We developed maximum clique-based algorithms for spot matching for two-dimensional gel electrophoresis images, protein structure alignment and protein side-chain packing, where these problems are known to be NP-hard. Algorithms based on direct reductions to the maximum clique can find optimal solutions for instances of size (the number of points or residues) up to 50-150 using a standard PC. We...

The template activities of protein-free SV40 DNA and SV40 minichromosomes for DNA re-replication are compared in in vitro replication assays. Density substitution experiments and two-dimensional gel electrophoresis show that protein-free DNA can replicate for at least two cycles whereas salt-treated minichromosomes replicate only once. Re-replication of minichromosomes is blocked at the stage o...

Escherichia coli contains the CspA family, consisting of nine proteins (CspA to CspI), in which CspA, CspB, and CspG have been shown to be cold shock inducible and CspD has been shown to be stationary-phase inducible. The cspI gene is located at 35.2 min on the E. coli chromosome map, and CspI shows 70, 70, and 79% identity to CspA, CspB, and CspG, respectively. Analyses of cspI-lacZ fusion con...

Conformational transitions in topologically constrained duplex DNA necessarily affect and are affected by other transitional processes throughout the entire molecule. This conformational interdependence of discrete sequences within a given superhelical domain arises through a requisite competition for the free energy of supercoiling. Here we present a generalized statistical mechanical analysis...

Sample preparation is key to the success of proteomics studies. In the present study, two sample preparation methods were tested for their suitability on the mature, recalcitrant leaves of six representative perennial plants (grape, plum, pear, peach, orange, and ramie). An improved sample preparation method was obtained: Tris and Triton X-100 were added together instead of CHAPS to the lysis b...

Background: Lipopolysaccharides (LPSs) and several antigenic proteins of Brucella have been considered for preparation of diagnostic reagents and subunit vaccines. The objective of this study was to identify and compare immunogens of B. abortus S19 which induce humoral immune responses in human, goat and rabbit. Material and Methods: The bacterial whole cell extract was prepared in extraction b...

The recent development of microarray technology has led statisticians and bioinformaticians to develop new statistical methodologies for comparing different biological samples. The objective is to identify a small number of differentially expressed genes from among thousands. In quantitative proteomics, analysis of protein expression using two-dimensional gel electrophoresis shows some similari...

We describe a two-dimensional agarose gel electrophoresis procedure that improves the resolution of knotted DNA molecules. The first gel dimension is run at low voltage, and DNA knots migrate according to their compactness. The second gel dimension is run at high voltage, and DNA knots migrate according to other physical parameters such as shape and flexibility. In comparison with one-dimension...

Many cell biologists wish to know the subcellular localization of proteins of interest. Proteomics methods have the potential to describe the entire protein content of organelles. However, practical limitations in organelle isolation and analysis of low abundance proteins have meant that organelle proteomics has had, until recently, only limited success. Some examples of quantitative proteomic ...

Patterns of newly synthesized proteins of Vero cells in different growth states were obtained using two-dimensional gel electrophoresis. The 240 most prevalent peptide spots were then compared. Cells in exponential growth and in the stationary phase were found to have patterns of peptide spots characteristic of their state of growth. The transition between these patterns is progressive, and the...