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

Reversing Coffee-Ring Effect by Laser-Induced Differential Evaporation

Abstract The coffee-ring effect, ubiquitously present in the drying process of aqueous droplets, impedes the performance of a myriad of applications involving precipitation of particle suspensions in evaporating liquids on solid surfaces, such as liquid biopsy combinational analysis, microarray fabrication, and ink-jet printing, to name a few. We invented the methodology of laser-induced differential evaporation to remove the coffee-ring effect. Without any additives to the liquid or any morphology modifications of the solid surface the liquid rests on, we have eliminated the coffee-ring effect by engineering the liquid evaporation profile with a CO2 laser irradiating the apex of the droplets. The method of laser-induced differential evaporation transitions particle deposition patterns from coffee-ring patterns to central-peak patterns, bringing all particles (e.g. fluorescent double strand DNAs) in the droplet to a designated area of 100 μm diameter without leaving any stains outside. The technique also moves the drying process from the constant contact radius (CCR) mode to the constant contact angle (CCA) mode. Physical mechanisms of this method were experimentally studied by internal flow tracking and surface evaporation flux mapping, and theoretically investigated by development of an analytical model

A quantitative experimental study of wetting hysteresis on discrete and continuous chemical heterogeneities

Chemically heterogeneous surfaces are well known to induce contact angle hysteresis due to the local energy barriers that oppose contact line movement. In many cases, the surface heterogeneity is discontinuous, i.e. discrete regions of different wettability exist, which leads to pinning of the contact line at boundaries between regions. Pinning on individual rows of microscopic defects arranged in a square lattice can be sensed using a Wilhelmy balance to reveal discrete stick-slip motion. For defects more wettable than the matrix with a lattice spacing of 28 µm, the advancing contact line slips over ~10 rows in a single slip step, while the receding contact line stick-slips between individual rows of defects. Single, millimetre-scale defects were used to assess the energy involved when a contact line advances or recedes over a hydrophilic (more wettable) defect. Quantitative information about defect-induced hysteresis in relation to defect dimensions is obtained. The crucial importance of wetting boundaries is highlighted with an experimental example of a surface that is heterogeneous yet, due to the continuously changing pattern, does not exhibit contact angle hysteresis