Prolonging assembly through dissociation:A self assembly paradigm in microtubules

We study a one-dimensional model of microtubule assembly/disassembly in which GTP bound to tubulins within the microtubule undergoes stochastic hydrolysis. In contrast to models that only consider a cap of GTP-bound tubulin, stochastic hydrolysis allows GTP-bound tubulin remnants to exist within the microtubule. We find that these buried GTP remnants enable an alternative mechanism of recovery from shrinkage, and enhances fluctuations of filament lengths. Under conditions for which this alternative mechanism dominates, an increasing depolymerization rate leads to a decrease in dissociation rate and thus a net increase in assembly.Comment: accepted for publication in Physical Review

Self-limited self-assembly of chiral filaments

The assembly of filamentous bundles with controlled diameters is common in biological systems and desirable for the development of nanomaterials. We discuss dynamical simulations and free energy calculations on patchy spheres with chiral pair interactions that spontaneously assemble into filamentous bundles. The chirality frustrates long-range crystal order by introducing twist between interacting subunits. For some ranges of system parameters this constraint leads to bundles with a finite diameter as the equilibrium state, and in other cases frustration is relieved by the formation of defects. While some self-limited structures can be modeled as twisted filaments arranged with local hexagonal symmetry, other structures are surprising in their complexity.Comment: 5 pages, 5 figure

Neural network-based colonoscopic diagnosis using on-line learning and differential evolution

In this paper, on-line training of neural networks is investigated in the context of computer-assisted colonoscopic diagnosis. A memory-based adaptation of the learning rate for the on-line back-propagation (BP) is proposed and used to seed an on-line evolution process that applies a differential evolution (DE) strategy to (re-) adapt the neural network to modified environmental conditions. Our approach looks at on-line training from the perspective of tracking the changing location of an approximate solution of a pattern-based, and thus, dynamically changing, error function. The proposed hybrid strategy is compared with other standard training methods that have traditionally been used for training neural networks off-line. Results in interpreting colonoscopy images and frames of video sequences are promising and suggest that networks trained with this strategy detect malignant regions of interest with accuracy

Akt substrate TBC1D1 regulates GLUT1 expression through the mTOR pathway in 3T3-L1 adipocytes

Multiple studies have suggested that the protein kinase Akt/PKB (protein kinase B) is required for insulin-stimulated glucose transport in skeletal muscle and adipose cells. In an attempt to understand links between Akt activation and glucose transport regulation, we applied mass spectrometry-based proteomics and bioinformatics approaches to identify potential Akt substrates containing the phospho-Akt substrate motif RXRXXpS/T. The present study describes the identification of the Rab GAP (GTPase-activating protein)-domain containing protein TBC1D1 [TBC (Tre-2/Bub2/Cdc16) domain family, member 1], which is closely related to TBC1D4 [TBC domain family, member 4, also denoted AS160 (Akt substrate of 160 kDa)], as an Akt substrate that is phosphorylated at Thr(590). RNAi (RNA interference)-mediated silencing of TBC1D1 elevated basal deoxyglucose uptake by approx. 61% in 3T3-L1 mouse embryo adipocytes, while the suppression of TBC1D4 and RapGAP220 under the same conditions had little effect on basal and insulin-stimulated deoxyglucose uptake. Silencing of TBC1D1 strongly increased expression of the GLUT1 glucose transporter but not GLUT4 in cultured adipocytes, whereas the decrease in TBC1D4 had no effect. Remarkably, loss of TBC1D1 in 3T3-L1 adipocytes activated the mTOR (mammalian target of rapamycin)-p70 S6 protein kinase pathway, and the increase in GLUT1 expression in the cells treated with TBC1D1 siRNA (small interfering RNA) was blocked by the mTOR inhibitor rapamycin. Furthermore, overexpression of the mutant TBC1D1-T590A, lacking the putative Akt/PKB phosphorylation site, inhibited insulin stimulation of p70 S6 kinase phosphorylation at Thr(389), a phosphorylation induced by mTOR. Taken together, our data suggest that TBC1D1 may be involved in controlling GLUT1 glucose transporter expression through the mTOR-p70 S6 kinase pathway

Stress and Radiation-Induced Activation of Multiple Intracellular Signaling Pathways

Exposure of cells to a variety of stresses induces compensatory activations of multiple intracellular signaling pathways. These activations can play critical roles in controlling cell survival and repopulation effects in a stress-specific and cell type-dependent manner. Some stress-induced signaling pathways are those normally activated by mitogens such as the EGFR/RAS/PI3K-MAPK pathway. Other pathways activated by stresses such as ionizing radiation include those downstream of death receptors, including pro-caspases and the transcription factor NFKB. This review will attempt to describe some of the complex network of signals induced by ionizing radiation and other cellular stresses in animal cells, with particular attention to signaling by growth factor and death receptors. This includes radiation-induced signaling via the EGFR and IGFI-R to the PI3K, MAPK, JNK, and p38 pathways as well as FAS-R and TNF-R signaling to pro-caspases and NFKB. The roles of autocrine ligands in the responses of cells and bystander cells to radiation and cellular stresses will also be discussed. Based on the data currently available, it appears that radiation can simultaneously activate multiple signaling pathways in cells. Reactive oxygen and nitrogen species may play an important role in this process by inhibiting protein tyrosine phosphatase activity. The ability of radiation to activate signaling pathways may depend on the expression of growth factor receptors, autocrine factors, RAS mutation, and PTEN expression. In other words, just because pathway X is activated by radiation in one cell type does not mean that pathway X will be activated in a different cell type. Radiation-induced signaling through growth factor receptors such as the EGFR may provide radioprotective signals through multiple downstream pathways. In some cell types, enhanced basal signaling by proto-oncogenes such as RAS may provide a radioprotective signal. In many cell types, this may be through PI3K, in others potentially by NFKB or MAPK. Receptor signaling is often dependent on autocrine factors, and synthesis of autocrine factors will have an impact on the amount of radiation-induced pathway activity. For example, cells expressing TGFalpha and HB-EGF will generate protection primarily through EGFR. Heregulin and neuregulins will generate protective signals through ERBB4/ERBB3. The impact on radiation-induced signaling of other autocrine and paracrine ligands such as TGFbeta and interleukin 6 is likely to be as complicated as described above for the ERBB receptors.Fil: Dent, Paul. Virginia Commonwealth University; Estados UnidosFil: Yacoub, Adly. Virginia Commonwealth University; Estados UnidosFil: Contessa, Joseph. Virginia Commonwealth University; Estados UnidosFil: Caron, Ruben Walter. Virginia Commonwealth University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Medicina y Biología Experimental de Cuyo; ArgentinaFil: Amorino, Geroge. Virginia Commonwealth University; Estados UnidosFil: Valerie, Kristoffer. Virginia Commonwealth University; Estados UnidosFil: Hagan, Michael P.. Virginia Commonwealth University; Estados UnidosFil: Grant, Steven. Virginia Commonwealth University; Estados UnidosFil: Schmidt Ullrich, Rupert. Virginia Commonwealth University; Estados Unido

Pharmocologic inhibitors of the mitogen activated protein kinase cascade have the potential to interact with ionizing radiation exposure to induce cell death in carcinoma cells by multiple mechanisms

Recent studies have shown that inhibition of stress-induced signaling via the mitogen activated protein kinase (MAPK) pathway can potentiate the toxic effects of chemotherapeutic drugs and ionizing radiation. Because of these observations, we have further investigated the impact upon growth and survival of mammary (MDA-MB-231, MCF7, T47D), prostate (DU145, LNCaP, PC3) and squamous (A431) carcinoma cells following irradiation and combined long-term exposure to MEK1/2 inhibitors. Exposure of carcinoma cells to ionizing radiation resulted in MAPK pathway activation initially (0-4h) and modestly enhanced MAPK activity at later times (24h-96h). Inhibition of radiation-induced MAPK activation using MEK1/2 inhibitors potentiated radiation-induced apoptosis in two waves, at 21-30h and 96-144h after exposure. The potentiation of apoptosis was not observed in MCF7, LNCaP, or PC3 cells. At 24h, the potentiation of apoptosis was independent of radiation dose whereas at 108h, apoptosis correlated with increasing dose. Removal of the MEK1/2 inhibitor either 6h or 12h after exposure abolished the potentiation of apoptosis at 24h. At this time, the potentiation of apoptosis correlated with cleavage of pro-caspases -8, -9 and -3, and with release of cytochrome c into the cytosol. Inhibition of caspase function using a pan-caspase inhibitor ZVAD blocked the enhanced apoptotic response at 24h. Selective inhibition of caspase 9 with LEHD or caspase 8 with IETD partially blunted the apoptotic response in MDA-MB-231, DU145 and A431 cells, whereas inhibition of both caspases reduced the response by >90%. Removal of the MEK1/2 inhibitor either 24h or 48h after exposure abolished the potentiation of apoptosis at 108h. Incubation of cells with ZVAD for 108h also abolished the potentiation of apoptosis. In general agreement with the finding that prolonged inhibition of MEK1/2 was required to enhance radiation-induced apoptosis at 108h, omission of MEK1/2 inhibitor from the culture media during assessment of clonogenic survival resulted in either little or no significant alteration in radiosensitivity. Collectively, our data show that combined exposure to radiation and MEK1/2 inhibitors can reduce survival in some, but not all, tumor cell types. Prolonged blunting of MAPK pathway function following radiation exposure is required for MEK1/2 inhibitors to have any effect on carcinoma cell radiosensitivity.Fil: Qiao, Liang. Virginia Commonwealth University; Estados UnidosFil: Yacoub, Adly. Virginia Commonwealth University; Estados UnidosFil: McKinstry, Robert. Virginia Commonwealth University; Estados UnidosFil: Park, Jong Sung. Virginia Commonwealth University; Estados UnidosFil: Caron, Ruben Walter. Virginia Commonwealth University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Medicina y Biología Experimental de Cuyo; ArgentinaFil: Fisher, Paul B.. Columbia University. College of Physicians and Surgeons; Estados UnidosFil: Hagan, Michael P.. Virginia Commonwealth University; Estados UnidosFil: Grant, Steven. Virginia Commonwealth University; Estados UnidosFil: Dent, Paul. Virginia Commonwealth University; Estados Unido

Controlling Viral Capsid Assembly with Templating

We develop coarse-grained models that describe the dynamic encapsidation of functionalized nanoparticles by viral capsid proteins. We find that some forms of cooperative interactions between protein subunits and nanoparticles can dramatically enhance rates and robustness of assembly, as compared to the spontaneous assembly of subunits into empty capsids. For large core-subunit interactions, subunits adsorb onto core surfaces en masse in a disordered manner, and then undergo a cooperative rearrangement into an ordered capsid structure. These assembly pathways are unlike any identified for empty capsid formation. Our models can be directly applied to recent experiments in which viral capsid proteins assemble around the functionalized inorganic nanoparticles [Sun et al., Proc. Natl. Acad. Sci (2007) 104, 1354]. In addition, we discuss broader implications for understanding the dynamic encapsidation of single-stranded genomic molecules during viral replication and for developing multicomponent nanostructured materials.Comment: submitted to Phys. Rev.

Kinetic constraints on self-assembly into closed supramolecular structures

Many biological and synthetic systems exploit self-assembly to generate highly intricate closed supramolecular architectures, ranging from self-assembling cages to viral capsids. The fundamental design principles that control the structural determinants of the resulting assemblies are increasingly well-understood, but much less is known about the kinetics of such assembly phenomena and it remains a key challenge to elucidate how these systems can be engineered to assemble in an efficient manner and avoid kinetic trapping. We show here that simple scaling laws emerge from a set of kinetic equations describing the self-assembly of identical building blocks into closed supramolecular structures and that this scaling behavior provides general rules that determine efficient assembly in these systems. Using this framework, we uncover the existence of a narrow range of parameter space that supports efficient self-assembly and reveal that nature capitalizes on this behavior to direct the reliable assembly of viral capsids on biologically relevant timescales

Psychopathic traits influence amygdala-anterior cingulate cortex connectivity during facial emotion processing

There is accumulating evidence that youths with antisocial behavior or psychopathic traits show deficits in facial emotion recognition, but little is known about the neural mechanisms underlying these impairments. A number of neuroimaging studies have investigated brain activity during facial emotion processing in youths with Conduct Disorder (CD) and adults with psychopathy, but few of these studies tested for group differences in effective connectivity—i.e. changes in connectivity during emotion processing. Using functional magnetic resonance imaging and psycho-physiological interaction methods, we investigated the impact of CD and psychopathic traits on amygdala activity and effective connectivity in 46 male youths with CD and 25 typically-developing controls when processing emotional faces. All participants were aged 16–21 years. Relative to controls, youths with CD showed reduced amygdala activity when processing angry or sad faces relative to neutral faces, but the groups did not significantly differ in amygdala-related effective connectivity. In contrast, psychopathic traits were negatively correlated with amygdala–ventral anterior cingulate cortex connectivity for angry vs neutral faces, but were unrelated to amygdala responses to angry or sad faces. These findings suggest that CD and psychopathic traits have differential effects on amygdala activation and functional interactions between limbic regions during facial emotion processing