Morphological and molecular characteristics of a new species of Pasteuria parasitic on Meloidogyne ardenensis

A species of the hyper-parasitic bacterium Pasteuria was isolated from the root-knot nematode Meloidogyne ardenensis infecting the roots of ash (Fraxinus excelsior). It is morphologically different from some other Pasteuria pathogens of nematodes in that the spores lack a basal ring on the ventral side of the spore and have a unique clumping nature. Transmission electron microscopy (TEM) showed that the clumps of spores are not random aggregates but result from the disintegration of the suicide cells of the thalli. Sporulation within each vegetative mycelium was shown to be asynchronous. In addition to the novel morphological features 16S rRNA sequence analysis showed this to be a new species of Pasteuria which we have called P. hartismeri. Spores of P. hartismeri attach to juveniles of root-knot nematodes infecting a wide range of plants such as mint (Meloidogyne hapla), rye grass (unidentified Meloidogyne sp.) and potato (Meloidogyne fallax).

Dip in the gene pool: metagenomic survey of natural coccolithovirus communities

Despite the global oceanic distribution and recognized biogeochemical impact of coccolithoviruses (EhV), their diversity remains poorly understood. Here we employed a metagenomic approach to study the occurrence and progression of natural EhV community genomic variability. Analysis of EhV metagenomes from the early and late stages of an induced bloom led to three main discoveries. First, we observed resilient and specific genomic signatures in the EhV community associated with the Norwegian coast, which reinforce the existence of limitations to the capacity of dispersal and genomic exchange among EhV populations. Second, we identified a hyper-variable region (approximately 21 kbp long) in the coccolithovirus genome. Third, we observed a clear trend for EhV relative amino-acid diversity to reduce from early to late stages of the bloom. This study validated two new methodological combinations, and proved very useful in the discovery of new genomic features associated with coccolithovirus natural communities.

Dip in the gene pool: metagenomic survey of natural coccolithovirus communities

Despite the global oceanic distribution and recognised biogeochemical impact of coccolithoviruses (EhV), their diversity remains poorly understood. Here we employed a metagenomic approach to study the occurrence and progression of natural EhV community genomic variability. Analysis of EhV metagenomes from the early and late stages of an induced bloom led to three main discoveries. First, we observed resilient and specific genomic signatures in the EhV community associated with the Norwegian coast, which reinforce the existence of limitations to the capacity of dispersal and genomic exchange among EhV populations. Second, we identified a hyper-variable region (approximately 21kbp long) in the coccolithovirus genome. Third, we observed a clear trend for EhV relative amino-acid diversity to reduce from early to late stages of the bloom. This study validated two new methodological combinations, and proved very useful in the discovery of new genomic features associated with coccolithovirus natural communities.

Identification of Genes Involved in the C. elegans VAB-1 Eph Receptor Tyrosine Kinase Signaling Pathway

The generation of a functional nervous system requires that neuronal cells and axons navigate precisely to their appropriate targets. The Eph Receptor Tyrosine Kinases (RTKs) and their ephrin ligands have emerged as one of the important guidance cues for neuronal and axon navigation. However, the molecular mechanisms of how Eph RTKs regulate these processes are still incomplete. The purpose of this work was to contribute to the understanding of how Eph receptors regulate axon guidance by identifying and characterizing components of the Caenorhabditis elegans Eph RTK (VAB-1) signaling pathway. To achieve this objective I utilized a hyper active form of the VAB-1 Eph RTK (MYR-VAB-1) that caused penetrant axon guidance defects in the PLM mechanosensory neurons, and screened for suppressors of the MYR-VAB-1 phenotype. Through a candidate gene approach, I identified the adaptor NCK-1 as a downstream effector of VAB-1. Molecular and genetic analysis revealed that the nck-1 gene encodes for two isoforms (NCK-1A and NCK-1B) that share similar expression patterns in parts of the nervous system, but also have independent expression patterns in other tissues. Genetic rescue experiments showed that both NCK-1 isoforms can function in axon guidance, but each isoform also has specific functions. In vitro binding assays showed that NCK-1 binds to VAB-1 in a kinase dependent manner. In addition to NCK-1, WSP-1/N-WASP was also identified as an effector of VAB-1 signaling. Phenotypic analysis showed that nck-1 and wsp-1 mutants had PLM axon over extension defects similar to vab-1 animals. Furthermore, VAB-1, NCK-1 and WSP-1 formed a complex in vitro. Intriguingly, protein binding assays showed that NCK-1 can also bind to the actin regulator UNC-34/Ena, but genetic experiments suggest that unc-34 is an inhibitor of nck-1 function. Through various genetic and biochemical experiments, I provide evidence that VAB-1 can disrupt the NCK-1/UNC-34 complex, and negatively regulate UNC-34. Taken together, my work provides a model of how VAB-1 RTK signaling can inhibit axon extension. I propose that activated VAB-1 can prevent axon extension by inhibiting growth cone filopodia formation. This is accomplished by inhibiting UNC-34/Ena activity, and simultaneously activating Arp2/3 through a VAB-1/NCK-1/WSP-1 complex.

An 8000-year history of landscape, climate and copper exploitation in the Middle East: the Wadi Faynan and the Wadi Dana National Reserve in southern Jordan

Investigations of geomorphology, geoarchaeology, pollen, palynofacies, and charcoal indicate the comparative scales and significance of palaeoenvironmental changes throughout the Holocene at the junction between the hyper-arid hot Wadi â??Arabah desert and the front of the Mediterranean-belt Mountains of Edom in southern Jordan through a series of climatic changes and episodes of intense mining and smelting of copper ores. Early Holocene alluviation followed the impact of Neolithic grazers but climate drove fluvial geomorphic change in the Late Holocene, with a major arid episode corresponding chronologically with the â??Little Ice Ageâ?? causing widespread alluviation. The harvesting of wood for charcoal may have been sufficiently intense and widespread to affect the capacity of intensively harvested tree species to respond to a period of greater precipitation deduced for the Roman-Byzantine period - a property that affects both taphonomic and biogeographical bases for the interpretation of palynological evidence from arid-lands with substantial industrial histories. Studies of palynofacies have provided a record of human and climatic causes of soil erosion, and the changing intensity of the use of fire over time. The patterns of vegetational, climatic change and geomorphic changes are set out for this area for the last 8000 years.

Low-dose studies of bystander cell killing with targeted soft X rays

The Gray Cancer Institute ultrasoft X-ray microprobe was used to quantify the bystander response of individual V79 cells exposed to a focused carbon K-shell (278 eV) X-ray beam. The ultrasoft X-ray microprobe is designed to precisely assess the biological response of individual cells irradiated in vitro with a very fine beam of low-energy photons. Characteristic C-K X rays are generated by a focused beam of 10 keV electrons striking a graphite target. Circular diffraction gratings (i.e. zone plates) are then employed to focus the X-ray beam into a spot with a radius of 0.25 mum at the sample position. Using this microbeam technology, the correlation between the irradiated cells and their nonirradiated neighbors can be examined critically. The survival response of V79 cells irradiated with a C-K X-ray beam was measured in the 0-2-Gy dose range. The response when all cells were irradiated was compared to that obtained when only a single cell was exposed. The cell survival data exhibit a linear-quadratic response when all cells were targeted (with evidence for hyper-sensitivity at low doses). When only a single cell was targeted within the population, 10% cell killing was measured. In contrast to the binary bystander behavior reported by many other investigations, the effect detected was initially dependent on dose (200 mGy). In the low-dose region (

Adaptive automated construction of hybrid heuristics for exam timetabling and graph colouring problems

In this paper, we present a random iterative graph based hyper-heuristic to produce a collection of heuristic sequences to construct solutions of different quality. These heuristic sequences can be seen as dynamic hybridisations of different graph colouring heuristics that construct solutions step by step. Based on these sequences, we statistically analyse the way in which graph colouring heuristics are automatically hybridised. This, to our knowledge, represents a new direction in hyper-heuristic research. It is observed that spending the search effort on hybridising Largest Weighted Degree with Saturation Degree at the early stage of solution construction tends to generate high quality solutions. Based on these observations, an iterative hybrid approach is developed to adaptively hybridise these two graph colouring heuristics at different stages of solution construction. The overall aim here is to automate the heuristic design process, which draws upon an emerging research theme on developing computer methods to design and adapt heuristics automatically. Experimental results on benchmark exam timetabling and graph colouring problems demonstrate the effectiveness and generality of this adaptive hybrid approach compared with previous methods on automatically generating and adapting heuristics. Indeed, we also show that the approach is competitive with the state of the art human produced methods.

A Hybrid Evolutionary Approach to the Nurse Rostering Problem

Nurse rostering is a difficult search problem with many constraints. In the literature, a number of approaches have been investigated including penalty function methods to tackle these constraints within genetic algorithm frameworks. In this paper, we investigate an extension of a previously proposed stochastic ranking method, which has demonstrated superior performance to other constraint handling techniques when tested against a set of constrained optimisation benchmark problems. An initial experiment on nurse rostering problems demonstrates that the stochastic ranking method is better in finding feasible solutions but fails to obtain good results with regard to the objective function. To improve the performance of the algorithm, we hybridise it with a recently proposed simulated annealing hyper-heuristic within a local search and genetic algorithm framework. The hybrid algorithm shows significant improvement over both the genetic algorithm with stochastic ranking and the simulated annealing hyper-heuristic alone. The hybrid algorithm also considerably outperforms the methods in the literature which have the previously best known results.

Characterisation of the Thermal, Spectroscopic and Drug Dissolution Properties of Mefenamic Acid and Polyoxyethylene–Polyoxypropylene Solid Dispersions

The aim of this study was to investigate the solubility of mefenamic acid (MA), a highly cohesive, poorly water-soluble drug in a copolymer of polyoxyethylene–polyoxypropylene (Lutrol F681), and to understand the effect drug polymer solubility has on in vitro dissolution of MA. Solid dispersions (SD) of MA were prepared by a hot melt method, using Lutrol F681 as a thermoplastic polymeric platform. High-speed differential scanning calorimetry (Hyper-DSC), Raman spectroscopy, powder X-ray diffractometry (PXRD) and hot-stage/?uorescence microscopy were used to assess the solubility of the drug in molten and solid polymer. Drug dissolution studies were subsequently conducted on single-phase solid solutions and biphasic SD using phosphate buffer pH 6.8 as dissolution media. Solubility investigations using Hyper-DSC, Raman spectroscopy and hot-stage microscopy suggested MA was soluble in molten Lutrol F681 up to a concentration of 35% (w/w). Conversely, the solubility in the solidstate matrix was limited to<15% (w/w); determined by Raman spectroscopy, PXRD and ?uorescence microscopy. As expected the dissolution properties of MA were signi?cantly in?uenced by the solubility of the drug in the polymer matrix. At a concentration of 10% (w/w) MA (a single phase solid solution) dissolution of MA in phosphate buffer 6.8 was rapid, whereas at a concentration of 50% (w/w) MA (biphasic SD) dissolution was signi?cantly slower. This study has clearly demonstrated the complexity of drug– polymer binary blends and in particular de?ning the solubility of a drug within a polymeric platform. Moreover, this investigation has demonstrated the signi?cant effect drug solubility within a polymeric matrix has upon the in vitro dissolution properties of solid polymer/drug binary blends.

On the derived category of a regular toric scheme

Let X be a quasi-compact scheme, equipped with an open covering by affine schemes U s = Spec A s . A quasi-coherent sheaf on X gives rise, by taking sections over the U s , to a diagram of modules over the coordinate rings A s , indexed by the intersection poset S of the covering. If X is a regular toric scheme over an arbitrary commutative ring, we prove that the unbounded derived category of quasi-coherent sheaves on X can be obtained from a category of Sop-diagrams of chain complexes of modules by inverting maps which induce homology isomorphisms on hyper-derived inverse limits. Moreover, we show that there is a finite set of weak generators, one for each cone in the fan S. The approach taken uses the machinery of Bousfield–Hirschhorn colocalisation of model categories. The first step is to characterise colocal objects; these turn out to be homotopy sheaves in the sense that chain complexes over different open sets U s agree on intersections up to quasi-isomorphism. In a second step it is shown that the homotopy category of homotopy sheaves is equivalent to the derived category of X.

Vetting Sexual Offenders: State Over-extension, the Punishment Deficit and the Failure to Manage Risk

This article examines the state regulation of sexual offenders in the particular context of pre-employment vetting. A successive range of statutory frameworks have been put in place, culminating in the Safeguarding Vulnerable Groups Act 2006, to prevent unsuitable individuals from working with the vulnerable, and children in particular. Contemporary legislative and policy developments are set against a backdrop of broader concerns in the area of crime and justice, namely risk regulation, preventative governance and ‘precautionary logic.’ Proponents of these approaches have largely ignored concerns over their feasibility. This article specifically addresses this fissure within the specific field of vetting. It is argued that ‘hyper innovation’ and state over-extension in this area are particularly problematic and have resulted in exceptionally uncertain and unsafe policies. These difficulties relate principally to unrealistic public expectations about the state’s ability to control crime; unintended and ambiguous policy effects; and ultimately the failure of the state to deliver on its self-imposed regulatory mandate to effectively manage risk.

Long-term bone marrow culture profiles in patients with myelodysplastic syndromes are not explicable by defective apoptosis

It has been suggested that increased intramedullary apoptosis may explain the paradox between peripheral blood cytopenias and the hyper- or normo-cellular bone marrow observed in the myelodysplastic syndromes (MDS). We wished to see if culture performance could be related to the presence of apoptotic cells in a group of patients with MDS (12 patients) and other patients with peripheral blood cytopenias (six patients) which caused diagnostic difficulty. There was no correlation between LTBMC or adherent cell growth and the presence of apoptotic cells in the original marrow sample. A variable degree of apoptosis was observed in both groups of patients. LTBMC profiles correlated well with diagnosis but were unrelated to the extent of intramedullary apoptosis. This suggests that apoptosis is a much more ubiquitous process in disease than previously thought. (C) 1998 Elsevier Science Ltd. All rights reserved.

Construction of Drug–Polymer Thermodynamic Phase Diagrams Using Flory–Huggins Interaction Theory: Identifying the Relevance of Temperature and Drug Weight Fraction to Phase Separation within Solid Dispersions

Amorphous drug-polymer solid dispersions have the potential to enhance the dissolution performance and thus bioavailability of BCS class II drug compounds. The principle drawback of this approach is the limited physical stability of amorphous drug within the dispersion. Accurate determination of the solubility and miscibility of drug in the polymer matrix is the key to the successful design and development of such systems. In this paper, we propose a novel method, based on Flory-Huggins theory, to predict and compare the solubility and miscibility of drug in polymeric systems. The systems chosen for this study are (1) hydroxypropyl methylcellulose acetate succinate HF grade (HPMCAS-HF)-felodipine (FD) and (2) Soluplus (a graft copolymer of polyvinyl caprolactam-polyvinyl acetate-polyethylene glycol)-FD. Samples containing different drug compositions were mixed, ball milled, and then analyzed by differential scanning calorimetry (DSC). The value of the drug-polymer interaction parameter ? was calculated from the crystalline drug melting depression data and extrapolated to lower temperatures. The interaction parameter ? was also calculated at 25 °C for both systems using the van Krevelen solubility parameter method. The rank order of interaction parameters of the two systems obtained at this temperature was comparable. Diagrams of drug-polymer temperature-composition and free energy of mixing (?G mix) were constructed for both systems. The maximum crystalline drug solubility and amorphous drug miscibility may be predicted based on the phase diagrams. Hyper-DSC was used to assess the validity of constructed phase diagrams by annealing solid dispersions at specific drug loadings. Three different samples for each polymer were selected to represent different regions within the phase diagram

Targeting EGFR Induced Oxidative Stress by PARP1 Inhibition in Glioblastoma Therapy

Despite the critical role of Epidermal Growth Factor Receptor (EGFR) in glioblastoma pathogenesis [1,2], EGFR targeted therapies have achieved limited clinical efficacy [3]. Here we propose an alternate therapeutic strategy based on the conceptual framework of non-oncogene addiction [4,5]. A directed RNAi screen revealed that glioblastoma cells overexpressing EGFRvIII [6], an oncogenic variant of EGFR, become hyper-dependent on a variety of DNA repair genes. Among these, there was an enrichment of Base Excision Repair (BER) genes required for the repair of Reactive Oxygen Species (ROS)-induced DNA damage, including poly-ADP ribose polymerase 1 (PARP1). Subsequent studies revealed that EGFRvIII overexpression in glioblastoma cells caused increased levels of ROS, DNA strand break accumulation, and genome instability. In a panel of primary glioblastoma lines, sensitivity to PARP1 inhibition correlated with the levels of EGFR activation and oxidative stress. Gene expression analysis indicated that reduced expression of BER genes in glioblastomas with high EGFR expression correlated with improved patient survival. These observations suggest that oxidative stress secondary to EGFR hyperactivation necessitates increased cellular reliance on PARP1 mediated BER, and offer critical insights into clinical trial design.

A Unified Scheduler for Recursive and Task Dataflow Parallelism

Task dataflow languages simplify the specification of parallel programs by dynamically detecting and enforcing dependencies between tasks. These languages are, however, often restricted to a single level of parallelism. This language design is reflected in the runtime system, where a master thread explicitly generates a task graph and worker threads execute ready tasks and wake-up their dependents. Such an approach is incompatible with state-of-the-art schedulers such as the Cilk scheduler, that minimize the creation of idle tasks (work-first principle) and place all task creation and scheduling off the critical path. This paper proposes an extension to the Cilk scheduler in order to reconcile task dependencies with the work-first principle. We discuss the impact of task dependencies on the properties of the Cilk scheduler. Furthermore, we propose a low-overhead ticket-based technique for dependency tracking and enforcement at the object level. Our scheduler also supports renaming of objects in order to increase task-level parallelism. Renaming is implemented using versioned objects, a new type of hyper object. Experimental evaluation shows that the unified scheduler is as efficient as the Cilk scheduler when tasks have no dependencies. Moreover, the unified scheduler is more efficient than SMPSS, a particular implementation of a task dataflow language.