Molecular analysis of asymptomatic bacteriuria escherichia coli strain VR50 reveals adaptation to the urinary tract by gene acquisition

Urinary tract infections (UTIs) are among the most common infectious diseases of humans, with Escherichia coli responsible for >80% of all cases. One extreme of UTI is asymptomatic bacteriuria (ABU), which occurs as an asymptomatic carrier state that resembles commensalism. To understand the evolution and molecular mechanisms that underpin ABU, the genome of the ABU E. coli strain VR50 was sequenced. Analysis of the complete genome indicated that it most resembles E. coli K-12, with the addition of a 94-kb genomic island (GI-VR50-pheV), eight prophages, and multiple plasmids. GI-VR50-pheV has a mosaic structure and contains genes encoding a number of UTI-associated virulence factors, namely, Afa (afimbrial adhesin), two autotransporter proteins (Ag43 and Sat), and aerobactin. We demonstrated that the presence of this island in VR50 confers its ability to colonize the murine bladder, as a VR50 mutant with GI-VR50-pheV deleted was attenuated in a mouse model of UTI in vivo. We established that Afa is the island-encoded factor responsible for this phenotype using two independent deletion (Afa operon and AfaE adhesin) mutants. E. coli VR50afa and VR50afaE displayed significantly decreased ability to adhere to human bladder epithelial cells. In the mouse model of UTI, VR50afa and VR50afaE displayed reduced bladder colonization compared to wild-type VR50, similar to the colonization level of the GI-VR50-pheV mutant. Our study suggests that E. coli VR50 is a commensal-like strain that has acquired fitness factors that facilitate colonization of the human bladder.

Versatile single-layer sodium phosphidostannate(II): Strain-tunable electronic structure, excellent mechanical flexibility, and an ideal gap for photovoltaics

Density functional theory (DFT) calculations were performed to study the structural, mechanical, electrical, optical properties, and strain effects in single-layer sodium phosphidostannate(II) (NaSnP). We find the exfoliation of single-layer NaSnP from bulk form is highly feasible because the cleavage energy is comparable to graphite and MoS2. In addition, the breaking strain of the NaSnP monolayer is comparable to other widely studied 2D materials, indicating excellent mechanical flexibility of 2D NaSnP. Using the hybrid functional method, the calculated band gap of single-layer NaSnP is close to the ideal band gap of solar cell materials (1.5 eV), demonstrating great potential in future photovoltaic application. Furthermore, strain effect study shows that a moderate compression (2%) can trigger indirect-to-direct gap transition, which would enhance the ability of light absorption for the NaSnP monolayer. With sufficient compression (8%), the single-layer NaSnP can be tuned from semiconductor to metal, suggesting great applications in nanoelectronic devices based on strain engineering techniques.

Strain- and host species-specific inflammasome activation, IL-1β release, and cell death in macrophages infected with uropathogenic Escherichia coli

Uropathogenic Escherichia coli (UPEC) is the main etiological agent of urinary tract infections (UTIs). Little is known about interactions between UPEC and the inflammasome, a key innate immune pathway. Here we show that UPEC strains CFT073 and UTI89 trigger inflammasome activation and lytic cell death in human macrophages. Several other UPEC strains, including two multidrug-resistant ST131 isolates, did not kill macrophages. In mouse macrophages, UTI89 triggered cell death only at a high multiplicity of infection, and CFT073-mediated inflammasome responses were completely NLRP3-dependent. Surprisingly, CFT073- and UTI89-mediated responses only partially depended on NLRP3 in human macrophages. In these cells, NLRP3 was required for interleukin-1β (IL-1β) maturation, but contributed only marginally to cell death. Similarly, caspase-1 inhibition did not block cell death in human macrophages. In keeping with such differences, the pore-forming toxin α-hemolysin mediated a substantial proportion of CFT073-triggered IL-1β secretion in mouse but not human macrophages. There was also a more substantial α-hemolysin-independent cell death response in human vs. mouse macrophages. Thus, in mouse macrophages, CFT073-triggered inflammasome responses are completely NLRP3-dependent, and largely α-hemolysin-dependent. In contrast, UPEC activates an NLRP3-independent cell death pathway and an α-hemolysin-independent IL-1β secretion pathway in human macrophages. This has important implications for understanding UTI in humans.

Carbon concentration dependent grain growth of Cu2ZnSnS4thin films

Organic solvents are commonly used in ink precursors of Cu2ZnSnS4 (CZTS) nanocrystals to make thin films for applications such as solar cells. However, the traces of carbon residual left behind by the organic solvents after high-temperature annealing is generally considered to restrict the growth of nanocrystals to form large grains. This work reported the first systematic study on the influence of carbon content of organic solvents on the grain growth of CZTS nanomaterial during high temperature sulfurization annealing. Solvents with carbon atom per molecule varying from 3 to 10 were used to made ink of CZTS nanocrystals for thin film deposition. It has been found that, after high temperature sulfurization annealing, a bilayer structure was formed in the CZTS film using organic solvent containing 3 carbon atoms per solvent molecule based on glycerol and 1,3-propanediol. The top layer consisted of closelypacked large grains and the bottom layer was made of as-synthesized nanoparticles. In contrast, the CZTS film made with the solvent molecule with more carbon atoms including 1,5-pentanediol (5 carbon atoms) and 1,7-heptanediol (7 carbon atoms) consisted of nanoparticles embedded with large crystals. It is believed that the carbon residues left behind by the organic solvents affected the necking of CZTS nanocrystals to form large grains through influencing the surface property of nanocrystals. Furthermore, it has also been observed that the solvent affected the thickness of MoS2 layer which was formed between CZTS and Mo substrate. A thinner MoS2 film (50 nm) was obtained with the slurry using carbon-rich terpineol as solvent whereas the thickest MoS2 (350 nm) was obtained with the film made from 1,3-propanediol based solvent. The evaluation of the photoactivity of the CZTS thin films has demonstrated that a higher photocurrent was generated with the film containing more large grains.

Effects of metal ion concentration on electrodeposited CuZnSn film and its application in kesterite Cu2ZnSnS4solar cells

In this study, effects of concentrations of Cu(II), Zn(II) and Sn(II) ions in the electrolytic bath solution on the properties of electrochemically deposited CuZnSn (CZT) films were investigated. Study of the composition of a CZT film has shown that the metallic content (relative atomic ratio) in the film increased linearly with increase in the metal ion concentration. It is the first time that the relationship of the compositions of the alloy phases in the co-electrodeposited CZT film with the concentration of metal ions has been revealed. The results have confirmed that the formation and content of Cu6Sn5 and Cu5Zn8 alloy phases in the film were directly controlled by the concentration of Cu(II). SEM measurements have shown that Sn(II) has significant impact on film morphology, which became more porous as a result of the larger nucleation size of tin. The changes in the surface properties of the films was also confirmed by chronoamperometry characteristic (i–t) deposition curves. By optimization of metal ion concentrations in the electrolyte solution, a copper-poor and zinc-rich kesterite Cu2ZnSnS4 (CZTS) film was synthesized by the sulfurization of the deposited CZT film. The solar cell with the CZTS film showed an energy conversion efficiency of 2.15% under the illumination intensity of 100 mW cm 2.

Single layer lead iodide: Computational exploration of structural, electronic and optical properties, strain induced band modulation and the role of spin-orbital-coupling

Graphitic like layered materials exhibit intriguing electronic structures and thus the search for new types of two-dimensional (2D) monolayer materials is of great interest for developing novel nano-devices. By using density functional theory (DFT) method, here we for the first time investigate the structure, stability, electronic and optical properties of monolayer lead iodide (PbI2). The stability of PbI2 monolayer is first confirmed by phonon dispersion calculation. Compared to the calculation using generalized gradient approximation, screened hybrid functional and spin–orbit coupling effects can not only predicts an accurate bandgap (2.63 eV), but also the correct position of valence and conduction band edges. The biaxial strain can tune its bandgap size in a wide range from 1 eV to 3 eV, which can be understood by the strain induced uniformly change of electric field between Pb and I atomic layer. The calculated imaginary part of the dielectric function of 2D graphene/PbI2 van der Waals type hetero-structure shows significant red shift of absorption edge compared to that of a pure monolayer PbI2. Our findings highlight a new interesting 2D material with potential applications in nanoelectronics and optoelectronics.

Genome sequence of marine bacterium idiomarina sp. strain 28-8, isolated from Korean ark shells

Idiomarina sp. strain 28-8 is an aerobic, Gram-negative, flagellar bacterium isolated from the bodies of ark shells (Scapharca broughtonii) collected from underwater sediments in Gangjin Bay, South Korea. Here, we present the draft genome sequence of Idiomarina sp. 28-8 (2,971,606 bp, with a G+C content of 46.9%), containing 2,795 putative coding sequences.

Small gold nanoparticles as crystallization "catalysts": Effect of seed size and concentration on Au-ZnO hetero nanoparticles

This work reports the effect of seed nanoparticle size and concentration effects on heterogeneous crystal nucleation and growth in colloidal suspensions. We examined these effects in the Au nanoparticle-seeded growth of Au-ZnO hetero-nanocrystals under synthesis conditions that generate hexagonal, cone-shaped ZnO nanocrystals. It was observed that small (~ 4 nm) Au seed nanoparticles form one-to-one Au-ZnO hetero dimers and that Au nanoparticle seeds of this size can also act as crystallization ‘catalysts’ that readily promote the nucleation and growth of ZnO nanocrystals. Larger seed nanoparticles (~9 nm, ~ 11 nm) provided multiple, stable ZnO-nucleation sites, generating multi-crystalline hetero trimers, tetramers and oligomers.

Shaping development through mechanical strain: The transcriptional basis of diet-induced phenotypic plasticity in a cichlid fish

Adaptive phenotypic plasticity, the ability of an organism to change its phenotype to match local environments, is increasingly recognized for its contribution to evolution. However, few empirical studies have explored the molecular basis of plastic traits. The East African cichlid fish Astatoreochromis alluaudi displays adaptive phenotypic plasticity in its pharyngeal jaw apparatus, a structure that is widely seen as an evolutionary key innovation that has contributed to the remarkable diversity of cichlid fishes. It has previously been shown that in response to different diets, the pharyngeal jaws change their size, shape and dentition: hard diets induce an adaptive robust molariform tooth phenotype with short jaws and strong internal bone structures, while soft diets induce a gracile papilliform tooth phenotype with elongated jaws and slender internal bone structures. To gain insight into the molecular underpinnings of these adaptations and enable future investigations of the role that phenotypic plasticity plays during the formation of adaptive radiations, the transcriptomes of the two divergent jaw phenotypes were examined. Our study identified a total of 187 genes whose expression differs in response to hard and soft diets, including immediate early genes, extracellular matrix genes and inflammatory factors. Transcriptome results are interpreted in light of expression of candidate genesmarkers for tooth size and shape, bone cells and mechanically sensitive pathways. This study opens up new avenues of research at new levels of biological organization into the roles of phenotypic plasticity during speciation and radiation of cichlid fishes.

A Chlamydia trachomatis strain with a chemically generated amino acid substitution (P370L) in the cthtrA gene shows reduced elementary body production

Background Chlamydia (C.) trachomatis is the most prevalent bacterial sexually transmitted infection worldwide and the leading cause of preventable blindness. Genetic approaches to investigate C. trachomatis have been only recently developed due to the organism’s intracellular developmental cycle. HtrA is a critical stress response serine protease and chaperone for many bacteria and in C. trachomatis has been previously shown to be important for heat stress and the replicative phase of development using a chemical inhibitor of the CtHtrA activity. In this study, chemically-induced SNVs in the cthtrA gene that resulted in amino acid substitutions (A240V, G475E, and P370L) were identified and characterized. Methods SNVs were initially biochemically characterized in vitro using recombinant protein techniques to confirm a functional impact on proteolysis. The C. trachomatis strains containing the SNVs with marked reductions in proteolysis were investigated in cell culture to identify phenotypes that could be linked to CtHtrA function. Results The strain harboring the SNV with the most marked impact on proteolysis (cthtrAP370L) was detected to have a significant reduction in the production of infectious elementary bodies. Conclusions This provides genetic evidence that CtHtrA is critical for the C. trachomatis developmental cycle.

Hyaluronic acid enhances the mechanical properties of tissue-engineered cartilage constructs

There is a need for materials that are well suited for cartilage tissue engineering. Hydrogels have emerged as promising biomaterials for cartilage repair, since, like cartilage, they have high water content, and they allow cells to be encapsulated within the material in a genuinely three-dimensional microenvironment. In this study, we investigated the mechanical properties of tissue-engineered cartilage constructs using in vitro culture models incorporating human chondrocytes from osteoarthritis patients. We evaluated hydrogels formed from mixtures of photocrosslinkable gelatin-methacrylamide (Gel-MA) and varying concentrations (0–2%) of hyaluronic acid methacrylate (HA-MA). Initially, only small differences in the stiffness of each hydrogel existed. After 4 weeks of culture, and to a greater extent 8 weeks of culture, HA-MA had striking and concentration dependent impact on the changes in mechanical properties. For example, the initial compressive moduli of cell-laden constructs with 0 and 1% HA-MA were 29 and 41 kPa, respectively. After 8 weeks of culture, the moduli of these constructs had increased to 66 and 147 kPa respectively, representing a net improvement of 69 kPa for gels with 1% HA-MA. Similarly the equilibrium modulus, dynamic modulus, failure strength and failure strain were all improved in constructs containing HA-MA. Differences in mechanical properties did not correlate with glycosaminoglycan content, which did not vary greatly between groups, yet there were clear differences in aggrecan intensity and distribution as assessed using immunostaining. Based on the functional development with time in culture using human chondrocytes, mixtures of Gel-MA and HA-MA are promising candidates for cartilage tissue-engineering applications.

Influential parameters on particle concentration and size distribution in the mainstream of e-cigarettes

Electronic cigarette-generated mainstream aerosols were characterized in terms of particle number concentrations and size distributions through a Condensation Particle Counter and a Fast Mobility Particle Sizer spectrometer, respectively. A thermodilution system was also used to properly sample and dilute the mainstream aerosol. Different types of electronic cigarettes, liquid flavors, liquid nicotine contents, as well as different puffing times were tested. Conventional tobacco cigarettes were also investigated. The total particle number concentration peak (for 2-s puff), averaged across the different electronic cigarette types and liquids, was measured equal to 4.39 ± 0.42 × 109 part. cm−3, then comparable to the conventional cigarette one (3.14 ± 0.61 × 109 part. cm−3). Puffing times and nicotine contents were found to influence the particle concentration, whereas no significant differences were recognized in terms of flavors and types of cigarettes used. Particle number distribution modes of the electronic cigarette-generated aerosol were in the 120–165 nm range, then similar to the conventional cigarette one.

Dependence of light attenuation and backscattering on collagen concentration and chondrocyte density in agarose scaffolds

Optical coherence tomography (OCT) has been applied for high resolution imaging of articular cartilage. However, the contribution of individual structural elements of cartilage on OCT signal has not been thoroughly studied. We hypothesize that both collagen and chondrocytes, essential structural components of cartilage, act as important light scatterers and that variation in their concentrations can be detected by OCT through changes in backscattering and attenuation. To evaluate this hypothesis, we established a controlled model system using agarose scaffolds embedded with variable collagen concentrations and chondrocyte densities. Using OCT, we measured the backscattering coefficient (µb) and total attenuation coefficient (µt) in these scaffolds. Along our hypothesis, light backscattering and attenuation in agarose were dependent on collagen concentration and chondrocyte density. Significant correlations were found between µt and chondrocyte density (ρ = 0.853, p < 0.001) and between µt and collagen concentration (ρ = 0.694, p < 0.001). µb correlated significantly with chondrocyte density (ρ = 0.504, p < 0.001) but not with collagen concentration (ρ = 0.103, p = 0.422) of the scaffold. Thus, quantitation of light backscattering and, especially, attenuation could be valuable when evaluating the integrity of soft tissues, such as articular cartilage with OCT.

Role of enhanced vector transmission of a new West Nile virus strain in an outbreak of equine disease in Australia in 2011

Background In 2011, a variant of West Nile virus Kunjin strain (WNVKUN) caused an unprecedented epidemic of neurological disease in horses in southeast Australia, resulting in almost 1,000 cases and a 9% fatality rate. We investigated whether increased fitness of the virus in the primary vector, Culex annulirostris, and another potential vector, Culex australicus, contributed to the widespread nature of the outbreak. Methods Mosquitoes were exposed to infectious blood meals containing either the virus strain responsible for the outbreak, designated WNVKUN2011, or WNVKUN2009, a strain of low virulence that is typical of historical strains of this virus. WNVKUN infection in mosquito samples was detected using a fixed cell culture enzyme immunoassay and a WNVKUN- specific monoclonal antibody. Probit analysis was used to determine mosquito susceptibility to infection. Infection, dissemination and transmission rates for selected days post-exposure were compared using Fisher’s exact test. Virus titers in bodies and saliva expectorates were compared using t-tests. Results There were few significant differences between the two virus strains in the susceptibility of Cx. annulirostris to infection, the kinetics of virus replication and the ability of this mosquito species to transmit either strain. Both strains were transmitted by Cx. annulirostris for the first time on day 5 post-exposure. The highest transmission rates (proportion of mosquitoes with virus detected in saliva) observed were 68% for WNVKUN2011 on day 12 and 72% for WNVKUN2009 on day 14. On days 12 and 14 post-exposure, significantly more WNVKUN2011 than WNVKUN2009 was expectorated by infected mosquitoes. Infection, dissemination and transmission rates of the two strains were not significantly different in Culex australicus. However, transmission rates and the amount of virus expectorated were significantly lower in Cx. australicus than Cx. annulirostris. Conclusions The higher amount of WNVKUN2011 expectorated by infected mosquitoes may be an indication that this virus strain is transmitted more efficiently by Cx. annulirostris compared to other WNVKUN strains. Combined with other factors, such as a convergence of abundant mosquito and wading bird populations, and mammalian and avian feeding behaviour by Cx. annulirostris, this may have contributed to the scale of the 2011 equine epidemic.

Experimental studies on the performance of rail joints with modified wheel/railhead contact

Rail joints are provided with a gap to account for thermal movement and to maintain electrical insulation for the control of signals and/or broken rail detection circuits. The gap in the rail joint is regarded as a source of significant problems for the rail industry since it leads to a very short rail service life compared with other track components due to the various, and difficult to predict, failure modes – thus increasing the risk for train operations. Many attempts to improve the life of rail joints have led to a large number of patents around the world; notable attempts include strengthening through larger-sized joint bars, an increased number of bolts and the use of high yield materials. Unfortunately, no design to date has shown the ability to prolong the life of the rail joints to values close to those for continuously welded rail (CWR). This paper reports the results of a fundamental study that has revealed that the wheel contact at the free edge of the railhead is a major problem since it generates a singularity in the contact pressure and railhead stresses. A design was therefore developed using an optimisation framework that prevents wheel contact at the railhead edge. Finite element modelling of the design has shown that the contact pressure and railhead stress singularities are eliminated, thus increasing the potential to work as effectively as a CWR that does not have a geometric gap. An experimental validation of the finite element results is presented through an innovative non-contact measurement of strains. Some practical issues related to grinding rails to the optimal design are also discussed.