Quantitative analysis of ribosome–mRNA complexes at different translation stages

Inhibition of primer extension by ribosome–mRNA complexes (toeprinting) is a proven and powerful technique for studying mechanisms of mRNA translation. Here we have assayed an advanced toeprinting approach that employs fluorescently labeled DNA primers, followed by capillary electrophoresis utilizing standard instruments for sequencing and fragment analysis. We demonstrate that this improved technique is not merely fast and cost-effective, but also brings the primer extension inhibition method up to the next level. The electrophoretic pattern of the primer extension reaction can be characterized with a precision unattainable by the common toeprint analysis utilizing radioactive isotopes. This method allows us to detect and quantify stable ribosomal complexes at all stages of translation, including initiation, elongation and termination, generated during the complete translation process in both the in vitro reconstituted translation system and the cell lysate. We also point out the unique advantages of this new methodology, including the ability to assay sites of the ribosomal complex assembly on several mRNA species in the same reaction mixture

Mechanisms of gap gene expression canalization in the Drosophila blastoderm

<p>Abstract</p> <p>Background</p> <p>Extensive variation in early gap gene expression in the <it>Drosophila </it>blastoderm is reduced over time because of gap gene cross regulation. This phenomenon is a manifestation of canalization, the ability of an organism to produce a consistent phenotype despite variations in genotype or environment. The canalization of gap gene expression can be understood as arising from the actions of attractors in the gap gene dynamical system.</p> <p>Results</p> <p>In order to better understand the processes of developmental robustness and canalization in the early <it>Drosophila </it>embryo, we investigated the dynamical effects of varying spatial profiles of Bicoid protein concentration on the formation of the expression border of the gap gene <it>hunchback</it>. At several positions on the anterior-posterior axis of the embryo, we analyzed attractors and their basins of attraction in a dynamical model describing expression of four gap genes with the Bicoid concentration profile accounted as a given input in the model equations. This model was tested against a family of Bicoid gradients obtained from individual embryos. These gradients were normalized by two independent methods, which are based on distinct biological hypotheses and provide different magnitudes for Bicoid spatial variability. We showed how the border formation is dictated by the biological initial conditions (the concentration gradient of maternal Hunchback protein) being attracted to specific attracting sets in a local vicinity of the border. Different types of these attracting sets (point attractors or one dimensional attracting manifolds) define several possible mechanisms of border formation. The <it>hunchback </it>border formation is associated with intersection of the spatial gradient of the maternal Hunchback protein and a boundary between the attraction basins of two different point attractors. We demonstrated how the positional variability for <it>hunchback </it>is related to the corresponding variability of the basin boundaries. The observed reduction in variability of the <it>hunchback </it>gene expression can be accounted for by specific geometrical properties of the basin boundaries.</p> <p>Conclusion</p> <p>We clarified the mechanisms of gap gene expression canalization in early <it>Drosophila </it>embryos. These mechanisms were specified in the case of <it>hunchback </it>in well defined terms of the dynamical system theory.</p

The Numerical Simulation of Shallow Water: Estimation of the Roughness Coefficient on the Flood Stage

The results of the numerical simulations of the dynamics of shallow waters for Volga-Akhtuba Floodplain are discussed. The mathematical model is based on the system of Saint-Venant equations. Numerical solution applies a combined Lagrangian-Eulerian (cSPH-TVD) algorithm. We have investigated the features of the spring flood in 2011 and found the inapplicability of the hydrodynamical model with the constant roughness coefficient n M . We have found a good agreement between the results of numerical simulations and the observational data at gauging stations which allows us to estimate n M in low water n M min = 0.02 and the maximum water level in the river Volga n M max = 0.06–0.07

Structure, Thermal Properties and Proton Conductivity of the Sulfonated Polyphenylquinoxalines

This paper briefly reviews the results of scientific research on the proton conductivity of sulfonated polyphenylquinoxalines. Synthesis, structure (IR spectroscopy, SEM, quantum-chemical modeling, molecular weight distribution), moisture capacity, thermal properties, and proton conductivity of sulfonated polyphenylquinoxalines (sulfur content 2.6, 4.2, 5.5, and 7%) were studied. The relative stable configurations of sulfonated polyphenylquinoxalines with different positions of benzene rings and sulfogroups with the help of quantum chemical modeling were modeled. Sulfonation of the starting polyphenylquinoxalines was confirmed by IR spectroscopy and elemental analysis. The SEM method was used to study the surface of sulfonated polyphenylquinoxalines, and sulfonation regions were found. It was shown that sulfonated polyphenylquinoxalines contain water and are stable up to 250 &deg;C; on further heating, the decomposition of the sulfogroups occurs. The conductivity of the obtained polymer electrolytes was studied by impedance spectroscopy, and long-term tests were carried out. It is shown that the proton conductivity at an ambient humidity of 98 rel. % reaches values 10&minus;6&ndash;10&minus;3 S/cm depending on the degree of sulfonation. It was shown that even after long-term storage in air (7 years), samples of sulfonated polyphenylquinoxalines with a high sulfur content of 7% at 98% air humidity have a conductivity of 8 &times; 10&minus;4 S/cm

Comparative multi-modal, multi-scale residual stress evaluation in SLM 3D-printed Al-Si-Mg alloy (RS-300) parts

SLM additive manufacturing has demonstrated great potential for aerospace applications when structural elements of individual design and/or complex shape need to be promptly supplied. 3D-printable AlSi10Mg (RS-300) alloy is widely used for the fabrication of different structures in the aerospace industry. The importance of the evaluation of residual stresses that arise as a result of the 3D-printing process’ complex thermal history is widely discussed in literature, but systematic assessment remains lacking for their magnitude, spatial distribution, and comparative analysis of different evaluation techniques. In this study, we report the results of a systematic study of residual stresses in 3D-printed double tower shaped samples using several approaches: the contour method, blind hole drilling laser speckle interferometry, X-ray diffraction, and Xe pFIB-DIC micro-ring-core milling analysis. We show that a high level of tensile and compressive residual stresses is inherited from SLM 3D-printing and retained for longer than 6 months. The stresses vary (from −80 to +180 MPa) over a significant proportion of the material yield stress (from −⅓ to ¾). All residual stress evaluation techniques considered returned comparable values of residual stresses, regardless of dramatically different dimensional scales, which ranged from millimeters for the contour method, laser speckle interferometry, and XRD down to small fractions of a mm (70 μm) for Xe pFIB-DIC ring-core drilling. The use of residual stress evaluation is discussed in the context of optimizing printing strategies to enhance mechanical performance and long-term durability

Influence of Synthesis Conditions on the Crystal, Local Atomic, Electronic Structure, and Catalytic Properties of (Pr_1−<i>x</i>Yb_<i>x</i>)₂Zr₂O₇ (0 ≤ <i>x</i> ≤ 1) Powders

The influence of Yb3+ cations substitution for Pr3+ on the structure and catalytic activity of (Pr1−xYbx)2Zr2O7 powders synthesized via coprecipitation followed by calcination is studied using a combination of long- (s-XRD), medium- (Raman, FT-IR, and SEM-EDS) and short-range (XAFS) sensitive methods, as well as adsorption and catalytic techniques. It is established that chemical composition and calcination temperature are the two major factors that govern the phase composition, crystallographic, and local-structure parameters of these polycrystalline materials. The crystallographic and local-structure parameters of (Pr1−xYbx)2Zr2O7 samples prepared at 1400 °C/3 h demonstrate a tight correlation with their catalytic activity towards propane cracking. The progressive replacement of Pr3+ with Yb3+ cations gives rise to an increase in the catalytic activity. A mechanism of the catalytic cracking of propane is proposed, which considers the geometrical match between the metal–oxygen (Pr–O, Yb–O, and Zr–O) bond lengths within the active sites and the size of adsorbed propane molecule to be the decisive factor governing the reaction route