Psoroptic mange, caused by the Astigmatid mite Psoroptes ovis, is an ectoparasitic disease of significant economic importance to agriculture on a global scale and poses a serious welfare concern. With the current chemotherapeutic controls considered unsustainable, there is pressing need for novel control strategies. RNA interference has been proposed as a potential high throughput approach for the identification of novel therapeutic targets with high specificity, speed and at a relatively low cost compared to the existing methods. The presence of the components of the RNA interference (RNAi) pathway in P. ovis was first confirmed through in silico analyses of the P. ovis transcriptome and, following development of a non-invasive immersion method of double stranded RNA (dsRNA) delivery, gene silencing by RNAi was demonstrated in P. ovis. Statistically-significant reduction of transcript level was measured for the three genes targeted: P. ovis mite group 2 allergen (Pso o 2), P. ovis mu class glutathione S-transferase (PoGST-mu1) and P. ovis beta tubulin (Poβtub). This is the first demonstration of gene silencing by RNAi in P. ovis and provides a key mechanism for mining transcriptomic and genomic datasets in the future for novel targets of intervention against P. ovis. The first assessment of gene silencing was also performed in two related Astigmatid mites of high medical importance; the European house dust mite Dermatophagoides pteronyssinus and the scabies mite Sarcoptes scabiei. A statistically-significant reduction in expression of a D. pteronyssinus mu class glutathione S-transferase (DpGST-mu1) transcript was observed. No significant reduction in expression of a S. scabiei mu class glutathione S-transferase (SsGST-mu1) transcript was observed. Additionally, microRNAs (miRNAs) from the related miRNA pathway were identified in a P. ovis small RNA sample and were sequenced and annotated.

A soja (Glycine max) é uma das culturas mais importantes do mundo, os seus grãos servem tanto para a alimentação quanto para a extração de óleo para a fabricação do biodiesel. O vírus do mosaico do pepino (CMV, do inglês, “Cucumber mosaic virus”) é um vírus de RNA, patogênico a diversas plantas. O RNA de interferência é um sistema de silenciamento de RNA presente na maioria dos eucariotos no qual precursores de RNA de dupla fita (dsRNA) são processados em pequenos RNAs (sRNAs) de 21-24 nucleotídeos (nt), que podem regular a atividade de genes, elementos genéticos e vírus de uma maneira sequência específica. A integração de vírus de DNA e de retrovírus no genoma do hospedeiro já é bem conhecida tanto para sistemas eucarióticos quanto para procarióticos. Mais recentemente, foi observada a integração de vírus de RNA não retrovirais (NIRVs) em mamíferos. O presente trabalho é o primeiro a demonstrar tal evento no genoma de plantas. A partir das sequências dos sRNAs de 19-24 nt de 15 bibliotecas de sRNAs sequenciados de amostras de tecidos de soja, foram montadas sequências contíguas (“contigs”) pelo programa SOAP, algumas das quais apresentaram homologia de sequência ao RNA 1 do CMV. Por montagem de novo desses contigs foi obtida uma sequência de 3.092 nt do RNA 1 do CMV, presente em todas as bibliotecas pesquisadas de pelo menos cinco cultivares diferentes de soja. A presença dessa sequência foi confirmada em outras sete cultivares, exceto em "Willians". Foi observada uma maior presença de sRNAs derivados do CMV senso do que anti-senso nas 15 bibliotecas sequenciadas. Os sRNAs de 22-nt foram os mais abundantes. Para o vírus da mancha da vagem do feijoeiro (BPMV, do inglês “Bean pod mottle virus”) presente em uma das bibliotecas, os sRNAs de 21-nt e 22-nt representaram em torno de 80% do total de sRNAs. Foram encontrados sRNAs que variaram sob estresse biótico (Phakospora pachyrhizi) e abiótico (seca) e entre diferentes cultivares. A expressão do RNA 1 aumentou nas plantas sob estresse. Provavelmente o evento de integração ocorreu via recombinação à um retrotransposon. / The Soybean (Glycine max) is one of the world's most important crops, its seeds are used both as food and for the extraction of oil to manufacture biodiesel. The Cucumber mosaic virus (CMV) is a pathogenic RNA virus of plants. The RNA interference is a system of RNA silencing present in most eukaryotes in which precursors of double-stranded RNA (dsRNA) are processed into small RNAs (sRNAs) of 21-24 nucleotides (nt), which can regulate the activity of genes, genetic elements and virus in a sequence-specific manner. The integration of DNA virus and retrovirus into the host genome is well known both for prokaryotic and eukaryotic systems. The integration of non-retroviral RNA virus (NIRVs) in mammals was previously observed, but the present work is the first to demonstrate such an event in a plant genome. The sequences of the sRNAs ranging from 19 to 24 nt, in 15 libraries of sRNAs sequenced from samples of soybean tissues, were assembled in contigs by the program SOAP, with some preentering sequence homology to the RNA 1 of CMV. By de novo assembling of these contigs it was obtained a sequence of 3,092 nt of the CMV RNA 1, present in all libraries surveyed in at least five different varieties of soybeans. The presence of this sequence was confirmed by PCR in seven other cultivars, but in "Williams". We observed a greater presence of sRNAs derived from CMV of sense orientation than antisense in the 15 libraries sequenced. The 22-nt sRNAs were the most abundant. For the Bean pod mottle virus (BPMV), present in one of the libraries, the 21 and 22 nt sRNAs were represented by around 80% of all sRNAs. The sRNAs were found varying under biotic stress (Phakospora pachyrhizi) and abiotic (drought) and among different cultivars. RNA 1 expression increased in plants under stress. Probably the integration event occurred via recombination of a retrotransposon.

G-quadruplexes are non-canonical nucleic acid secondary structures of increasing biological and medicinal interest due to their proposed physiological functions in transcription, replication, translation and telomere biology. Aberrant G4 formation and stabilisation have been linked to genome instability, cancer and other diseases. However, the specific genes and pathways involved are largely unknown, and the work within this thesis aims to investigate this. Stabilisation of G4s by small molecules can perturb G4-mediated processes and initial studies suggest that this approach has chemotherapeutic potential. I therefore also aimed to identify cell genotypes sensitive to G4-ligand treatment that may offer further therapeutic opportunities. To address these aims, I present the first unbiased genome-wide genetic screen in cells where genes were silenced via short-hairpin RNAs (shRNAs) whilst being treated with either PDS or PhenDC3, two independent G4-stabilising small molecules. I explored gene deficiencies that enhance cell death (sensitisation) or provide a growth advantage (resistance) in the presence of these G4-ligands. Additionally, I present a validation screen, comprising hits uncovered via genome-wide screening, and also the use of this in another cell line of different origin. Sensitivities were enriched in DNA replication, cell cycle, DNA damage repair, splicing and ubiquitin-mediated proteolysis proteins and pathways. Ultimately, I uncovered four synthetic lethalities BRCA1, TOP1, DDX42, GAR1, independent of cell line and ligand. These were validated with three G4-stabilising ligands (PDS, PhenDC3 and CX-5461) using an independent siRNA approach. The latter siRNA methodology was used to screen 12 PDS derivatives with improved medicinal chemistry properties and ultimately identified SA-100-128, as a lead compound. The mechanism behind synthetic lethality with G4-stabilising ligands was explored further for DDX42, which I show has in vitro affinity for both RNA- and DNA-G4s and may represent a previously unknown G4-helicase. Also within this thesis, gene deficiencies that provided a growth advantage to PDS and/or PhenDC3 as uncovered by genome-wide and focused screening were explored. These showed enrichment in transcription, chromatin and lysosome-associated genes. The resistance phenotype of three gene deficiencies, TAF1, DDX39A and ZNF217 was further supported by additional siRNA experiments. Overall, I satisfied the primary aims and established many novel synthetic lethal and resistance interactions that may represent new therapeutic possibilities. Additionally, the results expand our knowledge of G4-biology by identifying genes, functions and subcellular locations previously not known to involve or regulate G4s.

One of the challenges in the 21st Century is to overcome the recalcitrance of lignocellulose for the production of liquid biofuels. Lignin is one of the key factors in this recalcitrance. Grasses such as Miscanthus and switchgrass could become major sources of lignocellulose. Barley has potential as a genetically-tractable research model for such novel bioenergy crops and also as a bioenergy crop itself. This thesis concerns the 4CL and the CCR enzymes on the lignin pathway which were chosen as the targets to manipulate lignin in barley. They were selected because there is evidence that suppression of each of them in dicot species can lead to increased saccharification. The 4CL and CCR genes constitute multigene families where members have different expression patterns. RNAi was used to down-regulate 4CL1 and CCR1 using a constitutive promoter via Agrobacterium-mediated transformation of barley. From an extensive screen of the primary transformants for changes in protein level and lignin content, six CCR and four 4CL lines were taken forward for detailed analysis. Antibodies were also raised against barley 4CL and CCR recombinant proteins and these showed substantial reductions in the respective target protein levels in the RNAi lines. Both 4CL and CCR transgenic lines had significant reductions in lignin content, and CCR lines had changes in lignin structure due to changes in the proportions of acid soluble and acid insoluble lignin. No substantial consistent adverse effects on key agronomic traits were apparent in the 4CL and CCR transgenics. Selected 4CL and CCR transgenics had improved saccharification yield after using three different pretreatment methods, which is a desirable feature for biofuel production.

Sequence-specific small interfering RNA (siRNA) duplexes can be used for gene silencing in mammalian cells and as mechanistic probes for determining gene function. Transfection of siRNA for specificity protein 1 (Sp1) in MCF-7 or ZR-75 cells decreased Sp1 protein in nuclear extracts, and immunohistochemical analysis showed that Sp1 protein in transfected MCF-7 cells was barely detectable. Decreased Sp1 protein in MCF-7 was accompanied by a decrease in basal and estrogen-induced transactivation and cell cycle progression. These results clearly demonstrate the key role of Sp1 protein in regulating growth and gene expression of breast cancer cells. The aryl hydrocarbon (AhR) is a ligand-activated nuclear transcription factor. siRNA for the AhR decreased TCDD-induced CYP1A1 protein, CYP1A1dependent activity, and luciferase activity in cells transfected with an Ah-responsive construct. 17β-Estradiol (E2) induces proliferation of MCF-7 cells, and this response is inhibited in cells cotreated with E2 plus TCDD. The effects of TCDD on E2-induced cell cycle progression were partially blocked in MCF-7 cells transfected with siRNA for AhR. The decrease in AhR protein in MCF-7 cells was also accompanied by increased G0/G1 → S phase progression. Surprisingly, TCDD alone induced G0/G1 → S phase progression and exhibited estrogenic activity in MCF-7 cells transfected with siRNA for the AhR. In contrast, degradation of the AhR in HepG2 liver cancer cells resulted in decreased G0/G1 → S phase progression, and this was accompanied by decreased expression of cyclin D1, cyclin E, cdk2 and cdk4. In the absence of ligand, the AhR exhibits growth inhibitory (MCF-7) and growth promoting (HepG2) activity that is cell context-dependent. Sp family proteins play a complex role in regulation of pancreatic cancer cells growth and expression of genes required for growth, angiogenesis and apoptosis. Sp1, Sp3 and Sp4 cooperatively activate VEGF promoter constructs in these cells; however, only Sp3 regulates cell proliferation. siRNA for Sp3 inhibits phosphorylation of retinoblastoma protein, blocks G0/G1 → S phase progression of Panc-1 cells, and upregulates p27 protein/promoter activity. Thus, Sp3 plays a critical role in angiogenesis (VEGF upregulation) and the proliferation of Panc-1 cells by a novel mechanism of Sp3-dependent suppression of the cyclin-dependent kinase inhibitor p27.

The non-receptor tyrosine kinase Src has been found to be overexpressed and activated in many human cancers, where it has been implicated in changes in cellular proliferation, adhesion, migration, apoptosis, angiogenesis, and tumour growth. In addition, several other members of the Src family have also been implicated in various cancer phenotypes. Our examination of a wide panel of colon, breast, and lung cancer cell lines revealed that not only Src, but also Yes, Fyn, Lyn, and Lck, were expressed at both the mRNA and protein levels in different combinations, and at varying levels, between cell lines. When examined for kinase activity, it was discovered that only a subset of the expressed Src family members had detectable kinase activity within a given cell line. To investigate the involvement of the Src family members in the proliferation, adhesion, migration, and colony forming ability of four selected cancer cell lines, both Src family kinase inhibitors, which inhibit the kinase activity of multiple Src family members, and RNA interference, which selectively decreases the expression of individual proteins, were used. It was found that the involvement of these proteins in all of the cellular processes investigated was cell line-specific, with the greatest effects observed in HT29 cells, which have relatively high Src protein levels and kinase activity. Furthermore, the consequences of Src family member inhibition were also inhibitor specific, as treatment with PP2 and SKI I generally had greater effects on the cellular processes examined than did treatment with SU6656 or SKI II. It was also found that the inhibition of multiple Src family kinases by at least one of the inhibitors generally resulted in greater effects on the cancer cell phenotypes investigated than were observed when the expression of Src, Fyn, or Yes was decreased using RNA interference. This suggests that multiple Src family members may need to be targeted in order to inhibit the increased proliferation, cell-matrix adhesion, migration, and colony forming ability exhibited by cancer cells. The identification of the cancer cell phenotypes in which particular Src family members are involved is of interest, as these proteins are attractive targets for cancer therapy.

The differentiation of plant vascular tissue is regulated by plant hormones and transcription factors. One of the key plant hormones involved in this process is auxin. Auxin signals are mediated by auxin response factor transcription factors (ARFs). These transcription factors are involved in the perception of auxin signals and the subsequent activation or deactivation of suites of downstream genes. Based on its mutant phenotype, one of the most interesting members of this family is the ARF MONOPTEROS (MP). This thesis investigates the role played by MP in secondary vascular differentiation, as well as taking a look at other molecular aspects of secondary vascular differentiation, with a focus on the model plants Arabidopsis thaliana and poplar (Populus trichocarpa and hybrid poplar). A dexamethasone inducible RNAi silencing strategy was developed, and transgenic Arabidopsis lines produced. When silencing was induced in these lines from germination, a phenotype closely resembling the mp mutant was observed. When MP silencing was induced in bolting stems, early senescence, as well as a dramatic reduction in interfascicular fibre production was observed, and these stems were thinner and less rigid than empty vector controls. RNA from these stems was isolated and used in a global transcript profiling microarray experiment. This experiment showed that several auxin-related genes, as well as several transcription factors, were differentially regulated in response to MP silencing. Because Arabidopsis is not a typical woody plant, further investigation into the role played by MP in wood formation was done using the model tree poplar. A BLAST search of a poplar xylem EST database identified a single promising partial sequence. Based on this sequence information, a poplar MP homolog was isolated and named PopMP1. The full-length sequence of this gene demonstrated remarkable structural conservation when compared with that of Arabidopsis. Subsequent complete sequencing of the poplar genome revealed a second copy of the MP gene in poplar and named PopMP2. Expression profiling across a range of tissues suggests that subfunctionalization has occurred between the two copies. Overexpression transgenic lines for PoptrMP1 were developed. AtHB8 is known to be regulated by MP in Arabidopsis, and a poplar HB8 homolog was upregulated in the transgenic lines. However, no obvious physical phenotype in these lines was apparent. To investigate the transcriptome-wide changes associated with initiation of cambium formation in poplar stems, a global transcript profiling experiment was performed. Out of 15400 genes tested, 2320 met an arbitrary cutoff of >1.3 fold and p-value <0.05 and were labeled differentially expressed (DE). These included several transcription factors and showed remarkable similarity to analogous data from Arabidopsis. The conclusions drawn from this thesis support the hypothesis that MP plays roles in later development, and do not rule out the possibility that MP is directly involved in wood development. The data reported also offer a large number of candidate for further investigation into the genetic control of wood development.

The differentiation of plant vascular tissue is regulated by plant hormones and transcription factors. One of the key plant hormones involved in this process is auxin. Auxin signals are mediated by auxin response factor transcription factors (ARFs). These transcription factors are involved in the perception of auxin signals and the subsequent activation or deactivation of suites of downstream genes. Based on its mutant phenotype, one of the most interesting members of this family is the ARF MONOPTEROS (MP). This thesis investigates the role played by MP in secondary vascular differentiation, as well as taking a look at other molecular aspects of secondary vascular differentiation, with a focus on the model plants Arabidopsis thaliana and poplar (Populus trichocarpa and hybrid poplar). A dexamethasone inducible RNAi silencing strategy was developed, and transgenic Arabidopsis lines produced. When silencing was induced in these lines from germination, a phenotype closely resembling the mp mutant was observed. When MP silencing was induced in bolting stems, early senescence, as well as a dramatic reduction in interfascicular fibre production was observed, and these stems were thinner and less rigid than empty vector controls. RNA from these stems was isolated and used in a global transcript profiling microarray experiment. This experiment showed that several auxin-related genes, as well as several transcription factors, were differentially regulated in response to MP silencing. Because Arabidopsis is not a typical woody plant, further investigation into the role played by MP in wood formation was done using the model tree poplar. A BLAST search of a poplar xylem EST database identified a single promising partial sequence. Based on this sequence information, a poplar MP homolog was isolated and named PopMP1. The full-length sequence of this gene demonstrated remarkable structural conservation when compared with that of Arabidopsis. Subsequent complete sequencing of the poplar genome revealed a second copy of the MP gene in poplar and named PopMP2. Expression profiling across a range of tissues suggests that subfunctionalization has occurred between the two copies. Overexpression transgenic lines for PoptrMP1 were developed. AtHB8 is known to be regulated by MP in Arabidopsis, and a poplar HB8 homolog was upregulated in the transgenic lines. However, no obvious physical phenotype in these lines was apparent. To investigate the transcriptome-wide changes associated with initiation of cambium formation in poplar stems, a global transcript profiling experiment was performed. Out of 15400 genes tested, 2320 met an arbitrary cutoff of >1.3 fold and p-value <0.05 and were labeled differentially expressed (DE). These included several transcription factors and showed remarkable similarity to analogous data from Arabidopsis. The conclusions drawn from this thesis support the hypothesis that MP plays roles in later development, and do not rule out the possibility that MP is directly involved in wood development. The data reported also offer a large number of candidate for further investigation into the genetic control of wood development.

The non-receptor tyrosine kinase Src has been found to be overexpressed and activated in many human cancers, where it has been implicated in changes in cellular proliferation, adhesion, migration, apoptosis, angiogenesis, and tumour growth. In addition, several other members of the Src family have also been implicated in various cancer phenotypes. Our examination of a wide panel of colon, breast, and lung cancer cell lines revealed that not only Src, but also Yes, Fyn, Lyn, and Lck, were expressed at both the mRNA and protein levels in different combinations, and at varying levels, between cell lines. When examined for kinase activity, it was discovered that only a subset of the expressed Src family members had detectable kinase activity within a given cell line. To investigate the involvement of the Src family members in the proliferation, adhesion, migration, and colony forming ability of four selected cancer cell lines, both Src family kinase inhibitors, which inhibit the kinase activity of multiple Src family members, and RNA interference, which selectively decreases the expression of individual proteins, were used. It was found that the involvement of these proteins in all of the cellular processes investigated was cell line-specific, with the greatest effects observed in HT29 cells, which have relatively high Src protein levels and kinase activity. Furthermore, the consequences of Src family member inhibition were also inhibitor specific, as treatment with PP2 and SKI I generally had greater effects on the cellular processes examined than did treatment with SU6656 or SKI II. It was also found that the inhibition of multiple Src family kinases by at least one of the inhibitors generally resulted in greater effects on the cancer cell phenotypes investigated than were observed when the expression of Src, Fyn, or Yes was decreased using RNA interference. This suggests that multiple Src family members may need to be targeted in order to inhibit the increased proliferation, cell-matrix adhesion, migration, and colony forming ability exhibited by cancer cells. The identification of the cancer cell phenotypes in which particular Src family members are involved is of interest, as these proteins are attractive targets for cancer therapy.

Tomato bushy stunt virus (TBSV) provides a good model system to investigate molecular virus-host interactions in plants. P22 and P19 proteins encoded by TBSV contribute to multiple invasion-associated functions. Green fluorescence-mediated visualization of TBSV invasion in this study suggests that virus exit from inoculated epidermal cells is a crucial event. Close examination of one P22 mutant showed that it had lost the capacity to move between epidermis and mesophyll which was possibly due to an altered subcellular localization. P19 is a potent suppressor of RNA interference (RNAi) in various systems by forming dimers that bind 21-nucleotide (nt) duplex siRNAs (short interfering RNAs), to affect the programming of the RNA-induced silencing complex (RISC). P19 is attractive for biotechnological and research purposes to prevent RNAi of certain value-added genes in plants. To obtain a good plant-based expression platform, a suppression-active mutant P19 was expressed in transgenic N. benthamiana lines. This is the first example of P19 accumulating to detectable levels in a transgenic plant and initial results suggest it is actively suppressing RNAi. Furthermore, to investigate the correlation between siRNA binding of P19 and its various biological roles, predicted siRNA-interacting sites of TBSV P19 were modified, and the corresponding TBSV mutants were used to inoculate plants. Substitutions on siRNA-contact sites on the central domain of P19 resulted in more severe symptoms in N. benthamiana compared to those affecting peripheral regions. All tested combinations of siRNA-binding mutations were associated with reduced accumulation of total TBSV-derived siRNAs, and loss of siRNA sequestration by P19. Additionally, some modifications were found to cause RNAi-mediated disappearance of viral and host materials in N. benthamiana but not in spinach. In conclusion, exit out of epidermal cells is a key host range determinant for TBSV and particular amino acids on P22 may influence this by regulating the proper subcellular localization. Mutant P19 transgenic plants were successfully established with minor physiological effects to be applied as a platform to study RNAi and to over-express proteins. Finally, a compromised P19-siRNA binding impacts symptom development, systemic invasion, integrity of virus plus host RNA and proteins, and that all in a hostdependent manner.