Systems Biology and Pangenome of Salmonella O-Antigens.

O-antigens are glycopolymers in lipopolysaccharides expressed on the cell surface of Gram-negative bacteria. Variability in the O-antigen structure constitutes the basis for the establishment of the serotyping schema. We pursued a two-pronged approach to define the basis for O-antigen structural diversity. First, we developed a bottom-up systems biology approach to O-antigen metabolism by building a reconstruction of Salmonella O-antigen biosynthesis and used it to (i) update 410 existing Salmonella strain-specific metabolic models, (ii) predict a strain's serogroup and its O-antigen glycan synthesis capability (yielding 98% agreement with experimental data), and (iii) extend our workflow to more than 1,400 Gram-negative strains. Second, we used a top-down pangenome analysis to elucidate the genetic basis for intraserogroup O-antigen structural variations. We assembled a database of O-antigen gene islands from over 11,000 sequenced Salmonella strains, revealing (i) that gene duplication, pseudogene formation, gene deletion, and bacteriophage insertion elements occur ubiquitously across serogroups; (ii) novel serotypes in the group O:4 B2 variant, as well as an additional genotype variant for group O:4, and (iii) two novel O-antigen gene islands in understudied subspecies. We thus comprehensively defined the genetic basis for O-antigen diversity.IMPORTANCE Lipopolysaccharides are a major component of the outer membrane in Gram-negative bacteria. They are composed of a conserved lipid structure that is embedded in the outer leaflet of the outer membrane and a polysaccharide known as the O-antigen. O-antigens are highly variable in structure across strains of a species and are crucial to a bacterium's interactions with its environment. They constitute the first line of defense against both the immune system and bacteriophage infections and have been shown to mediate antimicrobial resistance. The significance of our research is in identifying the metabolic and genetic differences within and across O-antigen groups in Salmonella strains. Our effort constitutes a first step toward characterizing the O-antigen metabolic network across Gram-negative organisms and a comprehensive overview of genetic variations in Salmonella

iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE.

Acinetobacter baumannii has become an urgent clinical threat due to the recent emergence of multi-drug resistant strains. There is thus a significant need to discover new therapeutic targets in this organism. One means for doing so is through the use of high-quality genome-scale reconstructions. Well-curated and accurate genome-scale models (GEMs) of A. baumannii would be useful for improving treatment options. We present an updated and improved genome-scale reconstruction of A. baumannii AYE, named iCN718, that improves and standardizes previous A. baumannii AYE reconstructions. iCN718 has 80% accuracy for predicting gene essentiality data and additionally can predict large-scale phenotypic data with as much as 89% accuracy, a new capability for an A. baumannii reconstruction. We further demonstrate that iCN718 can be used to analyze conserved metabolic functions in the A. baumannii core genome and to build strain-specific GEMs of 74 other A. baumannii strains from genome sequence alone. iCN718 will serve as a resource to integrate and synthesize new experimental data being generated for this urgent threat pathogen

Performance of Preload on Cohesionless Soils

Common occurrence of loose normally consolidated fine sands and silts extending to considerable depths necessitates the utilization of ground improvement techniques along the coasts of Arabian Peninsula. In the case considered, the soil profile consisted of twenty meter thick compressible sands, and preloading technique was suggested to stabilize the foundation soil. The paper presents the performance of the preloading and the level of soil improvement achieved. The observed settlements and settlement-time behaviour are compared with the values estimated from various methods. The soil parameters back calculated from measured field behaviour are reported

High carrier concentration induced effects on the bowing parameter and the temperature dependence of the band gap of Ga_xIn_1−xN

The influence of intrinsic carrier concentration on the compositional and temperature dependence of the bandgap of GaxIn1-xN is investigated in nominally undoped samples with Ga fractions of x = 0.019, 0.062, 0.324, 0.52, and 0.56. Hall Effect results show that the free carrier density has a very weak temperature dependence and increases about a factor of 4, when the Ga composition increases from x = 0.019 to 0.56. The photoluminescence (PL) peak energy has also weak temperature dependence shifting to higher energies and the PL line shape becomes increasingly asymmetrical and broadens with increasing Ga composition. The observed characteristics of the PL spectra are explained in terms of the transitions from free electron to localized tail states and the high electron density induced many-body effects. The bowing parameter of GaxIn1-xN is obtained from the raw PL data as 2.5 eV. However, when the high carrier density induced effects are taken into account, it increases by about 14% to 2.9 eV. Furthermore, the temperature dependence of the PL peak becomes more pronounced and follows the expected temperature dependence of the bandgap variation

Degradation of Toxic Indigo Carmine Dye by Electrosynthesized Ferrate (VI)

Response surface methodology was applied for optimizing indigo carmine (IC) dye removal by electrochemically produced ferrate (VI). Box-Behnken design was employed in this study, and design parameters were pH, Fe (VI) dose and initial dye concentration (Co). R2 and adjusted R2 values were very high that indicated very good accuracy for the employed model. Optimum operational conditions were: 4.08-7.69 for pH, 24-118.83 mg/L for Fe (VI) dose and 60.68-99.13 mg/L for complete removal of IC. Produced by electrochemical method Ferrate (VI) provides high effectiveness for IC dye-containing synthetic wastewater

CD10 expression in urothelial carcinoma of the bladder

Background. CD10 antigen is a 100-kDa-cell surface zinc metalloendopeptidase and it is expressed in a variety of normal and neoplastic lymphoid and nonlymphoid tissues. The aim of this study was to evaluate CD10 expression in urothelial carcinoma of the urinary bladder and to determine the correlation between immunohistochemical (IHC) CD10 expression and histopathologic parameters including grade and stage. Methods. 371 cases of urothelial bladder carcinomas, all from transurethral resections, were included in this study. Hematoxylin-eosin (HE) stained sections from each case were reevaluated histopathologically according to WHO 2004 grading system. The TNM system was used for pathologic staging. Selected slides were also studied by IHC and a semiquantitative scoring for CD10 expression based on the percentage of positive cells was performed. Results. 157 cases (42.3%) showed immunostaining while 214 cases (57.7%) were negative for CD10. 1+ staining was seen in 65 CD10 positive cases (41.4%), and 2+ in 92 cases (58.6%). Overall CD10 expression as well as 2+ immunostaining was significantly correlated with high histologic grade. Overall CD10 expression was also significantly higher in invasive pT1 and pT2-3 tumors compared to noninvasive pTa tumors. pT1 and pT2-3 tumors were also significantly correlated with 2+ immunostaining. Conclusion. To date, only a few comparative IHC studies have assessed CD10 expression in urothelial carcinoma of the urinary bladder and this study represents the largest series. Our findings indicate that CD10 expression is strongly correlated with high tumor grade and stage in urothelial carcinoma of the bladder, and that CD10 may be associated with tumor progression in bladder cancer pathogenesis. © 2009 Bahadir et al; licensee BioMed Central Ltd