Antibiotic resistant strains of bacteria continue to increase in prevalence, hindering the ability of clinicians to treat infection. One disease exacerbated by this trend is osteomyelitis, or bone infection. When osteomyelitis is induced by these antibiotic resistant strains, patients can experience prolonged hospital visits, greater economic burdens, amputation, and even death. Due to the limitations of antibiotics to clear these infections, we sought to identify new therapeutic options for osteomyelitis. Our aim was to first develop an in vivo implant-related model of osteomyelitis. We then wanted to explore the potential of novel CRISPR-Cas9 modified bacteriophage to treat infection. In vitro and in vivo investigations demonstrated that bacteriophage therapeutic may be a viable option for infection mitigation. Furthermore, our in vivo model of osteomyelitis proved to be reliable, consistent, and challenging. Future research will utilize this model as a platform for optimizing therapeutic regimen and delivery vehicle(s) for antimicrobial therapeutics.

Estudos envolvendo o emprego de novas técnicas de esterilização têm apresentado nítido crescimento nos últimos anos como alternativa aos processos convencionais. A grande possibilidade consiste no emprego do plasma como agente de esterilização. Essa tecnologia tem considerável potencial para desenvolver o meio mais eficiente e seguro de esterilização de artigos termossensíveis com ênfase para a indústria farmacêutica e médica e até mesmo em outras áreas industriais. O objetivo deste trabalho foi investigar a influência de alguns parâmetros de processos por plasma e correlacionar sua eficácia com processos por óxido de etileno. Neste trabalho, estudos foram realizados empregando tecnologia de esterilização por plasma usando reator Reactive Ion Etching (RIE). Os valores aplicados de potências de rádio-frequência, a 13,56 MHz foram 25 W, 50 W, 100 W e 150 W. Os gases testados foram oxigênio puro e misturas de oxigênio e peróxido de hidrogênio (190/10, 180/20 e 160/40 sccm) e fluxo constante de 200 sccm, pressão de 0,100 torr e temperatura abaixo de 60°C. Esterilizador por óxido de etileno foi empregado a 450 mg/L (Oxyfume 2002®), 55°C, 60% de umidade e -0,65 e 0,60 kgf/cm2 de pressão. Os indicadores biológicos empregados foram constituídos de esporos de Bacillus subtilis var. niger ATCC 9372, inoculados em lamínulas de vidro de 18 x 18 mm e discos de papel de 13 mm de diâmetro em uma carga de 2,0 x 107 UFC/suporte. Os tempos de exposição aos processos por plasma foram de 3 a 120 minutos. Reduções progressivas da contagem inicial de microrganismos foram observadas nos valores D: 215,91,55,55,9,19 e 2,91 minutos para processos por plasma com oxigênio puro, a 25 W, 50 W, 100 W e 150 W, respectivamente. Misturas de oxigênio e peróxido de hidrogênio apresentaram os seguintes valores D: 190/10 sccm (6,41 min), 180/20 sccm (6,47 min) e 160/40 sccm (4,02 min), a 100 W e 190/10 sccm (1,47 min), 180/20 sccm (3,11 min) e 160/40 sccm (1,94 min), a 150 W. Processos empregando óxido de etileno apresentaram valor D de 2,86 minutos. Análises por Microscopia Eletrônica de Varredura demonstraram danos causados ao córtex dos esporos. Sistema empregando plasma como principal agente de esterilização apresentou-se efetivo em desafios com indicadores biológicos. Os processos por plasma provaram ser a mais apropriada tecnologia de esterilização de materias termossensíveis e com grande potencial para substituir os métodos convencionais de esterilização em futuro próximo. / Studies involving new sterilization techniques have increased in the past few years as alternatives to conventional processes. The great possibility consists in the use of plasma as sterilization agent. This technology has the enormous potential to develop a more efficient and safer means of sterilization at thermo-sensitive matters, focusing the pharmaceutical and medical industry - even though it can be applied to other industrial areas. The aim of the present study was to investigate the influence at some parameters of plasma processes and correlate the effectiveness plasma with ethylene oxide sterilizer. In this work, studies were performed taking into account a plasma sterilization technology using a Reactive Ion Etching (RIE) reactor. Power was applied at 13.56 MHz using a 6 inch diameter electrode. The gases tested were pure oxygen and oxygen-hydrogen peroxide mixtures (190/10, 180/20, and 160/40 sccm), and gas flow held constant 200 sccm, pressure at 0.100 torr and radio-frequency power at 25 W, 50 W, 100 W, and 150 W and temperature below 60°C. Ethylene oxide sterilizer were performed using 450 mg/L (Oxyfume 2002®) at 55°C, 60% humidity and -0.65 and 0.60 kgf/cm2 pressure. The biological indicator used was Bacillus subtilis var. niger ATCC 9372, witch was inoculated in glass carries (18 x 18 mm) and paper discs (13 mm diameter) in a load of 2.0 x 107 CFU/support. The exposition times were 3 to 120 minutes. Progressive reductions of the initial microbial count could be observed in the D values witch were 215.91, 55.55, 9.19, and 2.91 minutes for pure oxygen plasma at 25 W, 50 W, 100 W and 150 W, respectively. Oxygen-hydrogen peroxide mixtures plasma showed D values: 190/10 sccm (6.41 min), 180/20 sccm (6.47 min) and 160/40 sccm (4.02 min) at 100 W and 190/10 sccm (1.47 min), 180/20 sccm (3.11 min) and 160/40 sccm (1.94 min) at 150 W. Ethylene oxide processes showed D value to 2.86 minutes. Scanning Electron Microscopy analyses showed some damage on the spore cortex. Processes using plasma as main sterilization agent are presented effective in challenge with biological indicators. The plasma proved to be the most appropriate sterilization technology in thermosensitive matters and to have a great potential to replace conventional sterilization methods in the near future.

Conselho Nacional de Desenvolvimento Científico e Tecnológico / Lignocellulosic agroindustrial wastes, such as rice husks (RH), are abundant, low cost, renewable sources, available to biotransformation in value-added products. Thus, the main objective of this study was to investigate the use of RH with the purpose of its biotransformation in lactic acid (LacA) starting from hydrolysates of this residual biomass. At the same time, aiming to contribute to the mitigation of the growing environmental concern about the illegal disposal of this waste in the State of Rio Grande do Sul the biggest Brazilian rice producer. For this, a central composite rotational design (CCRD) of the hydrolysis experiments of RH in pressurized conversion system with diluted HCl and H2SO4, revealed that experiments conducted at 175 °C, for 46 min, with acid concentrations of 2.2% v v-1, generate the highest glucose contents. For hydrolysis involving HCl, 17.8 g glucose L-1, with an yield of 106.6 mg glucose g-1 RH; for hydrolysis with H2SO4, 14.1 g glucose L-1, with an yield of 84.5 mg glucose g-1 RH. Previous fermentative experiments were carried out with the aim to select resilient and efficient micro-organisms for the LacA production and, also, to evaluate the need of supplementation of the RH hydrolyzate with specific nutrients. L. rhamnosus, in this study, was the most suitable bacteria for the lactic fermentation, among all the Lactobacillus tested, being able to to produce 5.6 g LacA L-1, with a yield of 33.8 mg LacA g-1 RH (hydrolysed with HCl, without nutrient addition, 96 h fermentation). The acid hydrolysis, in this particular case, was carried out at 160 °C, for 70 min, using 4.0% HCl v v-1, generating 14.7 g glucose L-1. The lactic fermentation via CCRD was batch conducted in 4 mL vials, at 37 °C, pH 6.0, using L. casei subsp. rhamnosus ATCC 10863, specialized in catabolization of both hexoses and pentoses (except arabinose). Experiments with RH hydrolysates containing nutrients added produced up to 18.8 g LacA L-1 (maximum yield of 997,1 mg LacA g-1 sugars) in substrate hydrolyzed with HCl, after 52 h fermentation; and 14.6 g LacA L-1 (maximum yield of 999.8 mg LacA g-1 sugars) in substrate hydrolyzed with H2SO4, after 24 h fermentation. Therefore, in this study, the choices of most influence in the LacA production were fermentation with sulfuric acid and employment of L. rhamnosus. / Resíduos lignocelulósicos agroindustriais, como a casca de arroz (CA), são fontes renováveis, abundantes e de baixo custo, disponíveis para a biotransformação em produtos com valor agregado. O principal objetivo deste trabalho foi investigar o aproveitamento da CA com vistas à sua biotransformação em ácido láctico (ALac), partindo-se de hidrolisados desta biomassa residual. Ao mesmo tempo, objetivou-se contribuir para a mitigação do crescente problema ambiental decorrente da disposição irregular deste resíduo no estado do Rio Grande do Sul, maior produtor brasileiro. Para tanto, o delineamento composto central rotacional (DCCR) do planejamento experimental da hidrólise ácida da CA em sistema de conversão à pressão, com HCl e H2SO4 diluídos, revelou que, experimentos conduzidos a 175 °C, por 46 min, com concentração de 2,2% (v v-1) de ácido, produziram os teores máximos de glicose. Para hidrólises envolvendo HCl, teor de 17,8 g de glicose L-1, com rendimento de 106,6 mg de glicose g-1 CA; para hidrólises com H2SO4, teor de 14,1 g de glicose L-1, com rendimento de 84,5 mg de glicose g-1 CA. Ensaios fermentativos prévios foram feitos com o intuito de selecionar micro-organismos resilientes e eficientes para a produção de ALac e, também, para avaliar a necessidade de suplementação do hidrolisado da CA com nutrientes específicos. L. rhamnosus, neste trabalho, foi a bactéria mais apropriada à fermentação láctica, dentre os Lactobacillus testados, sendo capaz de produzir 5,6 g ALac L-1, com rendimento de 33,8 mg ALac g-1 CA (hidrolisado com HCl, sem adição de nutrientes, 96 h de fermentação). A hidrólise ácida, neste caso específico, foi feita a 160 °C, por 70 min, com 4,0% HCl v v-1, gerando 14,7 g L-1 de glicose. A fermentação láctica via DCCR foi conduzida em vials de 4 mL, em batelada, a 37 °C, pH 6,0, empregando-se L. casei subsp. rhamnosus ATCC 10863, cepa especializada em catabolização de hexoses e pentoses (exceto arabinose). Experimentos com hidrolisados da CA adicionados de nutrientes produziram até 18,8 g ALac L-1 (rendimento máximo de 997,1 mg ALac g-1 açúcares) em substrato hidrolisado com HCl, após 52 h de fermentação; e 14,6 g ALac L-1 (rendimento máximo de 999,8 mg ALac g-1 açúcares) em substrato hidrolisado com H2SO4, após 24 h de fermentação. Portanto, neste trabalho, as escolhas de maior influência na produção de ALac foram a fermentação com hidrolisado sulfúrico e emprego de L. rhamnosus.

Estudos envolvendo o emprego de novas técnicas de esterilização têm apresentado nítido crescimento nos últimos anos como alternativa aos processos convencionais. A grande possibilidade consiste no emprego do plasma como agente de esterilização. Essa tecnologia tem considerável potencial para desenvolver o meio mais eficiente e seguro de esterilização de artigos termossensíveis com ênfase para a indústria farmacêutica e médica e até mesmo em outras áreas industriais. O objetivo deste trabalho foi investigar a influência de alguns parâmetros de processos por plasma e correlacionar sua eficácia com processos por óxido de etileno. Neste trabalho, estudos foram realizados empregando tecnologia de esterilização por plasma usando reator Reactive Ion Etching (RIE). Os valores aplicados de potências de rádio-frequência, a 13,56 MHz foram 25 W, 50 W, 100 W e 150 W. Os gases testados foram oxigênio puro e misturas de oxigênio e peróxido de hidrogênio (190/10, 180/20 e 160/40 sccm) e fluxo constante de 200 sccm, pressão de 0,100 torr e temperatura abaixo de 60°C. Esterilizador por óxido de etileno foi empregado a 450 mg/L (Oxyfume 2002®), 55°C, 60% de umidade e -0,65 e 0,60 kgf/cm2 de pressão. Os indicadores biológicos empregados foram constituídos de esporos de Bacillus subtilis var. niger ATCC 9372, inoculados em lamínulas de vidro de 18 x 18 mm e discos de papel de 13 mm de diâmetro em uma carga de 2,0 x 107 UFC/suporte. Os tempos de exposição aos processos por plasma foram de 3 a 120 minutos. Reduções progressivas da contagem inicial de microrganismos foram observadas nos valores D: 215,91,55,55,9,19 e 2,91 minutos para processos por plasma com oxigênio puro, a 25 W, 50 W, 100 W e 150 W, respectivamente. Misturas de oxigênio e peróxido de hidrogênio apresentaram os seguintes valores D: 190/10 sccm (6,41 min), 180/20 sccm (6,47 min) e 160/40 sccm (4,02 min), a 100 W e 190/10 sccm (1,47 min), 180/20 sccm (3,11 min) e 160/40 sccm (1,94 min), a 150 W. Processos empregando óxido de etileno apresentaram valor D de 2,86 minutos. Análises por Microscopia Eletrônica de Varredura demonstraram danos causados ao córtex dos esporos. Sistema empregando plasma como principal agente de esterilização apresentou-se efetivo em desafios com indicadores biológicos. Os processos por plasma provaram ser a mais apropriada tecnologia de esterilização de materias termossensíveis e com grande potencial para substituir os métodos convencionais de esterilização em futuro próximo. / Studies involving new sterilization techniques have increased in the past few years as alternatives to conventional processes. The great possibility consists in the use of plasma as sterilization agent. This technology has the enormous potential to develop a more efficient and safer means of sterilization at thermo-sensitive matters, focusing the pharmaceutical and medical industry - even though it can be applied to other industrial areas. The aim of the present study was to investigate the influence at some parameters of plasma processes and correlate the effectiveness plasma with ethylene oxide sterilizer. In this work, studies were performed taking into account a plasma sterilization technology using a Reactive Ion Etching (RIE) reactor. Power was applied at 13.56 MHz using a 6 inch diameter electrode. The gases tested were pure oxygen and oxygen-hydrogen peroxide mixtures (190/10, 180/20, and 160/40 sccm), and gas flow held constant 200 sccm, pressure at 0.100 torr and radio-frequency power at 25 W, 50 W, 100 W, and 150 W and temperature below 60°C. Ethylene oxide sterilizer were performed using 450 mg/L (Oxyfume 2002®) at 55°C, 60% humidity and -0.65 and 0.60 kgf/cm2 pressure. The biological indicator used was Bacillus subtilis var. niger ATCC 9372, witch was inoculated in glass carries (18 x 18 mm) and paper discs (13 mm diameter) in a load of 2.0 x 107 CFU/support. The exposition times were 3 to 120 minutes. Progressive reductions of the initial microbial count could be observed in the D values witch were 215.91, 55.55, 9.19, and 2.91 minutes for pure oxygen plasma at 25 W, 50 W, 100 W and 150 W, respectively. Oxygen-hydrogen peroxide mixtures plasma showed D values: 190/10 sccm (6.41 min), 180/20 sccm (6.47 min) and 160/40 sccm (4.02 min) at 100 W and 190/10 sccm (1.47 min), 180/20 sccm (3.11 min) and 160/40 sccm (1.94 min) at 150 W. Ethylene oxide processes showed D value to 2.86 minutes. Scanning Electron Microscopy analyses showed some damage on the spore cortex. Processes using plasma as main sterilization agent are presented effective in challenge with biological indicators. The plasma proved to be the most appropriate sterilization technology in thermosensitive matters and to have a great potential to replace conventional sterilization methods in the near future.

Acinetobacter baumanii fait aujourd’hui partie des bactéries les plus problématiques dans le monde. Responsable de nombreux pics épidémiques d’infections nosocomiales auxquelles sont associés de forts taux de mortalité, cette bactérie puise sa pathogénie dans de multiples caractéristiques qui lui permettent ainsi d’échapper au système immunitaire de l’hôte et à la plupart des traitements actuels. Capable d’adhérer à de multiples surfaces, A. baumanii persiste dans l’environnement hospitalier à travers un mode de vie communautaire au sein duquel ses capacités de survie sont exacerbées. Chez les espèces du genre Acinetobacter, le mode de vie communautaire peut prendre deux formes distinctes : le biofilm et la pellicule. Dans la première partie de cette thèse, nous avons cherché à discriminer ces deux modes de vie, chez la souche ATCC 17978, par une analyse protéomique à large échelle. Nous avons confirmé la présence de nombreux marqueurs communs aux deux communautés (transporteurs, systèmes de sécrétion, d’acquisition d’ions, adhésines et pili) et mis en exergue des systèmes spécifiquement reliés à la formation du biofilm (pilus Fim, T2SS, T1SS/pompe A1S_0535-38, LPS/LOS, motif capsulaire) et à celle de la pellicule (Gac). Grâce à l’étude de la souche A. baumannii SDF en mode biofilm, qui présente un génome plus compact, nous montrons que très peu de mécanismes moléculaires sont partagés par les deux souches étudiées. Ce résultat témoigne de la difficulté quant au développement d’un traitement dirigé contre les biofilms A. baumannii. Dans une deuxième partie, nous avons testé deux approches pour prévenir et éradiquer les biofilms à A. baumannii. La première a ciblé le Quorum Sensing (QS), système de communication essentielle à la coordination des cellules. Nous avons pu montrer que les acides gras mono-insaturés (acide palmitoléique et acide myristoléique), au même titre que la virstatine, limitait la formation de communautés à A. baumannii en inhibant l’expression du régulateur abaR nécessaire au QS. Dans une seconde stratégie, nous avons finalement évalué l’action antibactérienne et antibiofilm d’un nouveau composé d’origine naturelle : la squalamine. Dans cette étude, nous montrons pour la première fois qu’A. baumannii est capable d’entrer dans un état de dormance (persistant/VBNC) pour survivre à de fortes doses de ciprofloxacine, mais que la squalamine est capable d’éradiquer ces cellules persistantes grâce à des concentrations inférieures à la concentration hémolytique. / Today, Acinetobacter baumannii is one of the most problematic pathogens in the world. This bacterium is responsible for worldwide epidemic outbreaks associated with dramatic mortality rates. It possesses high capacities to evade the immune host system and to resist to numerous available antibacterial agents. A. baumannii is also able to persist into hospital environment due to high adhesion abilities which induce community development. This process is also associated to an enhanced survival rate. In Acinetobacter genus, community modes of lif can take two forms : biofilm and pellicle. In this study on the strain ATCC 17978, we tried to discriminate these two lifestyles by a large scale proteomic analysis. We have confirmed the presence of many common community markers (transporters, ion acquisition secretion systems, adhesins and pili) and highlighted systems specifically related to biofilm (pilus Fim, T2SS, T1SS / pump A1S_0535-38, LPS / LOS, capsular pattern) and pellicle communities. Furthermore the proteomic analysis of an avirulent A. baumannii strain, SDF, in biofilm allowed to highlight peculiar metabolic pathways, specific adhesion determinants but very few markers shared by ATCC 17978. This demonstrated the difficulty in developing a treatment directed against A. baumannii biofilm. Then, we tested different approaches to prevent and eradicate biofilms. The first one targeted the Quorum Sensing system (QS), an essential communication system for cell coordination. We have showed that monounsaturated fatty acids (palmitoleic acid and myristoleic acid), like virstatin prevent the community formation of A. baumannii by inhibiting the expression of the abaR regulator required for QS. In a second strategy, we have evaluated the antibacterial and antibiofilm activity of a new natural compound : the squalamine. We showed for the first time that if ciprofloxacin treatment was able to induce a dormancy population (persistent/VBNCs) in A. baumannii, squalamine was able to eradicate this population of dormant cells.

Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico / FundaÃÃo Cearense de Apoio ao Desenvolvimento Cientifico e TecnolÃgico / Este trabalho teve como objetivo estudar a utilizaÃÃo de glicerol oriundo da indÃstria do biodiesel (glicerol bruto) como substrato em ensaios fermentativos para a produÃÃo de etanol. Os ensaios foram realizados em mesa agitadora com velocidade de 200 rpm, nas temperaturas de 30 e 37 ÂC, respectivamente para os microrganismos Saccharomyces sp. 1238 e Escherichia coli 224 ATCC 25922. Nos experimentos realizados com a levedura Saccharomyces sp., variaram-se as concentraÃÃes de glicerol adicionado ao meio fermentativo em 0,5; 1,0 e 5,0 % v/v e fixou-se o volume de inÃculo em 1 % m/v. Observou-se que o microrganismo Saccharomyces sp. nÃo utilizou glicerol como fonte de carbono para produÃÃo de etanol, porÃm em ensaios teste com glicose P.A., observou-se que este substrato foi rapidamente consumido pelo microrganismo apresentando uma produÃÃo de etanol de 5,5 g/L. Nas fermentaÃÃes com a bactÃria Escherichia coli, variou-se a concentraÃÃo de glicerol adicionado ao meio fermentativo em: 1, 10, 15 e 20 g/L. Pela avaliaÃÃo da influÃncia da concentraÃÃo de substrato no meio atravÃs dos resultados obtidos, pode-se concluir que a melhor condiÃÃo para a produÃÃo de etanol com esse microrganismo foi a concentraÃÃo inicial de 10 g/L de glicerol. O consumo de glicerol pela bactÃria Escherichia coli foi afetado pela variaÃÃo deste substrato. Observou-se que o etanol foi produzido a partir de 8 h de cultivo nas fermentaÃÃes tanto com glicerol bruto quanto P.A. nas concentraÃÃes de 10, 15 e 20 g/L adicionado ao meio de cultivo. Observou-se tambÃm a formaÃÃo de Ãcido acÃtico nas primeiras horas da fermentaÃÃo. A produÃÃo de Ãcido acÃtico foi baixa, atingindo a concentraÃÃo de 0,15 g/L na fermentaÃÃo utilizando 10 g/L de glicerol bruto. Analisando os dois microrganismos estudados, verificou-se que apenas a bactÃria Escherichia coli 224 ATCC 25922 mostrou-se adequada ao objetivo desta pesquisa, jà que com a levedura nÃo foi produzido etanol em quantidade significativa. / The aim of this work was to investigate the use of glycerol from biodiesel industry (raw glycerol) as a substrate in fermentation assays for production of ethanol. The assays were performed in shaker with agitation of 200 rpm, at temperatures of 30 and 37 ÂC, respectively for the microorganisms Saccharomyces sp. 1238 and 224 Escherichia coli ATCC 25922. In experiments with yeast Saccharomyces sp., it was varied concentrations of glycerol from fermentation medium at 0.5, 1.0 and 5.0 % v/v and the inoculum was set to 1% w/v. It was observed that the microorganism Saccharomyces sp. could not use glycerol as carbon source for ethanol production, but in assays using glucose, this substrate was rapidly consumed by the microorganism achieving an ethanol production of 5.5 g/L. It was varied the concentration of glycerol added to the fermentation medium: 1, 10, 15 and 20 g/L when Escherichia coli was used. By analyzing the influence of substrate concentration in fermentations, it can be concluded that the best condition for ethanol production, with this microorganism, was initial concentration of glycerol of 10 g/L. The consumption of glycerol by Escherichia coli was affected by the change of substrate concentration. It was observed that ethanol was produced after 8 h of fermentation with both raw and PA glycerol at 10, 15 and 20 g/L. It also observed the formation of acetic acid in the first hours of fermentation. The production of acetic acid was low, reaching a concentration of 0.15 g/L in fermentation using 10 g/L of raw glycerol. Analyzing the two microorganisms studied, it was found that only 224 bacteria Escherichia coli ATCC 25922 was adequate to the aim of this research, since the yeast was not produced ethanol in significant amounts.

All members of the genus Xanthomonas are considered to be plant pathogenic, with specific pathovars infecting several high value agricultural crops. One of these pathovars, X. campestris pv. zeae (as this is only a proposed name it will further on be referred to as Xanthomonas BLSD) the causal agent of bacterial leaf steak of maize, has established itself as a widespread significant maize pathogen within South Africa. Insufficient information about the present distribution of the pathogen is available. The main aim of the study was thus to isolate and characterise the pathogen using molecular methods. Results demonstrated that the causal agent of bacterial leaf streak disease (Xanthomonas BLSD: potentially X. campestris pv. zeae) was widely distributed within the major maize cultivation regions of South Africa. Most of the isolates collected originated from the Highveld maize production provinces (North West, Free State, Gauteng and Mpumalanga provinces) as well as from irrigated maize fields in the Northern Cape province. The XgumD gene marker was used to determine if the isolates belonged to the genus Xanthomonas. The gumD gene fragment is located within the gumB-gumM region of the operon and is conserved among Xanthomonas species. This gene fragment is partially responsible for xanthan production. This marker was amplified from all isolates and a selected number were sequenced. The marker was only able to confirm that the causal agent was a member of the genus Xanthomonas. PCR methods were used for the characterisation of the isolates. This included PCR and sequencing of ribosomal RNA- gyraseB and gumD genes. A fingerprinting method BOX-PCR was also employed. Good quality DNA of sufficient quantities was obtained from the various isolates. Amplification produced no non-specific amplification products. This resulted in good quality sequences that could be analysed using bioinformatics tools. Phylogenetic analyses of the ribosomal RNA and gyraseB genes could not detect differences amongst the 47 Xanthomonas BLSD isolates. However, these genes were able to distinguish between the type strain of these isolates and various Xanthomonas species and pathovars. From all three neighbour joining trees the Xanthomonas BLSD isolates had close association with X. axonopodis pv. vasculorum strain ATCC 35938. For the 16S rRNA gene there exists no sequence differences between Xanthomonas BLSD and X. axonopodis pv. vasculorum strain ATCC 35938. A single nucleotide difference was observed between Xanthomonas BLSD and X. axonopodis pv. vasculorum strain ATCC 35938 for the 23S rRNA gene. The gyraseB gene detected a total of six nucleotide variations between these two Xanthomonas species. For all of the phylogenetic trees there was no clustering of Xanthomonas BLSD with X. campestris pathovars. Genetic profiling (via BOX-PCR) based on present/absent analysis revealed no variations amongst the Xanthomonas BLSD isolates. All isolates shared an identical pattern produced by 12 distinct PCR products. This profiling technique did differentiate between the isolates of Xanthomonas BLSD and X. axonopodis pv. vasculorum strain ATCC 35938. Their profiles shared common bands, but differed in the number and overall pattern of the bands. These results suggest two main conclusions: (i) Xanthomonas BLSD has a clonal origin with geographical separation not impacting genetic variation. The fact that all the isolates appear to be clonal may imply that when resistant maize cultivars are developed these should be resistant to all isolates of the pathovar irrespective of their geographical origin. This is a suggestion that will have to be corroborated using more isolates and additional genetic fingerprinting techniques (ii) the Xanthomonas BLSD isolates from this study may not belong to X. campestris. Further studies using other markers should be conducted to determine the real identity of Xanthomonas BLSD. / MSc Environmental Sciences, North-West University, Potchefstroom Campus, 2015

All members of the genus Xanthomonas are considered to be plant pathogenic, with specific pathovars infecting several high value agricultural crops. One of these pathovars, X. campestris pv. zeae (as this is only a proposed name it will further on be referred to as Xanthomonas BLSD) the causal agent of bacterial leaf steak of maize, has established itself as a widespread significant maize pathogen within South Africa. Insufficient information about the present distribution of the pathogen is available. The main aim of the study was thus to isolate and characterise the pathogen using molecular methods. Results demonstrated that the causal agent of bacterial leaf streak disease (Xanthomonas BLSD: potentially X. campestris pv. zeae) was widely distributed within the major maize cultivation regions of South Africa. Most of the isolates collected originated from the Highveld maize production provinces (North West, Free State, Gauteng and Mpumalanga provinces) as well as from irrigated maize fields in the Northern Cape province. The XgumD gene marker was used to determine if the isolates belonged to the genus Xanthomonas. The gumD gene fragment is located within the gumB-gumM region of the operon and is conserved among Xanthomonas species. This gene fragment is partially responsible for xanthan production. This marker was amplified from all isolates and a selected number were sequenced. The marker was only able to confirm that the causal agent was a member of the genus Xanthomonas. PCR methods were used for the characterisation of the isolates. This included PCR and sequencing of ribosomal RNA- gyraseB and gumD genes. A fingerprinting method BOX-PCR was also employed. Good quality DNA of sufficient quantities was obtained from the various isolates. Amplification produced no non-specific amplification products. This resulted in good quality sequences that could be analysed using bioinformatics tools. Phylogenetic analyses of the ribosomal RNA and gyraseB genes could not detect differences amongst the 47 Xanthomonas BLSD isolates. However, these genes were able to distinguish between the type strain of these isolates and various Xanthomonas species and pathovars. From all three neighbour joining trees the Xanthomonas BLSD isolates had close association with X. axonopodis pv. vasculorum strain ATCC 35938. For the 16S rRNA gene there exists no sequence differences between Xanthomonas BLSD and X. axonopodis pv. vasculorum strain ATCC 35938. A single nucleotide difference was observed between Xanthomonas BLSD and X. axonopodis pv. vasculorum strain ATCC 35938 for the 23S rRNA gene. The gyraseB gene detected a total of six nucleotide variations between these two Xanthomonas species. For all of the phylogenetic trees there was no clustering of Xanthomonas BLSD with X. campestris pathovars. Genetic profiling (via BOX-PCR) based on present/absent analysis revealed no variations amongst the Xanthomonas BLSD isolates. All isolates shared an identical pattern produced by 12 distinct PCR products. This profiling technique did differentiate between the isolates of Xanthomonas BLSD and X. axonopodis pv. vasculorum strain ATCC 35938. Their profiles shared common bands, but differed in the number and overall pattern of the bands. These results suggest two main conclusions: (i) Xanthomonas BLSD has a clonal origin with geographical separation not impacting genetic variation. The fact that all the isolates appear to be clonal may imply that when resistant maize cultivars are developed these should be resistant to all isolates of the pathovar irrespective of their geographical origin. This is a suggestion that will have to be corroborated using more isolates and additional genetic fingerprinting techniques (ii) the Xanthomonas BLSD isolates from this study may not belong to X. campestris. Further studies using other markers should be conducted to determine the real identity of Xanthomonas BLSD. / MSc Environmental Sciences, North-West University, Potchefstroom Campus, 2015

Serratia sp. ATCC 39006 (S39006) is known for producing carbapenem and prodiginine antibiotics; 1-carbapen-2-em-3-carboxylic acid (car) and prodigiosin. It displays different motility mechanisms, such as swimming and swarming aided by flagellar rotation and biosurfactant production. In addition, S39006 produces gas vesicles to float in aqueous environments and enable colonization of air-liquid interfaces. Gas vesicles are thought to be constructed solely from proteins expressed from a gene cluster composed of two contiguous operons, gvpA1-gvpY and gvrA-gvrC. Prior to this study, three cognate regulators, GvrA, GvrB, and GvrC, encoded by the right hand operon were known to be essential for gas vesicle synthesis. Post-transcriptional regulators such as RsmA-rsmB were also known to be involved in the inverse regulation of gas vesicles and flagella based motility. Furthermore, gas vesicle formation, antibiotic production, and motility in S39006 were affected by cell population densities and de-repressed at high cellular densities through a quorum sensing (QS) system. The aim of this research study was to identify novel regulatory inputs to gas vesicle production. Mutants were generated by random transposon mutagenesis followed by extensive screening, then sequencing and bioinformatic identification of the corresponding mutant genes. After screening, 31 mutants and seven novel regulatory genes impacting on cell buoyancy were identified. Phenotypic and genetic analysis revealed that the mutations were pleiotropic and involved in cell morphology, ion transport and central metabolism. Two new pleiotropic regulators were characterized in detail. Mutations in an ion transporter gene (trkH) and a putative transcriptional regulator gene (floR) showed opposite phenotypic impacts on flotation, flagella-based motility and prodigiosin, whereas production of the carbapenem antibiotic was affected in the transcription regulator mutant. Gene expression assays with reporter fusions, phenotypic assays in single and double mutants, and proteomics suggested that these regulatory genes couple different physiological inputs to QS and RsmA-dependent and RsmA-independent pathways.

With accellerating global warming and pollution problems a change of energy regime is necessary. Solar energy offers a clean and unlimited energy source of enormous potential. Due to it’s intermittenet nature solar energy must be stored - ideally in the chemical bond of a carrier molecule. Hydrogen gas, H2, an energy carrier with water as only emission when used in a fuel cell, is considered to be the choise for the future. In this context cyanobacteria show promising potential as future H2 factories since they can produce H2 from solar energy and water. The main enzymes directly involved in cyanobacterial hydrogen metabolism are nitrogenases and hydrogenases. Cyanobacterial hydrogenases are either uptake hydrogenases or bidirectional hydrogenases and their maturation requires assistance of six maturation proteins and two hydrogenase specific proteases. In this thesis the transcriptional regulation, maturation and function of the cyanobacterial uptake hydrogenases were investigated in the filamentous, heterocyst forming strains Nostoc punctiforme ATCC 29133 and Nostoc sp. strain PCC 7120. Five genes, encoding proteins putatively involved in the maturation of the uptake hydrogenase were identified upstream the known maturation genes. Two transcription factors, CalA and CalB, were found interacting with the stretch of DNA forming the upstream regions of the uptake hydrogenase structural genes and the novel maturation genes. The expression of the uptake hydrogenase were  heterocysts specific and the specificity mapped to a short promoter region starting -57 bp upstream the transcription start point. In addition, the function of the uptake hydrogenase was inserted in a metabolic context. Among the proteases, a conserved region was discovered possibly involved in determining the hydrogenase specificity. This thesis has given valuable information about the transcriptional regulation, maturation and function of the uptake hydrogenase in filamentous, heterocystous cyanobacteria and identified new targets for bioengineering of mutant strains with higher H2 production rates.