Structures of proteases for ubiqutin and ubiquitin-like modifiers

Post-translational modifiers can alter the function of proteins in many different ways. The conjugation of ubiquitin (Ub) and ubiqutin-like modifiers (Ubls) to proteins has been shown to be especially crucial in regulating a variety of cellular processes including the cell cycle, growth control, quality control, localization and many more. It is a highly dynamic process and involves a number of enzymes called E1, E2 and E3. Ub and Ubls are removed from the target proteins by deubiquitinating enzymes (DUBs) or Ubl-specific proteases (ULPs), thereby deconjugation can act as an additional level of control over the ubiquitin-conjugation system. In addition, DUBs and ULPs are responsible for activating Ub and Ubls from their inactive corresponding precursor forms. Here we review recent progress in molecular details of these deconjugating enzymes of Ubls.     

ASAP3 is a focal adhesion-associated Arf GAP that functions in cell migration and invasion

ASAP3, an Arf GTPase-activating protein previously called DDEFL1 and ACAP4, has been implicated in the pathogenesis of hepatocellular carcinoma. We have examined in vitro and in vivo functions of ASAP3 and compared it to the related Arf GAP ASAP1 that has also been implicated in oncogenesis. ASAP3 was biochemically similar to ASAP1: the pleckstrin homology domain affected function of the catalytic domain by more than 100-fold; catalysis was stimulated by phosphatidylinositol 4,5-bisphosphate; and Arf1, Arf5, and Arf6 were used as substrates in vitro. Like ASAP1, ASAP3 associated with focal adhesions and circular dorsal ruffles. Different than ASAP1, ASAP3 did not localize to invadopodia or podosomes. Cells, derived from a mammary carcinoma and from a glioblastoma, with reduced ASAP3 expression had fewer actin stress fiber, reduced levels of phosphomyosin, and migrated more slowly than control cells. Reducing ASAP3 expression also slowed invasion of mammary carcinoma cells. In contrast, reduction of ASAP1 expression had no effect on migration or invasion. We propose that ASAP3 functions nonredundantly with ASAP1 to control cell movement and may have a role in cancer cell invasion. In comparing ASAP1 and ASAP3, we also found that invadopodia are dispensable for the invasive behavior of cells derived from a mammary carcinoma.     

Dependence of ultrasonic attenuation on bone mass and microstructure in bovine cortical bone

The development of the axial transmission technique now enables in vivo evaluation of cortical bone quality, which plays an important role in bone fragility. Cortical bone is a complex multiscale material, which may be made of different types of microstructure. The interaction between ultrasound and cortical bone remains unclear and most studies have been confined to wave speed analysis. The first aim of this study is to investigate the dependence of the frequency-dependent attenuation on the type of bone microstructure. The second goal is to determine whether broadband ultrasonic attenuation (BUA) is related to volumetric bone mineral density (vBMD) and mass density. Parallelepipedic samples of bovine cortical bone were cut from three specimens and tested in the axial, radial and tangential directions using an ultrasonic transmission device. BUA was evaluated over a 1-MHz wide bandwidth around 4MHz. In addition, the microstructure of each sample was determined using an optical microscope. BUA values measured in porotic microstructure are significantly higher than in Haversian microstructure. The lowest BUA values are obtained for plexiform microstructure. For all structures, BUA in the axial direction is significantly smaller than in the radial and tangential directions. Moreover, BUA is correlated with both vBMD and density (determination coefficient (R2) equal to 0.44 and 0.65, respectively, in the axial direction). BUA variations can be explained by scattering and viscoelastic mechanisms. This study suggests that BUA measurements have the potential to discriminate among different cortical bone microstructures in addition to providing material properties.     

Apigenin inhibits the production of NO and PGE2 in microglia and inhibits neuronal cell death in a middle cerebral artery occlusion-induced focal ischemia mice model

Flavonoids have been intensively studied on their pharmacological activities such as anti-cancer, anti-oxidant and anti-inflammation. However, little is known about their neuroprotective effects. Recent studies suggest that inflammation mediated by microglia may play a role in neurodegenerative diseases. In this study, we evaluated the anti-inflammatory effect of various flavonoid compounds by using BV-2, a murine microglia cell line. Of the compounds that were evaluated, apigenin inhibited the production of nitric oxide and prostaglandin E(2) by suppressing the expression of inducible nitric oxide synthase and cyclooxygenase-2 protein, respectively. Moreover, apigenin suppressed p38 mitogen-activated protein kinase (MAPK), c-Jun N-terminal kinase (JNK) phosphorylation without affecting the activity of extracellular signal-regulated kinase (ERK). Apigenin was also found to protect neuronal cells from injury in middle cerebral artery occlusion.     

Investigations into the design principles in the chemotactic behavior of Escherichia coli

Inspired by the recent studies on the analysis of biased random walk behavior of Escherichia coli[Passino, K.M., 2002. Biomimicry of bacterial foraging for distributed optimization and control. IEEE Control Syst. Mag. 22 (3), 52-67; Passino, K.M., 2005. Biomimicry for Optimization, Control and Automation. Springer-Verlag, pp. 768-798; Liu, Y., Passino, K.M., 2002. Biomimicry of social foraging bacteria for distributed optimization: models, principles, and emergent behaviors. J. Optim. Theory Appl. 115 (3), 603-628], we have developed a model describing the motile behavior of E. coli by specifying some simple rules on the chemotaxis. Based on this model, we have analyzed the role of some key parameters involved in the chemotactic behavior to unravel the underlying design principles. By investigating the target tracking capability of E. coli in a maze through computer simulations, we found that E. coli clusters can be controlled as target trackers in a complex micro-scale-environment. In addition, we have explored the dynamical characteristics of this target tracking mechanism through perturbation of parameters under noisy environments. It turns out that the E. coli chemotaxis mechanism might be designed such that it is sensitive enough to efficiently track the target and also robust enough to overcome environmental noises.     

A neurocomputational model for optimal temporal processing

Humans can estimate the duration of intervals of time, and psychophysical experiments show that these estimations are subject to timing errors. According to standard theories of timing, these errors increase linearly with the interval to be estimated (Weber's law), and both at longer and shorter intervals, deviations from linearity are reported. This is not easily reconciled with the accumulation of neuronal noise, which would only lead to an increase with the square root of the interval. Here, we offer a neuronal model which explains the form of the error function as a result of a constrained optimization process. The model consists of a number of synfire chains with different transmission times, which project onto a set of readout neurons. We show that an increase in the transmission time corresponds to a superlinear increase of the timing errors. Under the assumption of a fixed chain length, the experimentally observed error function emerges from optimal selection of chains for each given interval. Furthermore, we show how this optimal selection could be implemented by competitive spike-timing dependent plasticity in the connections from the chains to the readout network, and discuss implications of our model on selective temporal learning and possible neural architectures of interval timing.     

Complex extracellular interactions of proteases and a protease inhibitor influence multicellular development of Streptomyces coelicolor

Streptomyces coelicolor produces an extracellular protease inhibitor protein, STI (Streptomyces trypsin inhibitor). We show that post-growth elimination of STI is needed for colonies to develop aerial mycelium efficiently. Inactivation of STI, and thus the normal progression of colony development, at least partly involves an extracellular protease specified by gene SCO5913. Two-hybrid analysis identified two possible targets of STI inhibition (the products of SCO1355 and SCO5447), both extracellular proteases containing a domain homologous with the P-domain of eukaryotic convertases, proteases that mediate the processing of many precursors with important cellular or developmental roles. At least the SCO1355 protease is needed for the normal progression of development. Two components of the proposed cascade are dependent on the tRNA for the rare UUA (leucine) codon, which is specified by the developmental gene bldA. A model is presented that links intracellular regulatory events with an extracellular protease cascade to facilitate normal development.     

Synthesis and antibacterial activity of the C-7 side chain of 3-aminoquinazolinediones

A novel series of bacterial topoisomerase (3-aminoquinazolinediones) inhibitors are described. The side-chain SAR against Gram-positive and Gram-negative organisms as well as DNA gyrase activity is reported.     

Water extracts ofAralia elata root bark enhances migration and matrix metalloproteinases secretion in porcine coronary artery endothelial cells

Aralia elata is an edible mountain vegetable. Angiogenesis, the formation of new blood vessels, is a process involving migration, proliferation and cell differentiation, as well as the formation of new capillary structures. Matrix metalloproteinases (MMPs) plays an important role in angiogenesis. The development of a functional vascular system requires a variety of growth factors, their receptors, and intracellular signals. This study examines the effects of water extracts from: (i)A. elata root bark (Aralia extracts); (ii) a combination of Aralia extracts and fibroblast growth factors (FGF-2) on cultured porcine coronary artery endothelial cells (PCAECs). Aralia extracts induced the migration of PCAECs, which was inhibited by MMPs inhibitors. Combining Aralia extracts and FGF-2 enhanced the migration and the secretion of MMP-2 and MMP-9 from PCAECs. We postulated that the Aralia extracts, which induced migrating activity in PCAECs, may be accomplished by increased secretion levels of MMP-2 and MMP-9.     

Selection of mediators for bioelectrochemical nitrate reduction

The bioelectrochemical reduction of nitrate in the presence of various mediators including methyl viologen and azure A was studied using a 3-electrode voltammetric system. The catalytic potential for the reduction of the mediators was observed in the reactor, which for methyl viologen and azure A were −0.74 V and −0.32 V, respectively, with respect to the potential of Ag/AgCl reference electrode. This potential was then applied to a working electrode to reduce each mediator for enzymatic nitrate reduction. Nitrite, the product of the reaction, was measured to observe the enzymatic nitrate reduction in the reaction media. Methyl viologen was observed as the most efficient mediator among those tested, while azure A showed the highest electron efficiency at the intrinsic reduction potential when the mediated enzyme reactions were carried out with the freely solubilized mediator. The electron transfer of azure A with respect to time was due to the adhesion of azure A to the hydrophilic surface during the reduction. In addition, the use of the adsorbed mediator on conductive activated carbon was proposed to inhibit the change in the electron transfer rate during the reaction by maintaining a constant mediator concentration and active surface area of the electrode. Azure A showed better than nitrite formation than methyl viologen when used with activated carbon.