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Molecular dynamics has been employed to study the effect of ion treatment on the stability of 14-nucleotide RNA hairpin of Coxsackievirus B3. Three AMBER force fields were used: AMBER94, AMBER98, and AMBER99, which showed no significant structural difference of the hairpin. Thereafter, we applied two different long-range electrostatic treatments that were reaction field and PME methods, and calculated the distribution of ions around the hairpin. Although the structural stabilities of the MD simulations using both methods were similar in 0.14 M Na+, ion environment around the hairpin was notably different. In particular, structural stabilition of the hairpin with increasing ion concentration and with ion Mg2+ cannot be accommodated by simulations using reaction field method. Furthermore, the MD simulations using PME method suggested the strong similarity in structural and dynamical properties of the hairpin with 0.14 M Na+, 0.50 M Na+, 1,03 M Na+, and 0.08 M Mg2+ concentrations. However, the simulations revealed different ion occupations of Na+ and Mg2+.
Structural characterization of a polymethylsilsesquioxane (PMSQ) and a DT-type methyl silicone resin (MeDT) has been carried out by various instrumental analyses including GPC, NMR, gas chromatography, and gas chromatography-mass spectrometry. Although the PMSQ had a Mw around 5000, the resin contained a significant amount of low molecular weight species consisting of T2 [MeSi(OH)O2/2] and T3 [MeSiO3/2] units, ranging from T34T23 to T38T22 including many isomers. One isomer of T36T22 was isolated of which structure was determined as a cage structure. The species are supposed to consist mainly of cyclotetra- and cyclopentasiloxanes, but presence of strained rings such as cyclotrisiloxane rings also was suggested. In MeDT, species in which the T2 units in the molecules from PMSQ is replaced with D2 [Me2SiO2/2] were found, for example, T36D22, suggesting that general silicone resins consist of similar structures as silsesquioxanes. The Mark-Houwink exponent for these methyl resins was ~0.3, indicating the molecular shape to be compact. Investigation on the formation chemistry of the cubic octamers indicates that siloxane bond rearrangement is an important mechanism in the molecule build-up process.
The title compound, C37H67NO13·2C2H6OS·1.43H2O, is a macrolide antibiotic with better solubility and better dermal penetration abilities than erythromycin A itself. The asymmetric unit of this form contains one erythromycin A molecule, two dimethyl sulfoxide (DMSO) solvent molecules, a fully occupied water molecule and a partially occupied water molecule with an occupancy factor of 0.432 (11). The 14-membered ring of the erythronolide fragment has a conformation which differs considerably from that in erythromycin A dihydrate [Stephenson, Stowell, Toma, Pfeiffer & Byrn (1997[Stephenson, G. A., Stowell, J. G., Toma, P. H., Pfeiffer, R. R. & Byrn, S. R. (1997). J. Pharm. Sci. 86, 1239-1244.]). J. Pharm. Sci. 86, 1239–1244]. One of the two DMSO molecules is disordered over two orientations; the orientation depends on the presence or absence of the second, partially occupied, water molecule. In the crystal, erythromycin molecules are connected by O—H⋯O hydrogen bonds involving the hydroxy groups and the fully occupied water molecule to form layers parallel to (010). These layers are connected along the b-axis direction only by a possible hydrogen-bonding contact involving the partially occupied water molecule.
The aromatic rings in the title compound, C13H8ClNO4, enclose a dihedral angle of 39.53 (3)°. The nitro group is almost coplanar with the ring to which it is attached [dihedral angle = 4.31 (1)°]. In the crystal, molecules are connected by C-H...O hydrogen bonds into chains running along [001]. Key indicators: single-crystal X-ray study; T = 173 K; mean σ(C–C) = 0.002 A°; R factor = 0.044; wR factor = 0.105; data-to-parameter ratio = 18.9.
C. elegans is used extensively as a model system in the neurosciences due to its well defined nervous system. However, the seeming simplicity of this nervous system in anatomical structure and neuronal connectivity, at least compared to higher animals, underlies a rich diversity of behaviors. The usefulness of the worm in genome-wide mutagenesis or RNAi screens, where thousands of strains are assessed for phenotype, emphasizes the need for computational methods for automated parameterization of generated behaviors. In addition, behaviors can be modulated upon external cues like temperature, O2 and CO2 concentrations, mechanosensory and chemosensory inputs. Different machine vision tools have been developed to aid researchers in their efforts to inventory and characterize defined behavioral “outputs”. Here we aim at providing an overview of different worm-tracking packages or video analysis tools designed to quantify different aspects of locomotion such as the occurrence of directional changes (turns, omega bends), curvature of the sinusoidal shape (amplitude, body bend angles) and velocity (speed, backward or forward movement).
Background: Gastrulation is a key transition in embryogenesis; it requires self-organized cellular coordination, which has to be both robust to allow efficient development and plastic to provide adaptability. Despite the conservation of gastrulation as a key event in Metazoan embryogenesis, the morphogenetic mechanisms of self-organization (how global order or coordination can arise from local interactions) are poorly understood.
Results: We report a modular structure of cell internalization in Caenorhabditis elegans gastrulation that reveals mechanisms of self-organization. Cells that internalize during gastrulation show apical contractile flows, which are correlated with centripetal extensions from surrounding cells. These extensions converge to seal over the internalizing cells in the form of rosettes. This process represents a distinct mode of monolayer remodeling, with gradual extrusion of the internalizing cells and simultaneous tissue closure without an actin purse-string. We further report that this self-organizing module can adapt to severe topological alterations, providing evidence of scalability and plasticity of actomyosin-based patterning. Finally, we show that globally, the surface cell layer undergoes coplanar division to thin out and spread over the internalizing mass, which resembles epiboly.
Conclusions: The combination of coplanar division-based spreading and recurrent local modules for piecemeal internalization constitutes a system-level solution of gradual volume rearrangement under spatial constraint. Our results suggest that the mode of C. elegans gastrulation can be unified with the general notions of monolayer remodeling and with distinct cellular mechanisms of actomyosin-based morphogenesis.
Inhibitors of Apoptosis Proteins (IAPs) are well-studied E3 ubiquitin ligases predominantly known for regulation of apoptosis. We uncovered that IAPs can function as a direct E3 ubiquitin ligase of RhoGTPase Rac1. cIAP1 and XIAP directly conjugate polyubiquitin chains to Lysine 147 of activated Rac1 and target it for proteasomal degradation. Consistently, loss of these IAPs by various strategies led to stabilization of Rac1 and mesenchymal mode of migration in tumor cells. IAPs also regulate Rac1 degradation upon RhoGDI1 depletion and CNF1 toxin treatment. Our observations revealed an evolutionarily conserved role of IAPs in regulating Rac1 stability shedding light on to the mechanisms behind ubiquitination–dependent inactivation of Rac1 signaling.
Folding of RNA molecules into their functional three-dimensional structures is often supported by RNA chaperones, some of which can catalyse the two elementary reactions helix disruption and helix formation. Hfq is one such RNA chaperone, but its strand displacement activity is controversial. Whereas some groups found Hfq to destabilize secondary structures, others did not observe such an activity with their RNA substrates. We studied Hfq’s activities using a set of short RNAs of different thermodynamic stabilities (GC-contents from 4.8% to 61.9%), but constant length. We show that Hfq’s strand displacement as well as its annealing activity are strongly dependent on the substrate’s GC-content. However, this is due to Hfq’s preferred binding of AU-rich sequences and not to the substrate’s thermodynamic stability. Importantly, Hfq catalyses both annealing and strand displacement with comparable rates for different substrates, hinting at RNA strand diffusion and annealing nucleation being rate-limiting for both reactions. Hfq’s strand displacement activity is a result of the thermodynamic destabilization of the RNA through preferred single-strand binding whereas annealing acceleration is independent from Hfq’s thermodynamic influence. Therefore, the two apparently disparate activities annealing acceleration and duplex destabilization are not in energetic conflict with each other.
The crystal packing of the title compound, C13H19NO·0.33C7H8, shows a channel at [001], which contains grossly disordered toluene solvent molecules. The angle between the benzene ring and the mean plane of the formamide group is 71.1 (1)°. The amide groups of neighbouring molecules are connected by N—H(...)O hydrogen bonds, forming 21 helical chains propagating along [001]. Molecules are also connected by weak intermolecular C—H(...)O hydrogen bonds, forming 61 helices.