High-throughput comparison of gene fitness among related bacteria

BACKGROUND: The contribution of a gene to the fitness of a bacterium can be assayed by whether and to what degree the bacterium tolerates transposon insertions in that gene. We use this fact to compare the fitness of syntenic homologous genes among related Salmonella strains and thereby reveal differences not apparent at the gene sequence level. RESULTS: A transposon Tn5 derivative was used to construct mutants in Salmonella Typhimurium ATCC14028 (STM1) and Salmonella Typhi Ty2 (STY1), which were then grown in rich media. The locations of 234,152 and 53,556 integration sites, respectively, were mapped by sequencing. These data were compared to similar data available for a different Ty2 isolate (STY2) and essential genes identified in E. coli K-12 (ECO). Of 277 genes considered essential in ECO, all had syntenic homologs in STM1, STY1, and STY2, and all but nine genes were either devoid of transposon insertions or had very few. For three of these nine genes, part of the annotated gene lacked transposon integrations (yejM, ftsN and murB). At least one of the other six genes, trpS, had a potentially functionally redundant gene encoded elsewhere in Salmonella but not in ECO. An additional 165 genes were almost entirely devoid of transposon integrations in all three Salmonella strains examined, including many genes associated with protein and DNA synthesis. Four of these genes (STM14_1498, STM14_2872, STM14_3360, and STM14_5442) are not found in E. coli. Notable differences in the extent of gene selection were also observed among the three different Salmonella isolates. Mutations in hns, for example, were selected against in STM1 but not in the two STY strains, which have a defect in rpoS rendering hns nonessential. CONCLUSIONS: Comparisons among transposon integration profiles from different members of a species and among related species, all grown in similar conditions, identify differences in gene contributions to fitness among syntenic homologs. Further differences in fitness profiles among shared genes can be expected in other selective environments, with potential relevance for comparative systems biology

The Wnt inhibitory factor 1 restoration in prostate cancer cells was associated with reduced tumor growth, decreased capacity of cell migration and invasion and a reversal of epithelial to mesenchymal transition

<p>Abstract</p> <p>Background</p> <p>Aberrations in the Wnt pathway have been reported to be involved in the metastasis of prostate cancer (PCa) to bone. We investigated the effect and underlying mechanism of a naturally-occurring Wnt inhibitor, WIF1, on the growth and cellular invasiveness of a bone metastatic PCa cell line, PC3.</p> <p>Results</p> <p>The WIF1 gene promoter was hypermethylated and its expression down-regulated in the majority (7 of 8) of PCa cell lines. Restoration of WIF1 expression in PC-3 cells resulted in a decreased cell motility and invasiveness via up-regulation of epithelial markers (E-cadherin, Keratin-8 and-18), down-regulation of mesenchymal markers (N-cadherin, Fibronectin and Vimentin) and decreased activity of MMP-2 and -9. PC3 cells transfected with WIF1 consistently demonstrated reduced expression of Epithelial-to-Mesenchymal Transition (EMT) transcription factors, Slug and Twist, and a change in morphology from mesenchymal to epithelial. Moreover, WIF1 expression significantly reduced tumor growth by approximately 63% in a xenograft mouse model. This was accompanied by an increased expression of E-cadherin and Keratin-18 and a decreased expression of vimentin in tumor tissues.</p> <p>Conclusion</p> <p>These data suggest that WIF1 regulates tumor invasion through EMT process and thus, may play an important role in controlling metastatic disease in PCa patients. Blocking Wnt signaling in PCa by WIF1 may represent a novel strategy in the future to reduce metastatic disease burden in PCa patients.</p

Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data

The recent development of methods for extracting precise measurements of spatial gene expression patterns from three-dimensional (3D) image data opens the way for new analyses of the complex gene regulatory networks controlling animal development. We present an integrated visualization and analysis framework that supports user-guided data clustering to aid exploration of these new complex datasets. The interplay of data visualization and clustering-based data classification leads to improved visualization and enables a more detailed analysis than previously possible. We discuss (i) integration of data clustering and visualization into one framework; (ii) application of data clustering to 3D gene expression data; (iii) evaluation of the number of clusters k in the context of 3D gene expression clustering; and (iv) improvement of overall analysis quality via dedicated post-processing of clustering results based on visualization. We discuss the use of this framework to objectively define spatial pattern boundaries and temporal profiles of genes and to analyze how mRNA patterns are controlled by their regulatory transcription factors

A 15 MeV proton diagnostic for DIII-D

A 15 MeV proton diagnostic that is patterned after the ASDEX proton probe is presently being fabricated for the DIII-D tokamak. A bellows assembly inserts a silicon detector into the vacuum for plasma operation and retracts it for baking. The detector preamplifier is situated in a reentrant tube (at atmosphere) beside the detector; electrically, the whole assembly is referenced to vessel potential. Orbit calculations in realistic magnetic field geometries predict a proton detection efficiency of O(10{sup {minus}7}). The diagnostic will be used for burnup studies at high {beta} and particle transport studies in the H-mode. 25 refs., 4 figs

Combustion space modelling of oxy-fuel fired glass melter

A three-dimensional heat transfer code based on the zonal method was applied to evaluate the oxygen-fuel firing of a cross-fired regenerative glass melter. A furnace end section which includes the bridge wall and a pair of the regenerator ports was modelled in detail for a base air case and several oxy-fuel firing cases. The firing rates of two oxy-fuel burners that matched the heat flux distribution of the base air case were determined. The effects of the height and angle of the oxy-fuel burners on the temperature and heat flux distributions were predicted to evaluate the optimum burner placement of the oxy-fuel burners. The main conclusions of the simulation are that; (1) in spite of the small flame diameters, the high momentum low flame temperature oxy-fuel burners can create temperature and heat flux distributions equivalent to those of the base air case with a wide flame and (2) both lower burner elevation and angling of the oxy-fuel burners toward the glass surface tend to increase heat transfer to glass surface and reduce the peak refractory temperatures. 12 refs., 21 figs., 4 tabs

Simultaneous stabilization using genetic algorithms

This paper considers the problem of simultaneously stabilizing a set of plants using full state feedback. The problem is converted to a simple optimization problem which is solved by a genetic algorithm. Several examples demonstrate the utility of this method. 14 refs., 8 figs

Ten Thousand Years of Solitude

This report documents the authors work as an expert team advising the US Department of Energy on modes of inadvertent intrusion over the next 10,000 years into the Waste Isolation Pilot Project (WIPP) nuclear waste repository. Credible types of potential future accidental intrusion into the WIPP are estimated as a basis for creating warning markers to prevent inadvertent intrusion. A six-step process is used to structure possible scenarios for such intrusion, and it is concluded that the probability of inadvertent intrusion into the WIPP repository over the next ten thousand years lies between one and twenty-five percent. 3 figs., 5 tabs

Removal of Dissolved and Suspended Radionuclides From Hanford Waste Vitrification Plant Liquid Wastes

It was determined during Preliminary Design of the Hanford Waste Vitrification Plant that certain intermediate process liquid waste streams should be decontaminated in a way that would permit the purge of dissolved chemical species from the process recycle shop. This capability is needed to ensure proper control of product glass chemical composition and to avoid excessive corrosion of process equipment. This paper discusses the process design of a system that will remove both radioactive particulates and certain dissolved fission products from process liquid waste streams. Supporting data obtained from literature sources as well as from laboratory- and pilot-scale tests are presented. 3 refs., 1 fig., 3 tabs