We developed JVirGel, a collection of tools for the simulation and analysis of proteomics data. The software creates and visualizes virtual two-dimensional (2D) protein gels based on the migration behaviour of proteins in dependence of their theoretical molecular weights in combination with their calculated isoelectric points. The utilization of all proteins of an organism of interest deduced f...

This work describes the formation, perfusion, and maturation of three-dimensional microvascular tubes in vitro. These tubes consisted of confluent monolayers of human endothelial cells that lined open, cylindrical channels within collagen gels. Perivascular cells could be directly embedded within the gels or added after endothelial cells grew to confluence. The tubes spanned the entire 5-7 mm e...

In proteomics 2-dimensional SDS-polyacrylamide gel electrophoresis (2D-PAGE) is the most widely used method for analyzing protein mixtures qualitatively. There are, however, a lot of noise and measurement biases which needs to be accounted for both in the localization of spots as well as in the quantitative measurement of protein expression. Previous techniques for denoising 2D gels are based o...

Methyl-accepting chemotaxis proteins are central to both the excitation and adaptation phases of chemotactic behavior. Using null mutations in the genes coding for the two major methyl-accepting proteins (tsr and tar), we identified the gene products among the membrane proteins of Escherichia coli visualized on one- and two-dimensional gels. On two-dimensional gels, both the tsr and the tar pro...

A novel high-throughput system, called the stacked slice-gel system for separation and reactions (4SR), was developed for the analysis of DNA/RNA and protein/peptide. The system provides a novel three-dimensional gel electrophoresis approach that exploits the property of stacked slice gels. It allows multiple samples simultaneously to react as well as to be separated, offering a two-dimensional...

Proteins from silver-stained gels can be digested enzymatically and the resulting peptides analyzed and sequenced by mass spectrometry. Standard proteins yield the same peptide maps when extracted from Coomassieand silver-stained gels, as judged by electrospray and MALDI mass spectrometry. The low nanogram range can be reached by the protocols described here, and the method is robust. A silver-...

multiple traveling salesman problem (mtsp) is one of the most popular operation research problem and is known as combinatorial optimization problems. mtsp is an extension version of the famous and widely used problem named traveling salesman problem (tsp). because of its benefices in various domains, many researchers have tried to solve that, and many methods have proposed so far. mtsp is a np-...

The major spore coat proteins (SP60, SP70, and SP96) of Dictyostelium discoideum have been analyzed by using two-dimensional nonequilibrium pH gradient electrophoresis. These proteins have been characterized with respect to electrophoretic behavior, metachromatic staining with silver, and posttranslational modifications; these techniques allow unambiguous identification of these proteins in sil...

The influence of thiol blocking on the resolution of basic proteins by two-dimensional electrophoresis was investigated. Cysteine blocking greatly increased resolution and decreased streaking, especially in the basic region of the gels. Two strategies for cysteine blocking were found to be efficient: classical alkylation with maleimide derivatives and mixed disulfide exchange with an excess of ...

A new method for aligning families of two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) images arising in proteomics studies is presented. Forward piecewise bilinear transformations are used to determine an ideal gel and to obtain an initial alignment of the family of gels to this ideal gel. Both the ideal landmarks and the coefficients defining the transformations are obtained by so...