Transmissible spongiform encephalopathies (TSEs) are a group of fatal neurodegenerative diseases that are characterised by long incubation periods, protein aggregation and vacuolation. During TSE pathogenesis the normal, cellular prion protein, (PrPC), which is encoded by the gene PRNP, misfolds and accumulates as abnormal disease associated prion protein, (PrPSc) within the central nervous system. Variants of the Prion protein gene are associated with susceptibility to TSE disease. For example sheep scrapie disease is modulated by several PRNP alleles, with certain alleles carried by susceptible animals being different from those carried by resistant animals. The mechanisms linking PRNP genetics and disease is poorly understood but may involve protein sequence, PrPC expression levels, and possibly differences in protein processing. Post-translational modification of PrPC leads to specific cleavage (alpha cleavage) between amino acids 115/116 of ovine PrP, producing two fragments C1 and N1. Cleavage of PrP may occur as a protective mechanism, as a response to changes in the cellular environment or as a feature of an as yet unknown biological function. In the context of TSEs, alpha cleavage may inadvertently provide a protective role by reducing available PrPC protein for conversion into PrPSc, assuming that the C1 fragment would be an inefficient substrate for conversion, the opposite theory was also proposed. The former hypothesis became the focus of this present study, with the idea that total full-length PrPC, total C1 or the ratio between full-length PrPC and C1 may be linked to differences in scrapie susceptibility. To investigate these aims the C1 fragment was measured as a percentage of total PrPC in different PRNP genotypes with varying degrees of susceptibility to scrapie and in different brain regions. This study found that PrPC alpha cleavage increased during development from the new born lamb to the adult sheep, which may have consequences for the susceptibility differences related to age. There are also variations in the amount of alpha cleavage between brain regions such as cortex and medulla that may influence scrapie strain targeting. Overall the amount of the C1 fragment in the different brain areas varied as much as 10x (range 5% to 60%). There was a significant difference in the ratio of C1 to the other PrPC forms between two PRNP genotype groups carrying the VRQ and ARQ allele but there was no correlation between C1 level and scrapie susceptibility or scrapie incubation period in our scrapie models. Alpha cleavage of PrPC also occurs in various transgenic mouse models expressing different ruminant PrP sequences. In PrPC over-expressing transgenic mouse models a higher ratio of C1 was observed, this may suggest a link between PrPC expression levels and alpha cleavage. Transgenic mice are therefore important models to further investigate the link between PrPC biology and scrapie disease phenotype. In conclusion, this thesis has shown for the first time that certain ovine PRNP alleles can influence alpha cleavage of the PrPC protein; however it appears not to be a significant indicator of TSE disease susceptibility in sheep.

Current FDA approved anti-cytomegalovirus antivirals are ganciclovir, foscarnet, and cidofovir. These drugs target the viral polymerase to inhibit DNA synthesis. Halogenated benzimidazoles target a step later in viral replication during packaging and cleavage of the viral genome. The compounds 2-Bromo-5,6-dichloro-1-(β-D-ribofuranosyl)benzimidazole (BDCRB) and 2,5,6-trichloro-1-(β-D-ribofuranosyl)benzimidazole (TCRB) are novel inhibitors of human cytomegalovirus (HCMV) and resistance to these compounds are found within the human cytomegalovirus viral terminase. Terminase is unique to the virus and in theory provides a good target for antiviral development. Beginning with a BDCRB resistant guinea pig cytomegalovirus observations found a single mutation located in the viral terminase gene UL89 and unique formation found in genomic ends. In guinea pigs, the virus continued to produce large amounts of monomer. This is in contrast to human cytomegalovirus treated with either BDCRB or TCRB. Both compounds produced very little monomer DNA but created a supergenomic species, called monomer-plus that migrates to the apparent size of 270-kb on a pulse field gel. A model was developed to explain formation of monomer plus and my project aims originated from the model. In the presence of BDCRB and TCRB, packaging is relaxed resulting in the normal cleavage site being skipped and cleavage occurring at the next available cleavage site creating a short-long-short genome. In guinea pigs, cleavage has been relaxed by premature cleavage of the terminal ends. Current antivirals do not block viral entry therefore, patients are infected with HCMV. Blocking entry of HCMV into cells would prevent HCMV infection. It has been shown that antibodies to epitopes within the gH/gL/UL128-131 complex can block viral entry into endothelial, epithelial, and other cell types while antibodies to gB block entry into fibroblasts. The majority of the current work on entry into epithelial cells has been performed in retinal pigment epithelium and epithelial cells derived from tumors. Viral entry into cell lines derived from mucosa cells was dependent on the complex gH/gL/UL128-131. Rabbit antibodies raised against UL130 and UL131 peptides neutralized epithelial entry with effects as potent as human seropositive sera. This suggests that the entry complex can be blocked by single epitopes.

Staphylococcal phage 80α can serve as a helper bacteriophage for a family of mobile genetic elements called Staphylococcus aureus pathogenicity islands (SaPIs). The prototype island, SaPI1, is able to hijack the 80α capsid assembly process and redirect capsid formation to yield smaller, phage-like transducing particles carrying SaPI DNA. Capsid size redirection is accomplished through two SaPI1-encoded gene products, CpmA and an alternate scaffold protein, CpmB. The normal 80α scaffold and the SaPI1 CpmB scaffold share a small block of conserved residues at their C-termini, several of which had been shown to be essential for CpmB function. This led to the hypothesis that the C-termini of both the phage and SaPI scaffolds interact in similar ways with the major capsid protein. The goal of this study was to test this hypothesis and to identify the amino acid residues at the capsid-scaffold interface, using a genetic approach.

The aim of this study is to examine two cleavages in a Swedish political context and how the political debate of parentel leave among the parliamental parties relates to the cleavages. The cleavages examined are the right-left-scale and the new cleavage GAL-TAN. To do so, the study examines party platforms and debate articles to see if the proposals and arguments used are mainly related to the right-left-scale or to GAL-TAN. The result shows that the debate mostly relates to GAL-TAN due to the fact that most parties use proposals and arguments that are connected to social and cultural values, such as equality and freedom of choice, rather than economic values. Even though the proposals and arguments for the most part relate more to GAL-TAN, the economic arguments are not insignificant. Almost all parties discuss economic values in some way but not in the same amount as social and cultural values. This is the case for all parties except for two who focuses on both sides equally much. The main conclusion that can be drawn from this study is that GAL-TAN is a cleavage that is able to organize Swedish party politics in some political areas and can therefore be seen as a complement to the rightleft-scale.

The non-sustainable nature of fossil fuels as feedstocks for valuable chemicals, combined with the environmental damage caused by their extraction and combustion, increases the need for the development of a bio-based economy. While industry and public opinion are slowly shifting towards acceptance of this change, efficient technologies for the depolymerization and subsequent separation of lignocellulosic biomass fall short of the ever-increasing demand. In particular, there are currently no efficient, sustainable mass scale methods to convert lignin, the most abundant source of aromatic molecules on Earth. The use of oxovanadium(V) catalyst complexes to aerobically cleave C‒C bonds has been demonstrated previously and remains an attractive option for incorporation into a sustainable bio-based economy. Two new triphenoxyamine oxovanadium(V) catalysts with reduced steric bulk and electron density at the metal center (vs. previously reported complexes) have been synthesized for aerobic oxidative diol C‒C bond cleavage. These complexes were found to cleave less activated and more complex substrates than previous generations, including cyclic diols and polyalcohols. Several insights into the reaction pathways of this class of complex were elucidated through a series of kinetic studies. Experimentally, the rate of C‒C bond cleavage of both pinacol and hydrobenzoin was determined to be unaffected by substitution of the O‒H bonds with deuterium, suggesting that currently proposed mechanisms need to be revised. Multiple catalytic regimes were observed during anaerobic reaction, which were not altered significantly by the brief addition of O2. A series of density functional theory calculations revealed a plausible mechanism for the trialkoxy complex that did not involve a proton transfer in the rate determining step, instead suggesting that ligand-arm dissociation-reassociation play a significant role in the reaction. In a second project, new bisphenoxyamine-N-appended base ligand with less steric hindrance and electron density at the metal center, has been synthesized utilizing similar design principles gained from work with triphenoxyamine catalysts. When reacting with lignin model compound 1,2-diphenyl-2-methoxyethanol, this new complex displays a higher selectivity towards aldehydes and esters (relative to previous bisphenoxyamine-N-appended ligands), leading to a higher rate of C‒C bond cleavage. Investigations into the mechanism of bisphenoxy complexes, as well as the role of the N-appended base in reactivity, were performed using substrate pre-complexed bisphenoxy compounds. Thermolysis at 60 and 100 °C produced almost exclusively oxidative C‒H bond cleavage product benzyl methyl ether, with evidence for overoxidation product benzoic acid observed. Thermolysis of labelled substrate pre-complexed revealed that N-appended base may impede C‒C cleavage of 1,2-diphenyl-2-methoxyethanol by forcing the methyl ether away from the oxovanadium(V) center. Through the use of these multidentate phenoxyamine ligands, advances have been made towards sustainable oxovanadium catalysis in the pursuit of efficient and selective lignocellulosic disassembly for a sustainable bio-based economy.

A dissertation submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of requirements for the degree of Master of Science. 11/30/2013. / A variety of mass movement and depositional geomorphic phenomena in the Golden Gate Highlands National Park have been described in the literature over the past few decades, yet notably, the prominent rockfalls remain understudied. The objective of the MSc study is to undertake detailed mapping of the GGHNP rockfalls, and in so doing ascertain a better understanding of their macro-morphologies, associated spatial-size dynamics and relationships to lithology, using both field-based and desktop image processing techniques. Ground truthing, using the highest possible resolution achievable through differential GPS (DGPS) and field measurements with an accuracy of cm to mm, serves to quantify the accuracy of mapping rockfall phenomena through 0.5 m GSD colour aerial imagery. In addition, field measurements are used as inputs for feature extraction, such that rockfalls associated with the Clarens, Elliot and Molteno Formation Sandstones may be defined using object orientated classification techniques. The dimensions, orientation and absolute coordinates of rockfalls for select representative sites were captured using both field based and desktop techniques. The rockfall coordinates were taken at the midpoint of each measured rock using a DGPS, with an accuracy of ~ 2 cm on the x, y and z axis. Object Based Image Analysis (OBIA) of Clarens and Molteno Fm. rockfalls was performed successfully using ground-truthed rockfall measurements to guide the creation of segmentation and classification rulesets. Multiple linear regression modelling can be used to model rockfall characteristics from ground-truthing with remotely sensed imagery, albeit to a very limited extent. Elliot Formation rockfalls could not be mapped and analysed mainly due to resolution limitations. Uni- and bi-variate statistics show promise in interpreting rockfall distribution and weighting with environmental variables derived from a DEM and geological vector. Point density analyses found that for the entire GGHNP ~2 and ~4 rockfalls are found per Km² of Clarens and Molteno Formation rockfall areas

Orientador: Prof. Dr. Vani Xavier de Oliveira Junior / Dissertação (mestrado) - Universidade Federal do ABC, Programa de Pós-Graduação em Ciência & Tecnologia - Química, 2014. / Peptídeos são biomoléculas formadas pela ligação de dois ou mais aminoácidos através de ligações peptídicas, entre um grupo amina de um aminoácido e o grupo carboxila de outro aminoácido. Atualmente, uma das metodologias de síntese aplicada é a síntese de peptídeos em fase sólida, pela estratégia t-Boc. No presente trabalho foi analisada a eficiência da etapa de clivagem, utilizando o método convencional a 5°C e 30°C e a clivagem assistida por micro-ondas. Nesse sentido, foram utilizadas como suporte sólido as resinas Merrifield, MBHA, BHA e PAM. Os resultados mostram que a etapa de clivagem é influenciada pelo tamanho e sequência peptídica e pela resina empregada. Os melhores rendimentos foram encontrados para as clivagens assistidas por micro-ondas com a resina BHA e entre as clivagens convencionais, os melhores resultados foram obtidos a 5ºC, com as resinas MBHA e BHA. / Peptides are biomolecules formed by connecting two or more amino acids by peptide bonds between an amino group of an amino acid and the carboxyl group of another amino acid. Currently, one of the methodologies applied synthesis is the synthesis of peptides solid phase by t-Boc strategy. The present study examined the efficiency of the cleavage step using the conventional method at 5°C and 30°C and cleavage by microwave assisted. Accordingly were used as solid support the Merrifield, MBHA, BHA and PAM resins. The results show that cleavage step is influenced by size and peptide sequence and the resin employed. The best yields were found for the microwave assisted with the BHA resin and between conventional cleavages, the best results were obtained at 5°C, with the BHA and MBHA resin cleavages.

No description available.

L’émergence récente de nouvelles thérapies antivirales efficaces est une avancée considérable pour lutter contre l'infection chronique par le virus de l'hépatite C (VHC). Cependant, un pic de carcinomes hépatocellulaires, représentant l'atteinte hépatique ultime liée à l'infection, est attendu dans la prochaine décennie. Approfondir les connaissances des différentes étapes du cycle viral et de l’interférence du VHC avec l'hépatocyte hôte permet de mieux comprendre la pathogénèse associée à ce virus. Les travaux présentés dans cette thèse ont eu pour objectif d'identifier le réseau de partenaires cellulaires et viraux de la protéine non-structurale NS2 du VHC et de mieux comprendre les mécanismes d'action et de régulation de cette protéine transmembranaire multi-fonctionnelle, qui est un acteur clé du clivage protéolytique de la polyprotéine virale et de la morphogénèse des virions. Dans une première partie, nous avons analysé comparativement les mécanismes moléculaires de l’activité enzymatique des protéines NS2 du VHC et de plusieurs hepacivirus non-humains, qui infectent des primates du Nouveau Monde (GBV-B) ou qui ont été récemment identifiés chez plusieurs autres espèces animales (NPHV, RHV, BHV et GHV). Des analyses phylogénétiques, des modèles structuraux tridimensionnels et des Études dans un contexte d'expression transitoire de précurseurs polypeptidiques viraux ou dans des modèles d'infection ont montré que l’activité des protéases NS2 de divers hepacivirus (1) s'exerce à la jonction NS2/NS3 sous la forme d'homodimères formant deux triades catalytiques composites ; (2) est régulée dans le contexte de la polyprotéine virale par quelques résidus de surface du domaine N-terminal de NS3 (NS3N) nécessaires à son activation ; (3) est efficace en l'absence complète de NS3N, suggérant un rôle négatif ou régulateur, plutôt qu'activateur de NS3N, contrairement au dogme en vigueur actuellement. Ces travaux soulignent l'importance fonctionnelle des mécanismes protéolytiques de NS2 conservés parmi les différents hepacivirus. Dans une deuxième partie, nous avons identifié un réseau de facteurs cellulaires et viraux interagissant avec NS2 au cours du cycle infectieux par un crible interactomique reposant sur la purification par affinité et l'analyse par spectrométrie de masse des complexes protéiques isolés de cellules hépatocytaires infectées, ainsi que par un test de complémentation enzymatique fonctionnelle. Par une approche d'ARN interférence, nous avons ensuite montré qu'un nombre limité de facteurs cellulaires interagissant avec NS2 sont impliqués dans la production et la sécrétion de particules virales infectieuses, incluant des protéines du complexe de la peptidase signal (SPCS) au sein du réticulum endoplasmique, des protéines chaperonnes (DNAJB11, HSPA5) et une protéine impliquée dans le transport intracellulaire (SURF4). Notamment, nos Études suggèrent que plusieurs membres du SPCS forment un complexe multi-protéique avec NS2, impliquant Également la glycoprotéine virale E2, qui jouerait un rôle dans une Étape précoce de l'assemblage ou lors de l’enveloppement de la particule virale. En conclusion, mes travaux de thèse ont permis d'identifier pour la première fois une série limitée de facteurs hépatocytaires interagissant spécifiquement avec la protéine NS2 du VHC au cours de l'infection et de déterminer parmi ceux-ci les facteurs essentiels la morphogenèse virale. Par ailleurs, nos résultats ont permis d’enrichir les connaissances naissantes des hepacivirus non-humains récemment identifiés et de montrer que ceux-ci partageaient avec le VHC des mécanismes clés mis en jeu au cours du cycle viral, ce qui contribue consolider leur intérêt comme modèles animaux de substitution. / The recent emergence of a panel of direct acting antivirals will certainly help combat chronic hepatitis C in the future. However, in the current context worldwide, a peak of hepatitis C virus (HCV)-induced hepatocellular carcinoma is expected in the next decade. Deepening our understanding of HCV life cycle and HCV interference with host cells may help monitor HCV-associated pathogenesis. The aim of my PhD work was to identify the network of host and viral interactors of HCV nonstructural protein 2 and to unravel the mechanisms of action and regulation of this multifunctional, transmembrane protein, which is key both for the viral polyprotein cleavage and virion morphogenesis.In the first part of the work, we comparatively characterized molecular mechanisms underlying the enzymatic activity of NS2 proteins from HCV and from various non-human hepaciviruses that infect small New World primates (GBV-B) or that were recently identified in the wild in several mammalian species (NPHV, RHV, BHV, GHV). A combination of phylogenetic analyses, tridimensional structural models, and studies relying on the transient expression of viral polypeptide precursors or on infection models showed that NS2 proteases of the various hepaciviruses (1) act as dimers with two composite active sites to ensure NS2/NS3 junction cleavage, (2) are regulated in the polyprotein backbone via a hydrophobic patch at the surface of NS3 N-terminal domain (NS3N) that is essential to activate NS2 protease, and (3) are efficient in the complete absence of NS3N, which is unprecedented and suggests that NS3N has rather a negative or regulating role on NS2 activity. These data underline the functional importance of NS2 proteolytic mechanisms that are conserved across hepaciviruses.In the second part, we identified a network of cellular factors and viral proteins that interact with NS2 in the course of HCV infection using an interactomic screen based on affinity purification and mass spectrometry analysis of protein complexes retrieved form HCV infected hepatoma cells, as well as a split-luciferase complementation assay. Next, using a gene silencing approach, we found that a limited set of NS2 interactors among these host factors were involved in HCV particle assembly and/or secretion. This includes members of the endoplasmic reticulum signal peptidase complex (SPCS), chaperone proteins (DNAJB11, HSPA5) and a factor involved in intracellular transport (SURF4). Notably, our data are in favor of the existence of a multiprotein complex involving NS2, several members of the SPCS, and the viral E2 glycoprotein, which likely plays a role in an early step of HCV particle assembly or during particle envelopment. Altogether, my PhD work allowed us to identify a limited set of hepatocyte factors interacting with HCV NS2 during infection and to pinpoint those that are essential for HCV morphogenesis. Additionally, our results contributed to the molecular characterization of the recently identified non-human hepaciviruses and revealed that these hepaciviruses share with HCV key mechanisms in the course of their infectious life cycles. This highlights the value of non-human hepaciviruses as surrogate animal models of HCV infection.

Hepatitis B virus chronically infects 350-400 million people worldwide. It often leads to hepatocellular carcinoma, which causes >1 million deaths yearly. Current therapies prevent new viral genome formation but do not target pre-existing viral genomic DNA, thus curing only ~1/2 of patients. We targeted hepatitis B virus DNA for cleavage using zinc finger nucleases, which cleave as dimers. Co-transfection of our zinc finger nuclease pair with a target plasmid containing the hepatitis B virus genome resulted in specific cleavage. After three days in culture, 26% of the target remained linear, while ~10% was cleaved and mis-joined tail-to-tail. A portion of cleaved plasmids are repaired in cells, often with deletions and insertions. To track misrepair, we introduced an XbaI restriction site in the spacer between the zinc finger nuclease sites. Targeted cleavage and misrepair destroys the XbaI site. After three days in culture, ~6% of plasmids were XbaI resistant. 13 of 16 clones sequenced contained frameshift mutations that would lead to dramatic truncations of the viral core protein. These results demonstrate for the first time the feasibility of targeting episomal viral DNA genomes in cells using zinc finger nucleases. This strategy is broadly applicable toward inactivating other DNA viruses within cells. A major concern for the therapeutic use of zinc finger nucleases is off-target cleavage. To measure specificity, we employed in vitro assays and developed a bioinformatics method to find off-target cleavage sites in cultured cells. These sites can then be PCR amplified and tested using a mutation detection assay that we developed.