Cette thèse de doctorat s’inscrit dans le développement et l’utilisation de méthodes mathématiques et informatiques qui exploitent les données temporelles d’expression des gènes issues de puces à ADN afin de rationaliser et de modéliser les réseaux de régulation génique. Dans cette optique, nous nous sommes principalement intéressés aux données d’expression des gènes de la drosophile (Drosophila melanogaster) pendant son développement, du stade embryonnaire au stade adulte. Nous avons également étudié des données concernant le développement d’autres eucaryotes supérieurs, la réponse d’une bactérie soumises à différents stress et le cycle cellulaire d’une levure. Ce travail a été réalisé selon trois volets principaux :la détection des stades de développement et des perturbations, les classifications de profils d’expression et la modélisation de réseaux de régulation.<p><p>Premièrement, l’observation des données d’expression utilisées nous a conduits à approfondir l’étude des phénomènes survenant lors des changements de stades de développement de la drosophile. Dans ce but, deux méthodes de détection automatique de ces changements ont été développées et appliquées aux données temporelles disponibles sur le développement d’eucaryotes supérieurs. Elles ont également été appliquées à des données temporelles relatives à des perturbations externes de bactéries. Cette étude à montré qu’une formulation mathématique simple permettait de retrouver les instants expérimentaux où une perturbation ou un changement de stade de développement est observé, à partir uniquement des profils d’expression. Par ailleurs, la réponse à une perturbation externe s’avère non distinguable d’une succession de stades de développement, sur la base des seuls profils temporels d’expression.<p><p>Deuxièmement, en raison des dimensions du problème constitué par les données d’expression de plusieurs milliers de gènes et de l’impossibilité de distinguer le rôle dans la régulation des gènes qui présentent des profils d’expression similaires, il s’est avéré nécessaire de classifier les gènes selon leurs profils d’expression. En nous basant sur les résultats obtenus lors de la détection des stades de développement, la démarche suivie est de regrouper les gènes qui présentent des profils temporels d’expression aux comportements similaires non seulement au cours de la série temporelle complète, mais également dans chacun des stades de développement. Dans cette optique, trois distances ont été proposées et utilisées dans une classification hiérarchique des données d’expression de la drosophile.<p><p>Troisièmement, des structures de modèles linéaires et non linéaires ainsi que des méthodes d’estimation et de réduction paramétriques ont été développées et utilisées pour reproduire les données d’expression du développement de la drosophile. Les résultats de ce travail ont montré qu’avec une structure de modèle linéaire simple, la reproduction des profils expérimentaux était excellente et que, dans ce cas, le réseau de régulation génique de la drosophile pouvait se contenter d’une faible connectivité (en moyenne 3 connexions par classe de gènes) et ce, sans hypothèse a priori. Toutefois, les modèles linéaires ont ensuite sérieusement été remis en question par des analyses de robustesse aux perturbations paramétriques et de stabilité des profils après extrapolation dans le temps. Dès lors, quatre structures de modèles non linéaires et cinq méthodes de réduction paramétrique ont été proposées et utilisées pour concilier les critères de reproduction des données, de robustesse et de stabilité des réseaux identifiés. En outre, ces méthodes de modélisation ont été appliquées à un sous-ensemble de 20 gènes impliqués dans le développement musculaire de la drosophile et pour lesquels 36 interactions ont été validées expérimentalement, ainsi qu’à des profils synthétiques bruités. Nous avons pu constater que plus de la moitié des connexions et non-connexions sont retrouvées par trois modèles non linéaires. Les résultats de cette étude ont permis d’éliminer certaines structures de modèle et méthodes de réduction et ont mis en lumière plusieurs directions futures à suivre dans la démarche de modélisation des réseaux de régulation génique. / Doctorat en Sciences de l'ingénieur / info:eu-repo/semantics/nonPublished

Ljungan virus (LV) is a recently identified picornavirus of the genus Parechovirus. LV has been isolated from voles trapped in Sweden and also in the United States. LV infected small rodents may suffer from diabetes type 1 and type 2 like symptoms, myocarditis and encephalitis. LV has been proposed as a human pathogen, with indications of causing diabetes type 1, myocarditis and intrauterine fetal deaths. In this thesis, cell culture adapted LV strains were utilised for development and adaptation of several basic methodological protocols to study the LV biology, e.g. real time PCR, highly specific antibodies and a reverse genetics system. These methods allowed detailed studies of this virus and how it interacts with the host cell. The genomic 5'-end was identified and modelling showed unique secondary structure folding of this region. The LV encodes an aphthovirus-like 2A protein with a DvExNPGP motif. This motif was found to mediate primary cleavage of the LV polyprotein in vitro and is proposed to constitute the carboxy terminus of the structural protein VP1 in LV. Rabbit polyclonal antibodies generated against recombinant structural proteins were used to verify that the LV virion is composed of the structural proteins VP0, VP1 and VP3. Cell culture studies showed that LV replicates to low titer with an absent or delayed cell lysis. LV is proposed to be able to spread by a, for picornaviruses, not previously demonstrated direct cell-to-cell transmission. All results taken together suggest a maintenance strategy of LV including low amounts of the LV genome and persistently infected hosts. Stability studies showed that the LV virion not only maintain activity in acidic and alkaline environments but also exhibit resistance to the commonly used disinfectant Virkon®.The results presented in this thesis show that LV has several unique properties, not previously observed for a picornavirus.

Les furanocoumarines (FCs) sont des métabolites secondaires principalement synthétisés chez quatre familles botaniques et dérivent de la voie de biosynthèse des phénylpropanoïdes. Ces phytoalexines interviennent dans les processus de défense de la plante et présentent un fort potentiel thérapeutique. Des travaux réalisés dans les années 1960 sur des cultures cellulaires en parallèle de l’utilisation de précurseurs radiomarqués ont permis de démontrer que de nombreuses enzymes impliquées dans cette voie appartenaient à la famille des cytochromes P450 (P450s). Seules deux d’entre elles avaient pu être identifiées d’un point de vue moléculaire au début de ce travail de thèse. Afin de générer des informations concernant le génome de plantes productrices de FCs, nous avons fait séquencer les ARNm extraits de feuilles de Pastinaca sativa, de Ruta graveolens et de Cullen cinereum. L’analyse in silico de ces trois banques de données a permis d’identifier près de 800 fragments d’ADNc codants pour des P450s. Des travaux antérieurs réalisés au laboratoire et l’analyse comparative des transcriptomes de ces 3 plantes nous ont amenés à nous focaliser sur la sous-famille CYP71AZ au travers d’une étude fine de CYP71AZ3 et CYP71AZ4. La caractérisation fonctionnelle de ces enzymes a été réalisée dans un système d’expression hétérologue eucaryote : Saccharomyces cerevisiae. Les résultats obtenus ont permis de montrer que CYP71AZ4 avait une spécificité de substrat assez large puisqu’elle pouvait métaboliser au moins une FC et 4 coumarines. L’analyse et la comparaison des constantes cinétiques pour chacun de ces substrats indiquent néanmoins que le psoralène est le substrat préférentiel. La caractérisation fonctionnelle de CYP71AZ3 a mis en évidence que cette enzyme pouvait hydroxyler l’esculétine, une coumarine, mais ne jouait aucun rôle dans la synthèse de FCs. Ces travaux mettent en évidence la diversité fonctionnelle au sein d’une même sous-famille enzymatique et permettent d’émettre des hypothèses nouvelles quant à l’apparition de cette voie de biosynthèse chez les Apiacées d’une part, et chez les autres familles botaniques d’autre part / Furanocoumarins (FCs) are secondary metabolites mainly synthetized in four botanical families deriving from the phenylpropanoid biosynthetic pathway. These phytoalexins are involved in plant defense mechanisms and present strong therapeutic potential. Early studies in the 1960s based on cell cultures and the use of radiolabeled precursors have shown that many enzymes involved in this pathway belong to the cytochrome P450 family (P450s). Only two of them had been identified from a molecular point of view at the beginning of this thesis. In order to generate information regarding the genome of plants producing FCs, we sequenced the mRNA extracted from leaves of Pastinaca sativa, Ruta graveolens, and Cullen cinereum. In silico analysis of these three libraries identified nearly 800 cDNA fragments encoding for P450s. Previous studies in the laboratory and comparative transcriptome analysis of these three plants have led us to focus on the subfamily CYP71AZ through a detailed study of CYP71AZ3 and CYP71AZ4. Functional characterization of these enzymes was performed in an eukaryote heterologous expression system: Saccharomyces cerevisiae. The results showed that CYP71AZ4 had a broad substrate specificity enough as it could metabolize one FC and 4 coumarins. The analysis and comparison of the kinetic constants for each of these substrates indicate, however, that the preferred substrate is psoralen. The functional characterization of CYP71AZ3 showed that this enzyme could hydroxylate esculetin, a coumarin, but played no role in the synthesis of FCs. This study highlights the functional diversity within a single enzyme subfamily and allows to issue new hypotheses about the emergence of this biosynthetic pathway in Apiaceae on one hand, and among other botanical families on the other hand

Die Bildung von Amyloidablagerungen ist ein Kennzeichen der Alzheimerschen Erkrankung. Hauptbestandteil dieser senilen Plaques sind sogenannte A beta Peptide, die durch proteolytische Prozessierung aus einem Vorläufermolekül (APP) gebildet werden. Die vorliegende Arbeit beschreibt die Klonierung des Meerschweinchen - APP. Diese cDNA-Sequenz zeigt auf DNA-Ebene eine Homologie zum Human-APP von ca. 90%, auf Proteinebene beträgt die Identität ca. 97 %. Damit wird ein weiterer experimenteller Beweis für die evolutionäre Konservierung des Amyloidvorläuferproteins in Säugetieren erbracht. APP mRNA wird in Meerschweinchen-Geweben ubiquitär exprimiert. Durch alternatives Spleißen wird ein zum Human-APP im wesentlichen ähnliches Isoformenmuster gebildet: Isoformen, welche eine Proteaseinhibitordomäne enthalten, werden dominierend in peripheren Organen exprimiert, dagegen ist im Zentralnervensystem das APP 695 mit über 60 % der Gesamttranskripte die bevorzugt exprimierte Isoform. Die klonierte cDNA des Meerschweinchen-APP wurde in prokaryontischen wie auch eukaryontischen Zellsystemen exprimiert. Dabei wurde die Eignung einer Anzahl von gegen Human-APP gewonnenen Antikörpern zur Detektion des Meerschweinchen-APP und seiner Prozessierungsprodukte gezeigt. Die Expression der neuronal dominierend exprimierten Isoform APP 695 des Meerschweinchen-APP in humanen Neuroblastom-Zellen zeigte keine Unterschiede hinsichtlich der APP-Prozessierung und A beta-Bildung im direkten Vergleich zu Human-APP 695. Die proteolytische Prozessierung des Proteins wurde durch Detektion der typischen Spaltprodukte in vivo (im Liquor) als auch in einem neu etablierten in vitro-Modell primär kultivierter neuronaler Zellen untersucht. Diese Zellkulturen wurden zunächst immunhistochemisch und biochemisch charakterisiert und als "mixed brain"-Typ mit einem hohen neuronalen Anteil beschrieben. Die Prozessierung des endogenen Meerschweinchen-APP in kultivierten Zellen führt dabei zur Bildung und Akkumulation aggregationsfähiger A beta - Peptide. Zur Detektion dieser Peptide wurde ein sensitiver Nachweis durch Western-Blot etabliert. Es wird damit ein Modellsystem für in vitro-Untersuchungen vorgeschlagen, welches ein Studium der Expression und Prozessierung des Amyloidvorläuferproteins unter angenähert physiologischen Bedingungen ermöglicht. / A beta peptides, the major component of neuritic plaques found in the brains of patients with Alzheimer’s disease, are derived by proteolytic processing from a larger precursor molecule (amyloid precursor protein - APP). A combination of PCR methods was used to clone and sequence APP cDNA from guinea pig (Cavia porcellus). Guinea pig APP exhibits extensive similarities to human APP in terms of primary structure, mRNA expression of differentially spliced isoforms as shown by Northern blot and RT-PCR analysis as well as proteolytic processing to amyloidogenic A beta peptides. In contrast to rat and mouse APP, guinea pig APP - recombinantly expressed in human neuroblastoma-cells - was processed indistinguishable from human APP thus excluding intrinsic sequence-specific factors influencing processing. Further studies were performed using newly established primary cell cultures of guinea pig neurons. Refined methods have been used to detect and characterize major proteolytic processing products of APP in vitro and in vivo. In conclusion, guinea pigs provide a model to study expression and processing of APP that closely resembles the physiological situation in humans and should, therefore, be important in elucidating potential strategies to prevent amyloid formation in Alzheimers Disease.

Human α-N-Acetylglucosaminidase (Naglu) is a lysosomal acid hydrolase implicated in tthe rare metabolic storage disorder known as mucopolysaccharidosis type IIIB (MPS IIIB; also Sanfilippo syndrome B). Absence of this enzyme results in cytotoxic accumulation of heparan sulphate in the central nervous system, causing mental retardation and a shortened lifespan. Enzyme replacement therapy is not currently effective to treat neurological symptoms due to the inability of exogenous Naglu to access the brain. This laboratory uses a Spodoptera frugiperda (Sf9) insect cell system to express Naglu fused to a synthetic protein transduction domain with the intent to facilitate delivery of Naglu across the blood-brain barrier. The project described herein may be broken down into three main sections. Firstly, the impact of two cryptic splice sites on Naglu expression levels was analyzed in both transiently expressing Sf9 cultures and stably selected cell lines. Secondly, the effectiveness of the native Naglu secretion-signaling peptide in the Sf9 system was examined. Finally, purification of a Naglu fusion protein from suspension culture medium was performed using hydrophobic interaction chromatographic techniques. The ultimate goal of this research is to develop an efficient system for economical, large-scale production of a human recombinant Naglu fusion protein that has the potential to be successfully used for enzyme replacement therapy to treat MPS IIIB. / Graduate

Cardiovascular diseases are a broad group of diseases, such as heart attack and heart failureaffecting the cardiovascular system. The primary cause of cardiovascular diseases isatherosclerosis, and its progression is brought about by oxidative stress and a complex chronicinflammation reaction cascade. Of central importance are proinflammatory cytokines, regulatedby multiple factors, including interleukin (IL) 17A. This project aims to investigate the effectof IL-17A on the inflammatory response of human vascular endothelial cells by quantifyingchemokine C-X-C motif ligand-1 (CXCL1) release when exposed or not to otherproinflammatory mediators such as TNF-𝛼, IL-6 and IL-1β. To investigate this, humanumbilical cord endothelial cells were cultured and then stimulated with IL-17A alone or incombination with other cytokines, namely IL-6/sIL6R, IL-1β, or TNF-𝛼. After an appropriateincubation time following the stimulations, the supernatants of the cells were collected, and theamount of CXCL1 was analysed with ELISA or qPCR, respectively. At a lower concentration(10ng/ml), IL-17A failed to induce a significant level of CXCL1 release from endothelial cells.However, IL-17A + TNF-𝛼 (5ng/ml) greatly enhanced, higher than inductions from individualtreatments combined, level of CXCL1 release from endothelial cells. Furthermore, combiningIL-17A with IL-1β or IL-6 induced non-abundant and abundant upregulation in CXCL1 release,respectively. On transcription level, the amount of CXCL1 mRNA induced by IL-17A alonewas non-significant, but stimulation with TNF-𝛼 and IL-17A + TNF-𝛼 induced significantlyupregulated expression of CXCL1. In conclusion, we found that IL-17A induced synergeticrelease of CXCL1 in human vascular endothelial cells with TNF-𝛼. In addition, the synergisticimpact of IL-17A and TNF-𝛼 in terms of CXCL1 induction in vascular endothelial cells wasevident on a transcriptional level. Our data imply that combined blockage of IL-17A and TNF-𝛼 could have an enhanced therapeutic effect on vascular inflammation.

Las pérdidas causadas por podredumbres durante la post-cosecha de frutos cítricos suelen suponer entre un 5 y un 10 % de la producción, siendo Penicillium digitatum el principal hongo patógeno, responsable de hasta el 80 % de las pérdidas causadas por podredumbres en frutos almacenados a temperatura ambiente. A pesar de la importancia económica de este patógeno nuestro conocimiento sobre los mecanismos de patogenicidad/ virulencia son muy escasos, en contraste con el avance experimentado en los últimos años en el conocimiento de las respuestas de defensa del fruto a la infección por este patógeno. Así, en el grupo de Fisiología y Biotecnología Postcosecha del IATA se está trabajando en la caracterización a nivel bioquímico y molecular de las respuestas de los frutos cítricos frente a la infección por P. digitatum y en el proceso de inducción de resistencia en frutos cítricos frente a la infección. Por este motivo en esta Tesis se han desarrollado un conjunto de herramientas esenciales para poder abordar la caracterización funcional de genes involucrados en virulencia/patogenicidad: transformación de P. digitatum mediada por Agrobacterium tumefaciens, utilización de la proteína verde fluorescente como marcadora, metodología para la obtención de mutantes de deleción de genes específicos, incluyendo mutantes nulos ¿ku80, vectores para silenciamiento génico mediante RNAi y la construcción de una genoteca de DNA genómico de P. digitatum. Se ha secuenciado y analizado el factor de transcripción PacC, que controla la expresión de un grupo de genes regulados por el pH ambiental. En P. digitatum se produce una acidificación del medio para adaptarlo al pH óptimo de su arsenal de enzimas. Se han obtenido mutantes de expresión constitutiva de PacC que presentan una disminución la capacidad infectiva en un 20 %. Mediante el empleo de técnicas de alto rendimiento se ha construido una genoteca substractiva de cDNA para obtener fragmentos de genes de P. digitatum que se inducen durante la infección de frutos de naranja y se ha analizado la expresión génica de los mismos y se ha elaborado una macromatriz conteniendo más de 1330 clones de la genoteca. El grupo de genes con mayor representación en la genoteca y con altos valores de inducción, corresponde a genes que codifican cinco proteasas diferentes. Además, en la genoteca substractiva también hay una alta representación de genes que codifican enzimas de degradación de la pared celular, y otras proteínas implicadas en glucólisis, respuesta a estrés o detoxificación. La ya demostrada importancia de las enzimas de degradación de la pared celular en la virulencia de hongos fitopatógenos, su abundancia y niveles de inducción en la macromatriz nos llevaron a estudiar más en profundidad algunos de estos genes (dos poligalacturonasas y una pectin liasa). Para comprobar su implicación en el proceso de infección se secuenciaron y se obtuvieron mutantes de P. digitatum en los que se eliminó el gen. La disminución de la virulencia de estos mutantes sobre frutos de naranja con respecto a la cepa silvestre fue de aproximadamente un 25 %. Del conjunto de genes relacionados con el metabolismo redox se seleccionó por su patrón de expresión el gen ris1, que codifica una naftaleno dioxigenasa posiblemente implicada en la detoxificación de compuestos aromáticos. A diferencia de los mutantes nulos en los genes de las poligalacturonasas o de la pectin liasa, los mutantes nulos ¿ris1 no presentaron ninguna alteración en su capacidad patogénica. / López Pérez, M. (2013). Estudio de los factores de patogenicidad/virulencia de Penicillium digitatum sobre frutos cítricos [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/34176

Die Komposition der Skelettmuskulatur resultiert aus der fein abgestimmten Balance von Proteinauf- und Abbaumechanismen. Die Skelettmuskelatrophie kann in verschiedenen Situationen entstehen bzw. von diversen Krankheiten ausgelöst werden (Altern, Hunger, Krebs, Nervenschädigung, Kachexie) und ist meist die Folge von gesteigertem Proteinabbau, der die Proteinsynthese überwiegt. Der Muskelabbau ist physiologisch teilweise sinnvoll und dient der Notversorgung von lebenswichtigen Organen mit Lipiden, Aminosäuren und Glukose. Insgesamt ist eine funktionsfähige Muskulatur sehr wichtig, sowohl für Gesunde als auch Erkrankte, da bei Muskelatrophie auslösenden Erkrankungen das Gesamtüberleben wesentlich verringert ist und die Lebensqualität der Patienten enorm reduziert ist. Der Abbau von strukturellen Muskelproteinen wurde hauptsächlich dem Ubiquitin-Proteasom System zugeschrieben, dessen Regulation und von seinen einzelnen Enzymen muss genauestens verstanden sein, um in der Zukunft zielgerichtete Therapien entwickeln zu können. Eines der zentralen Enzyme in der Skelett- und Herzmuskelatrophie ist die E3 Ubiquitin Ligase MuRF1. In nahezu allen Modellen für Muskelatrophie wurde eine starke Zunahme der Expression von MuRF1 beschrieben. Betrachtet man die sehr zentrale Rolle von MuRF1 im UPS, dort vermittelt MuRF1 den Abbau von strukturellen Proteinen des Sarkomers, und der beobachteten starken Regulation bei diversen Atrophie-Modellen, wird klar, wie wichtig das Verständnis der transkriptionellen Regulation von MuRF1 selbst ist. In den letzten Jahren wurden bereits einige Transkriptionsfaktoren identifiziert, die an der Regulation von MuRF1 bei verschiedenen Atrophie-Modellen beteiligt sind, die Studien zeigten aber auch, dass noch nicht alle Modelle erklärt werden konnten. Um die verbleibenden Wissenslücken zu füllen, wurde in dieser Studie nach neuen transkriptionellen Regulatoren von MuRF1 gesucht und deren Beteiligung an bereits bekannten Signalwegen analysiert. / Skeletal muscle mass is permanently balanced as a result of fine tuned protein synthesis and degradation mechanisms. Skeletal muscle atrophy occurs when protein degradation exceeds protein synthesis, which happens in a variety of conditions, such as aging, starvation, cancer, cachexia or denervation. Degradation of muscle mass can sometimes be useful, e.g. as source for lipids, amino acids and glucose in case of critical malnutrition as well as several other physiological conditions. But a solid composition and thereby functional maintenance of muscles is necessary for healthy individuals as well as individuals suffering from atrophy releasing diseases as to retain their mobility and to preserve full heart functions. Since degradation of structural proteins in muscle tissue has been addressed mainly to the ubiquitin-proteasome-system, the regulation of the participating components needs to be understood in detail to develop constructive treatments and therapies for atrophy prevention. One of the key enzymes in skeletal and heart muscle atrophy is the E3 ubiquitin ligase MuRF1. Its expression levels and protein content was found to be elevated in almost every know atrophy model. MuRF1 is very critical for the muscles composition and thus their functional integrity, as it marks and initiates degradation of structural and contractile proteins via the UPS. Since MuRF1 plays a prominent role in muscle atrophy, its transcriptional regulation needs to be well understood to develop effective therapies for all the different atrophy models MuRF1 has been linked to. Several transcription factors have been identified to regulate MuRF1 at different ratios and in diverse atrophy models. Importantly, they do not explain all MuRF1 inducing events observed. To fill some of the remaining knowledge gaps, the studies aims were to find new transcriptional regulators for MuRF1 and to analyze potential involvements of the obtained candidates in pathways affecting skeletal muscle atrophy.

Reverse genetics is an innovative molecular biology tool that enables the manipulation of viral genomes at the cDNA level in order to generate particular mutants or artificial viruses. The reverse genetics system for the influenza virus is arguably one of the best illustrations of the potential power of this technology. This reverse genetics system is the basis for the ability to regularly adapt influenza vaccines strains. Today, reverse genetic systems have been developed for many animal RNA viruses. Selection-free reverse genetics systems have been developed for the members of the Reoviridae family including, African horsesickness virus, bluetongue virus and orthoreovirus. This ground-breaking technology has led to the generation of valuable evidence regarding the replication and pathogenesis of these viruses. Unfortunately, extrapolating either the plasmid-based or transcript-based reverse genetics systems to rotavirus has not yet been successful. The development of a selection-free rotavirus reverse genetics system will enable the systematic investigation of poorly understood aspects of the rotavirus replication cycle and aid the development of more effective vaccines, amongst other research avenues. This study investigated the importance of co-expressed rotavirus proteins in the development of a selection-free rotavirus reverse genetics system. The consensus sequences of the rotavirus strains Wa (RVA/Human-tc/USA/WaCS/1974/G1P[8]) and SA11 (RVA/Simian-tc/ZAF/SA11/1958/G3P[2]) where used to design rotavirus expression plasmids. The consensus nucleotide sequence of a human rotavirus Wa strain was determined by sequence-independent cDNA synthesis and amplification combined with next-generation 454® pyrosequencing. A total of 4 novel nucleotide changes, which also resulted in amino acid changes, were detected in genome segment 7 (NSP3), genome segment 9 (VP7) and genome segment 10 (NSP4). In silico analysis indicated that none of the detected nucleotide changes, and consequent amino acid variations, had any significant effect on viral structure. Evolutionary analysis indicated that the sequenced rotavirus WaCS was closely related to the ParWa and VirWa variants, which were derived from the original 1974 Wa isolate. Despite serial passaging in animals, as well as cell cultures, the Wa genome seems to be stable. Considering that the current reference sequence for the Wa strain is a composite sequence of various Wa variants, the rotavirus WaCS may be a more appropriate reference sequence. The rotavirus Wa and SA11 strains were selected for plasmid-based expression of rotavirus proteins, under control of a T7 promoter sequence, due to the fact that they propagate well in MA104 cells and the availability of their consensus sequences. The T7 RNA polymerase was provided by a recombinant fowlpox virus. After extensive transfection optimisation on a variety of mammalian cell lines, MA104 cells proved to be the best suited for the expression rotavirus proteins from plasmids. The expression of rotavirus Wa and SA11 VP1, VP6, NSP2 and NSP5 could be confirmed with immunostaining in MA104 and HEK 293H cells. Another approach involved the codon-optimised expression of the rotavirus replication complex scaffold in MA104 cells under the control of a CMV promoter sequence. This system was independent from the recombinant fowlpox virus. All three plasmid expression sets were designed to be used in combination with the transcript-based reverse genetics system in order to improve the odds of developing a successful rotavirus reverse genetics system. Rotavirus transcripts were generated using transcriptively active rotavirus SA11 double layered particles (DLPs). MA104 and HEK293H cells proved to be the best suited for the expression of rotavirus transcripts although expression of rotavirus VP6 could be demonstrated in all cell cultures examined (MA104, HEK 293H, BSR and COS-7) using immunostaining. In addition, the expression of transcript derived rotavirus VP1, NSP2 and NSP5 could be confirmed with immunofluorescence in MA104 and HEK 293H cells. This is the first report of rotavirus transcripts being translated in cultured cells. A peculiar cell death pattern was observed within 24 hours in response to transfection of rotavirus transcripts. This observed cell death, however does not seem to be related to normal viral cytopathic effect as no viable rotavirus could be recovered. In an effort to combine the transcript- and plasmid systems, a dual transfection strategy was followed where plasmids encoding rotavirus proteins were transfected first followed, 12 hours later, by the transfection of rotavirus SA11 transcripts. The codon- optimised plasmid system was designed as it was postulated that expression of the DLP-complex (VP1, VP2, VP3 and VP6), the rotavirus replication complex would form and assist with replication and/or packaging. Transfecting codon- optimized plasmids first noticeably delayed the mass cell death observed when transfecting rotavirus transcripts on their own. None of the examined coexpression systems were able to produce a viable rotavirus. Finally, the innate immune responses elicited by rotavirus transcripts and plasmid-derived rotavirus Wa and SA11 proteins were investigated. Quantitative RT-PCR (qRT-PCR) experiments indicated that rotavirus transcripts induced high levels of the expression of the cytokines IFN- α1, IFN-1β, IFN-λ1 and CXCL10. The expression of certain viral proteins from plasmids (VP3, VP7 and NSP5/6) was more likely to stimulate specific interferon responses, while other viral proteins (VP1, VP2, VP4 and NSP1) seem to be able to actively suppress the expression of certain cytokines. In the light of these suppression results, specific rotavirus proteins were expressed from transfected plasmids to investigate their potential in supressing the interferon responses provoked by rotavirus transcripts. qRT-PCR results indicated that cells transfected with the plasmids encoding NSP1, NSP2 or a combination of NSP2 and NSP5 significantly reduced the expression of specific cytokines induced by rotavirus transcripts. These findings point to other possible viral innate suppression mechanisms in addition to the degradation of interferon regulatory factors by NSP1. The suppression of the strong innate immune response elicited by rotavirus transcripts might well prove to be vital in the quest to better understand the replication cycle of this virus and eventually lead to the development of a selection-free reverse genetics system for rotavirus. / PhD (Biochemistry), North-West University, Potchefstroom Campus, 2014

Reverse genetics is an innovative molecular biology tool that enables the manipulation of viral genomes at the cDNA level in order to generate particular mutants or artificial viruses. The reverse genetics system for the influenza virus is arguably one of the best illustrations of the potential power of this technology. This reverse genetics system is the basis for the ability to regularly adapt influenza vaccines strains. Today, reverse genetic systems have been developed for many animal RNA viruses. Selection-free reverse genetics systems have been developed for the members of the Reoviridae family including, African horsesickness virus, bluetongue virus and orthoreovirus. This ground-breaking technology has led to the generation of valuable evidence regarding the replication and pathogenesis of these viruses. Unfortunately, extrapolating either the plasmid-based or transcript-based reverse genetics systems to rotavirus has not yet been successful. The development of a selection-free rotavirus reverse genetics system will enable the systematic investigation of poorly understood aspects of the rotavirus replication cycle and aid the development of more effective vaccines, amongst other research avenues. This study investigated the importance of co-expressed rotavirus proteins in the development of a selection-free rotavirus reverse genetics system. The consensus sequences of the rotavirus strains Wa (RVA/Human-tc/USA/WaCS/1974/G1P[8]) and SA11 (RVA/Simian-tc/ZAF/SA11/1958/G3P[2]) where used to design rotavirus expression plasmids. The consensus nucleotide sequence of a human rotavirus Wa strain was determined by sequence-independent cDNA synthesis and amplification combined with next-generation 454® pyrosequencing. A total of 4 novel nucleotide changes, which also resulted in amino acid changes, were detected in genome segment 7 (NSP3), genome segment 9 (VP7) and genome segment 10 (NSP4). In silico analysis indicated that none of the detected nucleotide changes, and consequent amino acid variations, had any significant effect on viral structure. Evolutionary analysis indicated that the sequenced rotavirus WaCS was closely related to the ParWa and VirWa variants, which were derived from the original 1974 Wa isolate. Despite serial passaging in animals, as well as cell cultures, the Wa genome seems to be stable. Considering that the current reference sequence for the Wa strain is a composite sequence of various Wa variants, the rotavirus WaCS may be a more appropriate reference sequence. The rotavirus Wa and SA11 strains were selected for plasmid-based expression of rotavirus proteins, under control of a T7 promoter sequence, due to the fact that they propagate well in MA104 cells and the availability of their consensus sequences. The T7 RNA polymerase was provided by a recombinant fowlpox virus. After extensive transfection optimisation on a variety of mammalian cell lines, MA104 cells proved to be the best suited for the expression rotavirus proteins from plasmids. The expression of rotavirus Wa and SA11 VP1, VP6, NSP2 and NSP5 could be confirmed with immunostaining in MA104 and HEK 293H cells. Another approach involved the codon-optimised expression of the rotavirus replication complex scaffold in MA104 cells under the control of a CMV promoter sequence. This system was independent from the recombinant fowlpox virus. All three plasmid expression sets were designed to be used in combination with the transcript-based reverse genetics system in order to improve the odds of developing a successful rotavirus reverse genetics system. Rotavirus transcripts were generated using transcriptively active rotavirus SA11 double layered particles (DLPs). MA104 and HEK293H cells proved to be the best suited for the expression of rotavirus transcripts although expression of rotavirus VP6 could be demonstrated in all cell cultures examined (MA104, HEK 293H, BSR and COS-7) using immunostaining. In addition, the expression of transcript derived rotavirus VP1, NSP2 and NSP5 could be confirmed with immunofluorescence in MA104 and HEK 293H cells. This is the first report of rotavirus transcripts being translated in cultured cells. A peculiar cell death pattern was observed within 24 hours in response to transfection of rotavirus transcripts. This observed cell death, however does not seem to be related to normal viral cytopathic effect as no viable rotavirus could be recovered. In an effort to combine the transcript- and plasmid systems, a dual transfection strategy was followed where plasmids encoding rotavirus proteins were transfected first followed, 12 hours later, by the transfection of rotavirus SA11 transcripts. The codon- optimised plasmid system was designed as it was postulated that expression of the DLP-complex (VP1, VP2, VP3 and VP6), the rotavirus replication complex would form and assist with replication and/or packaging. Transfecting codon- optimized plasmids first noticeably delayed the mass cell death observed when transfecting rotavirus transcripts on their own. None of the examined coexpression systems were able to produce a viable rotavirus. Finally, the innate immune responses elicited by rotavirus transcripts and plasmid-derived rotavirus Wa and SA11 proteins were investigated. Quantitative RT-PCR (qRT-PCR) experiments indicated that rotavirus transcripts induced high levels of the expression of the cytokines IFN- α1, IFN-1β, IFN-λ1 and CXCL10. The expression of certain viral proteins from plasmids (VP3, VP7 and NSP5/6) was more likely to stimulate specific interferon responses, while other viral proteins (VP1, VP2, VP4 and NSP1) seem to be able to actively suppress the expression of certain cytokines. In the light of these suppression results, specific rotavirus proteins were expressed from transfected plasmids to investigate their potential in supressing the interferon responses provoked by rotavirus transcripts. qRT-PCR results indicated that cells transfected with the plasmids encoding NSP1, NSP2 or a combination of NSP2 and NSP5 significantly reduced the expression of specific cytokines induced by rotavirus transcripts. These findings point to other possible viral innate suppression mechanisms in addition to the degradation of interferon regulatory factors by NSP1. The suppression of the strong innate immune response elicited by rotavirus transcripts might well prove to be vital in the quest to better understand the replication cycle of this virus and eventually lead to the development of a selection-free reverse genetics system for rotavirus. / PhD (Biochemistry), North-West University, Potchefstroom Campus, 2014