Bad bugs and beleaguered bladders: Interplay between uropathogenic Escherichia coli and innate host defenses

Strains of uropathogenic Escherichia coli (UPEC) are the causative agents in the vast majority of all urinary tract infections. Upon entering the urinary tract, UPEC strains face a formidable array of host defenses, including the flow of urine and a panoply of antimicrobial factors. To gain an initial foothold within the bladder, most UPEC strains encode filamentous surface adhesive organelles called type 1 pili that can mediate bacterial attachment to, and invasion of, bladder epithelial cells. Invasion provides UPEC with a protective environment in which bacteria can either replicate or persist in a quiescent state. Infection with type 1-piliated E. coli can trigger a number of host responses, including cytokine production, inflammation, and the exfoliation of infected bladder epithelial cells. Despite numerous host defenses and even antibiotic treatments that can effectively sterilize the urine, recent studies demonstrate that uropathogens can persist within the bladder tissue. These bacteria may serve as a reservoir for recurrent infections, a common problem affecting millions each year.

Identification of a pathogenicity island required for Salmonella survival in host cells.

We have identified a region unique to the Salmonella typhimurium chromosome that is essential for virulence in mice. This region harbors at least three genes: two (spiA and spiB) encode products that are similar to proteins found in type III secretion systems, and a third (spiR) encodes a putative regulator. A strain with a mutation in spiA was unable to survive within macrophages but displayed wild-type levels of epithelial cell invasion. The culture supernatants of the spi mutants lacked a modified form of flagellin, which was present in the supernatant of the wild-type strain. This suggests that the Spi secretory apparatus exports a protease, or a protein that can alter the activity of a secreted protease. The "pathogenicity island" harboring the spi genes may encode the virulence determinants that set Salmonella apart from other enteric pathogens.

Identification of transferred DNA insertions within Arabidopsis genes involved in signal transduction and ion transport.

The transferred DNA (T-DNA) of Agrobacterium tumefaciens serves as an insertional mutagen once integrated into a host plant's genome. As a means of facilitating reverse genetic analysis in Arabidopsis thaliana, we have developed a method that allows one to search for plants carrying F-DNA insertions within any sequenced Arabidopsis gene. Using PCR, we screened a collection of 9100 independent T-DNA-transformed Arabidopsis lines and found 17 T-DNA insertions within the 63 genes analyzed. The genes surveyed include members of various gene families involved in signal transduction and ion transport. As an example, data are shown for a T-DNA insertion that was found within CPK-9, a member of the gene family encoding calmodulin-domain protein kinases.

Naturally occurring variation in copia expression is due to both element (cis) and host (trans) regulatory variation.

Significant differences in levels of copia [Drosophila long terminal repeat (LTR) retrotransposon] expression exist among six species representing the Drosophila melanogaster species complex (D. melanogaster, Drosophila mauritiana, Drosophila simulans, Drosophila sechellia, Drosophila yakuba, and Drosophila erecta) and a more distantly related species (Drosophila willistoni). These differences in expression are correlated with major size variation mapping to putative regulatory regions of the copia 5' LTR and adjacent untranslated leader region (ULR). Sequence analysis indicates that these size variants were derived from a series of regional duplication events. The ability of the copia LTR-ULR size variants to drive expression of a bacterial chloramphenicol acetyltransferase reporter gene was tested in each of the seven species. The results indicate that both element-encoded (cis) and host-genome-encoded (trans) genetic differences are responsible for the variability in copia expression within and between Drosophila species. This finding indicates that models purporting to explain the dynamics and distribution of retrotransposons in natural populations must consider the potential impact of both element-encoded and host-genome-encoded regulatory variation to be valid. We propose that interelement selection among retrotransposons may provide a molecular drive mechanism for the evolution of eukaryotic enhancers which can be subsequently distributed throughout the genome by retrotransposition.

A formal framework for modelling complex network management systems

Society today is completely dependent on computer networks, the Internet and distributed systems, which place at our disposal the necessary services to perform our daily tasks. Subconsciously, we rely increasingly on network management systems. These systems allow us to, in general, maintain, manage, configure, scale, adapt, modify, edit, protect, and enhance the main distributed systems. Their role is secondary and is unknown and transparent to the users. They provide the necessary support to maintain the distributed systems whose services we use every day. If we do not consider network management systems during the development stage of distributed systems, then there could be serious consequences or even total failures in the development of the distributed system. It is necessary, therefore, to consider the management of the systems within the design of the distributed systems and to systematise their design to minimise the impact of network management in distributed systems projects. In this paper, we present a framework that allows the design of network management systems systematically. To accomplish this goal, formal modelling tools are used for modelling different views sequentially proposed of the same problem. These views cover all the aspects that are involved in the system; based on process definitions for identifying responsible and defining the involved agents to propose the deployment in a distributed architecture that is both feasible and appropriate.

Footwear bio-modelling: An industrial approach

There is a growing need within the footwear sector to customise the design of the last from which a specific footwear style is to be produced. This customisation is necessary for user comfort and health reasons, as the user needs to wear a suitable shoe. For this purpose, a relationship must be established between the user foot and the last with which the style will be made; up until now, no model has existed that integrates both elements. On the one hand, traditional customised footwear manufacturing techniques are based on purely artisanal procedures which make the process arduous and complex; on the other hand, geometric models proposed by different authors present the impossibility of implementing them in an industrial environment with limited resources for the acquisition of morphometric and structural data for the foot, apart from the fact that they do not prove to be sufficiently accurate given the non-similarity of the foot and last. In this paper, two interrelated geometric models are defined, the first, a bio-deformable foot model and the second, a deformable last model. The experiments completed show the goodness of the model, with it obtaining satisfactory results in terms of comfort, efficiency and precision, which make it viable for use in the sector.

Conceptual Modelling of Complex Network Management Systems

Society, as we know it today, is completely dependent on computer networks, Internet and distributed systems, which place at our disposal the necessary services to perform our daily tasks. Moreover, and unconsciously, all services and distributed systems require network management systems. These systems allow us to, in general, maintain, manage, configure, scale, adapt, modify, edit, protect or improve the main distributed systems. Their role is secondary and is unknown and transparent to the users. They provide the necessary support to maintain the distributed systems whose services we use every day. If we don’t consider network management systems during the development stage of main distributed systems, then there could be serious consequences or even total failures in the development of the distributed systems. It is necessary, therefore, to consider the management of the systems within the design of distributed systems and systematize their conception to minimize the impact of the management of networks within the project of distributed systems. In this paper, we present a formalization method of the conceptual modelling for design of a network management system through the use of formal modelling tools, thus allowing from the definition of processes to identify those responsible for these. Finally we will propose a use case to design a conceptual model intrusion detection system in network.

Modelling of the surface emission of the low magnetic field magnetar SGR 0418+5729

We perform a detailed modelling of the post-outburst surface emission of the low magnetic field magnetar SGR 0418+5729. The dipolar magnetic field of this source, B=6×1012G estimated from its spin-down rate, is in the observed range of magnetic fields for normal pulsars. The source is further characterized by a high pulse fraction and a single-peak profile. Using synthetic temperature distribution profiles, and fully accounting for the general-relativistic effects of light deflection and gravitational redshift, we generate synthetic X-ray spectra and pulse profiles that we fit to the observations. We find that asymmetric and symmetric surface temperature distributions can reproduce equally well the observed pulse profiles and spectra of SGR 0418. None the less, the modelling allows us to place constraints on the system geometry (i.e. the angles ψ and ξ that the rotation axis makes with the line of sight and the dipolar axis, respectively), as well as on the spot size and temperature contrast on the neutron star surface. After performing an analysis iterating between the pulse profile and spectra, as done in similar previous works, we further employed, for the first time in this context, a Markov-Chain Monte Carlo approach to extract constraints on the model parameters from the pulse profiles and spectra, simultaneously. We find that, to reproduce the observed spectrum and flux modulation: (a) the angles must be restricted to 65° ≲ ψ + ξ ≲ 125° or 235° ≲ ψ + ξ ≲ 295°; (b) the temperature contrast between the poles and the equator must be at least a factor of ∼6, and (c) the size of the hottest region ranges between 0.2 and 0.7 km (including uncertainties on the source distance). Lastly, we interpret our findings within the context of internal and external heating models.

Simulating Granite Emplacement and Deformation with Centrifuge Analogue Modelling

The Greater Himalayan leucogranites are a discontinuous suite of intrusions emplaced in a thickened crust during the Miocene southward ductile extrusion of the Himalayan metamorphic core. Melt-induced weakening is thought to have played a critical role in strain localization that facilitated the extrusion. Recent advancements in centrifuge analogue modelling techniques allow for the replication of a broader range of crustal deformation behaviors, enhancing our understanding of large hot orogens. Polydimethylsiloxane (PDMS) is commonly used in centrifuge experiments to model weak melt zones. Difficulties in handling PDMS had, until now, limited its emplacement in models prior to any deformation. A new modelling technique has been developed where PDMS is emplaced into models that have been subjected to some shortening. This technique aims to better understand the effects of melt on strain localization and potential decoupling between structural levels within an evolving orogenic system. Models are subjected to an early stage of shortening, followed by the introduction of PDMS, and then a final stage of shortening. Theoretical percentages of partial melt and their effect on rock strength are considered when adding a specific percentage of PDMS in each model. Due to the limited size of the models, only PDMS sheets of 3 mm thickness were used, which varied in length and width. Within undeformed packages, minimal surface and internal deformation occurred when PDMS is emplaced in the lower layer of the model, showing a vertical volume increase of ~20% within the package; whereas the emplacement of PDMS into the middle layer showed internal dragging of the middle laminations into the lower layer and a vertical volume increase ~30%. Emplacement of PDMS results in ~7% shortening for undeformed and deformed models. Deformed models undergo ~20% additional shortening after two rounds of deformation. Strain localization and decoupling between units occur in deformed models where the degree of deformation changes based on the amount of partial melt present. Surface deformation visible by the formation of a bulge, mode 1 extension cracks and varying surface strain ellipses varies depending if PDMS is present. Better control during emplacement is exhibited when PDMS is added into cooler models, resulting in reduced internal deformation within the middle layer.

Transferability of Regional Permafrost Disturbance Susceptibility Modelling Using Generalized Linear and Generalized Additive Models

To effectively assess and mitigate risk of permafrost disturbance, disturbance-p rone areas can be predicted through the application of susceptibility models. In this study we developed regional susceptibility models for permafrost disturbances using a field disturbance inventory to test the transferability of the model to a broader region in the Canadian High Arctic. Resulting maps of susceptibility were then used to explore the effect of terrain variables on the occurrence of disturbances within this region. To account for a large range of landscape charac- teristics, the model was calibrated using two locations: Sabine Peninsula, Melville Island, NU, and Fosheim Pen- insula, Ellesmere Island, NU. Spatial patterns of disturbance were predicted with a generalized linear model (GLM) and generalized additive model (GAM), each calibrated using disturbed and randomized undisturbed lo- cations from both locations and GIS-derived terrain predictor variables including slope, potential incoming solar radiation, wetness index, topographic position index, elevation, and distance to water. Each model was validated for the Sabine and Fosheim Peninsulas using independent data sets while the transferability of the model to an independent site was assessed at Cape Bounty, Melville Island, NU. The regional GLM and GAM validated well for both calibration sites (Sabine and Fosheim) with the area under the receiver operating curves (AUROC) N 0.79. Both models were applied directly to Cape Bounty without calibration and validated equally with AUROC's of 0.76; however, each model predicted disturbed and undisturbed samples differently. Addition- ally, the sensitivity of the transferred model was assessed using data sets with different sample sizes. Results in- dicated that models based on larger sample sizes transferred more consistently and captured the variability within the terrain attributes in the respective study areas. Terrain attributes associated with the initiation of dis- turbances were similar regardless of the location. Disturbances commonly occurred on slopes between 4 and 15°, below Holocene marine limit, and in areas with low potential incoming solar radiation

Host insulin stimulates Echinococcus multilocularis insulin signalling pathways and larval development.

BACKGROUND The metacestode of the tapeworm Echinococcus multilocularis is the causative agent of alveolar echinococcosis, a lethal zoonosis. Infections are initiated through establishment of parasite larvae within the intermediate host's liver, where high concentrations of insulin are present, followed by tumour-like growth of the metacestode in host organs. The molecular mechanisms determining the organ tropism of E. multilocularis or the influences of host hormones on parasite proliferation are poorly understood. RESULTS Using in vitro cultivation systems for parasite larvae we show that physiological concentrations (10 nM) of human insulin significantly stimulate the formation of metacestode larvae from parasite stem cells and promote asexual growth of the metacestode. Addition of human insulin to parasite larvae led to increased glucose uptake and enhanced phosphorylation of Echinococcus insulin signalling components, including an insulin receptor-like kinase, EmIR1, for which we demonstrate predominant expression in the parasite's glycogen storage cells. We also characterized a second insulin receptor family member, EmIR2, and demonstrated interaction of its ligand binding domain with human insulin in the yeast two-hybrid system. Addition of an insulin receptor inhibitor resulted in metacestode killing, prevented metacestode development from parasite stem cells, and impaired the activation of insulin signalling pathways through host insulin. CONCLUSIONS Our data indicate that host insulin acts as a stimulant for parasite development within the host liver and that E. multilocularis senses the host hormone through an evolutionarily conserved insulin signalling pathway. Hormonal host-parasite cross-communication, facilitated by the relatively close phylogenetic relationship between E. multilocularis and its mammalian hosts, thus appears to be important in the pathology of alveolar echinococcosis. This contributes to a closer understanding of organ tropism and parasite persistence in larval cestode infections. Furthermore, our data show that Echinococcus insulin signalling pathways are promising targets for the development of novel drugs.

Regulation of host cell survival by intracellular Plasmodium and Theileria parasites

Plasmodium and Theileria parasites are obligate intracellular protozoa of the phylum Apicomplexa. Theileria infection of bovine leukocytes induces transformation of host cells and infected leukocytes can be kept indefinitely in culture. Theileria-dependent host cell transformation has been the subject of interest for many years and the molecular basis of this unique phenomenon is quite well understood. The equivalent life cycle stage of Plasmodium is the infection of mammalian hepatocytes, where parasites reside for 2-7 days depending on the species. Some of the molecular details of parasite-host interactions in P. berghei-infected hepatocytes have emerged only very recently. Similar to what has been shown for Theileria-infected leukocytes these data suggest that malaria parasites within hepatocytes also protect their host cell from programmed cell death. However, the strategies employed to inhibit host cell apoptotic pathways appear to be different to those used by Theileria. This review discusses similarities and differences at the molecular level of Plasmodium- and Theileria-induced regulation of the host cell survival machinery.

Do upwelled waters from the California Undercurrent contribute to high pCO2 within the fjord system of Nootka Sound, BC?

Senior thesis written for Oceanography 445

Modelling the effect of shear history on activated sludge flocculation

The aim of this paper is to investigate the effect of shear history on activated sludge flocculation dynamics and to model the observed relationships using population balances. Activated sludge flocs are exposed to dramatic changes in the shear rate within the treatment process, as they pass through localised high and low mixing intensities within the aeration basin and are cycled through the different unit operations of the treatment process. We will show that shear history is a key factor in determining floc size, and that the floc size varies irreversibly with changes in shear rate. A population balance model of the flocculation process is also introduced and evaluated.

Functional recycling of C2 domains throughout evolution: A comparative study of synaptotagmin, protein kinase C and phospholipase C by sequence, structural and modelling approaches

The C2 domain is one of the most frequent and widely distributed calcium-binding motifs. Its structure comprises an eight-stranded beta-sandwich with two structural types as if the result of a circular permutation. Combining sequence, structural and modelling information, we have explored, at different levels of granularity, the functional characteristics of several families of C2 domains. At the coarsest level,the similarity correlates with key structural determinants of the C2 domain fold and, at the finest level, with the domain architecture of the proteins containing them, highlighting the functional diversity between the various subfamilies. The functional diversity appears as different conserved surface patches throughout this common fold. In some cases, these patches are related to substrate-binding sites whereas in others they correspond to interfaces of presumably permanent interaction between other domains within the same polypeptide chain. For those related to substrate-binding sites, the predictions overlap with biochemical data in addition to providing some novel observations. For those acting as protein-protein interfaces' our modelling analysis suggests that slight variations between families are a result of not only complementary adaptations in the interfaces involved but also different domain architecture. In the light of the sequence and structural genomic projects, the work presented here shows that modelling approaches along with careful sub-typing of protein families will be a powerful combination for a broader coverage in proteomics. (C) 2003 Elsevier Ltd. All rights reserved.