Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia

Pochonia chlamydosporia is a worldwide-distributed soil fungus with a great capacity to infect and destroy the eggs and kill females of plant-parasitic nematodes. Additionally, it has the ability to colonize endophytically roots of economically-important crop plants, thereby promoting their growth and eliciting plant defenses. This multitrophic behavior makes P. chlamydosporia a potentially useful tool for sustainable agriculture approaches. We sequenced and assembled ∼41 Mb of P. chlamydosporia genomic DNA and predicted 12,122 gene models, of which many were homologous to genes of fungal pathogens of invertebrates and fungal plant pathogens. Predicted genes (65%) were functionally annotated according to Gene Ontology, and 16% of them found to share homology with genes in the Pathogen Host Interactions (PHI) database. The genome of this fungus is highly enriched in genes encoding hydrolytic enzymes, such as proteases, glycoside hydrolases and carbohydrate esterases. We used RNA-Seq technology in order to identify the genes expressed during endophytic behavior of P. chlamydosporia when colonizing barley roots. Functional annotation of these genes showed that hydrolytic enzymes and transporters are expressed during endophytism. This structural and functional analysis of the P. chlamydosporia genome provides a starting point for understanding the molecular mechanisms involved in the multitrophic lifestyle of this fungus. The genomic information provided here should also prove useful for enhancing the capabilities of this fungus as a biocontrol agent of plant-parasitic nematodes and as a plant growth-promoting organism.

The nuclear pore complex and its transporters : from virus-host interactors to subverting the innate antiviral immunity

Les virus ont besoin d’interagir avec des facteurs cellulaires pour se répliquer et se propager dans les cellules d’hôtes. Une étude de l'interactome des protéines du virus d'hépatite C (VHC) par Germain et al. (2014) a permis d'élucider de nouvelles interactions virus-hôte. L'étude a également démontré que la majorité des facteurs de l'hôte n'avaient pas d'effet sur la réplication du virus. Ces travaux suggèrent que la majorité des protéines ont un rôle dans d'autres processus cellulaires tel que la réponse innée antivirale et ciblées pas le virus dans des mécanismes d'évasion immune. Pour tester cette hypothèse, 132 interactant virus-hôtes ont été sélectionnés et évalués par silençage génique dans un criblage d'ARNi sur la production interferon-beta (IFNB1). Nous avons ainsi observé que les réductions de l'expression de 53 interactants virus-hôte modulent la réponse antivirale innée. Une étude dans les termes de gène d'ontologie (GO) démontre un enrichissement de ces protéines au transport nucléocytoplasmique et au complexe du pore nucléaire. De plus, les gènes associés avec ces termes (CSE1L, KPNB1, RAN, TNPO1 et XPO1) ont été caractérisé comme des interactant de la protéine NS3/4A par Germain et al. (2014), et comme des régulateurs positives de la réponse innée antivirale. Comme le VHC se réplique dans le cytoplasme, nous proposons que ces interactions à des protéines associées avec le noyau confèrent un avantage de réplication et bénéficient au virus en interférant avec des processus cellulaire tel que la réponse innée. Cette réponse innée antivirale requiert la translocation nucléaire des facteurs transcriptionnelles IRF3 et NF-κB p65 pour la production des IFNs de type I. Un essai de microscopie a été développé afin d'évaluer l’effet du silençage de 60 gènes exprimant des protéines associés au complexe du pore nucléaire et au transport nucléocytoplasmique sur la translocation d’IRF3 et NF-κB p65 par un criblage ARNi lors d’une cinétique d'infection virale. En conclusion, l’étude démontre qu’il y a plusieurs protéines qui sont impliqués dans le transport de ces facteurs transcriptionnelles pendant une infection virale et peut affecter la production IFNB1 à différents niveaux de la réponse d'immunité antivirale. L'étude aussi suggère que l'effet de ces facteurs de transport sur la réponse innée est peut être un mécanisme d'évasion par des virus comme VHC.

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.

Host and Environmental Correlates of Multi-Drug Resistance in Kenyan Children with Acute Bacterial Diarrhea

Thesis (Master's)--University of Washington, 2016-06

Biology and phenology of the eriophyid mite, Floracarus perrepae, on its native host in Australia, Old World climbing fern, Lygodium microphyllum

The biology and phenology of the eriophyid mite, Floracarus perrepae Knihinicki and Boczek,a potential biological control agent of Lygodium microphyllum (Cav.) R. Br., was studied in its native range - Queensland, Australia. F. perrepae forms leaf roll galls oil tile subpinnae of L. microphyllum. It has a simple biology, with females and males produced throughout the year. Tile Population was female biased at 10.5 to 1. The immature development time was 8.9 ± 0.1 and 7.0 ± 0.1 days; adult longevity was 30.6 ± 1.6 and 19.4 ± 1.2 days and mean fecundity per female was 54.5 ± 3.2 and 38.5 ± 1.6 eggs at 21 and 26 ° C, all respectively. Field studies showed that tile mite was active year round, with populations peaking when temperatures were cool and soil moisture levels were highest. Two species of predatory mites, Tarsonemus sp. and a species of Tydeidae, along with the pathogen Hirsutella thompsonii, had significant effects oil all life stages of F. perrepae. Despite high levels of predators and the pathogen, F. perrepae caused consistent damage to L. microphyllum at all the field sites over the entire 2 years of the study.

Discrimination among host plants (Leucaena species and accessions) by the psyllid pest Heteropsylla cubana and implications for understanding resistance

1 The herbivorous bug Heteropsylla cubana Crawford (Homoptera: Psyllidae) is a pest of the cattle fodder crop Leucaena (Leguminosae: Mimosoideae). The interaction between the psyllid and three varieties of its Leucaena host plant was investigated in relation to the apparent resistance of some Leucaena varieties (Leucaena leucocephala, Leucaena pallida and their hybrids) to attack. 2 Field trials demonstrated that adult psyllids distinguished among the different varieties of Leucaena over a distance, and were attracted to L. leucocephala in significantly higher numbers than to L. pallida or to the hybrid. Pesticide treatment increased the attractiveness of Leucaena plants, even of those deemed to be psyllid resistant. Numbers of psyllid eggs and nymphs, sampled in the field, reflect the arrival rates of adults at the three plant varieties. 3 Wavelength reflectance data of the three Leucaena varieties were not significantly different from one another, suggesting that psyllids cannot discriminate among the three plants using brightness or wavelength cues. There was a differential release of caryophyllene among the three varieties. Release of caryophyllene in L. leucocephala and the hybrid appeared to be influenced by environmental conditions. 4 Experiments demonstrated that caryophyllene (at least on its own) did not influence the behaviour of leucaena psyllids in relation to leucaena plants. 5 The results suggest that host plant volatiles cannot be dismissed as significant in the interaction between the leucaena psyllid and its Leucaena host plants. Further avenues for investigation are recommended and these are related to novel ways of understanding resistance in insect plant inter-relationships.

Information technologies for vaccine research

Vaccinology is a combinatorial science which studies the diversity of pathogens and the human immune system, and formulations that can modulate immune responses and prevent or cure disease. Huge amounts of data are produced by genomics and proteomics projects and large-scale screening of pathogen-host and antigen-host interactions. Current developments in computational vaccinology mainly support the analysis of antigen processing and presentation and the characterization of targets of immune response. Future development will also include systemic models of vaccine responses. Immunomics, the large-scale screening of immune processes which includes powerful immunoinformatic tools, offers great promise for future translation of basic immunology research advances into successful vaccines.

Temperature dependence of the crystal structure and g-values of [(HC(Ph2PO)(3))(2)Cu] (ClO4)(2)center dot 2H(2)O: Influence of dynamic Jahn-Teller coupling and lattice strain interactions

The temperature dependence of the X-ray crystal structure and powder EPR spectrum of [(HC(Ph2PO)(3))(2)CU]-(ClO4)(2)center dot 2H(2)O is reported, and the structure at room temperature confirms that reported previously. Below similar to 100 K, the data imply a geometry with near elongated tetragonal symmetry for the [(HC(Ph2PO)(3))(2)Cu](2+) complex, but on warming the two higher Cu-O bond lengths and g-values progressively converge, and by 340 K the bond lengths correspond to a compressed tetragonal geometry. The data may be interpreted satisfactorily assuming an equilibrium among the energy levels of a Cu-O-6 polyhedron subjected to Jahn-Teller vibronic coupling and a lattice strain. However, agreement with the experiment is obtained only if the orthorhombic component of the lattice strain decreases to a negligible value as the temperature approaches 340 K.

Analysis of the Pasteurella multocida outer membrane sub-proteome and its response to the in vivo environment of the natural host

This study describes the identification of outer membrane proteins (OMPs) of the bacterial pathogen Pasteurella multocida and an analysis of how the expression of these proteins changes during infection of the natural host. We analysed the sarcosine-insoluble membrane fractions, which are highly enriched for OMPs, from bacteria grown under a range of conditions. Initially, the OMP-containing fractions were resolved by 2-DE and the proteins identified by MALDI-TOF MS. In addition, the OMP-containing fractions were separated by 1-D SDS-PAGE and protein identifications were made using nano LC MS/MS. Using these two methods a total of 35 proteins was identified from samples obtained from organisms grown in rich culture medium. Six of the proteins were identified only by 2-DE MALDI-TOF MS, whilst 17 proteins were identified only by 1-D LC MS/MS. We then analysed the OMPs from P. multocida which had been isolated from the bloodstream of infected chickens (a natural host) or grown in iron-depleted medium. Three proteins were found to be significantly up-regulated during growth in vivo and one of these (Pm0803) was also up-regulated during growth in iron-depleted medium. After bioinformatic analysis of the protein matches, it was predicted that over one third of the combined OMPs predicted by the bioinformatics sub-cellular localisation tools PSORTB and Proteome Analyst, had been identified during this study. This is the first comprehensive proteomic analysis of the P. multocida outer membrane and the first proteomic analysis of how a bacterial pathogen modifies its outer membrane proteome during infection.

Influence of lattice interactions on the jahn-teller distortion of the [Cu(H2O)(6)](2+) ion: Dependence of the crystal structure of K-2[Cu(H2O)(6)](SO4)(2x)(SeO4)(2-2x) upon the sulfate/selenate ratio

The temperature dependence of the structure of the mixed-anion Tutton salt K-2[Cu(H2O)(6)](SO4)(2x)(SeO4)(2-2x) has been determined for crystals with 0, 17, 25, 68, 78, and 100% sulfate over the temperature range of 85-320 K. In every case, the [Cu(H2O)(6)](2+) ion adopts a tetragonally elongated coordination geometry with an orthorhombic distortion. However, for the compounds with 0, 17, and 25% sulfate, the long and intermediate bonds occur on a different pair of water molecules from those with 68, 78, and 100% sulfate. A thermal equilibrium between the two forms is observed for each crystal, with this developing more readily as the proportions of the two counterions become more similar. Attempts to prepare a crystal with approximately equal amounts of sulfate and selenate were unsuccessful. The temperature dependence of the bond lengths has been analyzed using a model in which the Jahn-Teller potential surface of the [Cu(H2O)(6)](2+) ion is perturbed by a lattice-strain interaction. The magnitude and sign of the orthorhombic component of this strain interaction depends on the proportion of sulfate to selenate. Significant deviations from Boltzmann statistics are observed for those crystals exhibiting a large temperature dependence of the average bond lengths, and this may be explained by cooperative interactions between neighboring complexes.

Perspective on the host response to human metapneumovirus infection: what can we learn from respiratory syncytial virus infections?

Human metapneumovirus (HMPV) is a recently discovered pathogen first identified in respiratory specimens from young children suffering from clinical respiratory syndromes ranging from mild to severe lower respiratory tract illness. HMPV has worldwide prevalence, and is a leading cause of respiratory tract infection in the first years of life, with a spectrum of disease similar to respiratory syncytial virus (RSV). The disease burden associated with HMPV infection has not been fully elucidated; however, studies indicate that HMPV may cause upper or lower respiratory tract illness in patients between ages 2 months and 87 years, may co-circulate with RSV, and HMPV infection may be associated with asthma exacerbation. The mechanisms and effector pathways contributing to immunity or disease pathogenesis following infection are not fully understood; however, given the clinical significance of HMPV, there is a need for a fundamental understanding of the immune and pathophysiological processes that occur following infection to provide the foundation necessary for the development of effective vaccine or therapeutic intervention strategies. This review provides a current perspective on the processes associated with HMPV infection, immunity, and disease pathogenesis. (c) 2005 Elsevier SAS. All rights reserved.

Host-specificity of monogenean (platyhelminth) parasites: a role for anterior adhesive areas?

Monogeneans (flatworms) are among the most host-specific of parasites in general and may be the most host-specific of all fish parasites. Specificity, in terms of a restricted spatial distribution within an environment, is not unique to parasites and is displayed by some fungi, insects, birds, symbionts and pelagic larvae of free-living marine invertebrates. The nature of cues, how habitats are recognised and how interactions between partners are mediated and maintained is of interest across these diverse associations. We review some experiments that demonstrate important factors that contribute to host-specificity at the level of infective stages (larvae of oviparous monogeneans; juveniles of viviparous gyrodactylids) and adult parasites. Recent research on immune responses by fish to monogenean infections is considered. We emphasise the critical importance of host epidermis to the Monogenea. Monogeneans live on host epidermis, they live in its products (e.g. mucus), monopisthocotyleans feed on it, some of its products are attractants and it may be an inhospitable surface because of its immunological activity. We focus attention on fish but reference is made to amphibian hosts. We develop the concept for a potential role in host-speciality by the anterior adhesive areas, either the specialised tegument and/or anterior secretions produced by monogeneans for temporary but firm attachment during locomotion on host epithelial surfaces. Initial contact between the anterior adhesive areas of infective stages and host epidermis may serve two important purposes. (1) Appropriate sense organs or receptors on the parasite interact with a specific chemical or chemicals or with surface structures on host epidermis. (2) A specific but instant recognition or reaction occurs between component(s) of host mucus and the adhesive(s) secreted by monogeneans. The chemical composition of fish skin is known to be species-specific and our preliminary analysis of the chemistry of some monogenean adhesives indicates they are novel proteins that display some differences between parasite families and species. (C) 2000 Australian Society for Parasitology Inc. Published by Elsevier Science Ltd. All rights reserved.

Cellular interactions with hydrogels

An efficient means of evaluating potential biomaterials is to use the in vitro fibroblast cell culture model. However, the chemistry which influences cell adhesion on polymer substrates is poorly understood. The work in this thesis aims to rationalise several theories of current opinion and introduce new chemical techniques that may predict cellular behaviour. The keratoprosthesis is a typical example of the need to be able to manipulate cell adhesion of materials since both adhesive and non adhesive sections are needed for proper integration and optical function. Calcein AM/ethidium homodimer-1 and DAPI assays were carried out using 3T3 and EKl.BR cells. Poly(HEMA) was found to be the most cell adhesive hydrogel tested. The reactivity of monomers and the resulting sequence distribution were found to affect surface properties and this may explain the poor levels of cell adhesion seen on NVP/MMA copolymers. Surface free energy is shown to be dependent on the polar and non polar groups present along the backbone chain of the polymers. Dehydrated and hydrated contact angle measurements show the effect of rotation of surface groups around the backbone chain. This effect is most apparent on hydrogels containing methacrylic acid. Dynamic contact angle measurements confirm sequence distribution irregularities and demonstrate the mobility of surface groups. Incorporation of NVI or DEAEMA into the hydrogels does not affect the mobility of the surface groups despite their bulkiness. Foetal calf serum was used for the first time as a test solution in an attempt to mimic a biological environment during surface experiments. A Vroman effect may be present, and may involve different surface proteins for each material tested. This interdisciplinary study combines surface characterisation and biological testing to further the knowledge of the biomaterial/host interface. Surface chemistry techniques appear to be insufficiently sensitive to predict cellular behaviour. The degree of ionisation of hydrogels containing ionic groups depends on the nature of the functional groups as well as the concentration and this is an important parameter to consider when comparing charged materials.

Expatriate-local interactions:an investigation in China

Purpose: This study aims to build on recent research, by investigating and examining how likely it is that Chinese locals (i.e. host country nationals (HCNs)) would offer support to expatriates from India and the USA. Design/methodology/approach: Data were gathered from 222 participants in Chinese organizations, asking them to respond to questions about their willingness to offer support to expatriates. Findings: As predicted, perceived values similarity was significantly related to higher dogmatism, which had a significant positive relationship with ethnocentrism. Further, ethnocentrism had a significant negative relationship with willingness to offer support. Research limitations/implications: All data were collected from the participants at one point in time, so the study's results are subject to common method bias. Also, it only included India and the USA, as the two countries of origin of the expatriates. Practical implications: Given HCNs do not automatically offer support to all expatriates, organizations might consider sending expatriates who are culturally similar to HCNs, as they are more likely to receive support, which will help their adjustment and thus organizational effectiveness. Originality/value: This study adds to the small, but growing, number of empirical investigations of HCN willingness to support expatriates. © Emerald Group Publishing Limited.

Biomaterial interactions with compromised tissue surfaces

This thesis is concerned with the nature of biomaterial interactions with compromised host tissue sites. Both ocular and dermal tissues can be wounded, following injury, disease or surgery, and consequently require the use of a biomaterial. Clear analogies exist between the cornea/tear film/contact lens and the dermal wound bed/wound fluid/skin adhesive wound dressing. The work described in this thesis builds upon established biochemistry to examine specific aspects of the interaction of biomaterials with compromised ocular and dermal tissue sites, with a particular focus on the role of vitronectin. Vitronectin is a prominent cell adhesion glycoprotein present in both tear fluid and wound fluid, and has a role in the regulation and upregulation of plasmin. The interaction of contact lenses with the cornea was assessed by a novel on-lens cell-based vitronectin assay technique. Vitronectin mapping showed that vitronectin-mediated cell adhesion to contact lens surfaces was due to the contact lens-corneal mechanical interaction rather than deposition out of the tear film. This deposition is associated predominantly with the peripheral region of the posterior contact lens surface. The locus of vitronectin deposition on the contact lens surface, which is affected by material modulus, is potentially an important factor in the generation of plasmin in the posterior tear film. Use of the vitronectin mapping technique on ex vivo bandage contact lenses revealed greater vitronectin-mediated cell adhesion to the contact lens surfaces in comparison to lenses worn in the healthy eye. The results suggest that vitronectin is more readily deposited from the impaired corneal tissue bed than the intact healthy tissue bed. Significantly, subjects with a deficient tear film were found to deposit high vitronectin-mediated cell adhesion levels to the BCL surface, thus highlighting the influence of the contact lens-tissue interaction upon deposition. Biomimetic principles imply that adhesive materials for wound applications, including hydrogels and hydrocolloids, should closely match the surface energy parameters of skin. The surface properties of hydrocolloid adhesives were found to be easily modified by contact with siliconised plastic release liners. In contrast, paper release liners did not significantly affect the adhesive surface properties. In order to characterise such materials in the actual wound environment, which is an extremely challenging task, preliminary considerations for the design of an artificial wound fluid model from an animal serum base were addressed.