Analysis of genomic sequences by Chaos Game Representation.

MOTIVATION: Chaos Game Representation (CGR) is an iterative mapping technique that processes sequences of units, such as nucleotides in a DNA sequence or amino acids in a protein, in order to find the coordinates for their position in a continuous space. This distribution of positions has two properties: it is unique, and the source sequence can be recovered from the coordinates such that distance between positions measures similarity between the corresponding sequences. The possibility of using the latter property to identify succession schemes have been entirely overlooked in previous studies which raises the possibility that CGR may be upgraded from a mere representation technique to a sequence modeling tool. RESULTS: The distribution of positions in the CGR plane were shown to be a generalization of Markov chain probability tables that accommodates non-integer orders. Therefore, Markov models are particular cases of CGR models rather than the reverse, as currently accepted. In addition, the CGR generalization has both practical (computational efficiency) and fundamental (scale independence) advantages. These results are illustrated by using Escherichia coli K-12 as a test data-set, in particular, the genes thrA, thrB and thrC of the threonine operon.

Reversible induction of ATP synthesis by DNA damage and repair in Escherichia coli. In vivo NMR studies.

Early metabolic events in Escherichia coli exposed to nalidixic acid, a topoisomerase II inhibitor and an inducer of the SOS system, were investigated by in vivo NMR spectroscopy, a technique that permits monitoring of bacteria under controlled physiological conditions. The energetics of AB1157 (wild type) and of its isogenic, SOS-defective mutants, recBC, lexA, and DeltarecA, were studied by 31P and 19F NMR before, during, and after exposure to nalidixic acid. The content of the NTP in E. coli embedded in agarose beads and perfused at 36 degreesC was found to be 4.3 +/- 1.1 x 10(-18) mol/cell, yielding a concentration of approximately 2.7 +/- 0.7 mM. Nalidixic acid induced in the wild type and mutants a rapid 2-fold increase in the content of the NTP, predominantly ATP. This induction did not involve synthesis of uracil derivatives or breakdown of RNA and caused cell proliferation to stop. Removal of nalidixic acid after 40 min of treatment rescued the cells and resulted in a decrease of ATP to control levels and resumption of proliferation. However, in DeltarecA cells, which were more sensitive to the activity of the drug, ATP elevation could not be reversed, and ATP content continued to increase faster than in control cells. The results ruled out association between the elevation of ATP and the induction of the SOS system and suggested involvement of a process reminiscent of apoptosis in the stimulation of ATP synthesis. Thus, the presence of the RecA protein was found to be essential for reversing the ATP increase and cell rescue, possibly by its function in repair of DNA damage.

Angiogenic response of MCF7 human breast cancer to hormonal treatment: assessment by dynamic GdDTPA-enhanced MRI at high spatial resolution.

Dynamic gadolinium diethylenetriamine pentaacetic acid (Gd-DTPA)-enhanced MRI was followed during growth and regression of MCF7 human breast tumors implanted in nude mice in the presence of estrogen and tamoxifen, respectively. Gradient-echo and spin-echo sequences were applied at a temporal resolution of 12 and 100 seconds, respectively, and a spatial resolution of 195 x 390 x 1000 microns. Maps of initial rates of contrast enhancement demonstrated stimulation of local growth of permeable microcapillaries at regions bordering necrotic areas, resulting from tamoxifen treatment. This localized angiogenic stimulation was confirmed by immunohistochemical staining of endothelial cells. After 1 week of tamoxifen treatment, the fraction of tumor pixels exhibiting rapid initial rate of contrast enhancement increased significantly from .28 +/- .05 to .46 +/- .06. In parallel, the fraction of tumor area showing contrast enhancement 3 minutes after Gd-DTPA injection also increased significantly, from .42 +/- .06 to .58 +/- .06. On the basis of these changes, it was possible to assess the response to tamoxifen therapy at an early stage.

Tamoxifen enhances cell death in implanted MCF7 breast cancer by inhibiting endothelium growth.

Magnetic resonance imaging at high spatial resolution and histochemical staining were applied to monitor the influence of tamoxifen versus estrogen on the growth, endothelial density, and extent of necrosis in tumors of MCF7 human breast cancer cells implanted in nude mice. Concomitantly with tamoxifen growth arrest, a highly significant decrease, by more than 2-fold, in the endothelial density of viable tumor regions had occurred, together with a significant increase in the extent of necrosis. The results suggest that the antiestrogenic activity of tamoxifen in breast cancer, which results in enhanced necrosis and tumor regression, is due to the inhibition of angiogenesis and of endothelial growth, thus reducing vascularization and impairing tumor perfusion.