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

Highly efficient separation of actinides from lanthanides by a phenanthroline-derived bis-triazine ligand

The synthesis, lanthanide complexation, and solvent ex- traction of actinide(III) and lanthanide(III) radiotracers from nitric acid solutions by a phenanthroline-derived quadridentate bis-triazine ligand are described. The ligand separates Am(III) and Cm(III) from the lanthanides with remarkably high efficiency, high selectivity, and fast extraction kinetics compared to its 2,2'-bipyridine counterpart. Structures of the 1:2 bis-complexes of the ligand with Eu(III) and Yb(III) were elucidated by X-ray crystallography and force field calculations, respec-tively. The Eu(III) bis-complex is the first 1:2 bis-complex of a quadridentate bis-triazine ligand to be characterized by crystallography. The faster rates of extraction were verified by kinetics measurements using the rotating membrane cell technique in several diluents. The improved kinetics of metal ion extraction are related to the higher surface activity of the ligand at the phase interface. The improvement in the ligand's properties on replacing the bipyridine unit with a phenanthroline unit far exceeds what was anticipated based on ligand design alone

Dependency of Contact Angles on Three-Phase Contact Line: A Review

The wetted area of a sessile droplet on a practical substrate is limited by the three-phase contact line and characterized by contact angle, contact radius and drop height. Although, contact angles of droplets have been studied for more than two hundred years, there are still some unanswered questions. In the last two decades, it was experimentally proven that the advancing and receding contact angles, and the contact angle hysteresis of rough and chemically heterogeneous surfaces, are determined by interactions of the liquid and the solid at the three-phase contact line alone, and the interfacial area within the contact perimeter is irrelevant. However, confusion and misunderstanding still exist in this field regarding the relationship between contact angle and surface roughness and chemical heterogeneity. An extensive review was published on the debate for the dependence of apparent contact angles on drop contact area or the three-phase contact line in 2014. Following this old review, several new articles were published on the same subject. This article presents a review of the novel articles (mostly published after 2014 to present) on the dependency of contact angles on the three-phase contact line, after a short summary is given for this long-lasting debate. Recently, some improvements have been made; for example, a relationship of the apparent contact angle with the properties of the three-phase line was obtained by replacing the solid–vapor interfacial tension term, γSV, with a string tension term containing the edge energy, γSLV, and curvature of the triple contact line, km, terms. In addition, a novel Gibbsian thermodynamics composite system was developed for a liquid drop resting on a heterogeneous multiphase and also on a homogeneous rough solid substrate at equilibrium conditions, and this approach led to the same conclusions given above. Moreover, some publications on the line energy concept along the three-phase contact line, and on the “modified” Cassie equations were also examined in this review

Surface Modification of 3D Printed PLA Objects by Fused Deposition Modeling: A Review

Polylactic acid (PLA) filaments are very popular as a thermoplastic source used in the 3D printing field by the &#8220;Fused Deposition Modeling&#8222; method in the last decade. The PLA market is expected to reach 5.2 billion US dollars in 2020 for all of its industrial uses. On the other hand, 3D printing is an expanding technology that has a large economic potential in many industries where PLA is one of the main choices as the source polymer due to its ease of printing, environmentally friendly nature, glossiness and multicolor appearance properties. In this review, we first reported the chemical structure, production methods, general properties, and present market of the PLA. Then, the chemical modification possibilities of PLA and its use in 3D printers, present drawbacks, and the surface modification methods of PLA polymers in many different fields were discussed. Specifically, the 3D printing method where the PLA filaments are used in the extrusion-based 3D printing technologies is reviewed in this article. Many methods have been proposed for the permanent surface modifications of the PLA where covalent attachments were formed such as alkaline surface hydrolysis, atom transfer polymerization, photografting by UV light, plasma treatment, and chemical reactions after plasma treatment. Some of these methods can be applied for surface modifications of PLA objects obtained by 3D printing for better performance in biomedical uses and other fields. Some recent publications reporting the surface modification of 3D printed PLA objects were also discussed