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Of Interest

GenePaint: Visualizing Developmental Expression

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…

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Wrapping up a Week of Just FAK

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…

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FAK and Phosphatidyl Inositol in Cell Polarity

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…

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Dissecting Molecular Interactions Between FAK and Paxillin

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…

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FAK and Lamellipodia

Yesterday, I ended a post about FAK, Pyk2 and regulation of RhoA activity by asking “So, what about Rac regulation by [FAK] and Pyk2?” Today, let’s discuss a paper relating FAK/Pyk2 function studies on Rac1: Regulation of lamellipodial persistence, adhesion turnover, and motility in macrophages by focal adhesion kinase. Katherine Owen, et al., focus on…

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FAK, Pyk2, and p190RhoGEF in Cell Motility

Focal adhesion kinase is an important signaling molecule in integrin-mediated cell signaling and cell adhesion. In FAK genetic knockout (FAK-null) cells, its closely homologous relative proline-rich kinase (Pyk2) is upregulated in FAK-null fibroblasts to partially compensate, but the mechanisms of Pyk2 upregulation and compensation remain undefined1. A recent study by Yangmi Lim, David Schlaepfer, and…

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Love in Mendel’s Garden

It’s February… the end of winter is in sight and with Valentine’s day approaching, romance is in the air in Mendel’s Garden. In case you don’t know it, Mendel’s Garden is a delicious box of brain candy – a phenylethylamine-packed, monthly collection of blog articles on gene expression, development and evolutionary genetics. This month we…

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A New Unnatural Base-Pair

You know about adenine, thymine, guanine, cytosine. Now get used to SICS and MMO2. In this JACS article published this month, researchers at the Scripps Institute reported the identification of these two artificial bases. They are efficiently incorporated during in vivo DNA synthesis by the Klenow fragment of E.coli DNA polymerase and pair together with…

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Metabolism as Biogenesis

One of the several popular views regarding the origin of life stems from thermodynamics. Harold Morowitz refers to it as “Metabolism recapitulates biogenesis”. In PLoS Biology there’s an interesting essay that was submitted posthumously by the chemist Leslie Orgel on this subject – The Implausibility of Metabolic Cycles on the Prebiotic Earth. Orgel takes a…

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Geometries of Cells

Form follows physics in the fly eye, say Sascha Hilgenfeldt, Sinem Erisken, and Richard Carthew Simple forces, complex shapes: While most biological features appear complex in their geometries and varieties of components, appearances can be deceiving. That finding is supported by a recent modeling study by Hilgenfeldt, et al., looking at the arrangement of cone…

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Worms: Models of Development

Continuing with the recent theme on model organisms, there is the nematode (roundworm) Caenorhabditis elegans. This organisms is particularly useful owing to the fact that it has very defined development patterns involving fixed numbers of cells, and it can be rapidly assayed for abnormalities. Further, strains are cheap to breed and can be frozen. When…

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Xenopus as a Model for Early Development

Another popular model organism is the African Clawed Frog, Xenopus laevis, which is extremely useful for studying development and cellular physiology, owing to its particularly large and easy manipulable oocytes and embryo.

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Dictyostelium as a Model

As noted in the previous post on Model Organisms, Dictyostelium discoideum is a popular model for studying fundamental aspects of cell-cell communication and chemotaxis. This is a soil-living social amoeba grows as separate, independent cells that interact to form multicellular structures when challenged by adverse conditions such as starvation. Up to 100,000 cells signal each…

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Model Organisms in Biomedical Research

The term “model organism” is often used in research, to describe species that are extensively studied to understand particular biological phenomena. We say “model,” because there is usually the expectation that discoveries made in the organism model will be representative of related taxonomic groups. In particular, model organisms are widely used to explore potential causes…

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In Which I Agree with the Corporations

In Deserting the hungry?, a Nature essay argues today that “Monsanto and Syngenta are wrong to withdraw from an international assessment on agriculture.” The assessment, titled the International Assessment of Agricultural Science and Technology, is an ambitious, 4-year, US$10-million project that aims to do for hunger and poverty what the Intergovernmental Panel on Climate Change…

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Closer to the Genetic Roots of Autism

To go with this past Friday’s post on Alzheimer’s, recent progress is being made in understanding Autism. That’s the claim coming from an initial identification of a gene called CNTNAP2, which when mutated, this gene indicated a predisposition to autism in a specific population of Old Order Amish children from Pennsylvania. Three separate studies recently…

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Seeing Bacterial Bones with Cryo-EM Tomography

Until this decade, the notion that bacteria had cytoskeletons that maintained their cylindrical morphologies was not seriously considered. “People more or less thought the bacterial cell was a swimming pool and the chromosome was this ball of spaghetti,” says Stanford microbiologist Lucy Shapiro. The lack of apparent internal organization to bacteria supported this view. But…

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Curing Alzheimer’s through TNF?

One of the more dreaded diseases that plague our elders is Alzheimer’s disease, which robs the afflicted of not just their memories, but their dignities as well. Research on the role of cytokines in disease progression has illuminated a therapy with great potential, according to a recent study. Edward Tobinick and Hyman Gross, in a…

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Kinase Structures and Autoinhibition

Here’s a comment on work published about 6 months ago that was relevant to me, given my graduate studies on FAK with Jun-Lin Guan. The relations between protein structures and evolution are quite interesting indeed. As more structures are being solved for multimodular signaling proteins, the regulatory kinetics (on, off, and everything in between) is…

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The Big Story of 2007: Cellular Alchemy

Amid the political controversy and obstructions to conducting stem cell research, scientists this year managed to turn lead into gold… Genetically manipulating fibroblasts to become ESC(embryonic stem cell)-like sort of sounds like alchemy in a way, doesn’t it? The product of these papers, inducible pluripotent stem (iPS) cells, were created by transfecting four factors into…

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