Characterization and simulation of cDNA microarray spots using a novel mathematical model

<p>Abstract</p> <p>Background</p> <p>The quality of cDNA microarray data is crucial for expanding its application to other research areas, such as the study of gene regulatory networks. Despite the fact that a number of algorithms have been suggested to increase the accuracy of microarray gene expression data, it is necessary to obtain reliable microarray images by improving wet-lab experiments. As the first step of a cDNA microarray experiment, spotting cDNA probes is critical to determining the quality of spot images.</p> <p>Results</p> <p>We developed a governing equation of cDNA deposition during evaporation of a drop in the microarray spotting process. The governing equation included four parameters: the surface site density on the support, the extrapolated equilibrium constant for the binding of cDNA molecules with surface sites on glass slides, the macromolecular interaction factor, and the volume constant of a drop of cDNA solution. We simulated cDNA deposition from the single model equation by varying the value of the parameters. The morphology of the resulting cDNA deposit can be classified into three types: a doughnut shape, a peak shape, and a volcano shape. The spot morphology can be changed into a flat shape by varying the experimental conditions while considering the parameters of the governing equation of cDNA deposition. The four parameters were estimated by fitting the governing equation to the real microarray images. With the results of the simulation and the parameter estimation, the phenomenon of the formation of cDNA deposits in each type was investigated.</p> <p>Conclusion</p> <p>This study explains how various spot shapes can exist and suggests which parameters are to be adjusted for obtaining a good spot. This system is able to explore the cDNA microarray spotting process in a predictable, manageable and descriptive manner. We hope it can provide a way to predict the incidents that can occur during a real cDNA microarray experiment, and produce useful data for several research applications involving cDNA microarrays.</p

Consequences of H-dimerization on the photophysics and photochemistry of oxacarbocyanines

The photophysical/photochemical behaviour of the monomers and the H dimers of four oxacarbocyanines (dyes D-G in the scheme) was investigated in water. In contrast with the usually observed effect of H dimerization, the dimers of dyes D-G were found to fluoresce with efficiencies comparable to or larger than those of the corresponding monomers. Analysis of the decay paths of the lowest excited singlet state showed, however, that dimerization causes a decrease of the radiative rate constants and an enhancement of intersystem crossing to the triplet manifold, as expected from application of exciton theory to a model H dimer. Twisting about one of the polymethine bonds contributes to the decay from the spectroscopic minimum of monomers, though yielding a rather small amount of a distorted cis isomer. The process is inhibited in dimers, likely due to a pronounced increase of activation energy connected with a loss of van der Waals attractive energy at the twisted geometry

Solvent dependent iodide oxidation in metal-halide perovskite precursor solutions

Solar cell absorbing layers made of metal-halide perovskites (MHPs) are usually deposited from solution phase precursors, which is one of the reasons why these materials received huge research attention in the last few years. A detailed knowledge of the solution chemistry is critical to understand the formation of MHP thin films and thus to control their optoelectronic properties and the reproducibility issues that usually affect their synthesis. In this regard, the concentration of triiodide, I-3(-), is one factor known to have an influence on regulating important aspects such as the particle size in the solution and the defect concentration in the film. In this study, we highlight an underestimated source of I-3(-), namely the iodide salt solutions ubiquitously employed in MHP synthetic routes, which not only lead to the formation of I-3(-) but also detracts available I- for the MHP synthesis, thus establishing under-stoichiometric conditions. Particularly, we show how the oxidation of I- to I-3(-) changes in time with both the iodide salt counter-cation (K+, CH3NH3+) and the used solvent, meaning that variable quantities of I-3(-) are found depending on the synthesis conditions, with enhanced oxidation found in the gamma-butyrolactone (GBL) solvent. Though these differences are generally small, we shed light on a hidden and ever-present reaction which is likely to be related to the overall processing quality of MHP thin films