Dissertations / Theses on the topic 'Host resistance'

The 1985 and 1986 Cotton Reports have the same publication and P-Series numbers.
Cotton breeding stocks were evaluated for resistance to pink bollworm. Resistance is being transferred into improved agronomic stocks.

Significant differences were observed among 79 geographically diverse Arabidopsis accessions in response to the wheat powdery mildew pathogen, Blumeria graminis f.sp. tritici (Bgt) and the wheat leaf rust pathogen Puccinia triticina (Ptr). In response to Bgt genotypes classified into two major classes based on the degree of compatibility, Wc-1 an accession from Germany expressed significantly high frequency of penetration. Interestingly, in response to Ptr, a high frequency of guard cell death and sub-stomata vesicle formation (SVF) was observed on Wa-1, an accession from Poland. Attempted Ptr infection induced the production of reaction oxygen intermediates (ROI), nitric oxide, salicylic acid (SA) and camalexin. The expression of SA, jasmonic acid and ROI-dependent genes were also detected. Multiple small-to-medium effect quantitative trait loci (QTL) were identified that govern the expression of NMR in Arabidopsis against Ptr. In response to Bgt, a leaf collapse phenotype was observed in Ler when it was pre-treated with Cytochalasin E, an inhibitor of actin microfilament polymerization. Whereas, Col did not express a similar phenotype. This reaction showed a complicated genetic basis with the involvement of several genes. Our genetic analysis revealed two major QTLs on chromosomes one and three with the existence of episatsis effects. A role for ASYMMETRIC LEAVES1 (AS1) in plant immunity has recently been identified. My experiments showed a conserved regulatory function for NSPHAN, an orthologue of ASI gene in Nicotiana sylvestris when challenged with host and nonhost pathogens. This regulatory gene action remained consistent when the as1 mutant was coupled with key Arabidopsis defence related mutants.

Plant innate immunity is activated upon pathogen attack by recognizing their avirulent (avr) genes by Resistant (R) genes leading to R-gene resistance or host resistance. Another form of innate immunity is non-host resistance that is exhibited by a given plant species to most strains of a microbial species. R-gene resistance activates salicylic acid (SA) that is synthesized from methyl salicylic acid (MeSA) by Salicylic Acid Binding Protein 2 (SABP2). It was hypothesized that SABP2 plays the similar role in non-host resistance also. Growth experiments and non-host related gene analysis experiments were conducted on tobacco plants using P.s tabaci and P.s. phaseolicola that are host and non-host pathogens on tobacco respectively. Tobacco control plant C3 that expresses SABP2 and 1-2 that is RNAi silenced in SABP2 expression were used in this study. Results suggest that SABP2 may not have any significant role in tobacco non-host resistance.

In this work we take an evolutionary invasion analysis approach to modelling evolution and use it to describe the selection pressures underlying epidemiological traits in natural host populations harboring endemic infections. Throughout this work a logistic form for host-birth rate allows for disease dependent population dynamics so that the detrimental e ects of infection can be modelled and we also consider the more neglected detrimental e ect whereby infection is linked to infertility. To begin with we give a theoretical introduction to the framework of adaptive dynamics and illustrate it through the established example of the evolution of parasite virulence. We then extend the results to account for condition dependent virulence which is an interaction between host condition (i.e. host stress) and virulence, that has recently generated much attention from empiricists. Many natural systems are seasonal, potentially leading to seasonal stress, and we show how to conduct a study for seasonal host populations and analyse its role in the evolution of density dependent virulence. We then turn our attention to the evolution of resistance beginning with a perspective on the relationship between investment in acquired immunity and the lifespan of hosts and parasites. In our penultimate chapter we derive explicit expressions for optimal investment in the various modes of resistance for a range of epidemiological scenarios. These expressions are then key to understanding our nal chapter where we elaborate further on the established theory by allowing for parasite diversity. The nal chapter highlights the central role played by speci city in the evolution of host defence. Since our approach throughout has been to build complexity onto a baseline model we conclude our discussion with a short section interpreting established results on the coevolution of virulence and resistance from the perspective of our results on the evolution of virulence and resistance.

The ability to mount an efficient immune response should be an important life-history trait as parasitism can impact upon an individual's fecundity and survival prospects, and hence its fitness. However, immune function is likely to be costly as resources must be divided between many important traits. Whilst many studies have examined host resistance to particular parasite types, fewer have considered general immune responses. Studies that have considered general immune responses tend to do so in vertebrate models. However, the complexity of the vertebrate immune system makes the examination of evolutionary aspects of immune function difficult. Using larvae of the genus Spodoptera (Lepidoptera: Noctuidae) as a model system, this study examines' genetic and phenotypic aspects of innate immunity. The aims were to assess the levels of additive genetic variation maintained in immune traits, to consider possible costs that could maintain this variation, and to assess the role of phenotypic plasticity in ameliorating those costs. A key finding of this study was that high levels of additive genetic variation were maintained in all of the measured Immune traits. Analysis of the genetic correlations between traits revealed potential trade-offs within the immune system and between immune components and body condition. In addition, it was shown that larvae living at high densities invest more in immune function than those living in solitary conditions, suggesting that larvae can minimise the costs of immune function by employing them only when the risk of pathogenesis is high.

Salmonella cause a broad spectrum of diseases in humans ranging from asymptomatic carriage to life-threatening sepsis. The disease outcome depends partly on the host genetic background.
The contribution of genes controlling the late phase of a Salmonella infection was studied using a model based on the inoculation of a sublethal dose of S. Enteritidis in 129S6 and C57BL/6J mice. C57BL/6J mice were able to eliminate completely S. Enteritidis from their RES, whereas 129S6 mice could not. Linkage analysis of 302 (C57BL/6J X 129S6) F2 progeny identified three QTLs, Ses1, Ses2, and Ses3. They were associated with disease susceptibility in 129S6 mice, and their estimated effects on bacterial clearance were greater in females. A statistical interaction was detected between Ses1 and Ses2. The model included the QTLs, the interaction and sex as a covariate, and explained 32% of the phenotypic variance suggesting that unidentified modifiers contributed to the phenotype.
A two-locus epistasis QTL linkage analysis conducted separately in the F2 females and males identified additional QTLs with individual effects and epistasic QTLs associated with the Salmonella carrier state of 129S6 mice. The model for females included Ses3 and two significant interactions (Ses1-D7Mit267 and Ses1-DXMit48 ) accounting for 47% of the total phenotypic variance. The model for males included Ses1.1, three interactions (Ses1-D9Mit218, D2Mit197-D4Mit2 and D3Mit256-D13Mit36) and explained 47% of the phenotypic variance.
We constructed congenic mice carrying the Ses1.1, Ses1, Ses2 and Ses3 regions to validate their existence in vivo and to study their impact on Salmonella clearance (129.136). Double congenic mice Ses1/Ses2 were constructed to test functionally the statistical interaction between these QTLs. Phenotypic analysis confirmed that Ses1 and Ses1.1 contribute to bacterial clearance.
The candidacy of Nramp1 as the gene underlying Ses1 was evaluated using Nramp1-deficient mice. 129S6-Nramp1tm1Mcg mice have a significantly lower bacterial load compared to 129S6 mice, suggesting that Nramp1 influences the S. Enteritidis clearance during the late phase of infection. We observed that the 129S6 mice mounted an early and strong TH1 response, whereas the 129S6-Nramp1 tm1Mcg mice mounted an earlier and more vigorous TH 2 response that seems to improve the late phase Salmonella clearance.

Root-knot nematodes (Meloidogyne spp.) are serious root pathogens that affect commercial crops world-wide. The overall aim of this study was to develop techniques to identify plant genes expressed in specialised cells induced to feed these nematodes in order to develop a novel approach to host resistance. Little data exists on which root-knot nematode species are present in Western Australia. An initial study was carried out to identify species present in the major horticultural areas of WA. M. incognita, M. hapla, M. arenaria and M. javanica were isolated from a variety of crops with M. javanica found to be the most prevalent and widespread species. As a result, M. javanica was used as the nematode to develop an infection system for the molecular study of the host/parasite interaction with tomato as the host plant. Several molecular approaches for developing host resistance to root knot nematodes have been suggested and are discussed. Root-knot nematodes parasitise the host plant root by modifying host cells from which the nematode feeds. These feeding structures are large, multinucleate cells termed "giant cells". Knowledge of giant cell-specific gene expression in the host plant is needed to develop synthetic resistance genes and to aid understanding of the host/nematode interaction. In an attempt to clone giant cell specific transcripts, a published PCR-based method for creating cDNA libraries from limited amounts of plant tissue was followed without success. As a result, considerable effort was expended to generate a new method for creating subtracted cDNA libraries. This new method involved the use of paramagnetic oligo-dT Dynabeads for the mRNA isolation directly from microgram quantities of crude giant cell enriched tissue homogenate, first strand synthesis on the beads using reverse transcriptase then tailing of the cDNA strand with dGTP so that a pool of second strand cDNA could be generated with a novel primer. This pool of second strand cDNA was then subtracted with a healthy root cDNA driver bound to Dynabeads for easy removal after each of three rounds of subtraction. The remaining giant cell enriched cDNA transcripts were then PCR amplified by use of primers with engineered restriction digest sites that allow direct cloning to create the cDNA library. Development of this original protocol and its benefits over existing techniques are discussed. Thirteen clones from a giant cell enriched cDNA library were analysed by sequencing and hybridisation to DNA and RNA from plants and nematodes. Several clones were identified which have homology to known sequences.

Yellow rust, caused by Puccinia striiformis West., is an important foliar disease of wheat and barley throughout the world, and the development of resistant cultivars is the most economical and environmentally friendly method of control. Breeding for resistance to yellow rust has, for decades, been based on the use of race-specific resistance genes, which have shown to be short-lived. Non-host resistance has been studied as a possible source of durable resistance. Two major genes, as well as an undetermined number of minor genes, for non-host resistance to the barley attacking form of yellow rust, P. striiformis f. sp. hordei, have been previously detected in the wheat cultivar ‘Lemhi’. The present study aimed at quantifying and mapping those genes using QTL (quantitative trait loci) mapping procedures. For that purpose, an F2 population of 114 individuals resulting from the cross of resistant ‘Lemhi’ with ‘Chinese 166’, a wheat cultivar susceptible to barley yellow rust, was used as the mapping population. QTL effects and significance were estimated by means of interval mapping and MQM mapping procedures. A map for the F2 population was constructed which included 116 DNA markers (14 SSRs and 102 AFLPs). Two major QTLs have been mapped to chromosome arms 1DS (Psh1) and 2BL (Psh2), with significant LOD values. These two QTLs account for 76.7% of the phenotypic variance for resistance to barley yellow rust. Two other QTLs, with a minor effect, were mapped to chromosome arms 5AL (Psh3) and 6AL (Psh4), explaining 5.1% and 10.9% of the phenotypic variation, respectively. The QTL on 5A was derived from the susceptible variety, ‘Chinese 166’. In all cases the resistance towards P. striiformis f.sp. hordei was associated with a visual chlorosis/necrosis response typical of race-specific, host resistance.
A ferrugem amarela, cujo agente causal é Puccinia striiformis Westend, é uma doença particularmente importante nas produções de trigo e cevada em todo o mundo, principalmente em regiões de clima fresco e húmido (EVERSMEYER & KRAMER, 2000). Infecções severas deste patogénio podem causar drásticas reduções na altura da planta, no número de grãos por espiga, e no peso e qualidade dos grãos (MA & SINGH, 1996b). A espécie P. striiformis encontra-se dividida em formae speciales, em função do género vegetal que ataca. Por exemplo, o trigo é considerado hospedeiro para P. striiformis f. sp. tritici, a ferrugem amarela do trigo, mas não para a f. sp. hordei, a forma da ferrugem amarela que ataca a cevada. No entanto, a divisão de P. striiformis em formae speciales, e em particular a separação em f. sp. tritici e f. sp. hordei, tem sido fortemente questionada, uma vez que existem vários exemplos de formae speciales com capacidade de atacar genótipos de espécies que estão supostamente fora do seu leque de hospedeiros (hospedeiros ‘inapropriados’) (JOHNSON & LOVELL, 1994; CHEN et al., 1995). O desenvolvimento de cultivares resistentes à ferrugem amarela é actualmente considerado o melhor método de controlo da doença, tanto a nível económico como ambiental. No entanto, o melhoramento para a resistência a esta doença tem assentado, ao longo das últimas décadas, no uso de genes de resistência específica de planta hospedeira, que, na maioria dos casos, têm demonstrado baixa durabilidade (WELLINGS & MCINTOSH, 1990; BAYLES et al., 2000; SING & HUERTA-ESPINO, 2001). O uso generalizado de cultivares portadoras deste tipo de resistência resulta geralmente numa elevada pressão de selecção sobre o patogénio e na sua consequente evolução para novas formas de virulência (BROWN, 1995). Formas de resistência alternativas à resistência específica têm sido estudadas como possíveis fontes de resistência durável. A resistência de planta não hospedeira é considerada por vários autores, a forma mais eficaz de obter durabilidade (HEATH, 1991; CRUTE & PINK, 1996). Na sua generalidade, este tipo de resistência envolve um controlo genético complexo e uma multiplicidade de factores de defesa que impedem o microrganismo de formar uma interacção básica (compatível) com a planta (HEATH, 1991). No entanto, interacções não-hospedeiro entre espécies vegetais filogeneticamente próximas (como é o caso do trigo e da cevada) e formae speciales do mesmo patogénio (P. striiformis f. sp. hordei e P. striiformis f. sp. tritici) parecem envolver mecanismos de resistência semelhantes aos envolvidos na resistência específica de planta hospedeira, que geralmente estão associados ao retardamento do desenvolvimento do patogénio na fase pós-haustorial e à morte das células invadidas (reacção de hipersensibilidade) (NIKS, 1988; GARROOD, 2001). As estratégias de exploração da resistência de planta não hospedeira, assim como a sua durabilidade efectiva, irão, neste sentido, depender de a resistência ser controlada por mecanismos de defesa específicos ou não-específicos (HEATH, 2001). Torna-se, portanto, indispensável a existência de informação detalhada sobre os genes que controlam os mecanismos de resistência de planta não hospedeira, por forma a determinar a viabilidade do uso deste tipo de resistência como fonte de resistência durável. O progresso nos sistemas de marcadores moleculares de DNA e nos programas informáticos de análise genética tornou possível o mapeamento de genes e a identificação de QTLs (Quantitative Trait loci, loci para características quantitativas) com relativa precisão, o que permitiu uma revisão dos métodos de análise genética e das estratégias de melhoramento. A análise de QTLs, i.e., a dissecção genética de características quantitativas, atenta na determinação do número de loci envolvidos na resistência, assim como na localização no genoma da planta e contribuição para o fenótipo de cada um desses loci, através da associação entre a variação de marcadores genéticos numa população segregante e a variação fenotípica para a resistência apresentada por essa mesma população (MOHAN et al., 1997). A tecnologia de microsatélites ou SSRs (Simple Sequence Repeats, repetições de sequências simples), que consistem em repetições em tandem de motivos básicos de 2 a 6 bases (TAUTZ, 1989), emergiu na última década como o sistema de escolha no mapeamento molecular em plantas, e em particular no trigo. Tal ocorre devido ao elevado número de SSRs existente nos genomas das plantas, e porque nesta tecnologia se reúnem as principais vantagens dos diferentes sistemas de marcadores moleculares: são específicos do cromossoma, altamente informativos, co-dominantes, com uma boa cobertura do genoma e com elevado potencial de automatização (MORGANTE & OLIVIERI, 1993; RÖDER et al., 1995; POWELL et al., 1996a; KORZUN et al., 1997). Têm como principal inconveniente o elevado custo de identificação e produção (POWELL et al., 1996a). Vários mapas de ligação foram já desenvolvidos para o trigo baseados neste tipo de marcadores moleculares (DEVOS et al., 1995; PLASCHKE et al., 1995; RÖDER et al., 1995, 1998a, b; BRYAN et al., 1997; STEPHENSON et al., 1998; PESTSOVA et al., 2000; VARSHNEY et al., 2000; SOURDILLE et al., 2001; GUPTA et al., 2002), e têm sido amplamente usados na localização de genes e QTLs responsáveis por resistências a doenças, incluindo a resistência à ferrugem amarela (e.g. CHAGUÉ et al., 1999; PENG et al., 1999, 2000a, b; BOUKHATEM et al., 2002; SUN et al., 2002). Com base num cruzamento entre as cultivares de trigo ‘Lemhi’ (resistente à ferrugem amarela da cevada) e ‘Chinese 166’ (susceptível à doença), JOHNSON & LOVELL (1994) identificaram dois genes major, independentes e dominantes, responsáveis pela resistência de planta não hospedeira à ferrugem amarela da cevada na cv. ‘Lemhi’. Foi igualmente detectada a existência de um número indeterminado de genes minor, alguns dos quais com possível origem na cv. ‘Chinese 166’. Pretendeu-se com o presente trabalho: 1) desenvolver um mapa genético para uma população F2, constituída por 114 indivíduos, derivada do cruzamento ‘Lemhi’ x ‘Chinese 166’ usando marcadores do tipo SSR; 2) adicionar estes marcadores a um mapa de AFLPs previamente construído para a mesma população; e 3) localizar os genes responsáveis pela resistência do trigo à ferrugem amarela da cevada em segregação na população F2 ‘Lemhi’ x ‘Chinese 166’. Cento e dezoito indivíduos da população F2 ‘Lemhi’ x ‘Chinese 166’, assim como as plantas progenitoras desta população, foram previamente testados para resistência/susceptibilidade ao referido patogénio. ‘Lemhi’ apresentou um fenótipo totalmente resistente, enquanto ‘Chinese 166’ se apresentou moderadamente susceptível, o que confirmou a presença de gene(s) minor nesta cultivar. Os 118 indivíduos da F2 analisados fenotipicamente segregaram 115 resistentes : 3 susceptíveis, sugerindo que a resistência de ‘Lemhi’ à ferrugem amarela é efectivamente controlada por dois genes major. Foram testados 88 pares de primers de SSRs para a presença de polimorfismos entre ‘Lemhi’ e ‘Chinese 166’. Desta análise resultou um total de 41 SSRs polimórficos, que foram analisados em 114 indivíduos da população F2. Com base nestes SSRs e em 172 AFLPs (Amplified Fragment Length Polymorphisms, polimorfismos do comprimento dos fragmentos amplificados) anteriormente desenvolvidos para a mesma população, e recorrendo ao programa informático de análise genética JoinMap® versão 3.0 (VAN OOIJEN & VOORRIPS, 2001), foi construído um mapa molecular com 18 mapas de ligação, integrando 116 marcadores de DNA (14 SSRs e 102 AFLPs), e abrangendo 680 cM, com uma densidade média de 1 marcador por cada 6 cM. Os restantes 97 marcadores moleculares não foram integrados no mapa, provavelmente por, dada a extensão do genoma do trigo, não haver marcadores suficientes para criar ligação entre eles. Oito dos 18 grupos de ligação foram ancorados a seis cromossomas (1D, 2B, 3A, 5A, 6A e 6B) pela presença de SSRs. Uma vez que os restantes grupos de ligação não foram associados a nenhum QTL (ver parágrafo seguinte), não foram desenvolvidos esforços no sentido de identificar SSRs específicos para esses grupos de ligação. A identificação de QTLs foi efectuada usando o programa informático de análise de QTLs MapQTL™ versão 4.0 (VAN OOIJEN et al., 2002). Os efeitos dos QTLs e a sua significância para a variação fenotípica total da resistência à ferrugem amarela da cevada foram estimados pelos métodos Interval Mapping e MQM Mapping. Através do método Interval Mapping foram identificados dois QTLs major, localizados nos cromossomas 1DS (Psh1) e 2BL (Psh2), com origem na cv. ‘Lemhi’. Por forma a detectar possíveis QTLs minor mascarados por estes QTLs major, foi aplicado o método MQM Mapping. Neste método, recorre-se ao uso dos marcadores que flanqueiam os QTLs detectados por Interval Mapping como co-factores para eliminar o efeito daqueles e detectar QTLs minor. Após análise por MQM Mapping, foram localizados dois QTLs minor nos cromossomas 5AL (Psh3) e 6AL (Psh4), sendo que o QTL presente no cromossoma 5A deriva da variedade susceptível ‘Chinese 166’. Os quatro QTLs detectados explicam, no seu conjunto, 92,7% da variação fenotípica total da resistência à doença, o que indica que, provavelmente, todos os loci que contribuem para a resistência de planta não hospedeira foram identificados. Neste estudo, verificou-se que a resistência à ferrugem amarela da cevada estava associada a uma resposta fenotípica de clorose/necrose, típica de resistência específica de planta hospedeira. Para além disso, os genes Psh1 e Psh2, genes de resistência de planta não hospedeira à ferrugem amarela da cevada, foram identificados em regiões do genoma do trigo onde se pensa (no caso do Psh1) e onde se sabe (no caso de Psh2) existirem genes de resistência de planta hospedeira (genes Yr) à ferrugem amarela do trigo. Tendo em atenção estes factos, pode considerar-se a possibilidade de uma ligação entre genes Psh e genes Yr, que, a confirmar-se, pode levar a supor que se trata de genes que evoluíram de um mesmo gene de resistência ancestral, possuindo portanto estrutura e modo de acção semelhantes. Se tal se vier a verificar, então a durabilidade de ambos seria, também ela, semelhante. Patologistas e melhoradores teriam que repensar seriamente a validade da busca de genes de resistência de planta não hospedeira como fonte de resistência durável. A clonagem destes genes é, neste sentido, essencial para que estudos bioquímicos e de funcionamento dos genes possam ser posteriormente desenvolvidos, e para que seja determinada a viabilidade do uso dos genes Psh como genes de resistência com efeito duradouro.

Erythrocytes infected by mature forms of the Plasmodium falciparum parasite adhere to other components of the vascular space, a behavior considered critical to the pathogenesis of severe malaria. Adhesion is mediated by the P. falciparum erythrocyte membrane protein 1 (PfEMP1), a highly variant antigen expressed by the parasite and subject to switching during the course of an infection. The host ligands of PfEMP1 include CD36, ICAM-1 and the ABO antigens. By employing a series of population- and family-based association studies from multiple African populations, we examined whether variation in the genes underlying these molecules affects susceptibility to severe malaria. Our results suggest that a common frameshift mutation in the ABO glycosyltransferase, responsible for blood group O, is associated with protection from severe malarial phenotypes (P=2x10⁻⁷), particularly severe malarial anaemia. However, we found no significant disease associations with variation in either the ICAM1 or CD36 genes. We focused on two particular functional polymorphisms, the missense ICAM-1Kilifi and the CD36 nonsense mutation T1264G. We genotyped both markers in around 10,000 individuals, but neither demonstrated an association with severe malarial phenotypes. Malaria has been a profound selection pressure shaping human genetic diversity. The last decade has seen the development of several haplotype-based methods to detect signatures of recent positive evolutionary selection. These techniques are potentially invaluable tools in our hunt for genetic variants that protect from life threatening malaria. We used simulations and empirical data from the International HapMap Project to demonstrate the validity of searching for long regions of haplotype homozygosity, as an approach to finding alleles undergoing selective sweeps. We analysed genetic data from a range of populations, particularly those utilized by HapMap, to investigate whether our candidate genes were associated with signals of recent positive selection. We characterized the distribution of a selection event associated with the CD36 1264G allele, focused in Central-West Africa, and demonstrated a novel signal of low population differentiation at the ABO gene, suggestive of longstanding balancing selection. Our work confirms that variation in the host ligands of PfEMP1 modulates severe malaria susceptibility, and highlights the value of using signals of selection, along with functional experiments and genetic association studies, to dissect the biology of severe malaria.

Puccinia graminis f. sp. tritici (Pgt) is the causal agent of the devastating stem rust disease in wheat. In recent years, new super virulent races of the fungus have emerged causing large scale epidemics. In an attempt to clone the stem rust resistance gene Sr44, we generated and screened an ethyl methane sulphonate (EMS) mutant population of an Sr44 wheat-alien introgression line. We identified twelve independent susceptible mutants from 1171 M2 families and sequenced the nucleotide binding leucine-rich repeat (NLR) genes in ten of the mutants and the wild-type. However, sequence comparison did not reveal a clear candidate. To investigate meristem cell fate in wheat, we phenotyped the sister spikes of ten Sr44 M2 families which segregated for susceptibility in the main spike. Ninety-two percent of the tested spikes were found to be resistant suggesting that they are genetically distinct from the main tiller. To improve the immunity of barley against wheat stem rust, we transformed the previously cloned wheat Sr22, Sr33, and Sr45 genes into barley. The resultant transgenic lines expressed high-level resistance to Pgt indicating wheat Sr genes can be transferred into barley. Nucleotide sequence analysis of the Sr22 locus revealed that some alleles have undergone historical sequence exchange in the LRR region. We also generated and phenotyped wheat transgenics to confirm the gene postulation of two previously identified Sr22 alleles. Stacking of multiple Sr genes at a single transgene locus is expected to result in more durable resistance. We have attempted to use CRISPR/Cas9 to repair the hygromycin phosphotransferase II (HPTII) gene as a proof-of-concept to in vivo sequential stacking of multiple Sr genes. Super transformation of barley T0 and T1 transgenics containing a landing pad did not yield positive transformants. However, we identified one deletion event out of twenty-four calli of T0 transgenics, indicating functional CRISPR/Cas9 activity.

Studying evolutionary dynamics is crucial for epidemiological containment and/or eradication of viral diseases. With recent advancements in genetic sequencing, the spread of viruses can be monitored and sequenced almost in real-time as epidemics unfold, and sophisticated statistical analytical methods allow for the inference of population genetic and evolutionary characteristics directly from epidemiologic and genetic data. In this thesis, I have investigated various evolutionary aspects of the human immunodeficiency virus, the causative agent of AIDS, in the context of (a) within-host evolution of the virus in the emergence of resistance to CCR5 antagonist anti-retroviral agents and (b) between-host global evolutionary dynamics of the virus including an investigation of closely related simian immunodeficiency virus endemic in simian hosts. The main outcomes of my work have been, firstly, the development of a novel computational predictor for determining viral tropism from genetic sequences and a study investigating the efficacy of utilising this approach, and other genotypic methods, for screening patients prior to therapy; secondly, the characterisation of complex within-host mutational pathways and population genetic dynamics that give rise to the emergence of a rare form of resistance to CCR5 antagonists, namely the ability for the virus to utilise antagonist-bound CCR5 coreceptor; thirdly, an investigation of the global spread of HIV-1 group O and a proposed reconciliation of previous attempts to characterise genetic diversity observed which were discordant; and fourthly, en exploratory study comparing differences in rates of intrinsic disorder in both HIV and species-specific SIV, as well as human host genes and homologous simian host genes, and investigating the hypothesis that HIV pathogenicity might be attributable to promiscuous protein-protein interactions facilitated through protein intrinsic disorder. These studies have all highlighted aspects that are collectively important for epidemiological and genomic surveillance of infectious disease, especially in characterising transmission dynamics, monitoring changes and adaptation of viruses. Ultimately, I hope that these contributions will asset the wealth of knowledge that exists in this field, which collectively guides research into the development of new drugs and treatment regimens, as well as guidance on public health measures for control of infectious disease.

Quambalaria shoot blight (QSB) caused by the non-native pathogen Quambalaria pitereka has been recently introduced to south-west Western Australia (SWWA). It affects the leaves, buds, flowers, and fruits of the keystone tree species Corymbia calophylla (marri) and can lead to the death of young trees. This project examined the potential to establish a disease resistance program for marri to QSB by (1) developing qPCR assays for the rapid and sensitive detection of Q. pitereka from plant tissues, (2) investigating the pathogenicity of Q. pitereka isolates collected in SWWA; (3) screening for QSB resistance of 3-month-old seedlings under glasshouse conditions; and (4) estimating the genetic control of growth traits and QSB resistance in four-, and six-year old trees in two common garden trials containing 165 - 170 open-pollinated families from 18 provenances of marri from across its natural range. As disease expression in QSB is similar to myrtle rust (Austropuccinia psidii), in a glasshouse experiment, seedlings were also screened for resistance to myrtle rust to test whether resistance to both diseases is linked. A qPCR assay for the rapid and sensitive detection of Q. pitereka from plant tissues was developed. Inoculation of seedlings with several Q. pitereka isolates demonstrated that they varied in their pathogenicity ranging from those that caused no disease symptoms to ones that were highly pathogenic in seedlings. There were significant differences in resistance to both QSB and myrtle rust between seedling provenances but no significant correlation between resistance to QSB and myrtle rust. In the common garden field trials, narrow-sense heritability for all growth traits and QSB damage were low to moderate (h2 = 0.11 - 0.26). A correlation between QSB damage and growth traits indicated that fastgrowing provenances were less damaged by QSB disease. The genetic correlation between the same traits at four and six years was strong, and the Type-B correlations were strongly positive for all traits. Both disease incidence and disease severity were assessed and gave similar results, but disease incidence is the easiest to assess in older trees. There was poor correlation between the provenance resistance assessed at the seedling stage and trees at four and six years of age. Provenances from cooler wetter regions showed higher resistance in the field trials than those from warmer, drier areas. Results suggest that selection for QSB resistance cannot be assessed in seedlings but may be reliably undertaken by assessing disease incidence on four-year old trees at the earliest. The results of this study indicate a strong potential for a resistance breeding program to develop populations of genetically diverse and resistant trees.

Abstract The scope of this study includes aspects of phage evolution and antagonistic/mutualistic coevolution between a phage and its host. As a basic study it may provide tools for developing phage resistant starters and offer regulatory elements and factors for biotechnological applications. The LL-H anti-receptor was characterized by isolation of spontaneous LL-H host range mutants and subsequent sequencing of candidate genes. All LL-H host range mutants carried a single point mutation at the 3' end of a minor tail protein encoding gene g71. The genomic location of g71 is congruent with the other verified anti-receptor genes found in the λ supergroup. The C-terminus of Gp71 determines the adsorption specificity of phage LL-H similarly for the number of phages infecting Gram-positive and Gram-negative bacteria. A Gp71 homolog of phage JCL1032 showed 62% identity to LL-H Gp71 within the last 300 amino acids at the C-terminus. Lactobacillus delbrueckii phage receptors were investigated by the purification of different cell surface structures. Certain Lb. delbrueckii phages from homology groups a and c including LL-H, LL-H host range mutants and JCL1032, were specifically inactivated by the LTAs. In structural analyses LTAs showed differences in the degree of α-glucosyl and ᴅ-alanyl substitution. α-glucose is necessary for LL-H adsorption. A high level of ᴅ-alanine esters in LTA backbones inhibited Lb. delbrueckii phage inactivation in general. Lysogenization of strain ATCC 15808 with the temperate phage JCL1032 revealed a rarely described coexistence of phage adsorption resistance and phage immunity, which could not be explained by lysogenic conversion. In this case the role of spontaneously induced JCL1032 may be significant. The LL-H early gene region was localized between the dysfunctional lysogeny module and the terminase encoding genes. The function of five ORFs could be connected to phage DNA replication and/or homologous recombination. Transcription of LL-H genes could be divided into two, possibly three, phases in which large gene clusters were sequentially transcribed. The intensity of the late transcripts exceeded the intensity of the early transcripts by several times. Two candidate genes for transcription regulators were found. One of the two candidates is the first ORF in the LL-H early gene region.

The Bcg/Ity/Lsh locus confers natural host resistance to mice infected with several unrelated species of intracellular pathogens. The Nramp1 gene was identified by Vidal and colleagues by positional cloning of candidate genes for the Bcg/Ity/Lsh locus. A single glycine-to-aspartate substitution at position 169 (G169D) in the predicted TM4 domain of the Nramp1 protein was found to be associated with susceptibility to infection. To initiate characterization of the Nramp1 gene and its role in infection, the Nramp1 genomic structure was analyzed including its exon-intron boundaries. Analysis of the 5' upstream region revealed the use of multiple transcription initiation sites mapping near possible initiator sequences and identified consensus DNA sequence motifs previously implicated in regulating cell-specific and inducible gene expression in macrophages. Transgenic mice were generated in which a genomic clone of the Nramp1 G169 allele was transferred onto a homozygous Nramp1 D169 allele genetic background. Expression of the Nramp1 (G169) protein in transgenic macrophages was concommitant with the emergence of resistance to infection with Mycobacterium bovis and Salmonella typhimurium. The gain of function detected in transgenic mice helped to establish that (1) Nramp1 and Bcg/Ity/Lsh are allelic, and (2) the Nramp1(D169) allele is the molecular basis for susceptibility to infection. Nramp1 gene expression was examined to help understand the role of Nramp1 during infection. Analysis of bone marrow-derived cell colonies found Nramp1 mRNA to be limited to mature professional phagocytes of myeloid lineage. Nramp1 mRNA expression was found to be upregulated by inflammatory and cytokine stimuli in a macrophage cell line and in vivo. To assay for Nramp1 function, an in vitro system was created where the Nramp1(D169) cDNA was transfected into the RAW264.7 macrophage cell line. Transfected Nramp1 protein was found to be in a membranous compartment, recruited to the membrane

Roughly one-third of cattle in sub-Saharan Africa are at risk of contracting "Nagana" - a disease caused by Trypanosoma parasites similar to those that cause human "Sleeping Sickness". Laboratory mice can also be infected by trypanosomes, and different mouse breeds show varying levels of susceptibility to infection, similar to what is seen between breeds of cattle. We have applied next-generation technologies to identify shared polymorphisms between susceptible mice, and annotated these for potential function alongside publicly available SNP data sets. By so doing, short lists of genes at the QTL have been created to aid functional testing in cattle. This includes two promising 'candidate genes': Pram1 and Cd244, which can now be tested to confirm their effect on response to trypanosome infection. The human-infective parasite Trypanosoma brucei rhodesiense generally causes an acute form of "sleeping sickness" across Eastern Africa, compared to the more chronic T b. gambiense infections found in Western Africa. The 1988-1993 Ugandan T b. rhodesiense outbreak constituted infections by parasites with differences in their clinical manifestation. Two such sub types, termed Busoga 17 (B 17) and Zambesi 310 (Z31O), caused more acute, and more chronic infections, respectively. In order to investigate whether the major QTL that regulates survival in T congolense infections (Tir 1) does so in a similar manner in T b. rhodesiense, mice congenic for the C5 7BL/ 6 allele (Tirl CC) at Tir 1 were infected with Z310 and B 1 7 zymodeme T b. rhodesiense parasites. Whilst Tir 1 was not found to have a significant effect on survival, all mice had a significantly shorter mean survival time when infected with B 17 (~1O. 7 days) than those infected with Z31 0 (~15.6 days), in line with previous observations of human infections. In order to identify genetic loci that might underlie differences in virulence between T b. rhodesiense zymodemes, cluster analysis was performed on the microsatellite genotypes of 31 T b. rhodesiense isolates that represented nine different zymodemes. Despite STRUCTURE identifying three population clusters, the Z310 and B 17 parasite populations could not be distinguished, suggesting that either multiple genes control virulence, that there is gene flow between similar parasite populations, or that the microsatellite genotyping is insufficient to distinguish between different parasite populations. Finally, we present the first whole-genome sequences of T b. rhodesiense field isolates, one each of Z310 and B 1 7. Genomic analysis of east African T b. rhodesiense and west African T b. gambiense has suggested that recombination may be occurring between them. SNP genotyping of 32 T b. rhodesiense isolates showed that differences in clinical phenotypes were associated with differences in alleles on chromosome 8. The genome sequence suggests that chromosome 8 is heterozygous for alleles of west African origin in the more virulent strain, suggesting that recombination may be associated with parasite virulence. This suggests that the human subspecies of T brucei are not genetically distinct, which has major implications for the control of the parasite, the spread of drug resistance and understanding the variation in virulence and the emergence of human infectivity. Further genetic analysis of T b. brucei populations from Western, central and Eastern Africa may be necessary to ascertain whether recombination is occurring directly between human-infective subspecies, or in the underlying animal-infective population.

Salicylic acid (SA) induces systemic acquired resistance (SAR) to a wide range of pathogenic microbes. The defensive signal transduction pathway branches downstream of SA in tobacco (Nicotiana tabacum) and Arabidopsis thaliana. One branch leads to resistance to fungi and bacteria. The other, antimycin A (AA)-induced, branch, the virus-specific signalling pathway (VSSP), leads to resistance to viruses. In this study I showed, using cDNA-AFLP, that certain genes induced or repressed in tobacco leaf tissue expressing SAR were also induced or repressed by the VSSP (induced using AA). The regulation of three of these genes was verified using RT-PCR. A preliminary investigation of the temporal and tissue-specific regulation one of these genes (B2) was carried out. B2 was constitutively expressed most strongly in the leaf lamina, less strongly in the vein, weakly in the stem and not at all in the roots of healthy tobacco plants. Following induction of SAR or the VSSP B2 transcript was found to increase steadily for up to 24 hours. B2 accumulation increased from the basal level only in the leaf lamina. B2 transcript was induced in both the pathogen inoculated and the distant (non-inoculated) leaves of tobacco resisting Tobacco mosaic virus (TMV)-infection. These experiments strengthened the correlation between B2 induction and resistance to viruses. Post-transcriptional gene silencing (PTGS) is another inducible anti-viral defence mechanism in plants. PTGS requires the activity of an RNA-dependent RNA polymerase (RdRp). The recent discovery of a SA-regulated, plant-encoded RdRp (NtRdRp1) in tobacco suggested that there is a link between PTGS and SA-dependent resistance. I found that although NtRdRp1 is indeed induced by SA, it is not induced by AA, and thus this gene is unlikely to be regulated by the VSSP. It has been proposed that the VSSP requires the activity of alternative oxidase (AOX), the terminal oxidase of the plant mitochondrial alternative respiratory pathway (AP). I tested this theory in transgenic tobacco lines with increased or decreased AP capacity, relative to untransformed tobacco. I found that TMV accumulation in inoculated tissue was similar in untreated transformed and untransformed plants.

Through specialised structures called haustoria, filamentous eukaryotic plant pathogens such as rusts and mildews can deliver “effector” proteins directly into plant cells in order to manipulate specific defence responses and processes. Hyaloperonospora arabidopsidis (Hpa) is a haustorium-producing biotrophic oomycete pathogen that causes downy mildew on Arabidopsis. Over 100 candidate effectors (called “HaRxLs”), carrying a characteristic RxLR protein motif, have been predicted from the Hpa genome sequence. This PhD work focused on the characterisation of some of these effectors and their interaction with plant defences. First, the Pseudomonas syringae pv. tomato (Pst) strain DC3000 type III secretion system was used to examine the effect of single oomycete effectors in planta. One of these, ATR13 from Hpa isolate Emco5 (ATR13Emco5) has been shown to be recognised in some Arabidopsis accessions by the RPP13 protein, preventing Hpa Emco5 from completing its life cycle on such resistant plants. Hpa Emco5 can however complete its life cycle on Ws-0 but paradoxically, ATR13Emco5 is also recognised in this accession. Here, I show that ATR13Emco5 is weakly recognised in Ws-0 by a single RPP13-independent, EDS1-independent dominant gene called RHA13, shown by rough mapping to position on Arabidopsis chromosome 4. Second, I contributed to two independent functional screens performed in our laboratory to experimentally characterise the Hpa effectorome. The first screen focused on HaRxLs effects on bacteria virulence using the EDV system. The second screen was based on HaRxLs subcellular localisation using Agrobacterium-mediated transient expression. As presented in this work, I showed that both screens identified putative interesting effectors which increased plant susceptibility to Pst and Hpa and localised to various plant subcellular compartments. One particular effector candidate, HaRxL79, localised to microtubules in planta and interacted with two microtubule-associated proteins in a yeast-two-hybrid assay. HaRxL79 was also found to interact with Arabidopsis histone chaperones (AtNAP1s) in the plant cytoplasm, which were observed to play a role in plant susceptibility to Hpa and partially to the necrotroph Botrytis cinerea, but not to the hemibiotrophs Pst and Phytophthora parasitica. AtNAP1s also interact with HaRxL67, a vacuole-associated Hpa effector. From this, I propose that AtNAP1s are susceptibility factors for Hpa, specifically targeted by Hpa effectors HaRxL67 and HaRxL79 in order to promote susceptibility and maintain biotrophy.

Fusarium head blight (FHB) is a major challenge in global wheat production. In the United States, the disease is predominantly caused by the fungus Fusarium graminearum. Utilization of FHB-resistant wheat cultivars integrated with other measures such as fungicide application is the most effective approach for the management of this disease. This study aimed to 1) identify novel quantitative trait loci (QTL) for resistance to FHB in a Brazilian spring wheat cultivar ‘Surpresa’ through bi-parental mapping, 2) detect QTL for FHB resistance in a global panel of 233 spring wheat accessions by genome-wide association analysis (GWAS), and 3) localize genomic regions governing traits associated with virulence in Fusarium graminearum. Using phenotypic and genotypic data from 187 recombinant inbred lines derived from the cross between Surpresa and a susceptible spring wheat cultivar ‘Wheaton’, four QTL (Qfhb.ndwp-2AS, Qfhb.ndwp-2AL, Qfhb.ndwp-3B, and Qfhb.ndwp-4D) were mapped on chromosomes 2A, 3B, and 4D of Surpresa, respectively. Qfhb.ndwp-2AS, Qfhb.ndwp-2AL, and Qfhb.ndwp-3B were found to be novel based on physical locations of the markers tightly linked to these QTL. Two significant marker-trait associations (Qfhb.ndwp-3A and Qfhb.ndwp-2BL) were detected by GWAS of 233 spring wheat accessions, which conferred type II and type III FHB resistance and mapped on chromosomes 3A and 2B, respectively. Both QTL were novel based on the physical locations of tightly linked markers. GWAS of virulence and fungicide sensitivity using 183 F. graminearum isolates collected from North Dakota identified two significant marker-trait associations in chromosomes 1 and 3 for virulence, and two for fungicide sensitivity. The genes associated with virulence that were detected in this study were not previously reported. Identification of these novel genes in metabolic pathways of F. graminearum could help to develop new strategies for the management FHB.

Cotton (Gossypium hirsutum L.) crop maturity is delayed by cotton fleahopper (Pseudatomoscelis seriatus Reuter) (fleahopper) feeding on early-season fruit forms which increases vulnerability to late-season pests such as Helicoverpa zea (Boddie) and Heliothis virescens (Fabricius). The objectives of this research were to evaluate methods of screening for resistance to fleahopper and to screen selected genotypes. Six fleahoppers were caged on plants in the insectary for 72 h. Numbers of live fleahoppers and percent square damage were determined 48 h following the removal of fleahoppers. Fleahopper numbers and percent square set were determined on randomly selected plants of 16 genotypes when grown under field conditions in 2002 and 2003. Across multiple sampling dates, the number of fleahoppers per plant was higher (p=0.05) in G. arboreum and Pilose (G. hirsutum), but no consistent differences were observed among the remaining 15 genotypes which represented several germplasm pools across the United States. Field and no-choice feeding tests suggested that Pilose, Lankart 142, Suregrow 747, and Stoneville 474 were more resistant hairy-leaf genotypes and not different (p=0.05) in resistance than the smooth-leaf genotypes, Deltapine 50 and TAM 96WD-69s. Pin-head, match-head, and one-third grown squares were removed from plants and placed on agar in petri-plates. Four fleahoppers were released per plate and allowed to feed for 48 h. Fleahopper damage, brown areas along the anthers and/or brown and shrunken pollen sacs was most evident in pin-head sized squares.

A pathosystem using Arabidopsis and wheat powdery mildew, Blumeria graminis f. sp. tritici (Bgt), for which Arabidopsis is a non-host, was employed to initiate the genetic dissection of non-host resistance (NHR). The EMS mutagenised population from the Arabidopsis line containing the GST1:LUC transgene, which can facilitate a high throughput mutant screening strategy, have been screened using an ultra low light imaging camera system. Following a mutant screen of approximately 100,000 M2 plants, a number of candidates have been identified that compromise the induction of the LUC transgene in response to attempted Bgt infection. Through this screening, nhr1 was isolated as a putative factor for non-host pathogen recognition. This mutant showed severely compromised GST1 induction and less hypersensitive cell death in response to Bgt inoculation, while exhibiting little difference against other host bacterial and fungal pathogens including Pseudomonas syringae p.v. tomato and Hyaloperonospora parasitica. In addition, nhr1 was sugar dependent in germination. We identified ads3 (ACTIVATED DISEASE SUSCEPTIBILTY 3), an Arabidopsis mutant showing drought resistant as well as disease susceptible phenotype against host and non-host pathogens. ads3 is emf1-D by enhanced expression of Embryonic Flower 1 (EMF1), which had been known as repressor of floral transition in plant. The susceptibility of emf1-D was recapitulated in transgenic Arabidopsis plants ectopically expressing EMF1. Conversely, conditionally decreased EMF1 level in the transgenic plant conveyed disease resistance. emf1-D was drought resistant and hypersensitive to abscisic acid (ABA). We show that ectopic expression of EMF1 modulates a ABA signalling, resulting in susceptibility to pathogens. The other plant link, which is the translationally controlled tumor protein (TCTP) over-expressing line, showed reduced NHR against Bgt. A leucine rich repeat receptor-like kinase (LRK) was isolated as a putative TCTP-interacting protein, and the KO line of the LRK showed less or delayed resistant response to non-host as well as host fungal pathogens. furthermore, the TCTP over-expressing line exhibited hypersensitivity towards ABA. These results suggest that ABA signalling could play a critical role in non-host resistance in plants.

Picea glauca (Moench) Voss (l’épinette blanche) est l’un des principaux hôtes de la tordeuse des bourgeons de l’épinette (TBE), le défoliateur épidémique le plus dommageable de l’est du Canada qui est à l’origine de la mortalité d’arbres et de pertes économiques d’envergure considérables. Un mécanisme constitutif de résistance contre la TBE a récemment été découvert. Dans la présente thèse, nous avons étudié ce mécanisme basé sur l’accumulation foliaire du picéol et du pungénol, deux acétophénones découlant de la surexpression du gène Pgglu-1. Ces trois facteurs sont désignés comme étant des «biomarqueurs de résistance». Nous avons aussi étudié la picéine, un acétophénone glycosilé qui est le précurseur du picéol, et l’ensemble des quatre facteurssont désignés «biomarqueurs de défense». La première partie de la thèse présente une approche de génétique quantitative s’appuyant sur l’analyse de 874 arbres représentant 33 familles et 71 lignées clonales répartis dans sept emplacements de l’est du Canada. Nos objectifs étaient : i) de déterminer le contrôle génétique des biomarqueurs de défense, ii) d’estimer les corrélations génétiques et phénotypiques entre les quatre traits de défense, iii) d’évaluer la présence de compromis entre les biomarqueurs de défense et la croissance primaire. Nous avons conclu que l’héritabilité au sens strict du picéol, du pungénol et de l’expression du gène Pgglu-1 était modérée (0,55, 0,50 et 0,58 respectivement), et obtenu des estimés un peu plus élevées pour l’héritabilité au sens large du picéol et du pungénol (0,66 et 0,60 respectivement), ce qui indique que ces traits de résistance sont soumis à un contrôle génétique additif. Les traits de résistance et la croissance montrent des corrélations génétiques positives (de 0,14 à 0,30), ce qui suggère que le mécanisme de résistance n’entraine pas un effet négatif sur la croissance de l’épinette blanche. Dans la deuxième partie de la thèse, nous avons étudié l’interaction insecte-hôte en menant des essais d’élevage d’insectes sur différents clones d’épinettes blanches. Nos objectifs étaient iv) de caractériser la variation développementale des acétophénones de défense, v) d’évaluer l’influence du stade phénologique de l’hôte sur le niveau de résistance indiqué par la performance biologique de la TBE et vi) de déterminer si les traits de résistance sont inductibles. Nous concluons que la variation des acétophénones dépend du phénotype de résistance de l’arbre, et que l’efficacité des traits de résistance dépend du synchronisme entre le Piceaglauca et l’alimentation des insectes. Finalement, nous avons démontré que ce mécanisme de résistance peut être inductible.
Picea glauca (Moench) Voss (white spruce) is one of the main hosts of the spruce budworm (SBW), anepidemic defoliator that is the most damaging in forests of eastern North America causing tree mortality and large economic losses. A constitutive resistance mechanism against the SBW was recently discovered. In this thesis, we studied this mechanism based on the foliar accumulation of aglycon acetophenones ̶piceol and pungenol ̶resulting from the expression of the Pgglu-1gene; and we refer to them as resistance biomarkers. Picein, the glycoside precursor of piceol was also investigated and we refer to all four traits togetheras defense biomarkers. The first part of this thesis presents a quantitative genetic study, which analysed 874 trees representing 33 full-sib families and 71 clonal lines from seven field locations in Eastern Canada. The goals were to i) determine the genetic control of the defense biomarkers, ii) estimate the genetic and phenotypic correlations among the four defensive traits and growth, and iii) evaluate the occurrence of trade-offs between the defense biomarkers and primary growth. Narrowsense heritability of piceol, pungenol and Pgglu-1 gene expression was moderate (0.55, 0.50 and 0.58, respectively). Slightly higher broad sense heritability estimates were obtained for acetophenones (0.66 and 0.60 respectively), indicating that additive genetic effects playa major role in these resistance biomarkers. Positive genetic correlations were found between the resistance traits and growth (from 0.14 to 0.30), suggesting that the resistance mechanism does not compromise growth in white spruce. In the second partof the thesis, we studied the insect-host interaction by use of insect rearing trials in severalwhite spruce clones. Our objectives were to iv) characterize the developmental and phenological variation of the defense acetophenones, v) evaluate the impact of the matched and delayed host phenology windows on the biological performance of the SBW, and vi) assess the inducibility potential of the resistance traits. Weshow that there are considerable variations in the acetophenone accumulation profiles between individual trees supporting their classification as Resistant (R) and Non-Resistant (NR); that the efficiency of the resistance traits is influenced by the synchronization between the P. glauca phenology and the insect feeding. Finally, we show that the resistance mechanism can be inducible.

The threat from infectious diseases dates as far back as prehistoric times. Pathogens continue to pose serious challenges to human health. The emergence and spread of diseases such as HIV/AIDS, Severe Acute Respiratory Syndrome (SARS), avian influenza, and the threats of bioterrorism have made infectious diseases major public health concerns. Despite many successes in the discovery of anti-infective medications, the treatment of infectious diseases faces serious challenges, which include (i) the emergence and reemergence of infectious pathogens, (ii) the ability of pathogens to adapt and develop resistance to drugs, and (ii) a shortage in the development and discovery of new anti-infective drugs. Host-Oriented Broad-Spectrum (HOBS) treatments have the promising potential to alleviate these problems. The HOBS treatment paradigm focuses on finding drug targets in human host that are simultaneously effective against a wide variety of infectious agents and toxins. In this dissertation, we present a computational approach to predict HOBS treatments by integrative analysis of three types of data, namely, (a) gene expression data representing host responses upon infection by a pathogen, (b) annotations of genes to pre-defined biological pathways and processes, and (iii) genes that are targets of known drugs. Our methods combine gene set-level enrichment with biclustering. We applied our approach to a compendium of gene expression data sets derived from host cells exposed to bacterial or to fungal pathogens, to functional annotation data from multiple databases, and to drug targets from DrugBank. We present putative host drug targets and drugs with extensive support in the literature for their potential to treat multiple bacterial and fungal infections. These results showcase the potential of our computational approach to predict HOBS drug targets that may be effective against two or more pathogens. Our study takes a clean-slate approach that promises to yield unsuspected or unknown associations between pathogens and biological processes, and thus discern candidate gene/proteins to be further probed as HOBS targets. Furthermore, by focusing on host responses to pathogens as captured by transcriptional data, our proposed approach stimulates host-oriented drug target identification, which has potential to alleviate the problem of drug resistance.
Ph. D.

The threat from infectious diseases dates as far back as prehistoric times. Pathogens continue to pose serious challenges to human health. The emergence and spread of diseases such as HIV/AIDS, Severe Acute Respiratory Syndrome (SARS), avian influenza, and the threats of bioterrorism have made infectious diseases major public health concerns. Despite many successes in the discovery of anti-infective medications, the treatment of infectious diseases faces serious challenges, which include (i) the emergence and reemergence of infectious pathogens, (ii) the ability of pathogens to adapt and develop resistance to drugs, and (ii) a shortage in the development and discovery of new anti-infective drugs. Host-Oriented Broad-Spectrum (HOBS) treatments have the promising potential to alleviate these problems. The HOBS treatment paradigm focuses on finding drug targets in human host that are simultaneously effective against a wide variety of infectious agents and toxins. In this dissertation, we present a computational approach to predict HOBS treatments by integrative analysis of three types of data, namely, (a) gene expression data representing host responses upon infection by a pathogen, (b) annotations of genes to pre-defined biological pathways and processes, and (iii) genes that are targets of known drugs. Our methods combine gene set-level enrichment with biclustering. We applied our approach to a compendium of gene expression data sets derived from host cells exposed to bacterial or to fungal pathogens, to functional annotation data from multiple databases, and to drug targets from DrugBank. We present putative host drug targets and drugs with extensive support in the literature for their potential to treat multiple bacterial and fungal infections. These results showcase the potential of our computational approach to predict HOBS drug targets that may be effective against two or more pathogens. Our study takes a clean-slate approach that promises to yield unsuspected or unknown associations between pathogens and biological processes, and thus discern candidate gene/proteins to be further probed as HOBS targets. Furthermore, by focusing on host responses to pathogens as captured by transcriptional data, our proposed approach stimulates host-oriented drug target identification, which has potential to alleviate the problem of drug resistance.
Ph. D.