Evolutionary rate variation and RNA secondary structure prediction

Predicting RNA secondary structure using evolutionary history can be carried out by using an alignment of related RNA sequences with conserved structure. Accurately determining evolutionary substitution rates for base pairs and single stranded nucleotides is a concern for methods based on this type of approach. Determining these rates can be hard to do reliably without a large and accurate initial alignment, which ideally also has structural annotation. Hence, one must often apply rates extracted from other RNA families with trusted alignments and structures. Here, we investigate this problem by applying rates derived from tRNA and rRNA to the prediction of the much more rapidly evolving 5'-region of HIV-1. We find that the HIV-1 prediction is in agreement with experimental data, even though the relative evolutionary rate between A and G is significantly increased, both in stem and loop regions. In addition we obtained an alignment of the 5' HIV-1 region that is more consistent with the structure than that currently in the database. We added randomized noise to the original values of the rates to investigate the stability of predictions to rate matrix deviations. We find that changes within a fairly large range still produce reliable predictions and conclude that using rates from a limited set of RNA sequences is valid over a broader range of sequences.     

X-ray structure and variable temperature NMR spectra of [meso-triarylcorrolato]copper(III)

The diamagnetic square planar d(8) complexes [meso-arylcorrolato]copper(III) become paramagnetic upon warming, indicative of the equilibrium between the [corrolato]copper(III) and the [corrolato](+)* copper(II) forms of the complex. [meso-Triphenylcorrolato]copper(III) was structurally characterized and found to be saddled.     

Transfer hydrogenation using recyclable polyurea-encapsulated palladium: efficient and chemoselective reduction of aryl ketones

A robust and recyclable palladium catalyst [Pd0EnCat] has been prepared by ligand exchange of polyurea-encapsulated palladium(II) acetate with formic acid, resulting in deposition of Pd(0) in the support material; Pd0EnCat is shown to be a highly efficient transfer hydrogenation catalyst for chemoselective reduction of a wide range of aryl ketones to benzyl alcohols.     

Capillary zone electrophoretic separation and determination of imidazolic antifungal drugs

Capillary zone electrophoresis (CZE) was adapted to the simultaneous determination of a mixture of three imidazolic antifungal drugs. Separation was achieved by using a fused-silica capillary column with an acetic acid-Tris buffer at pH 5.18 and UV detection at 196 nm. Several electrophoretic parameters were investigated: pH and buffer concentration, applied voltage, temperature and injection conditions. The optimized CZE method was applied to the individual determination of ketoconazole, clotrimazole and econazole in pharmaceutical forms, after a previous single extraction step in methanol, with recoveries of 98.00, 99.96 and 99.58% respectively. The antifungal drugs can be determined at a concentration level lower than 1.0 x 10(-7) M.     

Cooperative effects in phospholipid monolayers induced by a peptide from HIV-1 capsid protein

The study of interactions between biological molecules and model membranes is essential for the understanding of a number of physiological mechanisms involved in viral infections and dissemination. In this paper, the analysis of the interaction between a peptide from the p24 protein of Human Immunodeficiency Virus type 1 (HIV-1) and a phospholipid monolayer has pointed to a cooperative response in which very small amounts of peptide p24-1 (e.g. 0.05 mol%) can lead to measurable effects. Monolayer surface pressure and surface potential isotherms were affected for peptide concentrations as low as 0.05 mol%, with saturation at 0.5 mol%. The expansion effect from p24-1 is confirmed by changes in morphology of the monolayers using Brewster angle microscopy. Even though p24-1 is disordered in aqueous solutions, the interaction with dipalmitoyl phosphatidylcholine (DPPC) causes it to adopt an alpha-helix structure, as shown by circular dichroism (CD) data for multilamellar vesicles (MLV). The expansion of the phospholipid monolayer in a cooperative way may imply that p24-1 has potential antiviral activity, by participating in the cell rupture, with no need of specific receptors in the membrane.     

Analysis of metabolites of glucose pathways in human erythrocytes by analytical isotachophoresis

A method for the quantitative determination of the major anionic constituents of fountain solutions, typically mono-, di- and hydroxycarboxylates, alkylbenzenesulfonates, and inorganic anions, including orthophosphate and polyphosphates, is presented here for the first time. The analytical problems arising from extensive co-elution of many of these analytes on an ion-exchange column have been resolved through a combination of (i) careful selection of the concentration gradient of the sodium hydroxide eluent; (ii) parallel analysis by ion-exclusion chromatography; and (iii) determination of total phosphorus by inductively coupled plasma atomic emission spectrometry.     

Use of Silicon Substituents in the Syntheses of Natural and Non-natural Molecules

Trimethylsilyl groups have been used in our research as a director as well as a bulky and lipophilic group in our quest for natural and non-natural molecules.     

典型钙/镁基吸附剂对二氧化硒吸附特性研究

针对钙/镁基矿物吸附剂的主要组分CaO、CaCO₃、MgO在500-800 ℃下对Se的吸附特性进行研究，并选取天然矿物方解石、白云石研究其对Se的吸附效果，且对矿物煅烧所得CaO进行吸附实验。结果表明，三种组分中CaO的吸附效果最佳，800 ℃时单位质量CaO对Se的吸附量可达368 mg/g。CaCO₃对Se的吸附在700 ℃时效果最佳且其吸附产物的热稳定性较好。镁基吸附剂仅在中温段对Se具有一定吸附效果。方解石对Se的吸附效果随温度变化趋势与CaCO₃相似，因其较好的孔隙结构，吸附效果略优于CaCO₃。煅烧方解石得到的F-sor对Se的吸附效果优于CaO和CaCO₃煅烧得到的C-sor，这与其良好的比表面积、孔隙结构与抗烧结能力有关，且F-sor吸附产物的热稳定性相对较好。F-sor对Se的吸附量最高可达403 mg/g。     

Chaotic micromixers using two-layer crossing channels to exhibit fast mixing at low Reynolds numbers

We report two chaotic micromixers that exhibit fast mixing at low Reynolds numbers in this paper. Passive mixers usually use the channel geometry to stir the fluids, and many previously reported designs rely on inertial effects which are only available at moderate Re. In this paper, we propose two chaotic micromixers using two-layer crossing channels. Both numerical and experimental studies show that the mixers are very efficient for fluid manipulation at low Reynolds numbers, such as stretching and splitting, folding and recombination, through which chaotic advection can be generated and the mixing is significantly promoted. More importantly, the generation of chaotic advection does not rely on the fluid inertial forces, so the mixers work well at very low Re. The mixers are benchmarked against a three-dimensional serpentine mixer. Results show that the latter is inefficient at Re = 0.2, while the new design exhibits rapid mixing at Re = 0.2 and at Re of O(10(-2)). The new mixer design will benefit various microfluidic systems.     

Neuronal activation by GPI-linked neuroligin-1 displayed in synthetic lipid bilayer membranes

We have characterized, in vitro, interactions between hippocampal neuronal cells and silica microbeads coated with synthetic, fluid, lipid bilayer membranes containing the glycosylphosphatidyl inositol (GPI)-linked extracellular domain of the postsynaptic membrane protein neuroligin-1. These bilayer-neuroligin-1 beads activated neuronal cells to form presynaptic nerve terminals at the point of contact in a manner similar to that observed for live PC12 cells, ectopically expressing the full length neuroligin-1. The synthetic membranes exhibited biological activity at neuroligin-1 densities of approximately 1 to 6 proteins/microm(2). Polyolycarbonate beads with neuroligin-1 covalently attached to the surface failed to activate neurons despite the fact that neuroligin-1 binding activity is preserved. This implies that a lipid membrane environment is likely to be essential for neuroligin-1 activity. This technique allows the study of isolated proteins in an environment that has physical properties resembling those of a cell surface; proteins can diffuse freely within the membrane, retain their in vivo orientations, and are in a nondenatured state. In addition, the synthetic membrane environment affords control over both lipid and protein composition. This technology is easily implemented and can be applied to a wide variety of cellular studies.