This week, around the blogs is a bit heavy on the science posts, and light on the meta-science. First though, by way of Jake at Pure Pedantry, is an attractive visual demonstration of the cell cycle, from Sakaue-Sawano et al.:

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Yawn….

The awards season is upon us once again. Overpaid, under-worked and over-ego’d celebrities get together to slap each other’s backs and tell each other how great they are.

But little do they know where the real party in town is. The 2008 Thermostable Polymerase Awards (the THEPA’s) are underway and you have a front row seat.

Here are the winners: Read more »

One view on the aim of graduate studies towards a PhD is to foster critical learning and thinking habits, much more so than to simply learn facts. You’re supposed to learn how to “think like a scientist,” or develop and mature your intellectual behaviors in the discussions of difficult concepts (AKA, problems).

“Habits of Mind are the characteristics of what intelligent people do when they are confronted with problems, the resolutions of which are not immediately apparent,” (Costa & Kallick, below the fold). Read more »

Phenol extraction is a commonly used method for removing proteins from a DNA sample, e.g. to remove proteins from cell lysate during genomic DNA preparation. It’s commonly used, but not commonly understood.

If you want to know how it works so you can show off to all of your friends… read on. Read more »

In fields describable as functional or experimental biology, one tool that could be both useful and beautiful is a digital atlas of gene expression patterns in a representative mammal during development.

That’s just what GenePaint represents. In studying any individual gene product, its global function in the whole organism needs to be addressed. Clearly we can’t easily do this with an adult mouse, but we can with a mouse embryo. Take the image shown for instance, of focal adhesion kinase (which I chose arbitrarily, as something I’m familiar with), at day 14.5 of gestation (relatively late in development). Darker color indicates some expression of this protein. Now, some understanding of histology helps to understand what the image shows, but it is informative nonetheless. And, it’s beautiful, in a geeky sort of way. Read more »

Just Science week has been fun, reading four recent journal articles on focal adhesion kinase (FAK). It has helped me refresh myself on FAK as I got back to writing fellowship applications - although it had the added effect of taking time away from said writing activities. So today I thought a recap was in order, and add an insightful review that came out a year and a half ago which is still very helpful.

An excerpt from Integrin signaling in directed cell migration, by Konstandinos Moissoglu and Martin Alexander Schwartz: Read more »

Movie stars in the lab, debates and the destruction of creationism. There’s lots going on in the science blogs this week… here are the best bits… Read more »

After the past three days of blogging focal adhesion kinase (FAK), each focusing on an important regulator of cell adhesion dynamics and cell motility, I’m going to turn my attention to phosphatidyl inositol-3 kinase (PI3K). PI3K has a regulatory subunit (p85), and a catalytic subunit (p110) capable of catalyzing the phosphorylation of the D3 position of the inositol ring of a class of lipid components of the cell membrane. In the inactive state, p85 binds to p110, blocking its activity; but when the Src homology 2 (SH2) domain of p85 finds a phosphotyrosine-containing sequence in another protein that it likes, it dissociates from p110, which is then active.

Among the phosphotyrosine-containing activators of PI3K are FAK (through integrin receptors) and growth factor receptors (or receptor tyrosine kinases, RTK’s). In a recent study, Teet Velling and colleagues in Sweden sought to distinguish between FAK and RTK mechanisms of PI3K activation in EGFR and ?1 integrins utilize different signaling pathways to activate Akt. Read more »

Are you a visual, aural, read-write or kinesthetic learner?

If you don’t know, it could be a good idea to find out. Changing the way you learn, study and take notes to suit your learning tendencies can allow you to learn faster and make your newly-acquired knowledge stay with you for longer. Read more »

In keeping with this week’s trend of just science blogging on FAK, let’s take a look at another critical protein-protein interaction - this time with the scaffolding protein Paxillin. Specifically, how do FAK and Paxillin interact and why?

Conveniently, there’s a recent paper by Danielle Scheswohl et al., from the Schaller lab: Multiple paxillin binding sites regulate FAK function. The motivation to the paper can be found in the abstract: “Recent structural analyses have revealed two paxillin-binding sites in the [focal adhesion targeting, or FAT] domain of FAK. To define the role of paxillin binding to each site on FAK, point mutations have been engineered to specifically disrupt paxillin binding to each docking site on the FAT domain of FAK individually or in combination.” The paxillin binding sites are at the interface of ?-helices 1/4 and the interface of ?-helices 2/3 within the FAT domain (4 helices total). Paxillin is a scaffolding protein containing multiple domains that mediate protein-protein interactions, including five N-terminal LD motifs, four C-terminal LIM domains, and SH2 and SH3 domain binding sites. The second (LD2) and fourth LD motifs (LD4) of paxillin have been identified as FAK-binding sites and each of these sites binds to FAK with similar affinity. Read more »