Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops

BACKGROUND: Public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. The available data offers new opportunities to address questions about bacterial genome evolution, a task that requires reliable fine comparison data of closely related genomes. Recent analyses have shown, using pairwise whole genome alignments, that it is possible to segment bacterial genomes into a common conserved backbone and strain-specific sequences called loops. RESULTS: Here, we generalize this approach and propose a strategy that allows systematic and non-biased genome segmentation based on multiple genome alignments. Segmentation analyses, as applied to 13 different bacterial species, confirmed the feasibility of our approach to discern the 'mosaic' organization of bacterial genomes. Segmentation results are available through a Web interface permitting functional analysis, extraction and visualization of the backbone/loops structure of documented genomes. To illustrate the potential of this approach, we performed a precise analysis of the mosaic organization of three E. coli strains and functional characterization of the loops. CONCLUSION: The segmentation results including the backbone/loops structure of 13 bacterial species genomes are new and available for use by the scientific community at the URL:

A comparison of the molecular mechanisms underpinning high-intensity, pulsed polychromatic light and low-intensity UV-C hormesis in tomato fruit

Postharvest treatment of tomato fruit with high-intensity, pulsed polychromatic light (HIPPL) has previously been shown to induce delayed ripening and disease resistance comparable to that of low-intensity UV-C (LIUV). Little, however, is known of the mechanisms underpinning postharvest HIPPL hormesis in tomato fruit. Expression of genes involved in plant hormone biosynthesis, defence, secondary metabolism and ripening were monitored 24 h post treatment (24 HPT), 10 d post treatment (10 DPT) and 12 h post inoculation with Botrytis cinerea (12 HPI). All genes monitored were constitutively expressed and changes in expression profiles following treatment were highly similar for both HIPPL and LIUV treatments. Expression of pathogenesis-related proteins P4, β-1,3,-Glucanase and Chitinase 9 and a jasmonate biosynthesis enzyme (OPR3), were significantly upregulated at 10 DPT and 12 HPI. Both treatments significantly downregulated the expression of polygalacturonase and flavonol synthase at 10 DPT and 12 HPI. Ethylene biosynthesis enzyme ACO1 and β-carotene hydroxylase were significantly upregulated at 24 HPT, and phenylalanine ammonia-lyase (PAL) was significantly upregulated at 12 HPI. Both HIPPL and LIUV treatments stimulate defence responses that are mediated by salicylic acid, jasmonic acid and ethylene. This may lead to broad range resistance against both necrotrophic and biotrophic pathogens as well as abiotic stresses and herbivorous pests. Following inoculation with B. cinerea only PAL showed indication of a gene priming response for HIPPL- and LIUV-treated fruit

Effects of field parameters on IMRT plan quality for gynecological cancer: A case study

Traditional external beam radiotherapy of gynecological cancer consists of a 3D, four-field-box technique. The radiation treatment area is a large region of normal tissue, with greater inhomogeneity over the treatment volume, which could benefit more with intensity-modulated radiation therapy (IMRT). This is a case report of IMRT planning for a patient with endometrial cancer. The planning target volume (PTV) spanned the intrapelvic and periaortic lymph nodes to a 33-cm length. Planning and treatment were accomplished using double isocenters. The IMRT plan was compared with a 3D plan, and the effects of field parameters were studied. Delineated anatomical contours included the intrapelvic nodes (PTV), bone marrow, small bowel, bladder, rectum, sigmoid colon, periaortic nodes (PTV), spinal cord, left kidney, right kidney, large bowel, liver, and tissue (excluding the PTVs). Comparisons were made between IMRT and 3D plans, 23-MV and 6-MV energies, zero and rotated collimator angles, different numbers of segments, and opposite gantry angle configurations. The plans were evaluated based on dosevolume histograms (DVHs). Compared with the 3D plan, the IMRT plan ha