mRNA openers and closers: modulating AU-rich element-controlled mRNA stability by a molecular switch in mRNA secondary structure

Approximately 3 000 genes are regulated in a time-, tissue-, and stimulus-dependent manner by degradation or stabilization of their mRNAs. The process is mediated by interaction of AU-rich elements (AREs) in the mRNA's 3'-untranslated regions with trans-acting factors. AU-rich element-controlled genes of fundamentally different functional relevance depend for their activation on one positive regulator, HuR. Here we present a methodology to exploit this central regulatory process for specific manipulation of AU-rich element-controlled gene expression at the mRNA level. With a combination of single-molecule spectroscopy, computational biology, and molecular and cellular biochemistry, we show that mRNA recognition by HuR is dependent on the presentation of the sequence motif NNUUNNUUU in single-stranded conformation. The presentation of the HuR binding site in the mRNA secondary structure appears to act analogously to a regulatory on/off switch that specifically controls HuR access to mRNAs in cis. Based on this finding we present a methodology for manipulating ARE mRNA levels by actuating this conformational switch specifically in a target mRNA. Computationally designed oligonucleotides (openers) enhance the NNUUNNUUU accessibility by rearranging the mRNA conformation. Thereby they increase in vitro and endogenous HuR-mRNA complex formation which leads to specific mRNA stabilization (as demonstrated for TNFalpha and IL-2, respectively). Induced HuR binding both inside and outside the AU-rich element promotes functional IL-2 mRNA stabilization. This opener-induced mRNA stabilization mimics the endogenous IL-2 response to CD28 stimulation in human primary T-cells. We therefore propose that controlled modulation of the AU-rich element conformation by mRNA openers or closers allows message stabilization or destabilization in cis to be specifically triggered. The described methodology might provide a means for studying distinct pathways in a complex cellular network at the node of mRNA stability control. It allows ARE gene expression to be potentially silenced or boosted. This will be of particular value for drug-target validation, allowing the diseased phenotype to ameliorate or deteriorate. Finally, the mRNA openers provide a rational starting point for target-specific mRNA stability assays to screen for low-molecular-weight compounds acting as inhibitors or activators of an mRNA structure rearrangement.     

Simultaneous ac Susceptibility and Specific Heat Measurements of YBCO Ceramics

Simultaneous ac magnetic susceptibility and specific heat studies of YBCO ceramics permitted the correct correlation of the corresponding critical temperatures. The midpoint of the real component () and the maximum of the imaginary component () of ac susceptibility curves confirmed the T _c = 92 K critical temperature value determined by dc resistance measurements. The specific heat maximum's temperature (T _cc 93.6 K)—-taken as the calorimetric critical one—fell between T _c and T* (the pseudogap onset temperature). We suggest that T _cc signals the appearance of the first localized coherent pairs, while the temperature T _c marks their percolation. The existence of two different critical temperature values confirms the coexistence of partial coherent and coherent electron pairing phenomena in the region below T _cc of the superconducting phase diagram.     

Characterisation of single-mode fibres by near-field measurement

A new technique for the determination of the refractive-index profile of single-mode optical fibres from a simple near-field measurement is proposed. This permits one to deduce accurately all the important parameters of the fibre.     

Pattern recognition of collections

The task of simultaneously classifying a set of objects has unusual problems. Three categories of such problems are identified. Characteristics of context-dependent and context-independent classifications are considered. The effects of having parallepipeds or ellipsoids as decision regions are compared.     

Gramicidin Ion Channel-Based Biosensors: Construction, Stochastic Dynamical Models, and Statistical Detection Algorithms

This paper deals with the experimental construction, stochastic modeling, and statistical signal processing of a novel, artificially constructed biosensor comprised of biological ion channels. Such nanoscale biosensors have been built by incorporating dimeric gramicidin A (bis-gA) ion channels into bilayer membranes of giant unilamellar liposomes, and then excising small patches of the membrane loaded with ion channels. We present a stochastic model for the response of the biosensor and present statistical model validation tests to verify the adequacy of the model. We show that in the presence of specific target molecules, the statistics of the gating mechanisms of the gA channels are altered. By capturing the change in real time, we devise a maximum-likelihood detector to detect the presence of target molecules. To test the sensitivity of this model, we conducted patch-clamp experiments with two compounds known to inhibit conduction of the gA channels. We found experimentally that the real-time detection algorithm was able to accurately identify the addition of the compounds even when the alterations in the patch-clamp recordings were very small. This algorithm provides the sensitive detection system for ongoing development of lipid-based nanosensors.     

Thermische Ausdehnung,innere Spannungen und Porenverteilung in AlSiCp Metallmatrix‐ verbundwerkstoffen

Thermal expansion, internal stresses and porosity distribution in AlSiCp MMC AlSi7Mg/SiC/70p (AlSiC) is used for heat sinks because of its good thermal conductivity combined with a low coefficient of thermal expansion (CTE). These properties are important for power electronic devices where heat sinks have to provide efficient heat transfer to a cooling device. A low CTE is essential for a good surface bonding of the heat sink material to the isolating ceramics. Otherwise mismatch in thermal expansion would lead to damage of the bonding degrading the thermal contact within the electronic package. Therefore AlSiC replaces increasingly copper heat sinks. The CTE mismatch between isolation and a conventional metallic heat sink is transferred into the metal matrix composite (MMC). The stability of the external and internal interface bonding is essential for the heat sink function of AlSiC. In situ thermal cycling (RT – 400 °C) measurements of an AlSi7Mg/SiC/70p MMC are reported yielding the pore volume fraction and internal stresses between the matrix and the reinforcements in function of temperature. The changes in pore volume fractions are determined by synchrotron tomography and residual stresses by synchrotron diffraction at ESRF‐ID15A. The measurements show a relationship between thermal expansion, residual stresses and pore formation in the MMC. The results obtained from the in situ measurements reveal a thermo elastic range with inversion of the dominant tensile stresses in the matrix into compressive up to 200 °C followed by plastic matrix deformation reducing the volume of pores during heating. A reverse process takes place during cooling from 500 °C starting with elastic matrix strains converting into tensile stresses increasing the pore volume fraction again. Below 200 °C, the CTE behaves again according to thermo elastic calculations. Damage like in low cycle fatigue could be observed after multiple extreme cooling‐heating cycles between –100 °C and +400 °C, which increase the volume fraction and the size of the voids.     

沉积参数对CVD金刚石晶粒尺寸的影响

采用DC Arc Plasma Jet CVD方法制备了金刚石自支撑膜体,考察了温度分布、沉积腔压和CH4/H2等沉积参数对所制备金刚石膜体中的晶粒尺寸的影响.实验发现沿温度降低的方向和增加腔压会使晶粒尺寸变大,当CH4/H2超过15%后,有带刻面的晶粒出现.本次实验最大的晶粒对角线长度超过1mm.     

Performance analysis of parallel Schwarz preconditioners in the LES of turbulent channel flows

We present a comparative study of parallel Schwarz preconditioners in the solution of linear systems arising in a Large Eddy Simulation (LES) procedure for turbulent plane channel flows. This procedure applies a time-splitting technique to suitably filtered Navier–Stokes equations, in order to decouple the continuity and momentum equations, and uses a semi-implicit scheme for time integration and finite volumes for space discretisation. This approach requires the solution of four sparse linear systems at each time step, accounting for a large part of the overall simulation; hence the linear system solvers are a crucial component in the whole procedure. Several preconditioners are applied in the simulation of a reference test case for the LES community, using discretisation grids of different sizes, with the aim of analysing the effects of different algorithmic choices defining the preconditioners, and identifying the most effective ones for the selected problem. The preconditioners, coupled with the GMRES method, are run within SParC-LES, a recently developed LES code based on the PSBLAS and MLD2P4 libraries for parallel sparse matrix computations and preconditioning.     

Experimental validation of the discrete-time MCS adaptive strategy

This paper is concerned with the implementation and experimental validation of a discrete-time model reference adaptive control strategy, known as Minimal Control Synthesis (MCS) algorithm. After discussing the proof of stability of the algorithm when applied to discretized models of continuous-time plants, the problem of controlling a highly nonlinear electro-mechanical device is taken as a representative case of study. It is shown that the discrete-time MCS is an effective strategy to solve the problem while guaranteeing robustness to unmodeled nonlinear dynamics over a wide range of test manoeuvres.