Photoisomerising effects in nitroazo flexoelectric dimeric nematic systems

The photoisomerisation of a flexoelectric chiral nematic bimesogen system dyed with an azo dye has been investigated. The host material has a pitch and field dependent tilt angle that are temperature independent. Upon illumination by ultra violet, the azo dye molecules undergo a shape change from their trans to cis isomer. The effect of the shape change of the dye on the mixture is to decrease the I-N* transition temperatures, to increase the response times and to decrease the transmitted optical intensity. For the same reduced temperatures, the tilt angles, pitch and threshold voltages for the transition from focal conic to homeotropic textures are unchanged. The macroscopic parameters observed suggest that the orientational order parameter of the system is reduced by UV illumination. The cis isomers do not appear to separate from the host material or significantly change the flexoelectric coefficient. © 2001 OPA (Overseas Publishers Association) N.V. Published by license under the Gordon and Breach Science Publishers imprint, a member of the Taylor & Francis Group.

Photomechanically Induced Phase Transitions in Ferroelectric Liquid Crystals

We report optically induced phase transtions occurring in two different host ferroelectric liquid crystals; SCE13 a multicomponentmixture optimised for room temperature performance, and CE8 a single component liquid crystal. These act as host liquid crystals for a novel guest azo dye, which can be made to photoisomerise using low power density U.V. illumination, resulting in dramatic changes in sample properties. We have shown that the magnitude of spontaneous polarisation of systems can be isothermally and reversibly induced or reduced, with the consequent appearance or disappearance of optical switching hysteresis. We discuss the parameters controlling the behaviour of the systems under U.V. illumination and suggest mechansims by which the transitions may occur. © 1993, Taylor & Francis Group, LLC. All rights reserved.

Effect of the electrostatic interactions of chromophores on the macroscopic second-order nonlinear optical properties of the polymer films

The polyetherketone (PEK-c) guest-host system thin films doped with 3-(1,1-dicyanothenyl)-1-phenyl-4,5-dihydro-1H-pryazole (DCNP) were prepared. Their second-order nonlinear optical (NLO) coefficients chi(33)((2)) were measured by using Maker fringe method for the polymer films doped with different weight percents of DCNP. Experimental results indicate that the second-order NLO properties of the poled polymer films could decrease with the chromophore loading increasing when the chromophore loading reaches a fairly high level. In this paper, the relationship between the macroscopic second-order NLO coefficient and the chromophore number density was modified under considering the role of the electrostatic interactions of chromophores in the polymer film. According to the modified relationship, the macroscopic second-order NLO coefficient is no longer in direct proportion with the chromophore number density in the polymer film. The effect of the electrostatic interactions of chromophores on second-order NLO properties was discussed. The attenuation of the macroscopic second-order NLO activity can be demonstrated by the role of the chromophore electrostatic interactions at high loading of chromophore in the polymer systems.

Enhanced amplified spontaneous emission by assistant Forster energy transfer in DCJTB-C545T-Alq(3) coguest-host system

Amplified spontaneous emission (ASE) characteristics of a red fluorescent dye 4-(dicyanomethylene)-2-t-butyl-6(1,1,7,7-tetramethyljulolidyl-9-enyl)-4H-pyran (DCJTB) were significantly improved by assistant Forster energy transfer. The coguest-host system was composed of an electron transport organic molecule tris(8-hydroxyquinoline) aluminum (Alq(3)) as host and a green fluorescent dye (10-(2-benzothiazolyl)-1,1,7,7-tetramethyl-2,3,6,7-tetrahydro-1H,5H,11H-[1]benzopyrano[6,7,8-ij]quinolizin-11-one) (C545T) as assistant dopant codoped with the guest red dye DCJTB as emitter in a matrix of polystyrene (PS).

Novel Oligo-9,9 '-spirobifluorenes through ortho-Linkage as Full Hydrocarbon Host for Highly Efficient Phosphorescent OLEDs

4-Bromo-9,9'-spirobifluorene is facilely synthesized, and from this precursor, two ortho-linked oligo-9,9'-spirobifluorenes, 44BSF and 24TSF, are constructed. Devices with 24TSF as the full-hydrocarbon host material and Ir(ppy)(3) or (ppq)(2)Ir(acac) as the triplet emitter show maximum external quantum efficiencies of 12.6 and 10.5% for green and red electrophosphorescence, respectively.

White electrolumineseence from a single-polymer system with simultaneous two-color emission: Polyfluorene as the blue host and a 2,1,3-benzothiadiazole derivative as the orange dopant on the main chain

New single-polymer electroluminescent systems containing two individual emission species - polyfluorenes as a blue host and 2,1,3-benzothiadiazole derivative units as an orange dopant on the main chain - have been designed and synthesized. The resulting single polymers are found to have highly efficient white electroluminescence with simultaneous blue(lambda(max) = 421 nm/445 nm) and orange emission (lambda(max) = 564 nm)from the corresponding emitting species. The influence of the photoluminescence (PL) efficiencies of both the blue and orange species on the electroluminescence (EL) efficiencies of white polymer light-emitting diodes (PLEDs) based on the single-polymer systems has been investigated. The introduction of the highly efficient 4,7-bis(4-(N-phenyl-N-(4-methylphenyl)amino)phenyl)-2,1,3-benzothiadiazole unit to the main chain of polyfluorene provides significant improvement in EL efficiency. For a single-layer device fabricated in air (indium tin oxide/poly(3,4-ethylenedioxythiophene): poly(styrene sulfonic acid/polymer/Ca/Al), pure-white electroluminescence with Commission Internationale de l'Eclairage (CIE) coordinates of (0.35,0.32), maximum brightness of 12 300 cd m(-2), luminance efficiency of 7.30 cd A(-1), and power efficiency of 3.34 lm W-1 can be obtained.

Expressed sequence tags from the zhikong scallop (Chlamys farreri): Discovery and annotation of host-defense genes

A high-quality cDNA library was constructed from whole body tissues of the zhikong scallop, Chlamys farreri, challenged by Listonella anguillarum. A total of 5720 clones were sequenced, yielding 5123 expressed sequence tags (ESTs). Among the 3326 unique genes identified, 2289 (69%) genes had no significant (E-value < 1e-5) matches to known sequences in public databases and 194 (6%) matched proteins of unknown functions. The remaining 843 (25%) genes that exhibited homology with genes of known functions, showed broad involvement in metabolic processes (31%), cell structure and motility (20%), gene and protein expression (12%), cell signaling and cell communication (8%), cell division (4%), and notably, 25% of those genes were related to immune function. They included stress response genes, complement-like genes, proteinase and proteinase inhibitors, immune recognition receptors and immune effectors. The EST collection obtained in this study provides a useful resource for gene discovery and especially for the identification of host-defense genes and systems in scallops and other molluscs. (C) 2009 Elsevier Ltd. All rights reserved.

Efficient End-Host Architecture for High Performance Communication Using User-level Sandboxing

Current low-level networking abstractions on modern operating systems are commonly implemented in the kernel to provide sufficient performance for general purpose applications. However, it is desirable for high performance applications to have more control over the networking subsystem to support optimizations for their specific needs. One approach is to allow networking services to be implemented at user-level. Unfortunately, this typically incurs costs due to scheduling overheads and unnecessary data copying via the kernel. In this paper, we describe a method to implement efficient application-specific network service extensions at user-level, that removes the cost of scheduling and provides protected access to lower-level system abstractions. We present a networking implementation that, with minor modifications to the Linux kernel, passes data between "sandboxed" extensions and the Ethernet device without copying or processing in the kernel. Using this mechanism, we put a customizable networking stack into a user-level sandbox and show how it can be used to efficiently process and forward data via proxies, or intermediate hosts, in the communication path of high performance data streams. Unlike other user-level networking implementations, our method makes no special hardware requirements to avoid unnecessary data copies. Results show that we achieve a substantial increase in throughput over comparable user-space methods using our networking stack implementation.

Plasmid biology of natural Lactococcus lactis strains and molecular mechanisms of bacteriophage-host interaction

Lacticin 3147, enterocin AS-48, lacticin 481, variacin, and sakacin P are bacteriocins offering promising perspectives in terms of preservation and shelf-life extension of food products and should find commercial application in the near future. The studies detailing their characterization and bio-preservative applications are reviewed. Transcriptomic analyses showed a cell wall-targeted response of Lactococcus lactis IL1403 during the early stages of infection with the lytic bacteriophage c2, which is probably orchestrated by a number of membrane stress proteins and involves D-alanylation of membrane lipoteichoic acids, restoration of the physiological proton motive force disrupted following bacteriophage infection, and energy conservation. Sequencing of the eight plasmids of L. lactis subsp. cremoris DPC3758 from raw milk cheese revealed three anti-phage restriction/modification (R/M) systems, immunity/resistance to nisin, lacticin 481, cadmium and copper, and six conjugative/mobilization regions. A food-grade derivative strain with enhanced bacteriophage resistance was generated via stacking of R/M plasmids. Sequencing and functional analysis of the four plasmids of L. lactis subsp. lactis biovar. diacetylactis DPC3901 from raw milk cheese revealed genes novel to Lactococcus and typical of bacteria associated with plants, in addition to genes associated with plant-derived lactococcal strains. The functionality of a novel high-affinity regulated system for cobalt uptake was demonstrated. The bacteriophage resistant and bacteriocin-producing plasmid pMRC01 places a metabolic burden on lactococcal hosts resulting in lowered growth rates and increased cell permeability and autolysis. The magnitude of these effects is strain dependent but not related to bacteriocin production. Starters’ acidification capacity is not significantly affected. Transcriptomic analyses showed that pMRC01 abortive infection (Abi) system is probably subjected to a complex regulatory control by Rgg-like ORF51 and CopG-like ORF58 proteins. These regulators are suggested to modulate the activity of the putative Abi effectors ORF50 and ORF49 exhibiting topology and functional similarities to the Rex system aborting bacteriophage λ lytic growth.

Characterisation of bacteriophage-host interactions in Lactococcus lactis

Lactococcus lactis is used extensively world-wide for the production of fermented dairy products. Bacteriophages (phages) infecting L. lactis can result in slow or incomplete fermentations, or may even cause total fermentation failure. Therefore, bacteriophages disrupting L. lactis fermentation are of economic concern. This thesis employed a multifaceted approach to investigate various molecular aspects of phage-host interaction in L. lactis. The genome sequence of an Irish dairy starter strain, the prophage-cured L. lactis subsp. cremoris UC509.9, was studied. The 2,250,427 bp circular chromosome represents the smallest among its sequenced lactococcal equivalents. The genome displays clear genetic adaptation to the dairy niche in the form of extensive reductive evolution. Gene prediction identified 2066 protein-encoding genes, including 104 which showed significant homology to transposase-specifying genes. Over 9 % of the identified genes appear to be inactivated through stop codons or frame shift mutations. Many pseudogenes were found in genes that are assigned to carbohydrate and amino acid transport and metabolism orthologous groups, reflecting L. lactis UC509.9’s adaptation to the lactose and casein-rich dairy environment. Sequence analysis of the eight plasmids of L. lactis revealed extensive adaptation to the dairy environment. Key industrial phenotypes were mapped and novel lactococcal plasmid-associated genes highlighted. In addition to chromosomally-encoded bacteriophage resistance systems, six functional such systems were identified, including two abortive infection systems, AbiB and AbiD1, explaining the observed phage resistance of L. lactis UC509.9 Molecular analysis suggests that the constitutive expression of AbiB is not lethal to cells, suggesting the protein is expressed in an un/inactivated form. Analysis of 936 species phage sk1-escape mutants of AbiB revealed that all such mutants harbour mutations in orf6, which encodes the major capsid protein. Results suggest that the major capsid protein is required for activation of the AbiB system, although this requires furrther investigations. Temporal transcriptomes of L. lactis UC509.9 undergoing lytic infection with either one of two distinct bacteriophages, Tuc2009 and c2, was determined and compared to the transcriptome of uninfected UC509.9 cells. Whole genome microarrays performed at various time-points post-infection demonstrated a rather modest impact on host transcription. Alterations in the UC509.9 transcriptome during lytic infection appear phage-specific, with a relatively small number of differentially transcribed genes shared between infection with either Tuc2009 or c2. Transcriptional profiles of both bacteriophages during lytic infection was shown to generally correlate with previous studies and allowed the confirmation of previously predicted promoter sequences. Bioinformatic analysis of genomic regions encoding the presumed cell wall polysaccharide (CW PS) biosynthesis gene cluster of several strains of L. lactis was performed. Results demonstrate the presence of three dominant genetic types of this gene cluster, termed type A, B and C. These regions were used for the development of a multiplex PCR to identify CW PS genotype of various lactococcal strains. Analysis of 936 species phage receptor binding protein phylogeny (RBP) and CW PS genotype revealed an apparent correlation between RBP phylogeny and CW PS type, thereby providing a partial explanation for the observed narrow host range of 936 phages. Further analysis of the genetic locus encompassing the presumed CW PS biosynthesis operon of eight strains identified as belonging to the CW PS C (geno)type, revealed the presence of a variable region among the examined strains. The obtained comparative analysis allowed for the identification of five subgroups of the C type, named C1 to C5. We purified an acidic polysaccharide from the cell wall of L. lactis 3107 (C2 subtype) and confirmed that it is structurally different from the CW PS of the C1 subtype L. lactis MG1363. Combinations of genes from the variable region of C2 subtype were amplified from L. lactis 3107 and introduced into a mutant of the C1 subtype L. lactis NZ9000 (a direct derivative of MG1363) deficient in CW PS biosynthesis. The resulting recombinant mutant synthesized a CW PS with a composition characteristic for that of the C2 subtype L. lactis 3107 and not the wildtype C1 L. lactis NZ9000. The recombinant mutant exhibited a changed phage resistance/sensitivity profile consistent with that of L. lactis 3107, which unambiguously demonstrated that L. lactis 3107 CW PS is the host cell surface receptor of two bacteriophages belonging to the P335 species as well as phages that are member of the 936 species. The research presented in this thesis has significantly advanced our understanding of L. lactis bacteriophage-host interactions in several ways. Firstly, the examination of plasmidencoded bacteriophage resistance systems has allowed inferences to be made regarding the mode of action of AbiB, thereby providing a platform for further elucidation of the molecular trigger of this system. Secondly, the phage infection transcriptome data presented, in addition to previous work, has made L. lactis a model organism in terms of transcriptomic studies of bacteriophage-host interactions. And finally, the research described in this thesis has for the first time explicitly revealed the nature of a carbohydrate bacteriophage receptor in L. lactis, while also providing a logical explanation for the observed narrow host ranges exhibited by 936 and P335 phages. Future research in discerning the structures of other L. lactis CW PS, combined with the determination of the molecular interplay between receptor binding proteins of these phages and CW PS will allow an in depth understanding of the mechanism by which the most prevalent lactococcal phages identify and adsorb to their specific host.

Oscillations by minimal bacterial suicide circuits reveal hidden facets of host-circuit physiology.

Synthetic biology seeks to enable programmed control of cellular behavior though engineered biological systems. These systems typically consist of synthetic circuits that function inside, and interact with, complex host cells possessing pre-existing metabolic and regulatory networks. Nevertheless, while designing systems, a simple well-defined interface between the synthetic gene circuit and the host is frequently assumed. We describe the generation of robust but unexpected oscillations in the densities of bacterium Escherichia coli populations by simple synthetic suicide circuits containing quorum components and a lysis gene. Contrary to design expectations, oscillations required neither the quorum sensing genes (luxR and luxI) nor known regulatory elements in the P(luxI) promoter. Instead, oscillations were likely due to density-dependent plasmid amplification that established a population-level negative feedback. A mathematical model based on this mechanism captures the key characteristics of oscillations, and model predictions regarding perturbations to plasmid amplification were experimentally validated. Our results underscore the importance of plasmid copy number and potential impact of "hidden interactions" on the behavior of engineered gene circuits - a major challenge for standardizing biological parts. As synthetic biology grows as a discipline, increasing value may be derived from tools that enable the assessment of parts in their final context.

Host genetics and HIV-1: the final phase?

This is a crucial transition time for human genetics in general, and for HIV host genetics in particular. After years of equivocal results from candidate gene analyses, several genome-wide association studies have been published that looked at plasma viral load or disease progression. Results from other studies that used various large-scale approaches (siRNA screens, transcriptome or proteome analysis, comparative genomics) have also shed new light on retroviral pathogenesis. However, most of the inter-individual variability in response to HIV-1 infection remains to be explained: genome resequencing and systems biology approaches are now required to progress toward a better understanding of the complex interactions between HIV-1 and its human host.

A forum on case-based reasoning. Guest editorial

Guest editorial

Computational modelling of multi-physics processes on high performance parallel computer systems

The demands of the process of engineering design, particularly for structural integrity, have exploited computational modelling techniques and software tools for decades. Frequently, the shape of structural components or assemblies is determined to optimise the flow distribution or heat transfer characteristics, and to ensure that the structural performance in service is adequate. From the perspective of computational modelling these activities are typically separated into: • fluid flow and the associated heat transfer analysis (possibly with chemical reactions), based upon Computational Fluid Dynamics (CFD) technology • structural analysis again possibly with heat transfer, based upon finite element analysis (FEA) techniques.

Fitting host-parasitoid models with CV² > 1 using hierarchical generalized linear models

The powerful general Pacala-Hassell host-parasitoid model for a patchy environment, which allows host density–dependent heterogeneity (HDD) to be distinguished from between-patch, host density–independent heterogeneity (HDI), is reformulated within the class of the generalized linear model (GLM) family. This improves accessibility through the provision of general software within well–known statistical systems, and allows a rich variety of models to be formulated. Covariates such as age class, host density and abiotic factors may be included easily. For the case where there is no HDI, the formulation is a simple GLM. When there is HDI in addition to HDD, the formulation is a hierarchical generalized linear model. Two forms of HDI model are considered, both with between-patch variability: one has binomial variation within patches and one has extra-binomial, overdispersed variation within patches. Examples are given demonstrating parameter estimation with standard errors, and hypothesis testing. For one example given, the extra-binomial component of the HDI heterogeneity in parasitism is itself shown to be strongly density dependent.