The fascinating field of molecular capsules has recently begun to see the creation of structures that, medicated by the encapsulation of guest molecules within their central cavity, are able to change the properties or reactivity of the substrate. The current capsule designs are however, prone to exchange of either part or whole ligands. This exchange or the capsule's subsequent disassembly can lead to loss of the cavity or modification of their external properties, and is a barrier to their more widespread application, a problem this work seeks to address by creating more a robust capsule structure. This thesis presents the design, synthesis and properties displayed by three novel capsules. All the species presented share a similar supramolecular tetrahedral structure, but their properties deviate significantly, showing either switchable behaviour, spin-crossover or a novel synthetic route to a kinetically inert structure. Improvements in the design have led to a final capsule that is water-soluble, robust, non-toxic and has been shown to encapsulate a range of guests. Chapter 1 includes an overview of the types of capsule constructed in literature and their possible application. The fundamental properties of these capsules are identified, with emphasis given to a discussion of mechanisms underlying their encapsulation phenomena. Chapter 2 describes efforts to construct a tetrahedral capsule based on iron(II) and an oxime ligand. While the use of an oxime motif achieved the aim of preventing exchange of the external groups, the capsule also displayed the surprising property of possessing a solvent responsive assembly-disassembly process. This potentially provides a basis for 'on-demand' encapsulation by being able to choose when to have hydrophobic cavity available for guests. Chapter 3 details the synthesis of a tetrahedral capsule containing iron (II) coordinated by a pyridyl-triazole bonding motif. the spin-crossover properties of the complex were initially demonstrated in the solid state, however, when in solution the capsule displayed the unusual ability of spin-crossover mediated structural rearrangement. Chapter 4 demonstrates the synthesis of a robust capsule. The synthetic route shown alleviates the problems surrounding the construction of inert species in a self-assembly process. Based around a cobalt (III) cation, the stability of the capsule to carious conditions is examined and its host-guest chemistry is explored, revealing some insights into the encapsulation behaviour of this structure.

published_or_final_version / Botany / Master / Master of Philosophy

Replication of the nonsegmented, plus-stranded RNA genome of Cucumber necrosis tombusvirus (CNV) requires two essential overlapping viral-coded replication proteins, the p33 replication co-factor and the p92 RNA-dependent RNA polymerase. In my thesis I describe (i) the effect of phosphorylation of p33, (ii) the RNA chaperone-like activity of p33, and (iii) the role of HSP70s a host proteins in the viral replication. To test the effect of phosphorylation on p33 function, I used in vitro phosphorylated p33. I found that phosphorylation inhibited the ability of p33 to bind to the viral RNA. Phosphorylation-mimicking mutations rendered p33 nonfunctional in plant protoplasts and in yeast. Based on these results, I propose that the primary function of phosphorylation of p33 is to regulate its RNA binding capacity, which could affect the assembly of new viral replicase complexes, recruitment of the viral RNA template into replication and/or release of viral RNA from replication. Thus, phosphorylation of p33 might help in switching the role of the viral RNA from replication to other processes, such as viral RNA encapsidation and cell-to-cell movement. Small plus-stranded RNA viruses do not code for RNA helicases that would facilitate the proper folding of viral RNAs during replication. Instead, small RNA viruses might use RNA chaperones for replication as shown here for the p33 replication protein. In vitro experiments demonstrated that the purified recombinant p33 facilitated RNA synthesis on plusstranded and double-stranded (ds)RNA templates up to 5-fold. In addition, p33 rendered dsRNA templates sensitive to single-strand specific S1 nuclease, suggesting that p33 can destabilize highly structured RNA. Altogether, the RNA chaperone activity of p33 might perform similar biological functions to the helicases. SSa a yeast HSP70 found in the viral replication complex and shown to facilitate viral replication (Serva and Nagy, 2006)To dissect the mode of action of SSA in the viral replication I used temperature sensitive and deletion mutants. Both showed miss localization of p33 compared to the wild type. Purified SSA rendered non functional bacterial expressed p92 functional in an in vitro replication assay. SSa might play a role in the transportation and assembly of viral replication proteins.

This thesis concerns the construction, use and modulation of various host–guest systems, from small bispidines for binding of inorganic ions to bisporphyrin clips for supramolecular systems. Small flexible molecules undergo fast conformational movements when in solution. These conformational movements generate time-averaged population-weighted chemical shifts, coupling constants and NOEs when analysed by NMR spectroscopy. A bisporphyrin clip was designed to be used as a host for restriction of conformational movements of small flexible molecules by ditopic metal-ligand binding. Based on conformational analysis in combination with NMR analysis of molecular flexibility in solution (NAMFIS), the relative stereochemistry of flexible alditol-derived diamines containing three or four consecutive stereocentres could be determined. To further explore the idea of conformational deconvolution via host–guest binding, two flexible molecular tweezers with photoswitchable moieties were developed. Upon photoswitching cis/trans isomerisation facilitates the opening and closing of these bisporphyrin hosts. A guest molecule could then be exposed to a “catch and stretch” or “catch and release” effect. Preliminary studies have shown that photoisomerisation of the constructed systems is possible without photodecomposition and preliminary binding studies have been conducted. Controlled modulation of molecular conformations is of interest especially if the conformational steering activates a unit working as a nucleator in a larger structure or facilitates a reaction. The protonation-triggered modulation of bispidine conformations has been investigated. In addition to previously reported conformations we have observed that upon diprotonation a bispidine derivative can be driven into the unusual boat-boat conformation. Finally, the unexpected formation of persistent organic radicals with a cyclophane motif from the reaction of N,N´-diphenyl-1-5-diazacyclooctane and AgBF4 is described. Interestingly, these diradicals exhibit features such as intramolecular π-stacking without lateral displacement and also intramolecular spin pairing.

<p>Malaria, caused by the apicomplexan parasite Plasmodium, is a disease which affects up to 500 million people each year. Historically, malaria infection has been combated both through the control of its vector, the Anopheles mosquito, and use of a variety of drugs, such as quinine (1800s) and chloroquine (1900s). However, with the evolution of resistance to the majority of available anti-malarial drugs, current approaches have settled upon combinatorial therapies. The most effective of these currently are ACTs (Artemisinin Combination Therapies - Artemisinin derivatives combined with a number of other drugs). However reports of Artemisinin resistance are continuing to emerge, suggesting that new approaches and increased understanding of the Plasmodium parasite is required.</p><p> Beginning with the complete sequencing of Plasmodium falciparum genome and continuing with comprehensive profiling of both the parasite's proteome and transcriptome, various genomic approaches applied in the study of malaria have led to significant new insights into the underlying biology of this parasite. While these new findings have greatly increased our understanding of genetic regulation within the malaria parasite, they largely have not yet translated into new therapeutic approaches. For this reason, considerable attention has been paid to the study of human genetic disorders which convey resistance to malaria, in the hopes that elucidating the mechanisms behind these resistances might lead to increased understanding of the parasite's biology and thus novel therapeutic approaches.</p><p> Sickle cell (HbS) erythrocytes are well known to resist malaria infection. However, the molecular basis of this resistance, long been recognized as multifactorial, contains elements which remain poorly understood. Here we show that the dysregulated erythrocytic microRNA composition, present in both HbAS and HbSS erythrocytes, is a significant determinant of resistance against the malaria parasite Plasmodium falciparum. During the intraerythrocytic lifecycle of P. falciparum, a subset of erythrocyte microRNAs translocate into the parasite. Two microRNAs, miR-451 and let-7i, were highly enriched in HbAS and HbSS erythrocytes and these miRNAs, along with miR-223, negatively regulated parasite growth. Surprisingly, we found that miR-451 and let-7i integrated into essential parasite mRNAs and, via impaired ribosomal loading, resulted in translational inhibition of the target mRNA. Hence, sickle cell erythrocytes exhibit cell-intrinsic resistance to malaria in part through an atypical microRNA activity which may present a novel host defense strategy against complex eukaryotic pathogens. In addition, the formation of these chimeric transcripts even in normal host erythrocytes illustrates a unique parasitic post-transcriptional adaptation to the host-cell environment.</p> / Dissertation

Leafflower plant/leafflower moth brood pollination mutualisms are widespread in the Paleotropics. Leafflower moths pollinate leafflower plants, but their larvae consume a subset of the hosts' seeds. These interactions are highly phylogenetically constrained: six clades of leafflower plants are each associated with a unique clade of leafflower moths (Epicephala). Here, we report a previously unrecognized basal seventh pollinating Epicephala lineageassociated with the highly derived leafflower clade Glochidionin Asia. Epicephala lanceolaria is a pollinator and seed predator of Glochidion lanceolarium. Phylogenetic inference indicates that the ancestor of E. lanceolaria most likely shifted onto the ancestor of G. lanceolarium and displaced the ancestral allospecific Epicephala pollinator in at least some host populations. The unusual and apparently coadapted aspects of the G. lanceolarium/E. lanceolaria reproductive cycles suggest that plant-pollinator coevolution may have played a role in this displacement and provide insights into the dynamics of host shifts and trait coevolution in this specialized mutualism.

Aflatoxins, toxic secondary metabolites produced by some Aspergillus species, are a universal agricultural economic problem and a critical health issue. Despite decades of control efforts, aflatoxin contamination is responsible for a global loss of millions of tons of crops each year. We show that host-induced gene silencing is an effective method for eliminating this toxin in transgenic maize. We transformed maize plants with a kernel-specific RNA interference (RNAi) gene cassette targeting the aflC gene, which encodes an enzyme in the Aspergillus aflatoxin biosynthetic pathway. After pathogen infection, aflatoxin could not be detected in kernels from these RNAi transgenic maize plants, while toxin loads reached thousands of parts per billion in nontransgenic control kernels. A comparison of transcripts in developing aflatoxin-free transgenic kernels with those from nontransgenic kernels showed no significant differences between these two groups. These results demonstrate that small interfering RNA molecules can be used to silence aflatoxin biosynthesis in maize, providing an attractive and precise engineering strategy that could also be extended to other crops to improve food security.

Current therapies for chronic inflammatory diseases often abrogate the immune functions required to fight infections. Human cathelicidin host defence peptide (HDP) LL-37 selectively suppresses pathogen-induced inflammation, without compromising resistance to infections. These unique dual abilities of LL-37 make it a promising candidate as an alternative therapeutic for treating chronic inflammatory diseases. The objective of this study was to investigate the effects of LL-37 and its derivative peptide IG-19 in cytokine-mediated inflammation. I demonstrated that LL-37 and IG-19 selectively suppressed cytokine IL-32γ-induced pro-inflammatory cytokines, without compromising the production of anti-inflammatory cytokines, and chemokines in human PBMC and macrophages. However, significant quantitative differences between LL-37 and IG-19-mediated chemokine productions suggested that the mechanisms underlying the activity of these two peptides were different. I showed that both peptides suppressed IL-32γ-mediated phosphorylation of the Src-kinase FYN(Y420), known to enhance inflammation. Contrastingly, phosphorylation of the dual phosphatase MKP-1(S359), a negative regulator of inflammation, was enhanced in response to both peptides. Similarly, both peptides increased the activity of p44/42MAPK, which phosphorylates and stabilizes MKP-1. These results suggested that MKP-1 may be a critical mediator of the immunomodulatory activity of these peptides. Bioinformatic interrogation revealed that direct interacting protein partners of MKP-1 were overrepresented in MAPK and NF-κB signalling pathways. Both peptides enhanced the phosphorylation of p38MAPK. However, contrasting to LL-37, IG-19 did not mediate the phosphorylation of JNK MAPK and IKK-α signaling intermediates involved in inflammation. This was consistent with observations that chemokine production was significantly lower in response to IG-19 compared to LL-37. These results suggested that IG-19 may be a better immunomodulatory therapeutic candidate compared to LL-37. As cytokine-mediated inflammation plays critical roles in the disease pathogenesis of inflammatory arthritis, I examined the effects of exogenous administration of IG-19 in a murine model of collagen-induced arthritis. Administration of IG-19 decreased disease severity, suppressed pro-inflammatory cytokines and anti-collagen antibodies, and mitigated cartilage destruction in the CIA mice. These results provide a rationale to further develop IG-19 as a therapeutic agent for chronic inflammatory arthritis. The advantage of HDP based therapy is the potential to control inflammation without compromising the patient’s ability to resolve infections. / May 2017

No description available.

Drosophila melanogaster has been extensively used as a model organism to study diverse facets of biology, including host-pathogen interactions and the basic biology of its pathogens. I have used the fruit fly as a model to study elementary aspects of Nora virus biology, such as the role of the different proteins encoded by the virus genome. Nora virus, an enteric virus transmitted via the feca-oral route, does not cause any obvious pathology in the fly, although the infection is persistent. Nora virus genome consists of a positive strand RNA that is translated in four open reading frames (ORF).  Since sequence homology studies did not yield much information about the different Nora virus proteins, I have used the cDNA clone of the virus to construct mutants to identify the specific function of each protein. My results have shown that, 1) The protein(s) encoded by ORF 1 are crucial for the replication of the virus genome. 2) The C-terminus of the ORF 1-encoded protein (VP1), is an inhibitor to the RNAi pathway. 3) The transmembrane domain in the N-terminus of the ORF2-encoded protein (VP2) is important for the formation of Nora virus virions. 4) The ORF 3-encoded protein (VP3) forms α-helical trimers and this protein is essential for the stability of Nora virus capsid.                                                     I have also performed RNA sequencing to investigate the transcriptional response of D. melanogaster in response to Nora virus infection and my results indicate that,                        5) The upregulation of genes related to cellular stress and protein synthesis and the downregulation of basal digestive machinery, together with the induction of upd3, implies major gut epithelium damage and subsequent regeneration.