Thesis (MSc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: The creation of nanometer-scale (nanoscale) materials has fascinated and inspired the scientific community for more than a quarter of a century because of the wide range of applications of these materials, e.g. applications in drug delivery, medicine, tissue engineering, memory storage, display and audio devices, semiconductors, etc. π-Conjugated dendrimers have a proposed flat packing arrangement. An alternating phenyl isoxazole dendrimer system was developed to investigate this phenomenon. The synthesis of this dendritic system was attempted by divergent and convergent approaches. Preparation of the second generation failed because some functional groups inhibited the monomers to react to the first generation. Other examples of nano materials that have attracted a vast amount of interest are the so-called discotic amphiphiles. Discotic amphiphilic molecules have the potential to self-assemble into helical architectures. Discotic systems bearing chiral polar side chains (one and three respectively) were developed. Their self-assembly was investigated in variable concentration and variable solvent composition experiments. These systems did show signs of aggregation in UV-vis and CD spectroscopy experiments. Thread-like helical structures were observed with transmission electron microscopy. / AFRIKAANSE OPSOMMING: Nanometer-skaal materiale inspireer en fassineer wetenskaplikes al vir meer as 25 jaar as gevolg van hulle wye verskeidenheid toepassings bv.: die vervoer van geneesmiddels, weefsel ontwerp, geheue stoorspasie, digitale skerms, klank toerusting, geleiers, ens. π-Gekonjugeerde dendrimere het 'n plat drie dimmensionele rangskikking. 'n Afwisselende feniel isoxazole dendrimer stelsel was ontwikkel om hierdie verskynsel te ondersoek. Die sintese van hierdie dendritiese stelsel is aangepak deur divergerende en konvergerende benaderings. Sintese van die tweede generasie het misluk omdat sommige funksionele groepe die monomere geïnhibeer het om te reageer met die eerste generasie. Ander interessante voorbeelde van nano materiale, is die sogenaamde skyfvormige amphiphiles. Skyfvormige amphiphiles het die potensiaal om spontaan te versamel in heliese strukture. Skyfvormige molekules met chirale polêre sykettings (een en drie onderskeidelik) is ontwikkel. Hulle potensiaal om spontaan te versamel is ondersoek met wisselende konsentrasie en wisselende oplosmiddel samestelling eksperimente. Hierdie stelsels het tekens van versameling gewys in UV-vis en CD-spektroskopiese eksperimente. Staaf-vormige heliese strukture is waargeneem met transmissie-elektronmikroskopie.

This study examined the dynamics, challenges and opportunities of developing innovation systems in low resource settings with a particular focus on Uganda. It applied perspectives of technoscience and concepts of innovation systems, triple helix as university-industry-government relationships, mode 2 knowledge production and situated knowledges in understanding the context, identifying key policy issues and suggesting ways to address them. A mixed methodology combining both quantitative and qualitative methods was used in the study. It involved review of key policy documents, key informant interviews, focus group discussions and meetings with scientists, business leaders in the target organizations and firms, community members as well as observations of production processes in firms. Findings underscore the need for greater interaction and learning among actors in the emerging innovation systems in Uganda and eastern Africa. An opportunity for this to happen may be the growing number of entrepreneurial initiatives at the university and some public research organizations in the country. These entrepreneurial initiatives are driven by scientists, who are enthusiastic about moving their research results and innovations to market. This makes it plausible, in low resource settings like in Uganda, to promote the university working closely with public research organizations and firms as a locus for research and innovation. However, enabling conditions, which foster interaction and learning among actors, should be put in place. First, there is need to formulate specific policies and strategies with clear goals and incentives to promote growth of particular innovation systems. Second, a clear national policy for financing research and innovation is needed, which involves on the one part core funding to universities and research organizations, and on the other, competitive grants for research and innovation. Third, business incubation services should be established and/or supported as places where entrepreneurial scientists and other persons develop and test their business ideas and models. Fourth, there is need for institutional reforms to make administrative processes less bureaucratic, more costeffective and efficient. These reforms are necessary for example in processes involving procurement and financial management, research project approvals (for ethics and safety), technology assessments, contracting and licensing and other registration services. The findings and conclusions from this study demonstrate that technoscientific perspectives and innovation systems approaches can be adapted and used as a framework for identifying and explaining conditions that promote or hamper innovation in low resource settings as well as policy options to address them.

Mechanics and biological function of nucleic acids are intimately coupled. The DNA double helix must be opened to allow base pairing of RNA during transcription; RNA must bend and fold in its many cellular functions. Presented in this dissertation are two investigations of mechanical deformations of nucleic acids, conducted with optical tweezers.In the introduction, the mechanical properties of DNA and RNA and their relevance to their cellular functions are introduced, to give the reader context for the results presented in the Chapters 2 and 3. This is followed by an introduction to the theory of semiflexible polymer elasticity. The optical tweezers instruments used in conducting these investigations are then presented, along with calibration procedures and a short introduction to optical trapping physics.Chapter 2 presents an investigation of the effect of downstream DNA tension on initiation by T7 RNA polymerase. A hidden Markov model is fit to force-dependent lifetimes obtained from optical tweezers experiments, allowing us to identify which steps in initiation are force-dependent and estimate rates and transition state distances. We find that 1-2 pN of tension is sufficient to turn o gene expression by causing transcription bubble collapse and destabilizing the bound state. Our force-dependence scheme and estimated transition distances provide independent supportfor the \scrunching" model of initiation.The effects of cation binding and screening on single-stranded helix formation in poly(A) RNA are presented in Chapter 3. Magnesium and calcium bind to poly(A), stabilize the helix, and change its mechanical properties. A new model of helix-coil transitions is presented and used to estimate energetics and mechanical properties.Chapter 4 presents the first fully objective algorithm for use in analyzing the noisy staircaselike data that is often produced by single-molecule fluorescence experiments. A test based on the SIC (BIC) statistic is used in conjunction with a progressive step-placement scheme to locate changepoints (steps) in noisy data. Its performance is compared to other step detection algorithms in use by biophysicists by repeating tests performed in a recent review.Experimental protocols and computer codes used in these investigations are presentedin detail in the appendices.

In this dissertation, techniques of high-resolution rotational spectroscopy have been used to measure the spectra of molecules in both laboratory and astronomical settings. In the laboratory, small metal-bearing molecules containing zinc, iron, nickel, titanium, yttrium, and scandium have been studied at microwave and millimeter/submillimeter wavelengths in order to determine their rotational, fine, and hyperfine constants. These molecules were synthesized in situ in direct-absorption and Fourier-transform microwave spectrometers using Broida-type ovens and laser ablation methods. From the spectroscopic parameters, information about fundamental physical propertes and electronic character could be obtained. Radio telescopes were used to measure the spectra of molecules in different interstellar environments. A new molecule, FeCN, was detected toward the circumstellar envelope of the carbon-rich asymtotic giant branch star, IRC+10216, marking the first iron-bearing molecule detected in the interstellar medium. The telescopes were also used to conduct a study of the evolved planetary nebula, NGC 7293, or the Helix Nebula. In the Helix, CO, HCO⁺, and H₂CO were observed at several positions offset from the central star to obtain densities and kinetic temperatures throughout the Helix. A map of the HCO⁺ J = 1→ 0 transition was also constructed, showing that HCO⁺ is widespread throughout the Helix, instead of being photodissociated and destroyed, as theoretical models of planetary nebulae predict.

Membrane proteins perform a variety of functions essential for the viability of the cell, including transport and signalling across the membrane. Most membrane proteins are formed from bundles of transmembrane helices. In this thesis molecular dynamics simulations have been used to investigate helix insertion into bilayers and helix association within bilayers. The potentials of mean force for the insertion of helices derived from the cystic fibrosis transmembrane conductance regulator into lipid bilayers were calculated using coarse-grained molecular dynamics simulations. The results showed that the insertion free energy increased with helix length and bilayer hydrophobic width. The insertion free energies obtained were significantly larger than comparable quantities obtained from translocon- mediated insertion experiments, consistent with a variety of previous studies. The implications of this observation for the interpretation of in vivo translocon-mediated insertion experiments, and the function of the translocon, are discussed. Coarse-grained and atomistic molecular dynamics simulations of the transmembrane region of the receptor tyrosine kinase EphA1 suggested that the transmembrane helix dimer was most stable when interacting via the glycine zipper motif, in agreement with a structure obtained by NMR spectroscopy. Coarse-grained simulations of the transmembrane region of EphA2 suggested that the dimer has two stable orientations, interacting via a glycine zipper or a heptad motif. Both structures showed right-handed dimers, although an NMR structure of the transmembrane region of EphA2 shows a left-handed dimer interacting via the heptad motif. Both structures obtained from coarse-grained simulations proved unstable when simulated at an atomistic level of detail. The potentials of mean force for dissociating the EphA1 and EphA2 dimers were calcu- lated using coarse-grained molecular dynamics calculations. Convergence of the detailed structure of the profiles was not conclusively shown, although association free energies cal- culated from the profiles were consistent over a variety of simulation times. The association free energies were slightly larger than experimental values obtained for comparable sys- tems, but consistent with similar computational calculations previously reported. However, direct comparisons are difficult owing to the influence of environmental factors on reported association free energies. The potential of mean force profiles showed that the interaction via the glycine zipper motif for EphA1 was significantly more stable than any other confor- mation. For EphA2 the potential of mean force profiles suggested that interaction via the glycine zipper and heptad motifs both provided stable or metastable conformations, with the interaction via the glycine zipper motif probably at least as stable as that via the heptad motif.

The land snail genus Helix comprises large gastropods distributed in from France to Iran and in North Africa. Some of them have close linkage to humans - are synanthropic or are collected and consumed. The genus is most diverse in eastern Mediterranean. Taxonomy of the genus is now being revised from morphological point of view, and a molecular study is needed as a counterpart to that study. Here I present first phylogenetic data for the genus Helix, including almost all currently recognised species. I have used samples from various sources including dried bodies and tissue remnants. I have sequenced two commonly used mitochondrial markers (16S, COI). Position of the genus within Helicidae cannot be inferred from the dataset. The genus should be delimited in a strict sense, excluding genera Maltzanella, Cantareus, Cryptomphalus and Lindholmia. Division into subgenera, as proposed by various authors until now, is not supported with the exception of a split between subgenera Pelasga and the nominotypical Helix. Relationships between species and their groups are poorly resolved. Regarding species limits, the data are largely in agreement with new opinions based on morphology. There might be surprisingly high variability in shell characters within a species, as few morphologically characteristic taxa seem to be...

Biotechnology entrepreneurship is a relatively new and distinct field of entrepreneurship. Most current empirical research is conducted in the developed economies and cannot be directly extrapolated to the developing economies. The paucity of empirical research and the lack of a conceptual framework for biotechnology entrepreneurship constitute gaps that this research addressed through the development of a proposed theoretical framework of biotechnology entrepreneurship based on empirical research conducted within the context of the developing economies of South Africa and Brazil. The current methodological approaches to research in biotechnology entrepreneurship predominantly make use of a nomothetic philosophical approach and employs quantitative methods. Current research is also often based on surveys conducted within one developing economy context. Consequently, few studies in biotechnology entrepreneurship use the qualitative multiple case study approach. This methodological gap is addressed in this research through the use of qualitative multiple case studies, in the idiographic philosophical tradition, in two developing economies; South Africa and Brazil. The data collection process included in-depth interviews, documents review and observations, which improved the quality of the research through data triangulation. Ten themes were identified, which formed the basis for developing the proposed theoretical framework. In addition, seven factors that influence the process of biotechnology entrepreneurship in South Africa and Brazil were identified as regulation; funding; infrastructure; skills; entrepreneurial and commercialisation capabilities; market for biotechnology products; and social development. This research shows that the individual-opportunity nexus of entrepreneurship does not entirely hold for biotechnology entrepreneurship in South Africa and Brazil. Instead, there is a nexus of research and development; and a governmentincentivised environment that is conducive for biotechnology entrepreneurship. The policy implications of these dynamics in South Africa and Brazil; as well as implications for the other stakeholders in the biotechnology industry are articulated as being linked to the control of the factors that influence biotechnology entrepreneurship by the various stakeholders. Hence, the implications for government are predominantly linked to regulation and infrastructure; and the implications for the other stakeholders are predominantly linked to funding and skills.

O propósito desta tese é investigar como a gestão do conhecimento e a colaboração universidade-empresa-governo incluindo as três hélices se relacionam influenciando o desempenho das organizações. Como principal contribuição, pretende-se propor um modelo analítico que relaciona as teorias da Gestão do Conhecimento e da Tripla Hélice, modelo mais referenciado para aprofundar esse tipo de cooperação, e as dimensões propostas (que são a estrutural, a relacional, a cognitiva e o contexto), considerando as particularidades do contexto brasileiro. No ambiente competitivo contemporâneo, a capacidade de as organizações criarem e utilizarem o conhecimento torna-se cada vez mais fundamental para a busca da vantagem competitiva sustentável, o que leva inclusive à busca de novas formas de arranjos interorganizacionais. A escolha do tema se justifica pela escassez de pesquisas empíricas que relacionem os tópicos de gestão do conhecimento e de colaboração universidade-empresa-governo de forma integrada com foco no contexto brasileiro. Os representantes desse tipo de colaboração selecionados para compor o estudo são Institutos Nacionais de Ciência e Tecnologia (INCTs). Como técnica qualitativa de análise de dados foi utilizada a análise de conteúdo categorial. Os principais resultados mostram que a estrutura organizacional (estrutural) influencia tanto o relacionamento entre os integrantes (relacional) quanto o fluxo de conhecimento (cognitiva), bem como os elementos relacionais (cultura colaborativa, confiança e liderança) facilitam o compartilhamento de conhecimento. Além disso, o contexto afeta essas três outras dimensões. Como principais barreiras no processo de transferência de conhecimento são identificadas as diferenças culturais, a burocracia e a realidade socioeconômica, e como facilitadores a presença de parques tecnológicos e incubadoras, a proximidade geográfica entre universidade e empresa e os incentivos governamentais. / This thesis focuses on an investigation into the way knowledge management and university-industry-government collaboration influence the performance of organizations. As the main contribution, an analytical model that relates the theories of Knowledge Management and the Triple Helix, the most referenced model for such cooperation, and the structural, relational, cognitive dimensions, as well as the context is proposed. The model takes into consideration the particularities of the Brazilian context. In todays competitive environment, the ability of organizations to create and use their knowledge has become fundamental for their pursuit of sustainable competitive advantages and new forms of organizational arrangements. The choice of the topic is justified by the scarcity of studies on the identification and analyses of the main aspects of this form of collaboration in an integrated way and focused on the Brazilian context. A categorical content analysis was used as a qualitative technique applied for a multiple case study of National Institutes of Science and Technology (INCTs). The results show both context and organizational structure (structural dimension) influence the relationship between members (relational dimension) and flow of knowledge (cognitive dimension) and the relational elements (collaborative culture, trust and leadership) facilitate knowledge sharing. Cultural differences, bureaucracy and socioeconomic reality were identified as the main barriers in the process of knowledge transfer, whereas facilitators included presence of science parks and incubators, geographical proximity between university and business and government incentives.

A presente dissertação trata do estudo experimental do comportamento estrutural de barras helicoidais assentadas sobre superfície cilíndrica e sujeitas a cargas de compressão. Aparato experimental específico foi projetado e construído para este fim. O projeto, bem como a aferição deste aparato, é descrito em detalhes. Este aparato permite ajustar as barras através de um sistema de apoios constituídos por uma série de rolamentos, que podem ser posicionados de forma a conferir liberdade de deslocamento à barra em duas direções distintas: radial (normal à superfície cilíndrica de assentamento) e lateral (tangencial; bi-normal). A aplicação de carga compressiva se faz na direção tangencial à hélice não-deformada. Barras com seção transversal circular e retangular, com diversos comprimentos livres de flambagem e para diferentes ângulos de assentamento, foram ensaiadas. Estudos preliminares, com barras retas, permitiram avaliar as condições efetivas de engastamento proporcionadas pelo aparato. Nestes casos foi possível induzir o fenômeno de flambagem, recuperando-se, consistentemente, os valores de cargas críticas previstas pela teoria de Euler e avaliando-se o grau de engastamento proporcionado pelo aparato experimental. Filmagem com câmera de alta velocidade permitiu observar o fenômeno de instabilidade. O comportamento estrutural das barras curvas, de seção circular e retangular, foi então estudado. Tanto o comprimento livre quanto o ângulo de assentamento foi variado. O estudo permitiu levantar base de dados experimentais do comportamento de barras helicoidais nessas condições de carregamento e de condições de contorno. No entanto, para nenhuma das diversas condições ensaiadas foi possível induzir o fenômeno de instabilidade. Tal fato poderia dar subsídios a inferências acerca do estudo da instabilidade de tubos flexíveis do tipo birdcaging. / This dissertation deals with an experimental study on the structural behavior of bars supported on a helical cylindrical surface and subject to compressive loads. A special experimental apparatus was designed and built for this purpose. The design, as well as the adjustment of such an apparatus is described in details. The device allows one adjusting the bars by using a system consisting of a series of bearings that can be positioned to give freedom to the structure in two different directions: radial (normal to the cylindrical surface) and lateral (tangential or bi-normal). The compressive load is applied in the tangential direction of the helix. Bars with circular and rectangular cross sections, with various buckling lengths and different helix angles, were tested. Preliminary studies with straight bars, have allowed to evaluate the boundary conditions offered by the apparatus. In these cases, it was possible to induce the phenomenon of buckling, obtaining, consistently, the values of critical loads provided by the theory of Euler and to evaluate the boundary conditions provided by the apparatus. The use of a high-speed camera allowed to observe the phenomenon of instability. The structural behavior of curved bars of circular and rectangular sections was also studied. Both, the test free length as the helix angle were varied. The study enabled us to get a huge amount of experimental data about the behavior of helical bars, subjected such loading and boundary conditions. However, the phenomenon of instability could not be induced, for any condition tested. This fact could collaborate for further inferences about the study of the birdcaging instability at flexible pipes.

A classe de proteínas das MEGs (codificadas por genes de micro-éxon) presente em Schistosoma mansoni, ganhou evidência após a publicação do genoma deste parasita, principalmente por ser majoritariamente secretada, estando em contato direito com moléculas do hospedeiro, e possuir alta taxa de variação, o que poderia ter relação com um possível um mecanismo de evasão do sistema imune. Assim, foram escolhidas proteínas da classe das MEGs, todas com predição de hélice anfipática em sua estrutura, para investigação neste trabalho. Hélices anfipáticas são amplamente descritas na literatura como tendo alta propensão à interação com membranas celulares e interessantes funções fisiológicas. O objetivo deste projeto foi estudar a dinâmica de interação com membranas e estabelecer possíveis indícios de função biológica das proteínas MEG-24 e MEG-27 a partir de técnicas biofísicas. Optou-se por trabalhar com essas proteínas produzidas a partir da síntese química. Utilizando as técnicas de CD, Fluorescência e DLS, observou-se que a presença de miméticos de membrana induzem o enovelamento e o aumento da estabilidade térmica de MEG-27, e interferem no seu estado oligomérico. Para MEG-24, também foi observado aumento da estabilidade térmica e influência no estado oligomérico na presença de sistemas miméticos de membrana. Utilizando OCD, inferiu-se que MEG-27 possivelmente interage com a superfície da membrana, a passo que MEG-24 se insere na bicamada. Adicionalmente, ambas foram capazes de interferir na dinâmica de vesículas, conforme observado pelo ensaio de vazamento de calceína e DSC. Utilizando células de eritrócito e um modelo de membrana a partir dessas células (ghosts) foram realizados ensaios biológicos, DSC e EPR. A capacidade de MEG-24 e MEG-27 realizarem hemólise e hemoaglutinação, respectivamente, reitera o potencial de interação destas proteínas com membranas biológicas. Os resultados de DSC apontaram que ambas interferem nas transições das proteínas de membrana embebidas na bicamada de ghosts de eritrócitos. Por EPR, notou-se que MEG-27 tem maior efeito na dinâmica de lipídios em detrimento a MEG-24, possivelmente devido a um mecanismo de acomodação envolvendo domínios raft e a diferença de orientação de interação entre ambas as proteínas. A expressão de MEG-27 exclusivamente na região da glândula do esôfago em vermes adultos verificada por WISH, sugere que a mesma deva entrar em contato com células recém ingeridas pelo parasita. Não foi observada atividade antimicrobiana para ambas e não foram encontrados parceiros de interação proteínas pela técnica de Duplo-híbrido para MEG-27. Concluiu-se que os peptídeos estudados interagem com membranas biológicas, podendo ter papéis importantes na interface de interação parasito-hospedeiro. / The class of MEGs proteins (coded by micro-exon genes) present in Schistosoma mansoni, drawn attention after the parasite genome publication. This proteins are mostly secreted, being in direct contact with host molecules and with a high rate of variation, which could be a mechanism of Imune system evasion. Thus, proteins of the MEGs class, all with amphipathic prediction in their structure, were chosen for investigation in this work. Amphipathic helices are widely described in the literature with high propensity to interact with membranes and, consequently, probability of related biological function. The objective of this project was to study the interaction dynamics with membranes and to establish possible indications of biological function of MEG-24 and MEG-27 proteins from biophysical techniques. We chose to work with these proteins produced by chemical synthesis. Using CD, Fluorescence and DLS techniques, it was observed that the presence of membrane mimetics induced the folding and increased thermal stability of MEG-27, and interfered with its oligomeric state. For MEG-24, an increase in thermal stability and influence on the oligomeric state was also observed when in the presence of membrane mimetic systems. The results of OCD suggest that MEG-27 possibly interacts with the membrane surface, whereas MEG-24 is inserted into the bilayer. Both were able to interfere with vesicle dynamics, as observed by the Leakage and DSC tests. Using a more realistic membrane model from erythrocyte cells, biological assays, DSC and EPR were performed. The ability of MEG-24 and MEG-27 to perform hemolysis and hemagglutination, respectively, provides evidence of the potential for interaction of these proteins with biological membranes. The DSC results indicated that both interfere with the transitions of the membrane proteins embedded in the bilayer of erythrocyte ghosts. By EPR, it was noted that MEG-27 has a greater effect on lipid dynamics than MEG-24, possibly due to an accommodation mechanism involving raft domains and the difference in orientation of interaction between both proteins. The expression of MEG-27 exclusively in the region of the esophagus gland in adult worms verified by WISH suggests that it should come into contact with cells just ingested by the parasite. No antimicrobial activity was observed for both and no protein interaction partners were found by the MEG-27 double-hybrid technique. It was concluded that the studied peptides interact with biological membranes and may have important roles in the parasite-host interaction interface.