The astacin metalloprotease moulting enzyme NAS-36 is required for normal cuticle ecdysis in free-living and parasitic nematodes

Nematodes represent one of the most abundant and species-rich groups of animals on the planet, with parasitic species causing chronic, debilitating infections in both livestock and humans worldwide. The prevalence and success of the nematodes is a direct consequence of the exceptionally protective properties of their cuticle. The synthesis of this cuticle is a complex multi-step process, which is repeated 4 times from hatchling to adult and has been investigated in detail in the free-living nematode, Caenorhabditis elegans. This process is known as moulting and involves numerous enzymes in the synthesis and degradation of the collagenous matrix. The nas-36 and nas-37 genes in C. elegans encode functionally conserved enzymes of the astacin metalloprotease family which, when mutated, result in a phenotype associated with the late-stage moulting defects, namely the inability to remove the preceding cuticle. Extensive genome searches in the gastrointestinal nematode of sheep, Haemonchus contortus, and in the filarial nematode of humans, Brugia malayi, identified NAS-36 but not NAS-37 homologues. Significantly, the nas-36 gene from B. malayi could successfully complement the moult defects associated with C. elegans nas-36, nas-37 and nas-36/nas-37 double mutants, suggesting a conserved function for NAS-36 between these diverse nematode species. This conservation between species was further indicated when the recombinant enzymes demonstrated a similar range of inhibitable metalloprotease activities

Framework for task scheduling in heterogeneous distributed computing using genetic algorithms

An algorithm has been developed to dynamically schedule heterogeneous tasks on heterogeneous processors in a distributed system. The scheduler operates in an environment with dynamically changing resources and adapts to variable system resources. It operates in a batch fashion and utilises a genetic algorithm to minimise the total execution time. We have compared our scheduler to six other schedulers, three batch-mode and three immediate-mode schedulers. Experiments show that the algorithm outperforms each of the others and can achieve near optimal efficiency, with up to 100,000 tasks being scheduled

Superbursts from Strange Stars

Recent models of carbon ignition on accreting neutron stars predict superburst ignition depths that are an order of magnitude larger than observed. We explore a possible solution to this problem, that the compact stars in low mass X-ray binaries that have shown superbursts are in fact strange stars with a crust of normal matter. We calculate the properties of superbursts on strange stars, and the resulting constraints on the properties of strange quark matter. We show that the observed ignition conditions exclude fast neutrino emission in the quark core, for example by the direct Urca process, which implies that strange quark matter at stellar densities should be in a color superconducting state. For slow neutrino emission in the quark matter core, we find that reproducing superburst properties requires a definite relation between three poorly constrained properties of strange quark matter: its thermal conductivity, its slow neutrino emissivity and the energy released by converting a nucleon into strange quark matter.Comment: 4 pages, submitted to Ap. J. Let

Adaptive Scheduling Across a Distributed Computation Platform

A programmable Java distributed system, which adapts to available resources, has been developed to minimise the overall processing time of computationally intensive problems. The system exploits the free resources of a heterogeneous set of computers linked together by a network, communicating using SUN Microsystems' Remote Method Invocation and Java sockets. It uses a multi-tiered distributed system model, which in principal allows for a system of unbounded size. The system consists of an n-ary tree of nodes where the internal nodes perform the scheduling and the leaves do the processing. The scheduler nodes communicate in a peer-to-peer manner and the processing nodes operate in a strictly client-server manner with their respective scheduler. The independent schedulers on each tier of the tree dynamically allocate resources between problems based on the constantly changing characteristics of the underlying network. The system has been evaluated over a network of 86 PCs with a bioinformatics application and the travelling salesman optimisation problem

Biosynthesis and enzymology of the Caenorhabditis elegans cuticle: identification and characterization of a novel serine protease inhibitor.

The nematode Caenorhabditis elegans represents an excellent model in which to examine nematode gene expression and function. A completed genome, straightforward transgenesis, available mutants and practical genome-wide RNAi approaches provide an invaluable toolkit in the characterization of nematode genes. We have performed a targeted RNAi screen in an attempt to identify components of the cuticle collagen biosynthetic pathway. Collagen biosynthesis and cuticle assembly are multi-step processes that involve numerous key enzymes involved in post-translational modification, trimer folding, procollagen processing and subsequent cross-linking stages. Many of these steps, the modifications and the enzymes are unique to nematodes and may represent attractive targets for the control of parasitic nematodes. A novel serine protease inhibitor was uncovered during our targeted screen, which is involved in collagen maturation, proper cuticle assembly and the moulting process. We have confirmed a link between this inhibitor and the previously uncharacterized bli-5 locus in C. elegans. The mutant phenotype, spatial expression pattern and the over-expression phenotype of the BLI-5 protease inhibitor and their relevance to collagen biosynthesis are discussed

Using Commodity Graphics Hardware for Real-Time Digital Hologram View-Reconstruction

View-reconstruction and display is an important part of many applications in digital holography such as computer vision and microscopy. Thus far, this has been an offline procedure for megapixel sized holograms. This paper introduces an implementation of real-time view-reconstruction using programmable graphics hardware. The theory of Fresnel-based view-reconstruction is introduced, after which an implementation using stream programming is presented. Two different fast Fourier transform (FFT)-based reconstruction methods are implemented, as well as two different FFT strategies. The efficiency of the methods is evaluated and compared to a CPU-based implementation, providing over 100 times speedup for a hologram size of 2048 x 2048

Using Commodity Graphics Hardware for Real-Time Digital Hologram View-Reconstruction

View-reconstruction and display is an important part of many applications in digital holography such as computer vision and microscopy. Thus far, this has been an offline procedure for megapixel sized holograms. This paper introduces an implementation of real-time view-reconstruction using programmable graphics hardware. The theory of Fresnel-based view-reconstruction is introduced, after which an implementation using stream programming is presented. Two different fast Fourier transform (FFT)-based reconstruction methods are implemented, as well as two different FFT strategies. The efficiency of the methods is evaluated and compared to a CPU-based implementation, providing over 100 times speedup for a hologram size of 2048 x 2048

Tatajuba: exploring the distribution of homopolymer tracts.

Length variation of homopolymeric tracts, which induces phase variation, is known to regulate gene expression leading to phenotypic variation in a wide range of bacterial species. There is no specialized bioinformatics software which can, at scale, exhaustively explore and describe these features from sequencing data. Identifying these is non-trivial as sequencing and bioinformatics methods are prone to introducing artefacts when presented with homopolymeric tracts due to the decreased base diversity. We present tatajuba, which can automatically identify potential homopolymeric tracts and help predict their putative phenotypic impact, allowing for rapid investigation. We use it to detect all tracts in two separate datasets, one of Campylobacter jejuni and one of three Bordetella species, and to highlight those tracts that are polymorphic across samples. With this we confirm homopolymer tract variation with phenotypic impact found in previous studies and additionally find many more with potential variability. The software is written in C and is available under the open source licence GNU GPLv3

Tatajuba: exploring the distribution of homopolymer tracts.

Length variation of homopolymeric tracts, which induces phase variation, is known to regulate gene expression leading to phenotypic variation in a wide range of bacterial species. There is no specialized bioinformatics software which can, at scale, exhaustively explore and describe these features from sequencing data. Identifying these is non-trivial as sequencing and bioinformatics methods are prone to introducing artefacts when presented with homopolymeric tracts due to the decreased base diversity. We present tatajuba, which can automatically identify potential homopolymeric tracts and help predict their putative phenotypic impact, allowing for rapid investigation. We use it to detect all tracts in two separate datasets, one of Campylobacter jejuni and one of three Bordetella species, and to highlight those tracts that are polymorphic across samples. With this we confirm homopolymer tract variation with phenotypic impact found in previous studies and additionally find many more with potential variability. The software is written in C and is available under the open source licence GNU GPLv3