My Science badges

During my (short) scientific life, I've worked in very different research projects: Alzheimer's, plant molecular biology, mRNA splicing and presently, circadian rhythms. This has had me doing research through diverse approaches and techniques, throughout the years. While some have criticized my allegedly "lack of focus", I value all of these experiences as I consider them to have helped me grow as a scientist, for example by studying biology through different perspectives, discussing science with lots of different people and attending seminars in a variety of topics, among other reasons.

So after reading about it over at Sandwalk, and considering my diverse experience in science, I've decided to join the Science Scouts ("Order of the Science Scouts of Exemplary Repute and Above Average Physique"), not only to promote this geeky funny initiative, but also (ok, mainly) as a somewhat small personal reward. Why reward, you may ask. As a Scout organization, Science Scouts awards badges for several different "achievements" in science. I just figured that working in different fields would get me more badges, considering the different things I've done, but apparently it's not the case :-P

For example, shall you clone something (and I've cloned a lot of stuff over the years), then you are awarded this nice badge:

Also, if you blog about science, they this badge is for you:

Anyway, there are lots of badges I look forward to obtaining, like the one awarded by publishing in Science or Nature.
Here are some of my other badges. Take a look at the Science Scout's site and learn what they mean.

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ATP synthase and its effects on grad students

I'll never forget the first time I saw an animation of the advance of the prokaryotic replication fork (I know the post is on ATP synthase. I'll get to that in a second). It was around 2005 while I was taking a MolBio course. Bruce Alberts (with whom I would later sit down for coffee on a cold morning in Chicago two years later, to discuss life as a biologist) came to visit our University in Chile and brought with him this video from HHMI (you can see other HHMI's animations here) which I posted a few months ago while discussing a recent paper on DNA replication [Polymerase Dynamics at the Eukaryotic DNA Replication Fork].

These sort of visual aids are of great help, in my opinion, in understanding complex phenomena as DNA replication, or other molecular processes.

Recently, Iddo at Byte Size Biology, pointed us to some very interesting videos, from John E. Walker’s lab, on the mechanism of ATP synthase, an enzyme capable of synthesizing ATP from ADP and Pi through a unique rotary mechanism, in which subunits move relative to one another, powered by an electrochemical gradient of H+ or Na+ across the membrane [Da Vinci, F0-F1 ATPase: a copyright-driven Update].

This is just one of them:

This animation (along with the several ones that have been created along the years) is a perfect example of the importance of animations in the teaching of complex phenomena in biology as it helps (along with reading the textbook and understanding the figures) to comprehend how this molecular assembly can lead to the generation of ATP, using an electrochemical gradient that powers mechanical rotation.

OK, enough with the background, and on to the REAL reason of this post: what would you get if you add geeky grad students, a camera and a seminar on the enzymatic mechanisms of ATP synthase (and maybe some beer)?

This (again, thanks Iddo!):

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Life in the Lab

So true... lol!

Image credit: GraphJam

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And now we play the waiting game...

As some of you know, I've been away from blogging for a while (actually I've done a little blogging, highlighting some sites and collections, but little to none reviewing of primary literature) as a result of writing my PhD Thesis project: in my school, early on your 2nd year you have to submit a thesis project which you will have to present and defend in your "Qualifying Exam". This project (a ~15-20 pages document) summarizes what you will do during your PhD, providing (of course) the background and stating the hypothesis, objectives and the means by which you plan to address them.

After working for over a year in my previous lab (in plant molecular biology), I decided to switch fields (for reasons I may share later) and enter the fascinating world of circadian rhythms, using fungi as model organisms. As I was already in my 2nd year, I knew that making such a decision will require a lot of work, as I would need to read a lot (and from scratch) to come up with an original (and "PI-satisfying") research project in little over a month.

Shortly after I downloaded all the articles necessary to get me into context, I realized the impact of the field: a LOT of CNS, G&D and PNAS articles flooded my folder, a view I longed since my days working in mRNA splicing in yeast in the US.
So I started reading and soon came up with an idea I felt was interesting and, more importantly, one that motivated me. So I ran it by my PI and he was totally on board with it. In fact, his words were "fascinating idea. In fact, I was kinda thinking the same thing". After deciding on a research topic, I had to read a lot more, now getting deeper on this subject and write something called a "pre-project", which is a 4-5 pages summary of your proposed project. The purpose of this pre-project is for the school to select your thesis committee accordingly. After turning that document in, they gave me ~1 month to write the final project, which had to be very detailed, particularly in the background info and the methods.

Needless to say, this resulted not only in the downloading of more and more papers, but also in the daily email from my PI stating something like "you should DEFINITELY include this paper" which is usually a 2 seconds-old (and 15 pages long) article.
In the end, and on the verge of losing it, I rationalized the reading, focused on the writing, and on my final week managed to have a draft 3 days before deadline, in my PI's inbox. After some corrections and a little fighting with Endnote, I managed to turn it in, 20 minutes before deadline, last Friday. I think it's a nice project, timely (which is a very good feature of any research project) and well-conceived (if I may praise myself a little).

As we ping-ponged the different versions of the manuscript with my PI, I realized I made a good decision not only in terms of changing labs, but in choosing my new PI: he was critical, yet supportive, never criticizing an approach or expression without providing an alternative or explaining (in some cases with extreme detail) why he thought I should think about the particular item from a different perspective or in a different way. Also, he's been in the US for this whole period (quick reminder: I'm attending grad school in Chile), but we talked and discussed ideas daily, not only through email, but also Skype!. I felt completely supported throughout this entire experience, which was great.

So, what's next? As the post title states, I now have to wait; wait for the committee to set a date for my exam. In the meantime, I keep studying and giving practice talks to my fellow lab members. Also (although I may do this less now) I've been invited to sit through (and comment on) the practice talks of some friends who are also at this stage.

I'll keep you posted!

(Image credit: Crashhanna, see here)

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Microorganisms invade PLoS One

PLoS One has set up a collection of articles describing whole genome sequence and/or comparative genomics of important prokaryotic organisms [The PLoS ONE Prokaryotic Genome Collection]. They will be highlighting articles in this field and including them as part of this collection from now on, so if you are interested in Microbiology this may be a good thing to keep in you bookmarks.

(Image from Miller et al. 2007)

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New MS protocol at Nature Protocols

I've been away from blogging for a while, because tomorrow I turn in my PhD Thesis Project, and a few weeks after that, I'll be taking my qualification exam: this means that for the last few weeks I've been reading my eyes out and studying, giving me little time to review articles and other items to highlight here at MolBio Research Highlights.

As part of my project (actually as an alternative approach) I've been thinking about using mass spectrometry (MS) to identify if the particular protein I'm studying is regulated through phosphorylation (sorry, can't give more details at the time). This is great as you can sequence phosphopeptides even if they are present at very low levels.
By some coincidence, while thinking about this, Nature Protocols alerted me of their latest FREE featured paper, a new MS protocol for the detection of peptide post-translational modifications.

Here's the link and reference:

Unwin RD, et al. (2009) A sensitive mass spectrometric method for hypothesis-driven detection of peptide post-translational modifications: multiple reaction monitoring-initiated detection and sequencing (MIDAS). Nature Protocols 4,870-877.

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Conference on Open Access

As you may know, I'm a strong supporter of Open Access and I've been promoting some of the activities regarding last year's Open Access Day and the 2009 Open Access Week at this blog [OA week will take place in October] (you can also see the banner on the right sidebar under "Coming soon").

This post is just to let you know about the 1st Conference on Open Access Scholarly Publishing (COASP), which will take place in mid-September (14-16).
More info here

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