Season's Greetings from MolBio Research Highlights

Merry Christmas from all of us at MolBio Research Highlights. We wish you love and happiness in this Holiday Season.

Oswald Avery (Image credit, modified by me)

Oswald Theodore Avery (1877-1955) was a distinguished Canadian-born bacteriologist and research physician and one of the founders of immunochemistry. He is best known for his discovery that deoxyribonucleic acid (DNA) serves as genetic material. The work of Avery and the members of his team at the Rockefeller Institute, observes Nobel laureate Dr. Joshua Lederberg, was "the historical platform of modern DNA research" and "betokened the molecular revolution in genetics and biomedical science generally."

Take a look at the The Oswald T. Avery Collection at the NIH.

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2010 - A year in review. We are now 2 years old!

Another year has gone by and it’s time to evaluate how 2010 was for us. Yesterday was my blogoversary, making MolBio Research Highlights 2 years old. In these two years, a lot has happened and this blog has evolved from being a place where I linked to papers I considered interesting, to a full blog where we discuss primary research articles in the field, link to interesting things in the web (including molbio blog posts), organize the MolBio Carnival, discuss life as a scientist and more (See here).

Let’s talk about some of this blog’s highlights for 2010 and some things worth mentioning about my professional life.

1) We were finalists for Best Expert Level Blog and I was a finalist for Research Twitterer of the Year in the 2010 ResearchBlogging Awards.

This was awesome. Even though we didn’t end up winning these awards, being a finalist among several candidates was enough for us.

I use Twitter a lot for topics surrounding research in the life sciences (I think the award was given to a “Science” Twitterer, rather than to a “Research” Twitterer, but anyway), and yesterday I used an application to make a word cloud for my Twitter updates for 2010.

The resulting cloud speaks for itself: I-tweet-science (see also below, where I discuss my Twitter use on an interview for Wiley). So, if you are interested in the life sciences I invite you to follow me!

As I tweet a lot about articles I consider interesting, let’s see what this cloud has to say regarding the topics I discussed in 2010.

Genome, transcription, genetics, RNA, chromatin, microRNAs, cancer, evolution, and lately, arsenic, are some of the most used tags.

Also, apparently I laughed a lot (I see “haha” in there) and talked to Chris Dieni and Psi regularly.

2) We started a series of posts under the title “The hottest molbio topics: the next few years”, which until now, has featured David Garcia and Keith Robison

We had a poll inviting people to vote for what they thought were going to be the hottest topics in the field in the next few years (see Which will be the hottest topic in molecular biology in a few years? The results), and I decided to share the results by accompanying them with blog posts by experts in the respective areas.

So far, David Garcia from You'd Prefer An Argonaute and Keith Robison from Omics! Omics! have talked about small RNAs and new sequencing technologies, respectively. Fascinating posts. Go check them out!

3) I got invited to write an article for LabTimes because of my blog post on Yeast Recombinational Cloning

I wrote a post discussing a very simple and efficient cloning strategy that we routinely use in our lab, called “yeast recombinational cloning” (See here). Some time after that, I was contacted by the people at Lab Times (“a new, free, Life Science journal for the whole of Europe”), and invited me to write an article for them discussing this methodology. I immediately accepted, wrote the article and it was featured in their 03-2010 issue. You can check it out here.

4) We took a top place in the 2010 HAL Medical Blog Awards, sponsored by Apredica, under the "Future Leaders of Biomed – Best Blog Award" category

As taken from their website:

“A search for “medical blog” in Google will get you more than 175 million results.

But of those 175 million results, which should you actually read? The 2010 HAL Medical Blog Awards, which highlight the very best blogs in health and medicine, aims to answer that question.”

Someone nominated us and we got a top place in the “Future Leaders of Biomed – Best Blog Award” category, which “recognizes the top blogs covering biology and medical issues that are by graduate students with exceptional promise”.

See my post about it here.

5) We started the “Direct Connection” Section

We created “Direct Connections”, a section which includes blog posts discussing primary research articles in the field, written by the authors themselves (see below). We have many of these in the works, but the first post of this series was written by Chris Dieni, who discussed his paper entitled “Regulation of glucose-6-phosphate dehydrogenase by reversible phosphorylation in liver of a freeze tolerant frog”.

Take a look at his post.

6) I was invited to write a post for Benchfly!

In early 2010, Benchfly organized the “Model Organism Week”, in which fellow science bloggers were invited to talk about some of the many organisms that have been instrumental for our current understanding of biology.

I wrote a piece for this initiative entitled “The Almighty Fungi: The Revolutionary Neurospora crassa”, in which I gave a historic view of the importance of this fungus for the advancement of modern molecular biology.

Go check it out!

7) We organized The MolBIo Carnival and hosted its first issue

A blog carnival discussing molecular and cellular biology was missing, so together with LabRat, Lucas Brouwers, Psi Wavefunction and Alex Knoll, we organized The MolBio Carnival, which groups together posts discussing peer-review articles, techniques, books and related topics in the field.

We hosted the first ever issue of this Carnival back in August (See The MolBio Carnival: the first edition) and this has been going one since then. The 6th one goes live on January 3rd, so there’s still time to get your posts in!

You can take a look at the Carnival’s history on its website.

8) I got interviewed for an article in Nature

That’s right. I was interviewed for an article discussing the "internationalization of science", which was part of a supplement entitled "Science masterclass", which commemorated the 60th Lindau Meeting of Nobel Laureates.

I won’t get into much detail and I encourage you to take a look to this article which was published back in October.

Francisco actually attended this meeting. Read his post entitled "My impressions on the recent Lindau Nobel Laureate Meeting"

9) I was selected as an Advisor for Wiley and was interviewed for their “Advisor Spotlight” section

The Wiley Science Advisors initiative aims to start a correspondence with young scientists and hear their perspectives on a variety of topics in science and publishing.

I’m currently involved in this program and recently, I was featured in their “Advisor Spotlight” section, for which I answered some questions regarding my online presence, i.e my blog and Twitter use.

Take a look!

10) I was interviewed by the PostDoc Forum

My interview for the PostDocs forum has just been published. I was kindly invited by Susan Steinhardt, who, despite of my "inattention to schedule", was continuously interested in featuring me.

Thanks Susan!

11) I’m a Mendeley advisor

This year I was selected as a Mendeley University Advisor. Mendeley “is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research”.

I’ve given some talks in Santiago to fellow researchers on the benefits of using Mendeley and actually convinced some people to switch from other platforms to Mendeley. If you have any questions regarding Mendeley, please send me an email or contact me through Twitter.

12) I won a F1000 twitter contest

Back in March, Richard Grant organized a fascinating Twitter contest, in which the idea was to "post your most embarrassing scientific error or egregious lab-based manipulation to Twitter with the #scifubar hashtag".

I contributed with this little thing…

Undergrad said he couldn't "paint" the black lines on the autoclave tape as good as his supervisor (he even bought a black marker) #scifubar,

which got me first place!  Read about it here.

___

Well, I guess that’s it. A whole year in review.

Thanks to everyone who has helped us throughout these two years and we hope to continue to be of service to all of our loyal readers.Yes, to all three of you :)

Happy holidays!

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Call for submissions MolBio Carnival #6

A new edition of the MolBio Carnival is coming! There's still time to get your posts in, as it goes live on Jan 3rd.

Read all about it here!



(Image credit)

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PostDocs Forum Featured Scientist

A (very) long time ago, Susan Steinhardt from the PostDocs Forum sent me an email with the idea of featuring me in their website. I immediately accepted, but I wasn't really diligent about it. I really appreciate Susan's continuous interest,  regardless of my  "inattention to schedule", as Keith Robison would say.

Anyway, my interview is now live at the Forum and I encourage you to take a look!

Also, be sure to check my Spotlight at Wiley Science Advisor's website.

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Top 5 papers of 2010

Go and take a look at the selection made by Faculty of 1000, which includes the article describing the structure of a bacterial complex I enzyme.

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The MolBio Carnival #5

The 5th edition of the MolBio Carnival is out at LabRat's blog. Go check it out!

If you didn't have time to get your post in this month's issue, don't worry! You can always submit to the next edition, which will be hosted at Phased.

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Middle Ages Science meets Present Times Science...

... and me!

Taken at the Karlsruhe Palace. Thanks to Alex Knoll for inviting me to his home while in Germany and for taking me sightseeing (and for taking the picture!).

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Quotes from the science blogosphere

I read the paper (Wolfe-Simon et al., 2010) and I can assure you that nothing in that paper is going into my biochemistry textbook. I predict that a year from now we'll have forgotten about this discovery. I'm not even sure it's going to be confirmed but, if it is, the result is pretty trivial. 

Larry Moran on the recent media hype about the paper "A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus".

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Powering the Cell: Mitochondria

From Biotechniques:

"Powering the Cell: Mitochondria" is a dynamic four-minute 3-D animation designed to help students understand the world inside mitochondria, the organelle that creates energy for eukaryotic cells in the form of adenosine triphosphates (ATP).

Enjoy!

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Quotes from the science blogosphere

Kary Mullis

"(....) Of course this record only applies to scientists who became quacks after getting the Nobel Prize. That lets Kary Mullis off the hook"

Larry Moran on his post entitled "Nobel Laureates Become Pseudoscientists"

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Advisor Spotlight

I'm part of Wiley Science Advisors, a project designed to connect with the next generation of scientists.

Every month an advisor is featured on the website and answers a few questions. This month was my turn and my Q&A was focused on my scientific online presence: how and why I use Twitter and blogs. 

Go and take a look!

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Oh, so I guess they just couldn't do the experiment again...

In 2005¹, the Liu lab described a new central element in the Neurospora circadian clock. They found that an RNA helicase with similarity to the yeast exosome cofactor Dob1p/Mtr4p, associated with FRQ, a core clock component essential for circadian clock function in this fungus (it was termed FRH, for "FRQ-interacting RNA helicase"). Their evidence suggested that FRH played an important role in the circadian negative-feedback loop. The same lab showed last year that FFC (the FRQ + FRH complex) and the exosome were "part of a posttranscriptional negative feedback loop that regulates frq transcript levels and the circadian output pathway"².

OK, so FRH is an important component of the central oscillator. As I have mentioned before, circadian systems are composed of a central oscillator and two signaling pathways: input pathways convey external signals to the oscillator, so that it can be synchronized with the environment, and output pathways allow the oscillator to temporally regulate diverse cellular processes.

Even though discussing both of these papers at length would be a great blogging topic, I just want to direct your attention to a little detail. Let's take a look at figure 5 from the 2005 paper:

You'll notice that  frq mRNA levels, as it had been known for many years now, oscillates in constant conditions (DD= constant darkness). Note that frq peaks at around DD16 and then at DD 36. As Cheng et al. show, this oscillation is absent in a strain in which frh has been downregulated (dsfrh), and frq mRNA levels remain high throughout the subjective day. Further, they show that the oscillation of an output gene³, ccg-2 (for clock-controlled gene 2), is also altered in the dsfrh strain as compared to the WT (lower panel).

This is all very nice and fascinating, but wait...what happened at DD24? You'll notice that there is a blank space in the Northern membrane for ccg-2.

This is what the authors say about it in the figure legend:

Figure 5. (A) Northern blot analyses showing the expression of frq and ccg-2 in DD. Cultures were harvested at the indicated hours in DD. QA was present in the medium for both strains.. The RNA samples at DD24 for ccg-2 were mishandled. (...)

(My emphasis)

"Mishandled"!? Really?

I realize that the conclusions of the paper do not depend on that particular time point and that the figure's general idea is perfectly clear without it [the downregulation of frh a) alters the rhythmic expression of a central clock component (frq) and b) disrupts circadian rhythmicity, as measured by the daily levels of ccg-2], but couldn't have they done the experiment again for the paper figure? I mean, they must have done it a couple of times to be sure that the result they were getting was reproducible, so why are they showing the Northern blot with the missing time point?

If I lose a sample, my PI ( and, basically common sense!) will tell me to do the experiment again, as I'm sure most PIs would. So, why they decided to go with this figure and justify the missing time point, instead of sending the figure with a different biological replicate, is a mystery to me.

Thoughts?


____

¹Cheng P, He Q, He Q, Wang L, & Liu Y (2005). Regulation of the Neurospora circadian clock by an RNA helicase. Genes & development, 19 (2), 234-41 PMID: 15625191

²Guo J, Cheng P, Yuan H, Liu Y. (2009) The exosome regulates circadian gene expression in a posttranscriptional negative feedback loop.Cell  138(6):1236-46. PMID:19747717

³ An output gene is basically (and traditionally) a gene whose time-of-day specific expression is dependent on the circadian oscillator and that it doesn't play any role on the functioning of the central clock. Its disruption then, has no impact on the functioning of the clock, even though it may lead to other phenotypes. 

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MolBio Carnival #4

A new edition of the MolBio Carnival is out at Skeptic Wonder. Be sure to check it out as great posts were featured.

If you didn't have time to get your post in this month's issue, don't worry! You can always submit to the next edition, which will be hosted by LabRat.

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Revise and Resubmit

Just hilarious...awesome British robotvoices...

(H/T: Comrade PhysioProf. I just had to spread the word about this video :)

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Quotes from the science blogosphere

The editing process requires interaction and patience, which may explain why some PIs choose to take over the draft of a developing student rather than teach them how to write it themselves. But, if we want to raise the level of writing in journals, books, and grants, this process can't be rushed. We should all to learn to edit just as well as, or even better than, we write.

-Dr O, on her post Editor's choice

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Generation X-change

A few months ago, I was interviewed for an article to be published in Nature, on the topic of the "internationalization of science". Basically, the idea was to interview scientists from different countries to address "whether or not the exchange of people and ideas is changing how science is done in countries all over the world".

The article, entitled "Generation X-change", was published today as part of the Nature supplement "Science masterclass", which commemorates the 60th Lindau Meeting of Nobel Laureates.

Go check it out... there's free full access to all articles in the supplement!

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Quotes: Publish like a pro

"Authors should try to resist the urge to let their findings trickle out over many years and many papers. Although the trend in the past may have been to turn each PhD thesis chapter into a manuscript, these days, even scientists at the postgraduate level should try to get one or two higher-profile papers rather than several lower-profile pieces (...)"

-Mark Hauber, in an interview in Nature entitled "Publications: Publish like a pro".

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Meeting of the Society of Biochem and MolBio + future meetings + small rant

I recently attended one of the largest scientific meetings in the country, the Annual Meeting of the Society of Biochemistry and Molecular Biology. It was held at “Gran Hotel Termas de Chillán”, a 5-star hotel right in the middle of the mountain. We had access to hot springs and pools and we were surrounded by the most beautiful scenery.

With two friends, outside the hotel

The meeting was fascinating, although a little too “biochem-oriented” for my taste (rather than molbio-oriented). I got to meet Rob Martienssen, a Professor at Cold Spring Harbor Laboratory working on plant epigenetics, with whom I shared a good number of wine bottles over dinner on various nights and many of what he referred to as “Chile Libre” (you know Cuba Libre right? Rum + Coke. Rob defined Chile Libre as Pisco + Coke). Meeting Rob (who invited me to visit his lab when I fly to the US, see below) was definitely one of the meeting highlights for me.

Rob Martienssen

The meeting was divided in a number of different Symposiums, with topics ranging from Virology, Plant Biochemistry and Biomedicine, to Cell Signalling and Bioinformatics, just to name a few.

A particularly interesting Symposium was the one on Plant Small RNAs, in which Rob, along with Scott Poethig and our very own Rodrigo Gutierrez, discussed a variety of small RNA-regulated processes in plants.

Also, we got to listen to David Holmes talk about the “challenges and opportunities for life at pH:1”, which focused on comparative genomics, and to Richard Garrat discuss the classification of protein domain folds (there's actually a protein chart with a number of different folds, resembling a periodic table).

Giancarlo de Ferrari, presently at Univ. Andrés Bello, also gave a very interesting talk on the role of Wnt signalling pathway in neurological diseases and how his group is using data derived from GWAS to address this.

With my PI, outside the hotel

All in all, I had a great time, I got to show my work to others (and almost got the prize for Best Poster - I was among the 3 finalists-) and bonded with my labmates, which is always important. My idea is to now attend two other meetings in the near future: one in Europe, from which I’m still waiting to hear back, and the very popular Fungal Genetics meeting, which will take place in Asilomar, California on March 2011. I have to somehow raise money to attend these meetings, so maybe I should get a paper route (or 10,000 of them!).

On another note and to wrap this up, here’s a small rant: it doesn’t matter where you are, you’ll always run into people that will try to cram 40 slides into 10-min talks. Obviously, they are not able to finish in time and so, when the session chair tells them they are out of time, they’ll keep on talking and fly through ten slides filled with data. What’s wrong with those guys? Session chairs should have the power to smack them in the head and send them outside to “think of what they’ve done”.

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Quotes from the science blogosphere

In this day and age, anyone who equates junk DNA with non-coding DNA isn't worth reading.

Larry Moran, discussing an article by Steve Talbott published in The New Atlantis.

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Quotes from the science blogosphere

Reviewer #3 is blaming our paper for not comparing our data to a very similar report that was published after we submitted it.

(..)

Trying to convince my collaborator to say that "our DeLorean was in the shop" in our reply to the editor.

@nantel on a recent rant on Twitter (not exactly from the blogosphere, but I want to keep the name of this Series).

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(Image credit)

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MolBio Carnival #3

A new issue of the Carnival was published on Monday. Go take a look at the great posts Alex Knoll has selected for the third issue of The MolBio Carnival!

If you didn't have time to get your post in this month's issue, don't worry! You can always submit to the next edition, which will be hosted by Psi Wavefunction over at Skeptic Wonder.  

And remember... The MolBio Carnival is posted on the first Monday of every month

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Music in the lab: how do you like it?

I would just go nuts without music. Hours of repetitive and mind-numbing tasks in the lab would take the best of me if it wasn't for my Sony MP4. Head banging at the laminar hood and dancing while setting a bacterial colony PCR are just one of my many daily moves.

Also, when I'm at my computer writing something or reading papers or whatever, I'm plugged in so that "lab noises" (which almost always include a chatty grad student) don't get in the way of my productivity. This has led to people talking to me for several minutes (to ask my opinion on some results or something) before noticing that I didn't even know they were talking to me! What can I say... I love my system and it helps me stay focused.

Were you talking to me?

There are some labs, however, that keep a radio on so that everyone can listen to it. They just pick a station and leave it there the whole day.

I was wondering then, what my readers preferred: do you rock to the beat of your personal selection of tunes? What's the music protocol in your lab? How do you feel about music while working in the lab?

Feel free to comment on these questions (as I really want to know), and if you listen to music in the lab, do you think sharing is a good thing?

Music in the lab: To share or not to share

(Image credits 1, 2)

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