Comparative genomic analysis of the Tribolium immune system

The annotation, and comparison with homologous genes in other species, of immunity-related genes in the Tribolium castaneum genome allowed the identification of around 300 candidate defense proteins, and revealed a framework of information on Tribolium immunity

Evolution of genes and repeats in the Nimrod superfamily

The recently identified Nimrod superfamily is characterized by the presence of a special type of EGF repeat, the NIM repeat, located right after a typical CCXGY/W amino acid motif. On the basis of structural features, nimrod genes can be divided into three types. The proteins encoded by Draper-type genes have an EMI domain at the N-terminal part and only one copy of the NIM motif, followed by a variable number of EGF-like repeats. The products of Nimrod B-type and Nimrod C-type genes (including the eater gene) have different kinds of N-terminal domains, and lack EGF-like repeats but contain a variable number of NIM repeats. Draper and Nimrod C-type (but not Nimrod B-type) proteins carry a transmembrane domain. Several members of the superfamily were claimed to function as receptors in phagocytosis and/or binding of bacteria, which indicates an important role in the cellular immunity and the elimination of apoptotic cells. In this paper, the evolution of the Nimrod superfamily is studied with various methods on the level of genes and repeats. A hypothesis is presented in which the NIM repeat, along with the EMI domain, emerged by structural reorganizations at the end of an EGF-like repeat chain, suggesting a mechanism for the formation of novel types of repeats. The analyses revealed diverse evolutionary patterns in the sequences containing multiple NIM repeats. Although in the Nimrod B and Nimrod C proteins show characteristics of independent evolution, many internal NIM repeats in Eater sequences seem to have undergone concerted evolution. An analysis of the nimrod genes has been performed using phylogenetic and other methods and an evolutionary scenario of the origin and diversification of the Nimrod superfamily is proposed. Our study presents an intriguing example how the evolution of multigene families may contribute to the complexity of the innate immune response

Tuning of the elastic modulus of a soft polythiophene through molecular doping

Molecular doping of a polythiophene with oligoethylene glycol side chains is found to strongly modulate not only the electrical but also the mechanical properties of the polymer. An oxidation level of up to 18% results in an electrical conductivity of more than 52 S cm(-1) and at the same time significantly enhances the elastic modulus from 8 to more than 200 MPa and toughness from 0.5 to 5.1 MJ m(-3). These changes arise because molecular doping strongly influences the glass transition temperature T-g and the degree of pi-stacking of the polymer, as indicated by both X-ray diffraction and molecular dynamics simulations. Surprisingly, a comparison of doped materials containing mono- or dianions reveals that - for a comparable oxidation level - the presence of multivalent counterions has little effect on the stiffness. Evidently, molecular doping is a powerful tool that can be used for the design of mechanically robust conducting materials, which may find use within the field of flexible and stretchable electronics

Obtaining accurate mean velocity measurements in high Reynolds number turbulent boundary layers using Pitot tubes

This article reports on one component of a larger study on measurement of the zero-pressure-gradient turbulent flat plate boundary layer, in which a detailed investigation was conducted of the suite of corrections required for mean velocity measurements performed using Pitot tubes. In particular, the corrections for velocity shear across the tube and for blockage effects which occur when the tube is in close proximity to the wall were investigated using measurements from Pitot tubes of five different diameters, in two different facilities, and at five different Reynolds numbers ranging from Re_θ = 11 100 to 67 000. Only small differences were found amongst commonly used corrections for velocity shear, but improvements were found for existing near-wall proximity corrections. Corrections for the nonlinear averaging of the velocity fluctuations were also investigated, and the results compared to hot-wire data taken as part of the same measurement campaign. The streamwise turbulence-intensity correction was found to be of comparable magnitude to that of the shear correction, and found to bring the hot-wire and Pitot results into closer agreement when applied to the data, along with the other corrections discussed and refined here

Wall roughness induces asymptotic ultimate turbulence

Turbulence is omnipresent in Nature and technology, governing the transport of heat, mass, and momentum on multiple scales. For real-world applications of wall-bounded turbulence, the underlying surfaces are virtually always rough; yet characterizing and understanding the effects of wall roughness for turbulence remains a challenge, especially for rotating and thermally driven turbulence. By combining extensive experiments and numerical simulations, here, taking as example the paradigmatic Taylor-Couette system (the closed flow between two independently rotating coaxial cylinders), we show how wall roughness greatly enhances the overall transport properties and the corresponding scaling exponents. If only one of the walls is rough, we reveal that the bulk velocity is slaved to the rough side, due to the much stronger coupling to that wall by the detaching flow structures. If both walls are rough, the viscosity dependence is thoroughly eliminated in the boundary layers and we thus achieve asymptotic ultimate turbulence, i.e. the upper limit of transport, whose existence had been predicted by Robert Kraichnan in 1962 (Phys. Fluids {\bf 5}, 1374 (1962)) and in which the scalings laws can be extrapolated to arbitrarily large Reynolds numbers

Origins of the open-circuit voltage in ternary organic solar cells and design rules for minimized voltage losses

The power conversion efficiency of ternary organic solar cells (TOSCs), consisting of one host binary blend and one guest component, remains limited by large voltage losses. The fundamental understanding of the open-circuit voltage (V OC) in TOSCs is controversial, limiting rational design of the guest component. In this study, we systematically investigate how the guest component affects the radiative and non-radiative related parts of V OC of a series of TOSCs using the detailed balanced principle. We highlight that the thermal population of charge-transfer and local exciton states provided by the guest binary blend (that is, the guest-component-based binary blend) has a significant influence on the non-radiative voltage losses. Ultimately, we provide two design rules for enhancing the V OC in TOSCs: high emission yield for the guest binary blend and similar charge-transfer-state energies for host/guest binary blends; high miscibility of the guest component with the low gap component in the host binary blend

Immune pathways and defence mechanisms in honey bees Apis mellifera

Social insects are able to mount both group-level and individual defences against pathogens. Here we focus on individual defences, by presenting a genome-wide analysis of immunity in a social insect, the honey bee Apis mellifera. We present honey bee models for each of four signalling pathways associated with immunity, identifying plausible orthologues for nearly all predicted pathway members. When compared to the sequenced Drosophila and Anopheles genomes, honey bees possess roughly one-third as many genes in 17 gene families implicated in insect immunity. We suggest that an implied reduction in immune flexibility in bees reflects either the strength of social barriers to disease, or a tendency for bees to be attacked by a limited set of highly coevolved pathogens

Nora Virus Persistent Infections Are Not Affected by the RNAi Machinery

Drosophila melanogaster is widely used to decipher the innate immune system in response to various pathogens. The innate immune response towards persistent virus infections is among the least studied in this model system. We recently discovered a picorna-like virus, the Nora virus which gives rise to persistent and essentially symptom-free infections in Drosophila melanogaster. Here, we have used this virus to study the interaction with its host and with some of the known Drosophila antiviral immune pathways. First, we find a striking variability in the course of the infection, even between flies of the same inbred stock. Some flies are able to clear the Nora virus but not others. This phenomenon seems to be threshold-dependent; flies with a high-titer infection establish stable persistent infections, whereas flies with a lower level of infection are able to clear the virus. Surprisingly, we find that both the clearance of low-level Nora virus infections and the stability of persistent infections are unaffected by mutations in the RNAi pathways. Nora virus infections are also unaffected by mutations in the Toll and Jak-Stat pathways. In these respects, the Nora virus differs from other studied Drosophila RNA viruses

Binding of protegrin-1 to Pseudomonas aeruginosa and Burkholderia cepacia

BACKGROUND: Pseudomonas aeruginosa and Burkholderia cepacia infections of cystic fibrosis patients' lungs are often resistant to conventional antibiotic therapy. Protegrins are antimicrobial peptides with potent activity against many bacteria, including P. aeruginosa. The present study evaluates the correlation between protegrin-1 (PG-1) sensitivity/resistance and protegrin binding in P. aeruginosa and B. cepacia. METHODS: The PG-1 sensitivity/resistance and PG-1 binding properties of P. aeruginosa and B. cepacia were assessed using radial diffusion assays, radioiodinated PG-1, and surface plasmon resonance (BiaCore). RESULTS: The six P. aeruginosa strains examined were very sensitive to PG-1, exhibiting minimal active concentrations from 0.0625–0.5 μg/ml in radial diffusion assays. In contrast, all five B. cepacia strains examined were greater than 10-fold to 100-fold more resistant, with minimal active concentrations ranging from 6–10 μg/ml. When incubated with a radioiodinated variant of PG-1, a sensitive P. aeruginosa strain bound considerably more protegrin molecules per cell than a resistant B. cepacia strain. Binding/diffusion and surface plasmon resonance assays revealed that isolated lipopolysaccharide (LPS) and lipid A from the sensitive P. aeruginosa strains bound PG-1 more effectively than LPS and lipid A from resistant B. cepacia strains. CONCLUSION: These findings support the hypothesis that the relative resistance of B. cepacia to protegrin is due to a reduced number of PG-1 binding sites on the lipid A moiety of its LPS

Carbohydrate metabolism genes and pathways in insects: insights from the honey bee genome

Carbohydrate-metabolizing enzymes may have particularly interesting roles in the honey bee, Apis mellifera, because this social insect has an extremely carbohydrate-rich diet, and nutrition plays important roles in caste determination and socially mediated behavioural plasticity. We annotated a total of 174 genes encoding carbohydrate-metabolizing enzymes and 28 genes encoding lipid-metabolizing enzymes, based on orthology to their counterparts in the fly, Drosophila melanogaster, and the mosquito, Anopheles gambiae. We found that the number of genes for carbohydrate metabolism appears to be more evolutionarily labile than for lipid metabolism. In particular, we identified striking changes in gene number or genomic organization for genes encoding glycolytic enzymes, cellulase, glucose oxidase and glucose dehydrogenases, glucose-methanol-choline (GMC) oxidoreductases, fucosyltransferases, and lysozymes