Soybean (Glycine max L. Merr.) is one of the most important crops of the world. Among the various viruses infecting soybean, peanut mottle virus is most commonly found on soybeans in areas where they are grown in close proximity to peanuts. This research was conducted with the primary objective of identifying new genes for resistance to peanut mottle virus. To assign a gene symbol to the resistance gene in cultivar CNS, it was crossed with 'Peking'. Both the F2 and F2:3 lines segregated in a ratio which is expected when one dominant and one recessive gene at two different loci are segregating. Previous studies indicate the presence of one dominant gene in CNS and one recessive gene in Peking for resistance against PMV. This clearly suggests that Peking and CNS possess different resistance genes, which are non-allelic to each other. Now that, all the allelism tests are complete, the resistance gene in CNS can be assigned a gene symbol of Rpv3. PI 486355, a resistant line, was crossed with susceptible cultivars Lee 68 and Essex to study the mode of inheritance of resistance. This PI was found to possess two independent dominant genes for resistance to peanut mottle virus. It was also crossed with 'York' and CNS which are known to have resistance genes at the Rpv1 and Rpv3 loci, respectively. Data from inoculations of F2 and F2:3 progenies indicated that one gene was allelic to Rpv1 and the other is at a locus different from both Rpv1 and Rpv3. PI 398593 was crossed with Lee 68, York, Peking and CNS for studying the nature of resistance genes present in it. No certain conclusions can be drawn regarding the nature of the resistance gene(s) at this stage because of inconsistent behavior of the PI itself. The F2 data of the crosses of PI 398593 with Lee 68, York and CNS supported a recessive nature of the resistance gene present in the PI. F2 plants of the cross PI 398593 x Peking segregated but, not in the expected ratio. F2:3 data of only one cross (PI 398593 x York) supported the recessive nature of the PI resistance gene whereas the other two crosses (PI 398593 x CNS and PI 398593 x Peking) did not support these findings. From the data available it appears that the resistance is at least partially influenced by the environment. The mode of inheritance of resistance in PI 96983, 'Kwanggyo', 'Toano', 'Jizuka', 'Raiden' and 'Suweon 97' was studied by crossing these cultivars with PMV susceptible cultivars and inoculating the F2 populations of these crosses. In all these cultivars resistance is governed by a single dominant gene. PI 96983, Toano, Jizuka and Suweon 97 were also crossed with York to determine the allelic relationships. Resistance genes in all these cultivars were found to be allelic to Rpv1. Since each of the cultivars also has a single dominant gene at the same locus for resistance to soybean mosaic virus, it is possible that resistance to both viruses is controlled by the same gene. / Master of Science

Acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) are blood cancers that are often treated with stem cell transplantation (SCT). Since SCT treatments have variable success, especially in adults with AML whose disease frequently relapses, novel and more effective solutions must be considered. In this thesis, I will explore one type of immunotherapy in murine models for ALL (L1210) and AML (C1498) using in vitro and in vivo techniques such as flow cytometry and transcriptomics. In my approach, I am attempting to enhance the immunogenicity of whole cell vaccines by pre-infecting the leukemia cells with oncolytic virus (OV) and thus producing leukemia infected cell vaccines (ICVs). While it has been previously shown that L1210-ICV pre-treatment works well in protecting mice from ALL challenge, I have found that pre-immunization with C1498-ICV has a limited efficacy in protecting animals from AML progression. By investigating the downstream effects of ICV, I was able to show that unlike C1498 cells, L1210 cells produce previously unknown immunogenic factors following OV infection.

La littérature décrit des différences fondamentales entre l’AAV2 sauvage et ses pendants recombinants. La forme sauvage serait plus efficiente en terme de production, d’encapsidation et d’infectieusité, allant de facteurs de deux à cents en fonction de la propriété étudiée. A cause de ces différences, la quantité de rAAV nécessaire pour traiter un patient atteint d’une maladie implique une injection systémique estimée à 1.1015 particules par kilogramme de tissue à traiter. C’est dans cette optique que s’inscrivent mes travaux de thèse. Essayer de comprendre qu’elles sont les différences entre l’AAV sauvageet les rAAV qui peuvent engendrer tant de différences en terme d’efficacité. L’étude du comportement du génome de l’AAV2 sauvage dans le système baculovirus/cellules Sf9, a permis de découvrir que la régulation de l’AAV2 sauvage était similaire en baculovirus. Nous avons aussi découvert, grâce à notre analyse transcriptomique que les promoteurs naturels del’AAV2 étaient actifs dans notre système, ce qui nous a permis d’imaginer de nouvelles constructions génétiques afin d’améliorer la quantité et la qualité des particules rAAV. Nous avons aussi réaliser des études structurales sur différentesparticules AAV afin d’améliorer notre connaissance de ces particules. / The literature describes several fundamental differences between WT AAV and rAAP properties. WT form obtains an one hundred higher production yield compared to rAAV, with the possibility to obtain only full particles, and most importantly, all the WT AAV particles are infectious, compared to only 1% for the rAAV. These lower values for rAAV, implied to inject up to 1.1015 particles per kilogram of tissue. These quantities induce a non-negligible cost for rAAV based gene therapies, even with the productions techniques improvements or the development of baculoviruses based techniques. It is with these ideas in mind that my PhD works were developed. Trying to understand differences between WT and rAAV, trying to produce WT AAV in baculovirus has bring important knowledges about AAV comportment in baculovirus. Our RNA-Seq results have demonstrated than the WT AAV natural promoters were all active, allowing us to design to genetic constructs in order to improve rAAV quantity and quality. We have also tried to solve the AAV crystal structure, to improve our knowledges about these particles.

Indiana University-Purdue University Indianapolis (IUPUI) / Vaccinia virus (VACV), the prototypical poxvirus, was used to eradicate smallpox worldwide and, in recent years, has received considerable attention as a vector for the development of vaccines against infectious diseases and oncolytic virus therapy. Studies have demonstrated that VACV exhibits an extremely strong bias for binding to and infection of primary human antigenpresenting cells (APCs) including monocytes, macrophages, and dendritic cells. However, very few studies have evaluated VACV binding to and infection of primary human B cells, a main type of professional APC. In this study, we evaluated the susceptibility of primary human peripheral B cells at different developmental stages to VACV binding, infection, and replication. We found that VACV exhibited strong binding but little entry into ex vivo B cells. Phenotypic analysis of B cells revealed that plasmablasts were the only subset resistant to VACV binding. Infection studies showed that plasma and mature-naïve B cells were resistant to VACV infection, while memory B cells were preferentially infected. Additionally, VACV infection was increased in larger and proliferative B cells suggesting a bias of VACV infection towards specific stages of differentiation and proliferative ability. VACV infection in B cells was abortive, and cessation of VACV infection was determined to occur at the stage of late viral gene expression. Interestingly, B cell function, measured by cytokine production, was not affected within 24 hours post-infection. In contrast to ex vivo B cells, stimulated B cells were permissive to productive VACV infection. These results demonstrate the value of B cells as a tool to aid in deciphering the intricacies of poxvirus infection in humans. Understanding VACV infection in primary human B cells at various stages of differentiation and maturation is important for the development of a safer smallpox vaccine and better vectors for vaccines against cancers and other infectious diseases.

Vaccinia virus has a large and still incompletely understood genome although several strains of this virus are already in clinical development. For the most part, clinical candidates have been attenuated from their wild type vaccine strains through deletion of metabolic genes like the viral thymidine kinase gene.In the present work, we thoroughly examined the genetic elements of vaccinia which could be modulated to tailor the virus as a cancer therapeutic. Using a variety of cancer cell lines and primary tumor explants, we performed a fitness assay that directly compares multiple wild-type Vaccinia strains to identify the genetic elements that together create an optimal “oncolytic engine”. Using a transposon insertion strategy and deep sequencing of viral populations we systematically examined Vaccinia genes that do or do not play a role in the therapeutic activity of the virus. Our studies allowed us to identify a variety of genes in the vaccinia genome that when deleted, augment the oncolytic activity of a newly engineered Vaccinia virus. In the context of this thesis, I define enhanced oncolytic activity as superior therapeutic activity, increased immunogenicity and an improved safety profile, all aspects which we used to compare this novel virus to Vaccinia viruses currently in the clinic.

The purpose of this study was to identify mutations in the basic core promoter and enhancer II region a* the hepatitis B virus (HBV) that might result in the hepatitis B virus e antigen (HBeAg)-negative phenotype and contribute to hepatocarcinogenesis in black African carriers of the virus. The basic core promoter/enhancer II overlaps the X gene. HBV DNAfrom serum of 47 asymptomatic carriers and 50 patients with hepatocellular carcinoma and from 29 tumorous and 10 nontumorous liver tissues was amplified and sequenced directly. That part of the enhancer II region not overlapping the basic core promoter was reasonably well conserved in all samples. Missense mutations at positions 1809 and 1812 were found in 80% of all sequences and may represent wiidtype sequence in southern African isolates. Nucleotide and amino acid divergences were higher in the basic core promoter of hepatocellular carcinoma patients than of asymptomatic carriers (p<0.0001). This applied particularly to the paired 1762 adenine to thymine (1762T) and 1764 guanine to adenine (1764*) missense mutations, the prevalence of which was 66% in patients with hepatocellular carcinoma compared with 11% in asymptomatic carriers (p<0.0001). There was no association between the presence of 1762T1764A and the rate of HBeAg negativity, although these mutations suppressed HBeAg titres in HBeAg-positive patients. Suppression of HBeAg expression as well as alteration of amino acid sequence of the X protein may be contributing factors in the development of hepatocarcinogenesis.

A dissertation submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfillment of the requirements for the degree of Master of Science in Medicine Johannesburg, 2017 / Hepatitis B is a global health problem that kills about 600 000 people annually. It is an infectious disease caused by the Hepatitis B Virus (HBV), which infects the liver and leads to liver inflammation and secondary complications such as cirrhosis and Hepatocellular Carcinoma (HCC). The available therapies are only partially effective and are associated with adverse side effects and viral drug resistance. RNA interference (RNAi) pathway is a gene silencing pathway found in diverse living systems including mammals. Harnessing of this pathway to inhibit HBV replication has shown a lot of promise, with highly effective anti-HBV RNAi activator sequences designed. However, the lack of safe and efficient delivery and expression systems for these sequences is one of the obstacles that need to be overcome before RNAi effectors can reach clinical application. For easy assessment of transduction efficiency, Helper Dependent Adenoviral vectors (HDAd) expressing β-galactosidase (encoded by lac Z gene) are commonly used to deliver anti-viral RNAi activators. However, this reporter protein has been blamed for induction of innate immune response and concomitant clearance of the HDAds by the host. For the first time, this study explored the use of lac Z-deficient HDAds to deliver anti-HBV RNAi activators expressed under the control of a liver-specific phosphoenolpyruvate carboxykinase (PEPCK) promoter. HDAd expressing Firefly luciferase resulted in a significant luminescence detected in cell culture lysates and a sustained bioluminescence in mice. HDAds expressing anti-HBV sequences transduced the liver efficiently and did not induce a pronounced inflammatory response or liver toxicity in mice. However, this did not translate into maximal anti-HBV sequence expression and HBV replication inhibition in vitro and in vivo. This suggests that the PEPCK promoter is inadequate for RNAi activator expression. This study highlights the importance of careful RNAi activator regulatory elements selection and presents the therapeutic potential and utility of HDAd vectors for hepatotropic delivery of antiviral sequences with markedly attenuated immune response stimulation and toxicity. For improved anti-HBV RNAi activator expression and HBV knockdown, a different liver specific promoter mouse transthyretin receptor (MTTR) promoter is currently being investigated in our lab. / MT2017

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Cancer is one of the leading causes of death worldwide, with currently assessed chances to develop at least one cancer in a lifetime for about 20%. High cases rates and mortality require the development of new anticancer therapies and treatment strategies. Another important concern is toxicity normally associated with conventional therapy methods, such as chemo- and radiotherapy. Among many proposed antitumoral agents, oncolytic viruses are still one of the promising and fast-developing fields of research with almost a hundred studies published data on over 3000 patients since the beginning of the new millennia. Among all oncolytic viruses, the Vaccinia virus is arguably one of the safest, with an extremely long and prominent history of use, since it was the one and only vaccine used in the Smallpox Eradication Program in the 1970s. Interestingly enough, it was the first oncolytic virus proven to have tumor tropism in vitro and in vivo in laboratory settings, and this year we can celebrate an unofficial 100th anniversary since the publication of the fact. While being highly immunogenic, Vaccinia virus DNA replication takes place in the cytoplasm of the infected cell, and virus genes never integrate into the host genome. Another advantage of using Vaccinia as an oncolytic agent is its high genome capacity, which allows inserting up to 25 kbps of exogenous genes, thus allowing to additionally arm the virus against the tumor. Oncolytic virus action consists of two major parts: direct oncolysis and immune activation against the tumor, with the latter being the key to successful treatment. To this moment, preclinical research data are mostly generated in immunocompromised xenograft models, which have hurdles to be properly translated for clinical use. In the first part of the current study, fourteen different recombinant Vaccinia virus strains were tested in two different murine tumor cell lines and corresponding immunocompetent animal models. We found, that Copenhagen backbone Vaccinia viruses while being extremely effective in cell culture, do not show significant oncolytic efficacy in animals. In contrast, several of the LIVP backbone viruses tested (specifically, IL-2 expressing ones) have little replication ability when compared to the Copenhagen strain, but are able to significantly delay tumor growth and prolong survival of the treated animals. We have also noted cytokine related toxicity of the animals to be mouse strain specific. We have also tested the virus with the highest therapeutic benefit in combination with romidepsin and cyclophosphamide. While the combination with histone deacetylase inhibitor romidepsin did not result in therapeutic benefit in our settings, the addition of cyclophosphamide significantly improved the efficacy of the treatment, at the same time reducing cytokine-associated toxicity of the IL-2 expressing virus. In the second part of the work, we analyzed the ability of adipose-derived mesenchymal stem cells to serve as a carrier for the oncolytic Vaccinia virus. We showed for the first time that the cells can be infected with the virus and can generate virus progeny. They are also able to survive for a substantially long time and, when injected into the bloodstream of tumor-bearing animals, produce the virus that is colonizing the tumor. Analysis of the systemic distribution of the cells after injection revealed that infected and uninfected cells are not distributed in the same manner, possibly suggesting that infected cells are getting recognized and cleared by an impaired immune system of athymic mice faster than non-infected cells. Despite this, injection of virus-loaded adipose-derived mesenchymal stem cells to human A549 tumor-bearing xenograft mice resulted in rapid tumor regression and reduced virus-related side effects of the treatment when compared to injection of the naked virus. In conclusion, we have tested two different approaches to augmenting oncolytic Vaccinia virus therapy. First, the combination of recombinant Vaccinia virus expressing IL-2 and cyclophosphamide showed promising results in a syngeneic mouse model, despite the low permissivity of murine cells to the virus. Second, we loaded the oncolytic Vaccinia virus into mesenchymal stem cells and have proven that they can potentially serve as a vehicle for the virus. / Krebs ist eine der häufigsten Todesursachen weltweit, wobei die Wahrscheinlichkeit, im Laufe des Lebens an mindestens einer Krebsart zu erkranken, derzeit auf etwa 20 % geschätzt wird. Die hohen Fallzahlen und die hohe Sterblichkeit erfordern die Entwicklung neuer Krebstherapien und Behandlungsstrategien. Ein weiteres wichtiges Problem ist die Toxizität, die normalerweise mit konventionellen Behandlungsmethoden, wie Chemo- und Strahlentherapie, einhergeht. Unter den vielen vorgeschlagenen antitumoralen Wirkstoffen sind onkolytische Viren nach wie vor eines der vielversprechendsten und sich schnell entwickelnden Forschungsgebiete mit fast hundert veröffentlichten Studien an über 3000 Patienten seit Beginn des neuen Jahrtausends. Unter allen onkolytischen Viren ist das Vaccinia Virus wohl eines der Sichersten und hat eine extrem lange und prominente Anwendungsgeschichte, da es der einzige Impfstoff war, der im Pockenausrottungsprogramm in den 1970er Jahren verwendet wurde. Interessanterweise war es das erste onkolytische Virus, dessen Tumortropismus in vitro und in vivo im Labor nachgewiesen wurde. In diesem Jahr (2022) können wir das inoffizielle 100-jährige Jubiläum seit der Veröffentlichung dieser Tatsache feiern. Obwohl Vaccinia hoch immunogen ist, findet die Replikation im Zytoplasma der infizierten Zelle statt, und die Virusgene werden niemals in das menschliche Genom integriert. Ein weiterer Vorteil der Verwendung von Vaccinia als onkolytisches Agens ist seine hohe Genomkapazität, die es ermöglicht, bis zu 25 kbit/s an exogenen Genen einzufügen, wodurch das Virus zusätzlich gegen den Tumor aufgerüstet werden kann. Die Wirkung des onkolytischen Virus besteht aus zwei Hauptbestandteilen: der direkten Onkolyse und die Aktivierung des Immunsystems gegen den Tumor, wobei letztere der Schlüssel zum Behandlungserfolg ist. Bislang wurden präklinische Forschungsdaten meist in immungeschwächten Xenotransplantationsmodellen gewonnen, die sich nur schwer für den klinischen Einsatz eignen. Im ersten Teil der aktuellen Studie wurden vierzehn verschiedene rekombinante Vaccinia-Virusstämme in zwei verschiedenen murinen Tumorzelllinien und in entsprechenden immunkompetenten Tiermodellen getestet. Wir fanden heraus, dass Kopenhagener Backbone-Vaccinia-Viren zwar in der Zellkultur äußerst wirksam sind, im Tiermodell jedoch keine signifikante onkolytische Wirksamkeit zeigen. Im Gegensatz dazu haben mehrere der getesteten LIVP-Backbone-Viren (insbesondere die IL-2 exprimierenden) im Vergleich zum Kopenhagener Stamm nur eine geringe Replikationsfähigkeit, sind aber in der Lage, das Tumorwachstum deutlich zu verzögern und das Überleben der behandelten Tiere zu verlängern. Wir haben auch festgestellt, dass die Zytokin-bedingte Toxizität der Tiere mausstammspezifisch ist. Wir haben auch das Virus mit dem höchsten therapeutischen Nutzen in Kombination mit Romidepsin und Cyclophosphamid getestet. Während die Kombination mit dem Histon-Deacetylase-Inhibitor Romidepsin in unseren Versuchsreihen keinen therapeutischen Nutzen erbrachte, verbesserte die Zugabe von Cyclophosphamid die Wirksamkeit der Behandlung erheblich und verringerte gleichzeitig die zytokinbedingte Toxizität des IL-2-exprimierenden Virus. Im zweiten Teil der Arbeit analysierten wir die Fähigkeit von aus Fettgewebe gewonnenen mesenchymalen Stammzellen, als Träger für das onkolytische Vaccinia-Virus zu dienen. Wir konnten zum ersten Mal zeigen, dass die Zellen mit dem Virus infiziert werden können und Virusnachkommen erzeugen können. Sie sind auch in der Lage, sehr lange zu überleben und, wenn sie in den Blutkreislauf von Tieren mit Tumoren injiziert werden, das Virus zu produzieren, das den Tumor besiedelt. Die Analyse der systemischen Verteilung der Zellen nach der Injektion ergab, dass infizierte und nicht infizierte Zellen nicht auf die gleiche Weise verteilt werden, was möglicherweise darauf hindeutet, dass infizierte Zellen von einem beeinträchtigten Immunsystem der athymischen Mäuse schneller erkannt und beseitigt werden, als nicht infizierte Zellen. Trotzdem führte die Injektion von virusbeladenen mesenchymalen Stammzellen aus Fettgewebe in A549-Tumor-tragende Xenograft-Mäuse zu einer schnellen Tumorregression und zu geringeren virusbedingten Nebenwirkungen der Behandlung, als bei der Injektion des nackten Virus. Zusammenfassend lässt sich sagen, dass wir zwei verschiedene Ansätze zur Verstärkung der onkolytischen Vaccinia-Virus-Therapie getestet haben. Erstens zeigte die Kombination aus rekombinantem Vaccinia-Virus, das IL-2 exprimiert, und Cyclophosphamid in einem syngenen Mausmodell vielversprechende Ergebnisse, trotz der geringen Permissivität der Mäusezellen für das Virus. Zweitens haben wir onkolytische Vaccinia-Viren in mesenchymale Stammzellen eingebracht und nachgewiesen, dass diese als Vehikel für das Virus dienen können.

Sequences of 33 Bean pod mottle virus (BPMV) isolates collected from Mississippi were obtained from four regions of the viral genome. Sequences were compared mutually and to subgroups I and II type isolates. Mississippi isolates collected have greater similarity to subgroup II. Helicase sequences obtained from Mississippi isolates showed characteristics of isolates producing mild or moderate symptoms. Biological comparison of isolates from Mississippi confirmed predictions from molecular data. Plant species were tested for susceptibility to BPMV. Seven of 52 species tested positive. Desmodium perplexum was infected by beetle feeding and served as an inoculum source for transmission of BPMV to soybeans. Beetle species collected from soybean and clover were tested to determine if they serve as BPMV vectors. Of eight species tested, Hypera postica transmitted BPMV to 1 of 14 test plants. Beetle overwintering transmission of BPMV was tested, but of 187 beetles collected, none transmitted the virus.