Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal.

L’ingénierie tissulaire vise à l’élaboration de prothèses biologiques par la régénération ou la culture, in vitro ou in vivo, de tissus ou d’organes. Dans la stratégie de culture in vitro, le développement de nouveaux outils, tels que des bioréacteurs, permettant la culture de cellules ou de tissus sous sollicitations mécaniques spécifiques au tissu est primordial. De plus, l’avancée de cette discipline dans la régénération des tissus nécessite de développer, dès à présent, des méthodes d’évaluation mécanique satisfaisantes permettant de comparer ces néo-tissus aux tissus sains selon des critères de sollicitations physiologiques. En effet, pour parvenir à une bonne évaluation de ces matériaux, il est nécessaire de pouvoir les tester sur des chargements représentatifs des sollicitations physiologiques auxquelles ils sont soumis. Nous avons ainsi, dans un premier temps, conçu et développé un bioréacteur de ligaments permettant la culture de cellules stimulées mécaniquement par des sollicitations cycliques de traction-torsion. Ce bioréacteur a été dimensionné afin de pouvoir obtenir des bio-prothèses de taille comparable aux ligaments et tendons à remplacer (4 à 5 cm de long). Nous avons, dans un deuxième temps, développé un modèle du comportement mécanique global de ces tissus à partir du formalisme thermodynamique développé au sein de notre laboratoire et des observations faites sur des tendons d’Achille de lapin. Ce modèle a pour but d’approfondir la compréhension des structures intervenant de façon prépondérante dans la qualité mécanique de ces tissus ainsi que l’évaluation et l’optimisation des matrices de support et des néo-tissus devant s’y substituer / Tissue Engineering aims to fabricate bio-prostheses by regenerating or culture, in vivo or in vitro, tissues or organs. In the in vitro strategy, developing new tools such as bioréactors which allow the culture of cells or tissues under their specific mechanical solicitations is a huge point. Moreover, the last advances of this discipline in regeneration of tissues require new mechanical model allowing their evaluation and comparison to native tissue under physiological loading. Indeed, in order to obtain a good evaluation of their mechanical quality, it is important to be able to applied mechanical solicitations linked to physiological ones. As a first step, a bioreactor of ligament allowing the culture of cells under mechanical solicitations of cyclic traction-torsion was designed and developed. This bioreactor was sized to potentially obtain a bio-prosthesis comparable to native tissue in term of size (4 to 5 cm long). In a second time, a mechanical model was elaborated based on a thermodynamic formalism developed in our laboratory and the observation made on rabbit Achilles tendons. The goals of this model are to improve our knowledge on the mayor structures involved into the mechanical quality of theses tissues and to evaluate and optimise the scaffolds and neo-tissues of substitution

La conservation au niveau population est extrêmement nécessaire pour limiter la perte de biodiversité au sein d'une espèce ou d'un complexe d'espèces. Ainsi, l'évaluation de la variabilité inter-populationnelle dans le complexe est reconnue comme première étape importante pour bien définir les plans de conservation des espèces menacées. Arenaria grandiflora form un complexe d'espèces herbacées pérennes à courte durée de vie (4 ans en moyenne) menacé dans certains sites de ses zones de distribution en Europe. A ce jour, sa taxonomie n'est pas bien résolue, ce qui entraîne des problèmes potentiels pour mettre en oeuvre une conservation efficace de ce taxon. Une variation inter-populationnelle du complexe d'espèces A. grandiflora est présentée dans cette étude aux niveaux génétiques, cytogénétiques et morphométriques. Quatre méthodes ont été utilisées : des marqueurs microsatellites nucléaires, une approche cytogénétique, la cytométrie en flux, et enfin la morphométrie sur les feuilles. De plus, les études phénotypiques de variation de taux de germination entre stocks de graines ont été développées. Une différenciation significative entre les profils de variations moléculaires, cytogénétiques et phénotypiques a été détectée dans le complexe d'espèces. Deux cytotypes (diploïdes 2n=2x=22 et tétraploïdes 2n = 4x = 44) ont été mis en évidence en utilisant à la fois des méthodes classiques et des méthodes plus récentes (marqueurs microsatellites, nombres chromosomiques et cytométrie de flux). Le complexe d'espèces d'A; grandiflora présente une forte variation de la valeur de l'ADN 2C, la taille du génome varie de 2.11 ± 0.74 pg à 2.70 ± 0.11 pg pour les populations diploïdes et de 4.30 ± 1.51 pg à 5.27 ± 0.14 pg pour les populations de tétraploïdes. En outre, les grains de tétraploïdes germent significativement mieux que les graines des diploïdes. Les feuilles diffèrent considérablement entre les diploïdes (aciculaires et linéaires) et les tétraploïdes (lancéolées). Cette étude peut être considérée comme préliminaire pour une révision taxonomique de ce complexe d'espèces. D'autre part, grâce à l'ensemble des résultats obtenus, il est également possible de revisiter le concept d'unités évolutives significatives (ESUs) dans le complexe d'espèces A. grandiflora et donc de définir les groupes de populations devant faire l'objet de mesures distinctes. Ainsi, il est possible d'évaluer la pertinence de plans déjà entrepris et de proposer de nouveaux plans de restauration efficaces pour l'avenir de ce complexe d'espèces. / Population-level conservation is being extremely required to restrain the biodiversity loss within a species. So, the assessment of the variability within the species complex is being renowned as an important first step to well implement the future conservation settings for threatened species. The species complex of Arenaria grandiflora is a short-lived perennial herbaceous and a threatened taxon in certain of sites of its distribution areas in Europe, with unresolved gentics and taxonomy, which lead to potential problems in the conservation and utilization of the resource. A differenciation among populations of the species complex of A. grandiflora is presented in this study based on the genetic, cytogenetic and phenotypic patterns. Intraspecific ploidy level varaition is an important aspect of numerous species, so, the present study explores this phenomenon within the A. grandiflora species complex in some type of populations (27 natural populations). To infer the intraspecific genetic and cytogenetic patterns of variability among the studied natural populations of the investigated species complex (A. grandiflora), three methods were used : nuclear microsatellite markers, cytogenetic and flow cytometry approaches. Moreover, the phenotypic patterns of variation among both the stock of seeds and the herbarium materials of A. grandiflora were defined. These patterns were detected using three methods of seed germination (in vitro culture, filter papers and potting soil) and morphometric approaches. A significant differentiation among populations' patterns of molecular, cytogenetic and phenotypic variation was detected within the A. grandiflora species complex. Presence of two closely related cytotypes (diploids 2n=2x=22 and tetraploids 2n=4x=44) was detected using both classical and more recent methods (chromosome number count and flow cytometry respectively). The species complex of A. grandiflora exhibits high variation in 2C-DNA value, the genome size ranges from 2.11 ± 0.74 pg to 2.70 ± 0.11 pg for the diploid populations and from 4.30 ± 1.51 pg to 5.27 ± 0.14 pg for the tetraploid populations. Moreover, the seeds of tetraploids germinate well and in high proportion than the seeds of the diploid ones. In addition, both acicular and linear leaves from the diploid populations differ significantly within the diploids and with the lanceolate leaves of the tetraploid ones. New protocol of seed germination for the tetraploids by in vitro culture after scarifying was described for th first time. The affected factors on seed germination percentages were determinated by an explanatory model of six predictors (altitude, longitude, latitude, ploidy levls, both period and condition of seed storage). Consequently, all these findings are fundamental for the determination of the evolutionarily significant units (ESUs) within A. grandiflora species complex and thus the definition of efficient restoration plans in the future. This study would consider as the preliminary signal for necessary revision for the intraspecific taxonomic keys problematic for this species complex.

Nas abordagens biotecnológicas de propagação de plantas, os meios de cultura devem ter uma composição química adequada à essa finalidade permitindo a otimização da produção. Como a bananeira (Musa sp.) é exigente em potássio, a busca do nível adequado desse macronutriente envolve não somente o comprometimento com o nível dos outros nutrientes (balanço iônico), mas também a relação entre eles. Para acompanhar os efeitos fisiológicos das relações de vários teores de K com os outros macro e micronutrientes é que explantes caulinares dos cvs. Nanica e Prata Anã foram cultivados em meio MS modificado em presença de BAP, sacarose, vitaminas, agar, suplementado com 6 diferentes doses de K: 5, 10, 15, 20, 25 e 30 mM, sendo que a dose 20 mM corresponde à concentração de K existente no MS básico, que foi adotado como controle.Foram feitas análises de massa de matéria seca (MMS),macro e micronutrientes na parte aérea, raiz e plântulas inteiras. Ao final do experimento foi determinado o número de plântulas e calculado o valor das relações N/K, K/P, K/Ca, K/Mg, K/Ca+Mg, K/S, K/Cu, K/Fe, K/Mn, K/Zn.Foram também dosados os teores da diamina putrescina e de poliaminas, e calculada a relação K/putrescina. Todos os parâmetros foram analisados segundo um delineamento experimental inteiramente casualizado. As plântulas que se desenvolveram em baixas concentrações de K apresentaram sintomas visuais de deficiência, como clorose e necrose das folhas mais velhas. Os cultivares apresentaram diferenças quantitativas entre si tanto em relação aos valores de MMS como em número de plântulas, relacionados às doses de K presentes nos meios de cultura. Em ambos os cultivares foi observada uma relação direta entre o desenvolvimento das plântulas e as concentrações de K com otimização ao redor de K 15 a 20 mM. Os teores de putrescina e de poliaminas foram maiores nos níveis mais baixos de K, atingindo o máximo na dose de K 5 mM. Em K 20 mM ocorreram maiores valores de MMS e em K 15 mM maior número de plântulas regeneradas. O íon K em geral foi mais intensamente absorvido do que os outros macro e micronutrientes sendo que estes tiveram sua absorção diminuída devido provavelmente a um efeito de diluição de seus teores pelo crescimento das plântulas in vitro. Esses resultados, inclusive os obtidos nas demais relações entre K e os outros macro e micronutrientes, as quais sempre foram crescentes (de K 5 a 30 mM), corroboram a essencialidade desse nutriente para os cvs. Nanica e Prata Anã. / Potassium is required in high dosis by the banana plant (Musa sp.) and interacts with other macro and micronutrients present in the medium in which banana tissues are maintained in vitro condition,with consequent modifications in the plant cell metabolism, mainly in nitrogen compounds, such as proteins and amino acids. When K is present in concentrations lower than the required, diamines such as putrescine, and polyamines, such as spermidine and spermine are formed. In order to establish the best dosis of K and follow the physiological consequences of the relationships N/K, K/P, K/Ca, K/Mg, K/Ca+Mg, K/S, K/Cu, K/Fe, K/Mn, K/Zn and K/putrescine, shoot apex of two banana cvs. Nanica and Prata Anã were maintained in asseptic conditions in modified MS media in the presence of 6 different dosis of K: 5, 10, 15, 20, 25 and 30 mM, K 20 mM being the K concentration in basic MS medium, and then transferred to rooting media with the same different K dosis. Dry wt., macro and micronutrients were measured in the shoots, roots and the intire plantlet, and number of plantlets produced determined, the data being analysed estatistically. Putrescine and polyamines were also determined. Visual symptoms of K deficiency such as clorosis and necrosis in the older leaves of all plantlets under low dosis of K were observed. The levels of putrescine and polyamines increased as K decreased in the medium, reaching the maximum value at K 5 mM, both cultivars presenting similar bahavior in relation to the diamine in some K concentrations. Quantitative differences were obtained among the two cultivars pertained to dry wt. values, number of in vitro regenerated banana plantlets and K concentration with optimization around K 15 and 20 mM. In general K absorption was more intense than the other nutrients, the absorption of the later being decreased probably due to a dilution effect of their values as the banana plantlets developed in vitro. These results, including those pertained to the relationships between K and the other nutrients, which always were high (from K 5 to 30 mM), corroborate the importance of potassium ion to the banana cvs. Nanica and Prata Anã.

Pilocarpus pennatifolius Lemmaire (Rutaceae) é uma espécie nativa que ocorre nas regiões Sul, Sudeste, Centro-Oeste e Nordeste do Brasil, e é popularmente conhecida por jaborandi. Essa e outras espécies de Pilocarpus encontram-se em risco de extinção devido ao extrativismo (uso como planta medicinal) e ao desmatamento. O cultivo in vitro de P. pennatifolius foi realizado como uma alternativa para a produção de pilocarpina (princípio ativo do jaborandi). A cultura de células foi obtida em meio MS semi-sólido, suplementado com sacarose, como fonte de carbono, e tendo como reguladores de crescimento BAP, IAA e NAA. O tempo de duplicação da cultura de calos foi de 22 dias. A concentração do alcalóide, determinada por técnicas cromatográficas, foi de aproximadamente 0,1 µg/ mg de biomassa. Os ensaios enzimáticos referentes à biossíntese da pilocarpina tiveram como objetivo elucidar a etapa inicial de formação do anel imidazólico, além da localização desta reação na planta. Os experimentos realizados indicaram a presença da enzima histidina amino-transferase (HAT, EC 2.6.1.38) cuja atividade catalítica foi de 46,09 nKat/ mg de proteína, apenas no extrato protéico das raízes de P. pennatifolius. A determinação da composição do óleo essencial por CG e CG/EM indicou como constituintes majoritários os hidrocarbonetos tridecano (56,8 %) e pentadecano (25,5 %). Os sesquiterpenos não oxigenados constituíram cerca de 15 % do óleo obtido. / Pilocarpus pennatifolius Lemmaire (Rutaceae) is a native Brazilian species which is commonly known as jaborandi. This species is endangered due to its exploitation as medicinal plant and the increasingly deforestation. A callus culture of P. pennatifolius was established as an alternative source for pilocarpine production (the active compound of jaborandi). The cell culture was obtained in a semi-solid media, supplemented with sucrose as carbon source and as growth regulators, BAP, IAA e NAA. The doubling time for the callus culture was determined as 22 days. The concentration of the alkaloid, obtained by chromatographic techniques was ca. 0.1 µg/ mg dry weight. The enzymatic assays related to pilocarpine biosynthesis were carried out with the aim to elucidate the imidazole ring formation beyond identify the site were this reaction takes place. The results indicated the presence of the enzyme histidine ammonia transferase (HAT, EC 2.6.1.38) only in the protein extract obtained from the roots of P. pennatifolius. The catalytic activity for this enzyme was 46.09 nKat/ mg protein. Volatile constituents from the leaves were analyzed by GC and GC/MS and the major compounds were determined as the hydrocarbons tridecane (56.8 %) and pentadecane (25.5 %). Almost 15 % of the total composition was constituted of non-oxygenated sesquiterpenes.

Sistemas de produção in vitro de embriões mamíferos muitas vezes requerem que o cultivo embrionário seja realizado de forma individualizada. Entretanto, os resultados obtidos com o cultivo in vitro (CIV) individual são inconstantes e, por vezes, inferiores ao CIV em grupo. Entre os sistemas que requerem o CIV individual, a técnica de handmade cloning (HMC) se destaca por produzir embriões sem zona pelúcida que não podem ser cultivados agrupados em protocolos convencionais de CIV. O objetivo deste experimento foi determinar as taxas de desenvolvimento in vitro e in vivo de embriões bovinos clonados pela técnica de HMC e submetidos a três diferentes sistemas de CIV em micropoços (Well of the well – WOW), sendo um industrial, confeccionado em polidimetilsiloxano (PDMS), que visou à padronização da configuração do sistema de CIV. Após 11 replicações, de 3.876 complexos cumuli-oócito bovinos maturados in vitro, 3.437 (88,6%) oócitos apresentaram a extrusão do 1º corpúsculo polar. Após a digestão da zona pelúcida, 2.992 estruturas foram bisseccionadas manualmente, com a produção de 2.288 hemi-citoplastos. Reconstruiram-se 1.011 embriões pela adesão de dois hemi-citoplastos a uma célula somática (célula-tronco mesenquimal bovina de uma fêmea adulta da raça Nelore), dos quais 751 (74,2%) embriões fusionaram após eletrofusão, sendo 715 ativados quimicamente. Os embriões clonados (n=705) foram então alocados aleatoriamente em três grupos experimentais para o CIV: Grupo 1 (G1) – micropoço modificado (WOW-modificado, FELTRIN et al., 2006a); Grupo 2 (G2) – micropoço convencional (WOW-convencional , VATJA et al., 2000); e Grupo 3 (G3) – micropoço – PDMS (WOW-PDMS) . Como grupo controle (FIV, Grupo 4, G4), 594 oócitos foram colocados em maturação, fecundação e cultivo in vitro, em paralelo aos grupos clonados. Os resultados das taxas de clivagem no Dia 2, de blastocisto no Dia 7 e de prenhez no Dia 30 de desenvolvimento foram analisados pelo teste do χ2 com nível de significância de 5%. Não houve diferença significativa quanto à taxa de clivagem nos diferentes grupos. Entretanto, a taxa de blastocisto (BL) no G1 (99/239; 41,4%) foi significativamente superior à observada no G2 (72/232; 31,0%) e no G3 (68/234; 29,1%), sendo estas últimas semelhantes entre si. A taxa de BL do grupo controle (315/594; 53,0%) foi superior aos três grupos experimentais. Finalmente, o desenvolvimento in vivo até o Dia 30 de prenhez não diferiu entre os grupos G1 (7/15; 46,7%), G2 (7/13; 53,9%) e G3 (6/16; 50,0%). O sistema em micropoço modificado promoveu melhores condições de CIV a embriões clonados por HMC, traduzido por maiores taxas de BL, não se refletindo, entretanto, em diferenças no desenvolvimento in vivo subseqüente à transferência para fêmeas receptoras. / In vitro production systems for mammalian embryos quite often require embryos to be cultured individually. However, results obtained after individual embryo in vitro culture (IVC) are frequently inconsistent and inferior to IVC in groups. The Handmade Cloning (HMC) procedure is among the systems that require individual IVC, since zona-free embryos cannot be grouped for culture by standard IVC protocols. The aim of this study was to evaluate the in vitro and in vivo development of bovine embryos cloned by HMC, after the IVC in three distinct microwell arrangements, including an industrial chip, manufactured in polydimethylsiloxane (PDMS), which aimed to standardize the pattern of the IVC system. After 11 replications, 3,437 (88.6%) oocytes were selected based on the extrusion of the first polar body, out of 3,876 in vitro-matured bovine cumuli-oocyte complexes. Following zona pellucida digestion, 2,992 structures were manually bisected, generating 2,288 hemi-cytoplasts. A total of 1,011 embryos were reconstructed by the adhesion of two hemi-cytoplasts to a somatic cell (bovine mesenchymal stem cells from an adult Nelore female), with 751 fusing (74.2%) following electrofusion, and 715 being chemically activated. Cloned embryos (n=705) were then randomly allocated to one of three IVC experimental groups: Group 1 (G1) – modified microwells (FELTRIN et al., 2006a); Group 2 (G2) – conventional microwells (VATJA et al., 2000); and Group 3 (G3) – microwells in PDMS. As control group (IVF, Group 4, G4), 594 oocytes were in vitro-matured, fertilized and cultured in parallel to the cloned groups. Cleavage, blastocyst and pregnancy rates evaluated on Days 2, 7 and 30 of development were analyzed by the χ2 test, for a significance level of 5%. No differences in cleavage rates were observed between groups. However, blastocyst rates in G1 (99/239; 41.4%) were significantly higher than in G2 (72/232; 31.0%) and in G3 (68/234; 29.1%), which did not differ between one another. Blastocyst rates in the IVF control group (315/594; 53.0%) were in turn higher than in all cloned experimental groups. Finally, in vivo development to Day 30 of pregnancy was not different between G1 (7/15; 46.7%), G2 (7/13; 53.9%) and G3 (6/16; 50.0%). In summary, the modified microwell system promoted superior development to the blastocyst stage than both the conventional and the DMPS-based microwell systems, with no impact on the subsequent in vivo development after transfer to female recipients.

La brûlure foliaire causée par Alternaria dauci est la maladie foliaire la plus dommageable pour les cultures de carottes, entravant la récolte mécanique. Seuls des cultivars partiellement résistants sont connus et commercialisés, mais leurs niveaux de résistance sont insuffisants. Les mécanismes de la résistance quantitative des plantes aux agents pathogènes sont mal caractérisés. Nous avons choisi d'étudier ces mécanismes dans l'interaction A. dauci-carotte. Auparavant, plusieurs résultats expérimentaux convergents ont montré que la résistance aux toxines fongiques entre en jeu dans cette interaction. Les tests de toxicité effectués avec des suspensions cellulaires de carotte ont révélé une corrélation entre la résistance des carottes à A.dauci et la résistance des cellules de carotte aux exsudats du champignon. Ces résultats nous ont incités à étudier les toxines impliquées dans le pouvoir pathogène d'A. dauci et afin de pouvoir étudier la réponse de la plante à celles –ci. En utilisant les profils HPLC de la phase organique d'exsudats de différentes souches de champignons, nous avons découvert une corrélation entre la production de toxines et l’agressivité de ces souches suggérant que la production de toxines joue un rôle majeur dans l’interaction A. dauci-carotte. Nous avons effectué l'extraction, la purification et la caractérisation de l'une des molécules candidates que nous avons nommé aldaulactone. Nous avons démontré sa toxicité grâce à un nouveau protocole de quantification de cellules mortes et vivantes. Un transcriptome d’A. dauci et une étude de l’expression des gènes en fonction de la production d’aldaulactone ont été utilisées pour étudier sa voie de biosynthèse. / Alternaria leaf blight, caused by the necrotrophic fungus Alternaria dauci, is the most damaging foliar disease of carrots, especially because it hampers leaf-pull harvesting. Only partially – and insufficiently – resistant cultivars exist. In general, partial resistance mechanisms are poorly understood, so we chose to study them in this interaction. Previous results obtained in the lab highlighted a correlation between plant resistance to the fungus and plant cell resistance toward fungal toxins. It was also shown using carrot cell suspensions that fungal exudates’ toxicity was only present in the organic phase. These results led us to better characterize the toxins produced by A. dauci, in order to get a deeper understanding of carrot cell resistance mechanisms toward those toxins. HPLC analysis of the exudates from different fungal strain uncovered a correlation between toxin production and the aggressiveness of the fungal strains, suggesting that toxin production is an important component of said aggressiveness. We extracted, purified and characterize one of these candidates, and named it aldaulactone. Using a new image analysis protocol, we demonstrated the toxicity of Aldaulactone on carrot cell suspensions. Transcriptomic data from Alternaria dauci were used to explore the biosynthesis pathway of Aldaulactone. Candidate Genes were selected and their level of expression compared with aldaulactone production in various A. dauci cultures.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal

HMPV was first reported in Australia by Nissen et al in 2002 from a group of 200 nasopharyngeal aspirate (NPA) specimens collected throughout 2001 from children presenting to the Royal Children’s Hospital, Brisbane. These specimens, previously negative for all common viral pathogens, were screened for hMPV by a polymerase chain reaction (PCR) assay based on known sequences. Molecular diagnostic assays including conventional reverse transcriptase PCR assay (RT-PCR) and real-time RT-PCR assays were subsequently developed, and molecular characterisation studies in our laboratory identified four genetic groups of hMPV. At the start of this project, little information were available regarding the virological characteristics of hMPV such as the isolation and replication kinetics of the virus in eukaryotic cells, molecular assays capable of detecting all virus subtypes, quantitation of viral load, genotyping and molecular epidemiology, correlation between virus subtypes and disease severity, and clinical spectrum of the infection. This project was designed to elucidate the virological features of hMPV that had not been explained by earlier studies on this virus. The project was limited to retrospective studies utilising the sera and nucleic acids obtained from positive subjects presenting to our hospital. The project provided relevant data in these areas, which helped in the early detection of infection and treatment, and also provided information for future research on antibody profiles and vaccine development. The study examined specific areas related to clinical and virological characteristics of hMPV with the aim of applying the results in patient management. During the project, five areas of hMPV research were undertaken, addressing each through detailed studies. An outline of the project aims and the conclusions derived from those experimental chapters is described below: 1. Isolation of the virus from clinical specimens obtained from infected subjects An optimised tissue culture protocol was successfully developed for isolating hMPV from positive nasopharyngeal aspirates, using LLC-MK2 cell lines. Viral stocks were prepared and maintained at stable conditions for future experiments. The demonstration of virus infection in the eukaryotic cells and titration of the infectious virions were performed using immunological assays developed and optimised in our laboratory, during the course of this study. 2. The complete genome sequence of an Australian hMPV isolate In this study, we described the ‘13,333 base pair’ complete genome sequence of the Queensland hMPV type-A strain, designated as AUS-001. Phylogenetic analyses of individual genes were used to generate ‘topological trees’ for systematic comparison of our local hMPV strain to that of international sequences. 3. A quantitative PCR assay (q.PCR) for hMPV A quantitative real-time reverse transcription PCR assay (qrt.RT-PCR) was developed for the simultaneous detection and quantification of hMPV in clinical samples. Serial dilutions of a synthetic RNA control were amplified after determining the absolute RNA copy numbers, and a standard curve was derived based on the cycle thresholds (Ct) values of the respective dilutions. Quantification of the hMPV RNA in clinical specimens was performed by extrapolating this data with Ct values of specimen dilutions obtained from the real-time assay. The dynamic range of the assay for hMPV genotypes A and B was determined. Validation of the inter- and intra- assay variations was completed using negative and positive controls along with a second assay targeting a different gene. 4. Determine the molecular epidemiology of hMPV genotypes This component of the project was designed to determine the molecular epidemiology of Queensland hMPV strains, using a selected ‘specimen population of hMPV positives’ representing the period 2001 to 2004. An RT-PCR assay based on P gene regions of hMPV was developed for the molecular typing of the above panel. Analyses of nucleotide and predicted amino acid sequences confirmed the heterogeneity of hMPV strains. In our study group, two genotypes (A and B) further classified into four subtypes (A1, A2, B1 and B2), were found to co-circulate during this period. General epidemiological features of the hMPV infections including seasonality, co-infections, incidence and prevalence in different age groups and in general population were described. 5. Clinical characteristics of hMPV infections The aim of this analysis was to illustrate the clinical spectrum of hMPV infections in a Queensland study population. We described the hMPV incidence pattern in different age groups and investigated the clinical severity scores of hMPV genotypes based on reported clinical features. We also undertook to identify any correlations between disease severity and other factors, including genotype, co-infections and viral load. Summary On completion, this PhD study provided valuable data on the isolation, molecular detection, epidemiological pattern and clinical severity of hMPV infections in Queensland. Overall hMPV was determined to be a serious respiratory pathogen in Queensland children. Data from this thesis will contribute to improved patient management and reduce the burden of hMPV-related disease in Queensland. These studies also formed the basis of further research involving respiratory viral pathogens in our laboratory and nationally.

HMPV was first reported in Australia by Nissen et al in 2002 from a group of 200 nasopharyngeal aspirate (NPA) specimens collected throughout 2001 from children presenting to the Royal Children’s Hospital, Brisbane. These specimens, previously negative for all common viral pathogens, were screened for hMPV by a polymerase chain reaction (PCR) assay based on known sequences. Molecular diagnostic assays including conventional reverse transcriptase PCR assay (RT-PCR) and real-time RT-PCR assays were subsequently developed, and molecular characterisation studies in our laboratory identified four genetic groups of hMPV. At the start of this project, little information were available regarding the virological characteristics of hMPV such as the isolation and replication kinetics of the virus in eukaryotic cells, molecular assays capable of detecting all virus subtypes, quantitation of viral load, genotyping and molecular epidemiology, correlation between virus subtypes and disease severity, and clinical spectrum of the infection. This project was designed to elucidate the virological features of hMPV that had not been explained by earlier studies on this virus. The project was limited to retrospective studies utilising the sera and nucleic acids obtained from positive subjects presenting to our hospital. The project provided relevant data in these areas, which helped in the early detection of infection and treatment, and also provided information for future research on antibody profiles and vaccine development. The study examined specific areas related to clinical and virological characteristics of hMPV with the aim of applying the results in patient management. During the project, five areas of hMPV research were undertaken, addressing each through detailed studies. An outline of the project aims and the conclusions derived from those experimental chapters is described below: 1. Isolation of the virus from clinical specimens obtained from infected subjects An optimised tissue culture protocol was successfully developed for isolating hMPV from positive nasopharyngeal aspirates, using LLC-MK2 cell lines. Viral stocks were prepared and maintained at stable conditions for future experiments. The demonstration of virus infection in the eukaryotic cells and titration of the infectious virions were performed using immunological assays developed and optimised in our laboratory, during the course of this study. 2. The complete genome sequence of an Australian hMPV isolate In this study, we described the ‘13,333 base pair’ complete genome sequence of the Queensland hMPV type-A strain, designated as AUS-001. Phylogenetic analyses of individual genes were used to generate ‘topological trees’ for systematic comparison of our local hMPV strain to that of international sequences. 3. A quantitative PCR assay (q.PCR) for hMPV A quantitative real-time reverse transcription PCR assay (qrt.RT-PCR) was developed for the simultaneous detection and quantification of hMPV in clinical samples. Serial dilutions of a synthetic RNA control were amplified after determining the absolute RNA copy numbers, and a standard curve was derived based on the cycle thresholds (Ct) values of the respective dilutions. Quantification of the hMPV RNA in clinical specimens was performed by extrapolating this data with Ct values of specimen dilutions obtained from the real-time assay. The dynamic range of the assay for hMPV genotypes A and B was determined. Validation of the inter- and intra- assay variations was completed using negative and positive controls along with a second assay targeting a different gene. 4. Determine the molecular epidemiology of hMPV genotypes This component of the project was designed to determine the molecular epidemiology of Queensland hMPV strains, using a selected ‘specimen population of hMPV positives’ representing the period 2001 to 2004. An RT-PCR assay based on P gene regions of hMPV was developed for the molecular typing of the above panel. Analyses of nucleotide and predicted amino acid sequences confirmed the heterogeneity of hMPV strains. In our study group, two genotypes (A and B) further classified into four subtypes (A1, A2, B1 and B2), were found to co-circulate during this period. General epidemiological features of the hMPV infections including seasonality, co-infections, incidence and prevalence in different age groups and in general population were described. 5. Clinical characteristics of hMPV infections The aim of this analysis was to illustrate the clinical spectrum of hMPV infections in a Queensland study population. We described the hMPV incidence pattern in different age groups and investigated the clinical severity scores of hMPV genotypes based on reported clinical features. We also undertook to identify any correlations between disease severity and other factors, including genotype, co-infections and viral load. Summary On completion, this PhD study provided valuable data on the isolation, molecular detection, epidemiological pattern and clinical severity of hMPV infections in Queensland. Overall hMPV was determined to be a serious respiratory pathogen in Queensland children. Data from this thesis will contribute to improved patient management and reduce the burden of hMPV-related disease in Queensland. These studies also formed the basis of further research involving respiratory viral pathogens in our laboratory and nationally.