Thursday, July 30, 2009

A few ideas for grad students in the life sciences to keep in mind



After 4 years of undergraduate education and a year in the US and here in Chile working as a tech, I finally applied and successfully made it into grad school, some time ago. I remember how anxious we all were (me and my new classmates) back then about entering a PhD program in molecular genetics and start doing research at this fascinating time in molecular biology.

I remember talking to a lot of professors about grad school and reading a whole lot of papers about life as a grad student before I started. Everyone has an opinion regarding the do’s and don’ts of grad school and a recent blog post over at BiteSize Bio [Pointers for New Graduate Students] prompted me to write down a few ideas and concepts I think should be considered by grad students in the life sciences.




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Monday, July 27, 2009

JANE: Journal and Author Name Estimator



ResearchBlogging.org

I've just read over at Scienceroll about two tools that “help you determine which journal you should choose for publication”, based on your abstract or keywords [See Journal and Author Name Estimator and Huge Steps in Changing Science].

The first one is part of ResearchGATE (a “scientific network that connects researchers”) and the second one (which has been around for some time, since early 2008) comes as a standalone web application called "Journal and Author Name Estimator" (JANE). Note that to use the tool at ResearchGATE you must sign in.



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Friday, July 24, 2009

Tom Cech on catalytic RNAs



Tom Cech is someone that doesn’t need much of an introduction around here. Due to the "discovery of catalytic properties of RNA", he won the Nobel Prize in Chemistry in 1989 (along with Sidney Altman). Tom and his coworkers discovered self-splicing as a property of the pre-rRNA transcripts of the 26S rRNA gene from Tetrahymena: the intron was excised from the pre-rRNA and the exons were spliced together in vitro, in the absence of any protein1,2,3. In other words, the 26S rRNA precursor was able to splice itself in vitro.

We conclude that splicing activity is intrinsic to the structure of the RNA, and that enzymes, small nuclear RNAs and folding of the pre-rRNA into an RNP are unnecessary for these reactions. We propose that the IVS portion of the RNA has several enzyme-like properties that enable it to break and reform phosphodiester bonds. The finding of autocatalytic rearrangements of RNA molecules has implications for the mechanism and the evolution of other reactions that involve RNA.”1
This was the first example of a particular class of self-catalytic (self-excising) introns we now classify as “group I introns4.

I first met Tom at the Twelfth Annual Meeting of the RNA Society in 2007, where he gave the keynote lecture ("From the RNA world to the RNP world") and later on in Argentina in 2008, at a Gene Expression and RNA Processing meeting, where this picture was taken (back when I still wore my hair long).

Here’s a short interview by Richard Sever, where Tom discusses, very generally, RNA as a catalyst. He talks a little about the seminal discovery stated above, compares RNA- and protein-based catalysis and briefly discusses the evolution of catalytic RNAs.

I recommend that you download the video (rather than wait for it to load), as it is a 125Mb file.

--
1Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR (1982) Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 31(1):147-57

2 Inoue T, Sullivan FX, Cech TR.(1985) Intermolecular exon ligation of the rRNA precursor of Tetrahymena: oligonucleotides can function as 5' exons. Cell 43 2:431-7.

3 Sullivan FX, Cech TR. (1985) Reversibility of cyclization of the Tetrahymena rRNA intervening sequence: implication for the mechanism of splice site choice. Cell 42(2):639-48.

4 Some group I introns can self-splice in vitro, but almost all are thought to be assisted by proteins in vivo.

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Monday, July 20, 2009

The Scientific article of the future



Cell Press has always been innovative [See Another one from Cell Press: free symposia! and references therein]. As a collaborative effort to redefine the way a scientific article is presented online, integrating the tools and capabilities of the online environment, Cell Press and Elsevier have launched a project called Article of the Future at its Beta Prototype site.

Together, they've compiled two prototypes with several features.
Some of them are:

A graphical abstract allows readers to quickly gain an understanding of the main take-home message of the paper. The graphical abstract is intended to encourage browsing, promote interdisciplinary scholarship and help readers identify more quickly which papers are most relevant to their research interests.
This is great as it helps you get the idea of the paper and its implications graphically. Note that this does not replace the written abstract; it's just an addition.

Research highlights provide a bulleted list of the key results of the article.

A figure that contains clickable areas so that it can be used as a navigation mechanism to directly access specific sub-sections of the results and figures.
And many others.

You can check the prototypes here. I particularly liked Prototype #1.

I think that taking full advantage of the most important platform used nowadays to search for and read articles (that is, online), is a great idea. As some have stated in the past (including my former PI) the print version of journals is inevitably heading towards disappearance unless it can find a way to compete with the complete set of tools provided by the Internet (commenting, sharing, rating, audio and video, etc) that enhances the reading (and science communicating) experience. Although I like my print version of Nature, as it allows me to read the News & Views section and editorials during my daily commute, I hardly use it to read the articles related to my research. I'd rather download them, file them, attach comments, etc and save them for good, without worrying about spilling my coffee over them or leaving them behind somewhere. Also, there's some great reference-managing software around nowadays to help you cope with the increasing amounts of articles being published so you can find a particular article in seconds, leaving the old days of diving into piles of photocopied articles to find the right one or visiting the library, behind.

But what about reading the articles online? Is it the same as downloading the article and reading it offline? This new approach by Cell Press and Elsevier, says no. The idea is to take advantage of the capabilities the online environment provides and to "allow readers individualized entry points and routes through the content, while using the latest advances in visualization techniques". Something not available in a simple PDF file.

You can download it just to have it backed up and organized and read it offline if you want to (although, who works offline nowadays?), but the idea behind the project is to enhance the reading experience by taking advantage of what the Internet has to offer.

I think that journals integrating and taking advantage of all the tools the online environment provides, benefits us all and can lead to better science communication.

Be sure to provide feedback to this project.


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Saturday, July 18, 2009

On Science cliches



Betsy Mason just published an article in Wired Science entitled "5 Atrocious Science Cliches to Throw Down a Black Hole" (thanks to @boraZ for the tweet).
In a nutshell, she argues that there are some "annoying and ubiquitous clichés" generally used in science writing that should be eliminated for good (the terms under fire are "Holy Grail", "Silver Bullet", "Shedding Light", "Missing Link", and "Paradigm Shift").

A few minutes later, a blog response at Mad Scientist Jr. called for the importance of these phrases in communicating science to the general public [In Defense of Cliches].

He says:
"(...)We need cliches. We depend upon cliches, and cliches are quite useful in the proper context. While it may be true that the above terms do get thrown about quite a bit, they're still quite useful. Science journalism is already a convoluted field that must continually walk the line between being too esoteric for its mainstream, non-scientist audience and maintaining proper accuracy to satisfy its scientific constituents, which keeps information flowing. Banning the use of any widely understood vehicles for explanation just raises the barrier to effective communication between science and the public. And when we, as a scientific community, have already made it clear that we're not usually pleased by the transmission of our findings to the public through the prism of science journalism, do we really need to throw in even more barriers? (...)"
I posted a comment at his blog post, which I share with you. Please note the text in blue was added for clarity and did not appear in the original blog response:

"(...) Even though I didn't initially think about this in terms of how we communicate science to the general public [I was thinking on their use in scientific papers, see below], the case you are making, makes complete sense and some of these so-called "cliches" may be, in this context, useful.

On the other hand, in technical writing [scientific papers, subjected to peer-review, published in scientific journals], some of those concepts may rightfully be discarded, but others (for example 'shedding light'), are, in no way misleading, ambiguous or confusing, and in my opinion, pose no problem to the way we write about science. In fact, in some cases are even welcomed, as they bring life to some very dull manuscripts. As long as they don't lead to any conflict or misunderstanding of the scientific ideas being discussed (and an example of such a conflicting term is indeed "missing link" -ugh-), I have no problem with them".

What do you think?

Note: for concepts that have been used loosely in primary research literature see [What is Epigenetics? An operational definition] and references therein.


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New journal from CSHL Press



A new review journal, covering all aspects of molecular biology, has recently been launched.

Cold Spring Harbor Perspectives in Biology (CSH Perspectives) is a monthly online publication from CSHL Press, with an outstanding editorial board (featuring renowned scientists like Tom Cech, Mark Estelle, Peter Lawrence, Tom Misteli, Paolo Sassone-Corsi and David Spector just to name a few), analyzing progress in emerging areas of molecular, cell, and developmental biology, genetics, evolutionary biology, neuroscience, cancer biology, and molecular pathology.

Interestingly, articles will be organized as "Subject Collections", which will "gradually accumulate articles as new issues of the journal are published and, when complete, each will represent a comprehensive survey of the field it covers".

This is a very attractive feature and I'm confident, considering its board, that the journal will keep up with the rapidly advancing pace of molecular biology.

Also you can follow the journal on twitter (http://twitter.com/cshperspectives) which is always a great addition.

We'll keep our eyes open.

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Tuesday, July 14, 2009

Great tweets of science





"Sckt it, Pauling!" lol.
(note the dates...)


Memorable.

(See it from its original source at PhD Comics)

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Sunday, July 12, 2009

The 100th post at MolBio Research Highlights



Our latest post, a discussion on the Cancer Stem Cell Hypothesis [Cancer Stem Cells: the root of all evil?], marked our 100th post.
I considered this to be a good time to talk a little about the ~7 months this blog has been around.

The blog, MolBio Research Highlights, was initially born to compile a list of articles, tools, websites and news in molecular biology I considered of interest [See So exactly, what is this blog about?]. With time, I decided I wanted to comment a little more extensively on the items I was posting and eventually these comments got lengthier and richer, as I sometimes discussed not only the item being highlighted but also related stuff. Indeed, some techniques in the field have also been posted, as an aid for interested young researchers [For example, see Analyzing the genome-wide chromatin landscape: ChIP-Seq].

As primary research literature in molecular biology was sometimes discussed, I decided it was a smart move to join Researchblogging.org, where blog posts on peer-reviewed research on different topics, are aggregated. Indeed, this attracted a whole lot of traffic to the site and also, through this initiative, I got the chance to learn about several science-related blogs with some very interesting writing. In this sense, I think MolBio Research Highlights stands aside, and through its novel approach joined a particular group of blogs: blogs where the content is written by scientists and more interestingly, for scientists, differing from many other blogs, for example, where science is discussed by some very talented, yet non-scientist/researcher bloggers, and are aimed at the general public, or others which are written by scientists but aimed at the general public. I consider all of these approaches valuable and needed at present, each within its particular niche.

Around that same time, Francisco Barriga, a cancer researcher at IRB Barcelona, joined the blog and his interesting insights in cancer biology have broadened our scope. Indeed, MolBio Research Highlights was featured for the first time in the Cancer Research Blog Carnival [Cancer Carnival #23] and we hope to participate in future editions.

I sincerely hope other young molecular biologists will follow Francisco’s example and get interested in participating in our blog to discuss new research and advances at this fascinating time in molecular biology. The doors are open.
You don’t have to be a regular writer to be featured here; if you occasionally find an article you’d like to write a post about, you are most certainly welcome to contact us with the idea.

We feel very satisfied with the way the blog has developed over the course of these few months, and even though we acknowledge there are still many things that can and must be improved, this has been a good start, in our opinion. We are particularly proud of some of our most-read articles, What is Epigenetics? An operational definition, On PLoS' article-level metrics and the rapid blogosphere hit Cancer Stem Cells: the root of all evil?

Please feel free and encouraged to comment on our posts and also to let us know who you are; do you also have a blog? Let us (and everyone else) know about it!

We hope to have been an interesting addition to the science-related blogosphere during these few months and to improve within the next ones.

Thanks to everyone who has been reading our blog.

[Image credit: Multitema]


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