Saprolegnia diclina IIIA and S. parasitica employ different infection strategies when colonizing eggs of Atlantic salmon, Salmo salar L.

Acknowledgements The work has been funded by the European Commission through the EU Marie Curie ITN project SAPRO (238550) (MMS, AW). We would also like to acknowledge support from the BBSRC and the University of Aberdeen (PvW) and Landcatch and AquaGen for providing salmon eggs. Elin Rolen's assistance with sequencing of the strains is highly appreciated.Peer reviewedPublisher PD

Cross-Functional Maintenance And Logistics Business Process Integration: Lessons From A Large Oil And Gas Company

The purpose of this research focused on integration and alignment of maintenance and logistics functions in a large ERP system in an oil and gas company to demonstrate how cross-functional integration can improve operations. A design science approach has been used based on a case study of a large oil and gas company. The study found that limited cross-functional integration involving the logistics function exists. Proposed process redesign involves activities include improved storage and picking strategies, information exchange, notification of fully received components at the warehouse and an improved shipping strategy. These improvement strategies have been tested through random questionnaires and most respondents support the improvements. This study shows that business process improvement facilitated by cross-functional process integration should realise substantial financial benefits. We have shown that warehouse operation strategies do have an impact on the work order performance through the on-time delivery of its components. In addition, regular communication and utilisation of the available information can also improve the scheduling of work order execution. These benefits are not limited to the company in question but the results show that if companies in general give more attention to cross-functional integration, substantial benefits are possible. The focus of this study is uncommon as it is the integration of logistics and maintenance functions within an organisation. We show substantial process improvements are possible. It therefore provides another opportunity for business process improvement experts to better align various systems and processes

Internuclear gene silencing in Phytophthora infestans is established through chromatin remodelling

In the plant pathogen Phytophthora infestans, nuclear integration of inf1 transgenic DNA sequences results in internuclear gene silencing of inf1. Although silencing is regulated at the transcriptional level, it also affects transcription from other nuclei within heterokaryotic cells of the mycelium. Here we report experiments exploring the mechanism of internuclear gene silencing in P. infestans. The DNA methylation inhibitor 5-azacytidine induced reversion of the inf1-silenced state. Also, the histone deacetylase inhibitor trichostatin-A was able to reverse inf1 silencing. inf1-expression levels returned to the silenced state when the inhibitors were removed except in non-transgenic inf1-silenced strains that were generated via internuclear gene silencing, where inf1 expression was restored permanently. Therefore, inf1-transgenic sequences are required to maintain the silenced state. Prolonged culture of non-transgenic inf1-silenced strains resulted in gradual reactivation of inf1 gene expression. Nuclease digestion of inf1-silenced and non-silenced nuclei showed that inf1 sequences in silenced nuclei were less rapidly degraded than non-silenced inf1 sequences. Bisulfite sequencing of the endogenous inf1 locus did not result in detection of any cytosine methylation. Our findings suggest that the inf1-silenced state is based on chromatin remodelling

On the Inconsistency of Fayet-Iliopoulos Terms in Supergravity Theories

Motivated by recent discussions, we revisit the issue of whether globally supersymmetric theories with non-zero Fayet-Iliopoulos terms may be consistently coupled to supergravity. In particular, we examine claims that a fundamental inconsistency arises due to the conflicting requirements which are imposed on the $R$-symmetry properties of the theory by the supergravity framework. We also prove that certain kinds of Fayet-Iliopoulos contributions to the supercurrent supermultiplets of theories with non-zero Fayet-Iliopoulos terms fail to exist. A key feature of our discussion is an explicit comparison between results from the chiral (or ``old minimal'') and linear (or ``new minimal'') formulations of supergravity, and the effects within each of these formalisms that are induced by the presence of non-zero Fayet-Iliopoulos terms.Comment: Comments: 69 pages, LaTeX, 2 figures, 7 tables. Significant new material on conformal-compensator formalisms added, previous results clarified and extended, references adde

Diffusion in a Time-dependent External Field

The problem of diffusion in a time-dependent (and generally inhomogeneous) external field is considered on the basis of a generalized master equation with two times, introduced in [1,2]. We consider the case of the quasi Fokker-Planck approximation, when the probability transition function for diffusion (PTD-function) does not possess a long tail in coordinate space and can be expanded as a function of instantaneous displacements. The more complicated case of long tails in the PTD will be discussed separately. We also discuss diffusion on the basis of hydrodynamic and kinetic equations and show the validity of the phenomenological approach. A new type of "collision" integral is introduced for the description of diffusion in a system of particles, which can transfer from a moving state to the rest state (with some waiting time distribution). The solution of the appropriate kinetic equation in the external field also confirms the phenomenological approach of the generalized master equation.Comment: 18 pages, no figure

Molecular tools to unravel the role of genes from Phytophthora infestans

The oomycete plant pathogen Phytophthora infestans is the causal agent of potato late blight. P. infestans is undoubtedly the best known and most studied Phytophthora species today. This is mainly because it is such a devastating pathogen that can cause complete destruction of a potato field in only a few days. In this thesis, we describe the characterisation of four P. infestans genes with presumed functions in pathogenicity and virulence, and the development of tools to study expression and function of two of these genes in P. infestans . The four genes are the in planta -induced genes ipiB and ipiO , the elicitin gene inf1 , and the stress-induced gene ric1 . We used theβ-glucuronidase reporter gene for expression analysis of the ipiO gene, and homology-dependent gene silencing for functional analysis of the inf1 gene. The latter resulted in the discovery of a new phenomenon, which we named internuclear gene silencing.In Chapter 2, we describe the characterisation of the in planta -induced genes ipiB and ipiO . IpiB constitutes a gene family with at least three members, ipiB1 , ipiB2 and ipiB3 , which are clustered in a head-to-tail arrangement. The ipiB genes are highly homologous throughout their promoter, coding and terminator sequences and encode three similar glycine-rich proteins of 301, 343 and 347 amino acids, respectively. The glycine-rich domains of the IPI-B proteins are predominantly composed of two repeats with the core sequences, A/V-G-A-G-L-Y-G-R and G-A-G-Y/V-G-G. The IPI-B proteins contain a putative signal peptide of 20 amino-acids, suggesting that the proteins are targeted to a specific organelle or to the outside of the cell. We speculate that the IPI-B proteins are structural proteins associated with the cell wall that are possibly involved in the development of infection structures. Also ipiO is a small gene family. Two members, ipiO1 and ipiO2 are closely linked and arranged in an inverted orientation. The ipiO genes encode almost identical 152 amino acid-proteins which do not have any significant homology with sequences present in data libraries. The IPI-O proteins contain a putative signal peptide which may target them to the extracellular matrix. A putative cell attachment sequence (RGD), functional in mammalian systems, was identified.Expression of the ipiO gene was analysed during several developmental stages of the life cycle of P. infestans (Chapter 3). IpiO mRNA was detected in zoospores, cysts, and germinating cysts, but not in sporangia or in mycelia grown in vitro . IpiO is also expressed during colonisation of potato leaves. In disease lesions, ipiO mRNA was detected in the water-soaked area and the surrounding healthy-looking plant tissue. IpiO mRNA could not be detected in necrotised tissue and sporulating areas of a lesion. Cytological assays were performed to determine more precisely the location and time of ipiO gene expression in planta . P. infestans transformants expressing a transcriptional fusion between the ipiO1 promoter and theβ-glucuronidase (GUS) reporter gene showed that GUS staining was specifically found in the subapical and vacuolated area of tips of invading hyphae. Therefore, we concluded that ipiO is expressed in hyphae during biotrophic stages of the infection process. We speculate that IPI-O has its function in the hyphal tips at the edge of the expanding lesion where the pathogen is invading healthy leaf cells. The IPI-O protein may well be localised at the interface between the invading hyphae and the plant cells, and could play a role in pathogenicity and/or virulence.To isolate more genes that might be involved in the interaction between P. infestans and potato, we used a small scale expressed sequence tag (EST) approach (Chapter 7). Twenty-two P. infestans cDNA clones were randomly selected from a potato- P. infestans interaction cDNA library. Five of these clones appeared to be derived from the same gene, ric1 . Two copies of the ric1 gene were identified and both genes share 98% homology at the nucleotide sequence level and 100% at the amino acid level. The open reading frame predicts a small protein sequence of 57 amino acids. The highly hydrophobic protein has two potential membrane spanning domains. The deduced amino acid sequence shows high homology with three putative plant proteins encoded by genes of which the expression is specifically induced during stress conditions. Expression of ric1 increased considerably during osmotic stress and at high pH. We hypothesise that RIC1 is a structural protein that is necessary to maintain membrane integrity, especially during unfavourable conditions.When culturing various Phytophthora species in liquid medium, all examined species secrete highly abundant 10 kDa proteins which have been shown to elicit a hypersensitive response when injected into tobacco leaves. It was hypothesised previously that these 10 kDa proteins, collectively called elicitins, function as plant species specific avirulence factors. In order to test this hypothesis, we set out to clone the elicitin gene inf1 , of P. infestans (Chapter 4) and subsequently generated mutants that no longer produced the INF1 protein (Chapter 5 & 6). An inf1 cDNA was isolated by heterologous hybridisation of a potato- P. infestans interaction cDNA library using parA1 , the gene encoding the major secreted elicitin of P. parasitica , as a probe. Inf1 encodes a 118 amino acid protein including a 20 amino acid signal peptide. Detailed expression studies show that inf1 is expressed in mycelium grown in various culture media, whereas expression was not detected in sporangia, zoospores, cysts and germinating cysts. The highest levels of expression of inf1 are observed in in vitro -grown mycelium and in planta during the late stages of infection when profuse sporulation and leaf necrosis occur. Expression is, however, down-regulated during early biotrophic stages of the interaction.To obtain P. infestans strains deficient in INF1 production, we explored a homology-dependent gene silencing strategy. Integrative transformation with antisense, sense and promoter-less constructs in P. infestans was performed to generate mutants. Inf1 mRNA and INF1 protein could not be detected in up to 20% of the transformants. The silenced state of the inf1 gene was shown to be mitotically stable under various conditions in vitro and in planta . In pathogenicity assays, the INF1-deficient strains remained pathogenic on the host plants potato and tomato. However, in contrast to the wild type and control transformant strains, INF1-deficient strains induced also disease lesions and extensive sporulation when inoculated on Nicotiana benthamiana . These results demonstrate that recognition of INF1 elicitin leads to active resistance in N. benthamiana to P. infestans and that INF1 functions as a plant species-specific avirulence factor.In Chapter 5, we describe experiments to identify the mechanism of silencing of the inf1 gene in P. infestans . Nuclear run-on assays showed that inf1 gene silencing is regulated at the transcriptional level. Interestingly, DNA methylation, a feature often associated with transcriptionally regulated gene silencing could not be detected in the inf1 gene sequences. Heterokaryons obtained by somatic fusion of an inf1 -silenced transgenic strain and a wild type strain displayed also stable gene silencing, demonstrating that inf1 silencing is dominant and acts in trans. The inf1 gene remained silenced in non-transgenic homokaryotic single zoospore isolates released from the silenced heterokaryons. Apparently, the presence of transgenes is not essential for maintaining the silenced status of the endogenous inf1 gene. Karyogamy was not demonstrated and hence, it is unlikely that the silenced state of the inf1 gene is transmitted from nucleus to nucleus by specific DNA-DNA interactions. Consequently, we propose a novel silencing phenomenon, called internuclear gene silencing, in which a diffusible silencing factor is involved in inducing stable gene silencing. We speculate that the proposed diffusible trans -acting silencing factor is either a protein, an aberrant RNA molecule or a complex consisting of RNA and protein. We envisage that such a molecule is transported from nucleus to nucleus where it may facilitate an inheritable change in inf1 -expression possibly initiated by changes in chromatin structure of the target gene or regions surrounding the target gene. Internuclear gene silencing is clearly a trans -inactivation phenomenon that is reminiscent of paramutation.In Chapter 8, we discuss how the results presented in this thesis will contribute to a better understanding of the biology and pathogenicity of P. infestans . On the long run, increased knowledge of this notorious pathogen will help in developing alternative methods to control potato late blight.</p

Graded Majorana spinors

In many mathematical and physical contexts spinors are treated as Grassmann odd valued fields. We show that it is possible to extend the classification of reality conditions on such spinors by a new type of Majorana condition. In order to define this graded Majorana condition we make use of pseudo-conjugation, a rather unfamiliar extension of complex conjugation to supernumbers. Like the symplectic Majorana condition, the graded Majorana condition may be imposed, for example, in spacetimes in which the standard Majorana condition is inconsistent. However, in contrast to the symplectic condition, which requires duplicating the number of spinor fields, the graded condition can be imposed on a single Dirac spinor. We illustrate how graded Majorana spinors can be applied to supersymmetry by constructing a globally supersymmetric field theory in three-dimensional Euclidean space, an example of a spacetime where standard Majorana spinors do not exist.Comment: 16 pages, version to appear in J. Phys. A; AFK previously published under the name A. F. Schunc

Dynamics of (SUSY) AdS Space Isometry Breaking

Actions governing the dynamics of the Nambu-Goldstone modes resulting from the spontaneous breaking of the SO(4,2) and $SU(2,2|1)$ isometries of five dimensional anti-de Sitter space ($AdS_{5}$) and SUSY $AdS_{5}\times S_1$ spaces respectively due to a restriction of the motion to embedded four dimensional $AdS_{4}$ space and four dimensional Minkowski space ($M_4$) probe branes are presented. The dilatonic Nambu-Goldstone mode governing the motion of the $M_4$ space probe brane into the covolume of the SUSY $AdS_5\times S_1$ space is found to be unstable. No such instablility appears in the other cases. Gauging these symmetries leads to an Einstein-Hilbert action containing, in addition to the gravitational vierbein, a massive Abelian vector field coupled to gravity.Comment: 6 pages, 0 figures, to appear in Proceedings of IRGAC 2006: 2nd International Conference on Quantum Theories and Renormalization Group in Gravity and Cosmology, Barcelon

A molecular insight into algal-oomycete warfare : cDNA analysis of Ectocarpus siliculosus infected with the basal oomycete Eurychasma dicksonii

Peer reviewedPublisher PD

A molecular insight into algal-oomycete warfare: cDNA analysis of <i>Ectocarpus siliculosus</i> infected with the basal oomycete <i>Eurychasma dicksonii</i>

Brown algae are the predominant primary producers in coastal habitats, and like land plants are subject to disease and parasitism. Eurychasma dicksonii is an abundant, and probably cosmopolitan, obligate biotrophic oomycete pathogen of marine brown algae. Oomycetes (or water moulds) are pathogenic or saprophytic non-photosynthetic Stramenopiles, mostly known for causing devastating agricultural and aquacultural diseases. Whilst molecular knowledge is restricted to crop pathogens, pathogenic oomycetes actually infect hosts from most eukaryotic lineages. Molecular evidence indicates that Eu. dicksonii belongs to the most early-branching oomycete clade known so far. Therefore Eu. dicksonii is of considerable interest due to its presumed environmental impact and phylogenetic position. Here we report the first large scale functional molecular data acquired on the most basal oomycete to date. 9873 unigenes, totalling over 3.5Mb of sequence data, were produced from Sanger-sequenced and pyrosequenced EST libraries of infected Ectocarpus siliculosus. 6787 unigenes (70%) were of algal origin, and 3086 (30%) oomycete origin. 57% of Eu. dicksonii sequences had no similarity to published sequence data, indicating that this dataset is largely unique. We were unable to positively identify sequences belonging to the RXLR and CRN groups of oomycete effectors identified in higher oomycetes, however we uncovered other unique pathogenicity factors. These included putative algal cell wall degrading enzymes, cell surface proteins, and cyclophilin-like proteins. A first look at the host response to infection has also revealed movement of the host nucleus to the site of infection as well as expression of genes responsible for strengthening the cell wall, and secretion of proteins such as protease inhibitors. We also found evidence of transcriptional reprogramming of E. siliculosus transposable elements and of a viral gene inserted in the host genome