Arcturus user's guide

This document describes the Arcturus programming environment, a first realization of an advanced programming environment based on the programming language Ada. It is the first environment that supplies interactive, "statement (or declaration) at a time" execution of Ada program fragments

An approximate theoretical method for modeling the static thrust performance of non-axisymmetric two-dimensional convergent-divergent nozzles

An analytical/numerical method has been developed to predict the static thrust performance of non-axisymmetric, two-dimensional convergent-divergent exhaust nozzles. Thermodynamic nozzle performance effects due to over- and underexpansion are modeled using one-dimensional compressible flow theory. Boundary layer development and skin friction losses are calculated using an approximate integral momentum method based on the classic karman-Polhausen solution. Angularity effects are included with these two models in a computational Nozzle Performance Analysis Code, NPAC. In four different case studies, results from NPAC are compared to experimental data obtained from subscale nozzle testing to demonstrate the capabilities and limitations of the NPAC method. In several cases, the NPAC prediction matched experimental gross thrust efficiency data to within 0.1 percent at a design NPR, and to within 0.5 percent at off-design conditions

SID-1 is a dsRNA-Selective dsRNA-gated Channel

Systemic RNAi in Caenorhabditis elegans requires the widely conserved transmembrane protein SID-1 to transport RNAi silencing signals between cells. When expressed in Drosophila S2 cells, C. elegans SID-1 enables passive dsRNA uptake from the culture medium, suggesting that SID-1 functions as a channel for the transport of double-stranded RNA (dsRNA). Here we show that nucleic acid transport by SID-1 is specific for dsRNA and that addition of dsRNA to SID-1 expressing cells results in changes in membrane conductance, which indicate that SID-1 is a dsRNA gated channel protein. Consistent with passive bidirectional transport, we find that the RNA induced silencing complex (RISC) is required to prevent the export of imported dsRNA and that retention of dsRNA by RISC does not seem to involve processing of retained dsRNA into siRNAs. Finally, we show that mimics of natural molecules that contain both single- and double-stranded dsRNA, such as hairpin RNA and pre-microRNA, can be transported by SID-1. These findings provide insight into the nature of potential endogenous RNA signaling molecules in animals.Molecular and Cellular Biolog

Spatiotemporal Statistical Downscaling for the Fusion of In-lake and Remote Sensing Data

This paper addresses the problem of fusing data from in-lake monitoring programmes with remote sensing data, through statistical downscaling. A Bayesian hierarchical model is developed, in order to fuse the in-lake and remote sensing data using spatially-varying coefficients. The model is applied to an example dataset of log(chlorophyll-a) data for Lake Erie, one of the Great Lakes of North America

Synthetic lethal analysis of Caenorhabditis elegans posterior embryonic patterning genes identifies conserved genetic interactions

Phenotypic robustness is evidenced when single-gene mutations do not result in an obvious phenotype. It has been suggested that such phenotypic stability results from 'buffering' activities of homologous genes as well as non-homologous genes acting in parallel pathways. One approach to characterizing mechanisms of phenotypic robustness is to identify genetic interactions, specifically, double mutants where buffering is compromised. To identify interactions among genes implicated in posterior patterning of the Caenorhabditis elegans embryo, we measured synthetic lethality following RNA interference of 22 genes in 15 mutant strains. A pair of homologous T-box transcription factors (tbx-8 and tbx-9) is found to interact in both C. elegans and C. briggsae, indicating that their compensatory function is conserved. Furthermore, a muscle module is defined by transitive interactions between the MyoD homolog hlh-1, another basic helix-loop-helix transcription factor, hnd-1, and the MADS-box transcription factor unc-120. Genetic interactions within a homologous set of genes involved in vertebrate myogenesis indicate broad conservation of the muscle module and suggest that other genetic modules identified in C. elegans will be conserved

Two Classes of Silencing RNAs Move between Caenorhabditis elegans Tissues

Organism-wide RNA interference (RNAi) is due to the transport of mobile silencing RNA throughout the organism, but the identities of these mobile RNA species in animals are unknown. Here, we present genetic evidence that both the initial double-stranded RNA (dsRNA), which triggers RNAi, and at least one dsRNA intermediate produced during RNAi can act as or generate mobile silencing RNA in C. elegans. This dsRNA intermediate requires the long dsRNA-binding protein RDE-4, the endonuclease DCR-1, which cleaves long dsRNA into double-stranded short-interfering RNA (ds-siRNA), and the putative nucleotidyltransferase MUT-2 (RDE-3). However, single-stranded siRNA and downstream secondary siRNA produced upon amplification by the RNA-dependent RNA polymerase RRF-1 do not generate mobile silencing RNA. Restricting intertissue transport to long dsRNA and directly processed siRNA intermediates rather than amplified siRNA may serve to modulate the extent of systemic silencing in proportion to available dsRNA.Molecular and Cellular Biolog

Renegotiating father’s identity following stillbirth: what and who am I?

This study examines the experiences of men following stillbirth in particular the challenges they face in claiming their identity as a father of an absent child. Fathers felt diminished when concerns about how they were coping were directed only to the women. Contrary to the notion that father’s experience suggests men suffer less distress, this research shows that men also deal with loss at an emotional level. This investigation into men’s accounts of loss forms part of a larger study in which 28 men and women participated in interviews and focus groups about their experiences of perinatal death. By listening to narrative accounts of loss, the passage to parenthood for bereaved men represents a disruption and re-evaluation of who they are, what they knew about the world as they negotiate the incomprehensibility of the death itself. Narratives by bereaved men also reveal how their sense of self and identity is mediated by the social and cultural milieu to which they belong and are largely disenfranchising experiences when friends, family and others, at times, fail to acknowledge the enormity of their loss. The findings suggest that recognition of the death of baby who is stillborn as well as the impact of the death for father’s is intertwined with personal identity. Men in this study needed to receive recognition as fathers, both at the time of their loss and after. In examining the reproductive and bereavement journey of men, several domains occurred to illuminate the experience of men including; men as support partners; the impact of the death; parenting an absent child [advocate, protector]. The findings from this study will offer insight into the experiences of men that will resonate for others including practitioners who support individuals going through similar experiences. Ethical approval for the study was granted by the University of Bristol Ethics Committee as part of doctoral research. Written informed consent was obtained by all study participants. No formal recruitment was obtained through the National Health Service or Government Institution and was entirely voluntary

Support System Effects on the DLR-F6 Transport Configuration in the National Transonic Facility

An experimental investigation of the DLR-F6 generic transport configuration was conducted in the NASA NTF for use in the Drag Prediction Workshop. As data from this experimental investigation was collected, a large difference in drag values was seen between the NTF test and an ONERA test that was conducted several years ago. After much investigation, it was determined that this difference was likely due to a sting effect correction applied to the ONERA data which NTF does not use. This insight led to the present work. In this study, a computational assessment has been undertaken to investigate model support system interference effects on the DLR-F6 transport configuration. The configurations computed during this investigation were the isolated wing-body, the wing-body with the full support system (blade and sting), the wing-body with just the blade, and the wing-body with just the sting. The results from this investigation show the same trends that ONERA saw when they conducted a similar experimental investigation in the S2MA tunnel. Computational results suggest that the blade contributed an interference type of effect, the sting contributed a general blockage effect, and the full support system combined these effects

Taxonomy, phylogeny and population biology of Mycosphaerella species occurring on Eucalyptus

Much research has been published on Mycosphaerella spp. causing Mycosphaerella Leaf Disease (MLD) on Eucalyptus spp. The first chapter of this thesis presents a review of the literature on this topic and focuses on the taxonomy, phylogeny and population biology of Mycosphaerella spp. occurring on Eucalyptus. From the published literature, it is clear that the majority of research conducted on MLD has focussed on the epidemiology and taxonomy of Mycosphaerella spp and the susceptibility of Eucalyptus hosts to species of Mycosphaerella. Advances in DNA-based technologies have, however, lead to extensive DNA sequence datasets of Mycosphaerella spp occurring on Eucalyptus. These datasets have provided substantial insight into species concepts for Mycosphaerella and have led to the realisation that many morphological species are complexes of several cryptic phylogenetic taxa. Furthermore, a recent application to the study of Mycosphaerella spp. occurring on Eucalyptus is that concerning their population dynamics. Such studies will aid in our understanding of the genetic structure of Mycosphaerella populations and their movement between countries. These population-based studies will aid forestry companies in establishing Eucalyptus breeding programmes to produce tolerant Eucalyptus genotypes that may be deployed in commercial forestry operations. Mycosphaerella spp. are difficult to identify, due to their conserved teleomorph morphology and the lack of natural occurrences of anamorph structures. DNA sequence data have, therefore, become the definitive technique used to identify Mycosphaerella spp. The Internal Transcribed Spacer (ITS) region of the ribosomal RNA operon has traditionally been targeted for DNA sequence comparisons. However, this gene region does not offer sufficient resolution to discriminate cryptic taxa or resolve deeper nodes within Mycosphaerella. Results presented in chapter two of this thesis present a multi-gene phylogeny for the identification of Mycosphaerella spp. occurring on Eucalyptus. This is based on DNA sequence data from four nuclear gene regions. The generation of these sequence datasets has allowed for competent elucidation of cryptic taxa, species complexes and the greater resolution of deeper nodes within Mycosphaerella. Furthermore, these results have also led to recognising that Mycosphaerella ambipyhlla and M. vespa is a synonym of Mycosphaerella molleriana and Pseudocercospora epispermogonia is recognised as the asexual state of Mycosphaerella marksii. A serious foliar disease of Eucalyptus camaldulensis and hybrids of this species has been known from Thailand and Vietnam for many years. This disease has been known to be caused by a species of Pseudocercospora and was attributed to the cosmopolitan Pseudocercospora eucalyptorum. Results of a study presented in chapter three of this thesis have, however, clearly shown that P. eucalyptorum is not the causal agent of the disease observed on E. camaldulensis in Thailand. By employing classical morphological techniques and DNA sequence data from four nuclear gene regions, I have shown that an undescribed species of Pseudocercospora is responsible for epidemics of this leaf disease. This species is formally described as Pseudocercospora flavomarginata. P. flavomarginata is only known from Thailand and Vietnam. However, considering that E. camaldulensis is planted in other south-east Asian countries and that E. camaldulensis is the most commonly found Eucalyptus sp. in Australia, further surveys in these areas will most likely lead to the discovery of the pathogen from these countries. Techniques that have been used to identify Mycosphaerella spp. include classical morphological comparisons and analyses of DNA sequence data. These techniques have, however, allowed only for the study of the evolutionary history within Mycosphaerella and for species identification. Recent advances in the field of population biology have led to the study of many fungal pathogens at a population level. One of the main tools used to study population biology involves applying DNA-based microsatellite markers. Chapter four of this thesis focuses on the development of DNA-based microsatellite markers for the Eucalyptus leaf pathogen Mycosphaerella nubilosa. By employing specific enrichment protocols, I was able to develop ten polymorphic microsatellite markers for M. nubilosa. These microsatellite markers exhibit high specificity for M. nubilosa and did not cross amplify with other Mycosphaerella spp. that are closely related to M. nubilosa. Mycosphaerella nubilosa has been extensively studied with respect to its taxonomy and epidemiology. However, nothing is known regarding the population biology of this important Eucalyptus leaf pathogen. Therefore, DNA-based microsatellite markers developed in chapter four of this thesis were used to study the population biology of M. nubilosa from several different geographic locations. Results presented in chapter five of this thesis show that populations of M. nubilosa from eastern Australia are genetically more diverse than those populations from western Australia, Africa and Europe. This indicates that eastern Australia is the likely centre of origin for M. nubilosa. Furthermore, based on shared haplotypes between M. nubilosa populations used in this study, I have proposed a pathway of gene flow of M. nubilosa. This suggests that the pathogen moved from eastern Australia to both western Australia and South Africa and then from South Africa into other countries in Africa and finally into Europe. An interesting result emerging from the population biology study presented in chapter five, is the finding that M. nubilosa appears to employ a homothallic mating strategy. Thus, opportunities exist, in countries with limited genetic diversity of M. nubilosa, to breed for Eucalyptus resistance. From the high number of M. nubilosa haplotypes observed in Australia and South Africa, it is also important that this pathogen be added to quarantine action lists to prevent the movement of contaminated Eucalyptus germplasm. This is necessary to prevent novel M. nubilosa haplotypes from moving into new environments where susceptible Eucalyptus spp. are propagated. Mycosphaerella nubilosa is one of the most pathogenic Mycosphaerella spp. causing MLD on Eucalyptus. Surveys of diseased Eucalyptus plantations from several countries where this pathogen occurs, have resulted in an extensive collection of M. nubilosa isolates. Recently, DNA-based studies have led to the hypothesis that M. nubilosa may represent two distinct taxa. Results of studies presented in chapter six of this thesis indicate that two distinct ITS phylogenetic lineages are represented by M. nubilosa sensu lato. These are characterized by defined geographic distributions and Eucalyptus host associations. M. nubilosa ITS lineage 1 is found exclusively in New Zealand, Tasmania and Victoria, eastern Australia occurring on E. globulus. M. nubilosa ITS lineage 2 has a broader geographic distribution and can be found in Spain, Portugal, Tanzania, Kenya, Ethiopia, South Africa, western Australia, Victoria and New South Wales, eastern Australia, where it occurs on E. globulus and several other Eucalyptus spp. that are used in commercial forestry including E. nitens. It is envisaged that results presented in chapter six will lead to more extensive studies into M. nubilosa sensu lato that may result in the description of a new Mycosphaerella sp. represented by M. nubilosa ITS lineage 1.Thesis (PhD)--University of Pretoria, 2011.Microbiology and Plant PathologyUnrestricte