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Ctenocephalides felis is a major pest of companion animals worldwide. This project aimed to generate novel genetic resources for C. felis and develop tools to aid drug-target identification and validation. Sample handling methods were assessed and candidate reference genes validated, to ensure quality of RNA samples and reliable gene expression normalisation. Piercing C. felis samples prior to storage in RNAlater ensured RNA integrity was maintained over time. Glyceraldehyde 3-phosphate dehydrogenase , 60S ribosomal protein L19 and elongation factor-1α were demonstrated as stable reference genes across all comparisons tested. A C. felis transcriptome encompassing multiple developmental stages, sexes and tissues was sequenced and de novo assemblies produced with two assemblers, Trinity and Oases. Each assembly contained >100000 contigs. Annotation of the assemblies generated functional insight, such as top BLAST hits, GO annotations and signal peptide predictions. The Trinity assembly was deemed the highest quality and searched for genes of interest, involved in development. Expression analysis of selected transcripts across stadia gave insight into developmental processes, and demonstrated the utility of the transcriptome. This study was the first to demonstrate that C. felis can mount an RNAi response upon exposure to dsRNA. Knockdown of glutathione S-transferase σ (GSTσ), was demonstrated in adult C. felis: ≈80 % knockdown following microinjection of dsGSTσ; ≈64 % knockdown after soaking in dsGSTσ; ≈96 % knockdown after continuous feeding on dsGSTσ. RNAi machinery was identified in C. felis. siRNAi pathway components, Dicer 2 and Argonaute 2, were upregulated following dsRNA exposure. Dicer 2 was knocked-down by soaking in dsDicer2, although results of an “RNAi of RNAi” experiment were inconclusive. Transcripts encoding machinery putatively involved in dsRNA uptake and breakdown were also identified. Through these studies, this project has generated novel insights into C. felis biology and opened up new avenues for research.

The presence of an unpaired copy of a gene during meiosis triggers the silencing of every copy of that gene in the diploid ascus cell of Neurospora crassa, a phenomenon called Meiotic Silencing. This phenomenon has two stages: trans-sensing and meiotic silencing. If a DNA region is not detected on the opposite homologous chromosome early in meiosis (a trans-sensing failure), a signal corresponding to the unpaired region is produced that transiently silences expression of all homologous sequences. Meiotic silencing is related to RNA Silencing, a phenomenon that employs RNA-dependent RNA Polymerases (RdRPs), Argonautes, and Dicers. Dicers cleave double-stranded RNA (dsRNA) into 21-23 nucleotide RNAs. In the filamentous fungus Neurospora crassa, two RNA silencing pathways have been identified; one is active during mitosis, and the other is active during meiosis. The mitotic RNA silencing pathway, known as “quelling”, involves an RdRP (quelling-deficient-1--qde-1), an Argonaute-like protein (quelling-deficient-2--qde-2), and two Dicer-like proteins (dicer-like-1--dcl-1 and dicer-like-2--dcl-2). Previous studies in N. crassa also revealed the involvement of an RdRP (Suppressor of ascus dominance-1--Sad-1) and an Argonaute-like protein (Suppressor of meiotic silencing-2--Sms-2) in meiotic silencing, suggesting that meiotic silencing is RNA-dependent and raising the question of whether a Dicer is involved in meiotic silencing. In this work, we tested the participation in meiotic silencing of the dcl-1 gene of N. crassa, which codes for a Dicer-like protein we call Suppressor of meiotic silencing-3--Sms-3. Crosses homozygous for mutant alleles of Sms-3 are barren, indicating that the gene is also essential for sexual development. Due to this homozygous sterility, we could only test the involvement of Sms-3 in meiotic silencing in heterozygous crosses. Under these conditions, we observed suppression of the meiotic silencing which would have otherwise been induced by the presence of unpaired DNA of reporter genes. We conclude that the Dicerlike protein Sms-3 is required for both meiotic RNA silencing and sexual development.

Salmonella enterica serovar Enteritidis (SE) is one of the most common food-borne pathogens that cause human salmonellosis. Contamination of consumed poultry products continues to be a global threat to public health. Genetic resistance using genomic approach provides a promising solution to controlling SE infection in poultry. The mechanism of SE resistance in chickens remains elusive. Three different approaches, microarray techology, gene silencing, and computational gene analysis, have been utilized to study SE-induced transcriptional changes of host immune response in the chicken. A whole genome chicken 44K microarray was used to analyze the transcriptome of heterophils from SE-resistant (line A) and SE-susceptible chickens (line B) with/without in vitro SE stimulation. Many differentially expressed immune-related genes were found in the SE-infected to non-infected comparison, where more immune-related genes were down-regulated in line B than line A. These results suggested a similar Toll-like receptor (TLR) regulatory network might exist in heterophils of both lines, and provided strong candidates for further investigating SE resistance and susceptibility in chickens. In the gene silencing study, small interfering RNAs (siRNA) were used to specifically inhibit the expression of NFkB1 in the chicken HD11 macrophage cell line with SE challenge. Genes related to the NF-kB signaling pathway were selected to examine the effect of NFkB1 inhibition on TLR pathway. With 36% inhibition of NFkB1 expression, the results showed an increased expression of TLR4 and interleukin (IL)-6 following SE challenge and suggested a likely inhibitory regulation of NFkB1 on TLR signal pathway. Finally, two novel chicken C-type lectin-like receptors were identified and annotated to chicken CD69 and CD94/NKG2-like with multiple evidences generated by computational (in-silico) sequence analysis. Both genes located in a region on chicken chromosome 1 that is syntenic to mammalian Nature Killer Receptor Complex (NKC) region, which may have existed before the divergence between mammals and aves. While siRNA lays the foundation of using loss-of-function approach on testifying gene-gene interactions, in-silico analysis aids in gathering information of unknown genes of great interest. Both approaches provide great potential to use for down-stream analysis following microarray study.

Engineered resistance mediated by RNA interference to control viral diseases in plants has shown great promise. However, the discovery that most known plant viruses encode RNAi suppressors which interfere with RNAi raised the issue to whether this type of engineered resistance can be durable in the presence of heterologous viruses in mixed infection. The overall goal of this study was to investigate the mechanism of suppression of RNAi-mediated resistance in transgenic plants in the presence of a virus carrying a strong suppressor of RNAi. Nicotiana benthamiana plants were transformed with a 1.2 kb from the 5' end of RCNMV RNA-1. Transgenic resistant lines were obtained. Resistance in two different transgenic lines was shown to be mediated by two different types of RNAi: constitutive RNAi in D2 line induced by doubles-stranded (ds) transgene transcripts and virus-induced RNAi in B1 line. We demonstrated that PVY differentially affected RNAi-mediated resistance in the two lines. D2 line is completely immune to RCNMV infection. D2 line contained multiple copies of the 1.2 kb transgene which are rearranged and produced dsRNAs. PVY did not break the resistance in this transgenic line however data showed that PVY interfered with RNAi which correlated to an increase of the 1.2 kb transgene mRNA. In addition, PVY infection induced accumulation of 21 nt siRNAs and did not alter the transcription of the transgene. In contrast, PVY infection suppressed resistance mediated by virus-induced RNAi in B1 line. B1 contains a single copy of the1.2 kb transgene and is initially susceptible to RCNMV infection however became resistant to RCNMV in newly merging leaves after 14 days post inoculation. PVY infection did not affect the accumulation of the 1.2 kb transgene mRNA nor the accumulation of 21 nt siRNA corresponding to the transgene. The differential effect of PVY infection on the two RNAi-mediated resistances in the two transgenic lines suggests that properly designed resistant plants might withstand mixed virus infections and the presence of a strong suppressor of RNAi. In addition, the differential effect of PVY on RNAi suggests that parallel but distinct pathways are involved in dsRNA-induced, virus-induced, and sense RNAi.

Influenza virus is a globally significant infectious agent with the potential to cause catastrophic pandemic outbreaks. Present treatment of influenza infections is restricted to only four anti-viral drugs, but there are increasing global reports of anti-viral resistance in several seasonal strains and also the 2009 pandemic swine-origin influenza virus H1N1. Possible future pandemic outbreaks, emerging new strains and drug resistance underscore the need to understand this complex virus and its pathogenicity with the goal that novel targets can be uncovered for future therapeutic development. Extensive lung tissue damage during influenza virus infection is proposed to contribute to the development of aberrant host immune responses. Strong evidence now demonstrates the significance of the cellular death pathway in promoting efficient influenza virus replication and disease progression. Viruses rely heavily on the machinery of their host for productive replication, which is also an Achilles’ heel that could be targeted for treatment. In pursuit of unraveling the complex nature of influenza virus replication, I carried out a global shRNA screen to identify specific host factors and signaling pathways that are involved in influenza-induced cell death and replication. In this study I identified 138 genes required for influenza viruses to induce infected host cell death. These genes were found to be involved in Protein Kinase A, NF-kB and PI3K signaling cascades. These signaling pathways are well known regulators of cell death and survival, which suggests influenza viruses may carefully regulate these pathways to reach a balance that suit their requirements for efficient proliferation, eventually at the cost of the host cell. I chose five candidate genes—BAD, MxB, TNFSF12-13,TNFSF13, and USP47—that were associated with apoptosis and the major signaling pathways determined in my network analysis to further verify the genome-wide screen as well as elucidate the role of these potentially novel host factors in influenza virus replication. I show in my study that influenza virus-induced cytopathology and cell death are considerably inhibited in BAD knockdown cells and both virus replication and viral protein production also are dramatically reduced. I also report here that MxB depletion protected cells from virus-mediated cytopathology and resulted in significant inhibition of influenza virus replication for H1N1 and H3N2 subtypes. Additionally, I report that TNFSF12-13, TFNSF13, and USP47, similarly, are required for efficient influenza virus replication and induction of cell death. Depletion of these proteins resulted in significant inhibition of viral propagation and conferred protection of host cells to virus killing. Overall, my study has provided a list of novel host factors that play significant roles during influenza virus infection. Further studies on these potential genes and their encoded protein products may uncover possible new targets for drug development for future therapeutic treatment. In addition to providing greater understanding of influenza virus infection, these studies will also highlight important fundamentals of cellular processes that may be broadly applicable to other fields of research.

Influenza virus is a globally significant infectious agent with the potential to cause catastrophic pandemic outbreaks. Present treatment of influenza infections is restricted to only four anti-viral drugs, but there are increasing global reports of anti-viral resistance in several seasonal strains and also the 2009 pandemic swine-origin influenza virus H1N1. Possible future pandemic outbreaks, emerging new strains and drug resistance underscore the need to understand this complex virus and its pathogenicity with the goal that novel targets can be uncovered for future therapeutic development. Extensive lung tissue damage during influenza virus infection is proposed to contribute to the development of aberrant host immune responses. Strong evidence now demonstrates the significance of the cellular death pathway in promoting efficient influenza virus replication and disease progression. Viruses rely heavily on the machinery of their host for productive replication, which is also an Achilles’ heel that could be targeted for treatment. In pursuit of unraveling the complex nature of influenza virus replication, I carried out a global shRNA screen to identify specific host factors and signaling pathways that are involved in influenza-induced cell death and replication. In this study I identified 138 genes required for influenza viruses to induce infected host cell death. These genes were found to be involved in Protein Kinase A, NF-kB and PI3K signaling cascades. These signaling pathways are well known regulators of cell death and survival, which suggests influenza viruses may carefully regulate these pathways to reach a balance that suit their requirements for efficient proliferation, eventually at the cost of the host cell. I chose five candidate genes—BAD, MxB, TNFSF12-13,TNFSF13, and USP47—that were associated with apoptosis and the major signaling pathways determined in my network analysis to further verify the genome-wide screen as well as elucidate the role of these potentially novel host factors in influenza virus replication. I show in my study that influenza virus-induced cytopathology and cell death are considerably inhibited in BAD knockdown cells and both virus replication and viral protein production also are dramatically reduced. I also report here that MxB depletion protected cells from virus-mediated cytopathology and resulted in significant inhibition of influenza virus replication for H1N1 and H3N2 subtypes. Additionally, I report that TNFSF12-13, TFNSF13, and USP47, similarly, are required for efficient influenza virus replication and induction of cell death. Depletion of these proteins resulted in significant inhibition of viral propagation and conferred protection of host cells to virus killing. Overall, my study has provided a list of novel host factors that play significant roles during influenza virus infection. Further studies on these potential genes and their encoded protein products may uncover possible new targets for drug development for future therapeutic treatment. In addition to providing greater understanding of influenza virus infection, these studies will also highlight important fundamentals of cellular processes that may be broadly applicable to other fields of research.

The ancient South American birds called tinamous (Tinamidae) have the smallest hearts known among birds and their cardiomyocytes have previously been shown to express significantly lower levels of the mitogen-activated protein kinase ERK compared to the more modern chicken (Gallus gallus). ERK is a well-known mediator of growth signalling in the heart, especially in hypertrophy. The aim of this project was to assess the effect of ERK knockdown on proliferation in cultured chicken cardiomyocytes. By transfecting these cells with a lipoplexed siRNA, ERK mRNA levels were knocked down to approximately half (45%, SD: 27%) compared to cells transfected with a negative control siRNA. The knockdown was coupled with a decreased proliferative response to insulin-like growth factor 1 (IGF-1) and foetal bovine serum (FBS). In conclusion, the ERK pathway was confirmed to be instrumental also in proliferative signalling. The results also support the notion that ERK itself is the rate-limiting step of this MAPK cascade. The low native expression of ERK in tinamou cardiomyocytes is expected to impose a strict limit on proliferative growth in response to various stimuli in these hearts. The genetic changes leading to higher expression levels, and with it the potential for larger hearts, in modern birds would have led to greatly increased evolutionary fitness by way of an increased aerobic scope and the ability to sustain flight.

Vesicular stomatitis virus (VSV) is considered a prototype for studying non-segmented negative-stranded ribonucleic acid (RNA) viruses. Livestock are naturally infected by VSV, causing severe economic impact due to lack of any effective treatment. RNA interference (RNAi)-based therapeutics are promising alternatives to control viral infections. Lentiviral vector systems deliver artificial short hairpin RNA (shRNA) into the genome of cells to activate the RNAi pathway. In this study, an RNAi-based approach to generate cell lines with reduced susceptibility to VSV (Indiana) infection was tested. First, eight shRNAs targeting either the nucleocapsid (N), phosphoprotein (P), or the polymerase (L) viral genes were designed and introduced into cell systems. To test the potency of the shRNAs for silencing the target viral transcripts, semi-quantitative polymerase chain reaction (PCR) analysis of viral N, P, and L transcripts was performed. Then, supernatants from infected groups were evaluated by microtitration and immunoblot. Finally, the effect of VSV genomic variability in the target region of shRNAs was predicted by partial sequencing field and laboratory-adapted strains. Viral transcripts were significantly reduced in cells stably expressing shRNAs targeting the N viral gene (nucleotides 67-97 or 1312-1332; p<0.05) or P gene (nucleotides 1772-1792; p&lt;0.05). Reduction in viral transcripts was not observed by other VSV-shRNAs tested. Reduction of viral transcripts by the N-shRNA (sh-1312) was accompanied by a decrease in viral protein. Also, a reduction in the viral particles shed from cells expressing N-shRNAs (nucleotides 67-97, p&lt;0.05) was noted. The results also showed complementarity of target gene sequences for shRNAs in the sequence from the laboratory-adapted strain and single base substitutions in the corresponding regions from VSV field isolates. However, these mismatches did not occur within the seed region of the shRNAs. In conclusion, partial silencing of viral transcripts by a single shRNA does not block VSIV replication; however, partial impairment of VSIV replication was observed in N-shRNAs expressing cells. During infection, the naturally high level of N gene transcription may have modulated the sh-RNA effect. The combination of the most potent shRNAs identified here into a multiple shRNA vector may result in further reduction of viral replication. These data contribute to ongoing development of effective RNAi-based technologies to combat viral diseases.

The ability of small interfering RNA (siRNA) to silence specific target genes offers not only a tool to study gene function but also represents a novel approach for the treatment of various human diseases, including cancers. The clinical use of siRNA, however, has been severely hampered by the inefficient delivery of these molecules to target cell populations due to their instability, inefficient cell entry, and poor pharmacokinetic profile. Much effort has therefore been devoted to the development of efficient in vivo siRNA delivery systems, with liposomes being the most widely employed vector. The traditional methods of packaging siRNA into liposomes, however, are often quite complex and labour-intensive, with the resulting products also being unstable at room temperature which limits their wide spread application in the clinic. The main aim of this research was to develop a simple, yet efficient, formulation technique to prepare stable siRNA-loaded liposomes which could be utilized as an efficient therapy for cancer treatment. Throughout this study, cervical cancer was used as the model system to assess the efficiency of various delivery systems. It is an ideal disease for siRNA therapy due to the cancer’s reliance on the expression of a single messenger RNA sequence which encodes two essential viral oncogenes, E6 and E7. Previous research has shown that targeting E6 and E7 by siRNA in cervical cancer cells in vitro results in either cell senescence or apoptosis. This thesis investigates the feasibility of applying E6/7 siRNA both intravaginally and intravenously to model the treatment of early-stage and end-stage cervical cancer, respectively. The practicability of applying E6/7 siRNA intravaginally for the treatment of localised cervical cancer tumours was firstly evaluated by administrating liposome-complexed siRNAs directly into the vaginal cavity of transgenic E7 mice. As no knockdown of E7 in cervical epithelium was observed for mice which received repeated treatments of E6/7 siRNA, the vaginal delivery efficiency of liposomes was further examined using fluorescently-labelled oligonucleotides. Contrary to previous reports, no delivery of lipoplexes into cervicovaginal tissues was detected irrespective of the dosage, type of lipid vector used, or the mouse estrus state at the time of administration. This lack of delivery was likely due to the poor retention of lipoplexes in the vaginal cavity as well as the inefficient penetration of lipoplexes across the mucosal layer lining the cervicovaginal epithelium. Overall, these findings indicated the necessity of developing more suitable and clinically acceptable vaginal siRNA delivery systems to enable this treatment strategy to become a reality. Despite the challenges of using liposomes to deliver siRNA via vaginal administration, their successful use in delivering siRNA intravenously to tumours was demonstrated in a subcutaneous cervical cancer mouse model. These experiments were carried out using PEGylated siRNA-loaded liposomes which were formulated using a novel Hydration-of-Freeze-Dried-Matrix (HFDM) technique. Compared to the existing formulation strategies, this method of preparation is less labour-intensive and the end product is also freeze-dried, ensuring product stability. It was found that the liposomes prepared using the HFDM method were stable in the presence of serum and they also possessed high siRNA entrapment and gene-silencing efficiencies. Following intravenous administration to mice, these particles were also found to accumulate in subcutaneous tumours to a similar degree compared to formulations prepared using a previously established technique. Importantly, these HFDM-formulated preparations showed superior stability over ones prepared using the traditional formulation method, with the particles still retaining 100% of their gene-silencing ability after storage for one month at room temperature. Using HFDM-formulated liposomes loaded with siRNA against Green Fluorescence Protein (GFP), a 50% knockdown of the GFP expression was achieved in tumours following intravenous administration. Additionally, the use of E6/7-targeted siRNA also resulted in a 50% reduction in tumour size when the siRNAs were delivered using HFDM-formulated liposomes. Importantly, this level of tumour growth suppression was comparable to that achieved from cisplatin, a clinically used chemotherapeutic for cervical cancer, at the clinically used dose. Overall, this research demonstrated that while there are still some challenges to overcome for siRNA to be used vaginally for cervical cancer treatment, HFDM-formulated PEGylated liposomes showed promise in bringing E6/7 siRNA forward as a treatment option for end-stage cervical cancer. In addition, the simplicity of preparation procedure along with superior product stability obtained from the HFDM method developed in this thesis will likely facilitate the translation of siRNA technology from laboratory to clinics for a range of other medical applications.