TOL plasmids of Pseudomonas putida encode enzymes for the degradation of toluene and related aromatics. These genes are organized into two operons regulated by the Xy1R and Xy1S transcriptional activators. Previous analysis of the TOL pDK1 catechol-2,3-dioxygenase gene (xy1E) and a comparison of this gene to xy1E from the related TOL plasmid pWW0, revealed the existance of a substantial level of sequence homology (82%).

Rhizobium leguminosarum is a Gram negative nitrogen-fixing soil bacterium. Due to the limited bioavailability of iron, bacteria utilize siderophores that scavenge and bind available iron. The transport of iron-siderophore complexes is achieved by the TonB-ExbB-ExbD complex. We have previously shown that a functional TonB protein is necessary for iron transport by creating ΔtonB mutants and assessing their growth and 55Fe-siderophore transport ability. We attempted to identify and characterize the roles of putative exbB and exbD genes using a similar approach. Growth curves and sequence analyses suggest putative exbB and exbD may be the tolpal-associated genes tolQ and tolR. Phenotypic and sensitivity assays showed mutants do not exhibit the characteristic tol phenotype and are not sensitive to detergents or changes in ionic strength of the growth medium. We also expressed and purified the 120 amino acid fragment of the TonB C-terminus for further physical and chemical characterization.

Wheat grain quality has a complex genetic architecture heavily influenced by the growing environment. Consistency in wheat quality not only affects the efficiency of milling and baking but also the quality of end-use products. The objectives of this study were to 1) analyze the different wheat quality parameters in Recombinant Inbred Lines (RILs) grown under different environments, and 2) to identify Quantitative Trait Loci (QTLs) associated with quality stability in RILs grown under different environments. A set of 180 RILs derived from two spring wheat lines 'Halberd' and 'Len' were grown at Uvalde and College Station TX, in the 2009/2010 growing season and at Chillicothe and College Station TX, in 2010/2011 growing seasons. The experiment was laid out in Randomized Complete Block Design (RCBD) with four replications within each location. Each line was tested for multiple quality traits that included grain hardness, protein content, dough mixing properties and bread baking quality using Single Kernel Characterization System (SKCS), Near-Infrared Reflectance Spectrometry (NIRS) analysis, mixograph and the Sodium Dodecyl Sulfate Sedimentation (SDSS) test. Genetic linkage map construction was carried out with 116 single nucleotide polymorphism (SNP) markers in the RILs. Then composite interval mapping was carried out to identify QTLs associated with quality traits. The SDSS column height was positively correlated across four environments. Similarly, it was found to have significant positive correlation with mixing tolerance and peak time within and also across locations. However, the SDSS was negatively correlated with the hardness index. The protein percent was not significant with any of the quality traits within and across environments. We were able to detect many QTLs for different quality traits but most of them were site specific. Only a few QTLs were consistent across environments. Most of the QTLs for quality traits i.e., SDSS, peak time, mixing tolerance and hardness index were identified on chromosome 1B. We were able to detect overlapped QTLs for SDSS column height and mixing tolerance on chromosome 1B. Furthermore, overlapping QTLs for mixing tolerance and peak time were detected on an unknown chromosome. We also detected overlapping QTLs for hardness index on chromosome 1B. We identified one stable QTL for SDSS column height on chromosome 4B. This QTL was detected based on the coefficient of variation (CV) for SDSS in four different environments.

Chez les bactéries à Gram-négatif, deux systèmes très bien conservés et essentiels à la survie de la cellule bactérienne ont été identifiés : les systèmes Tol et TonB. Ces deux systèmes utilisent la force proton motrice, issue de la membrane interne et transfert l’énergie associée pour le transport actif de molécules (TonB) ou nécessaire au maintien de l’intégrité membranaire (Tol). Ces 2 systèmes ont été détournés de leurs fonctions initiales et parasités par les colicines, leur conférant un rôle primordial dans le mécanisme d’import de la colicine. Une colicine est une bactériocine (toxine) produite par Escherichia coli pour tuer des souches apparentées. Ce sont des toxines spécifiques et hautement actives. Cependant E.coli a développé des mécanismes de protection afin de résister à l’action cytotoxique des colicines. Ces mécanismes de résistance consistent essentiellement à produire des protéines d’immunité, qui vont pour la plupart se fixer sur le domaine catalytique de la colicine et l’empêcher d’exercer son action létale. La bactérie Yersinia pestis, agent de la peste, possède une colicin-like bactériocine, la pesticine, dont l’activité est de dégrader le peptidoglycane. L’action de la pesticine est inhibée par une protéine d’immunité, Pim, localisée dans le périplasme. Le principal objectif de ce projet est de comprendre les mécanismes d’inhibition de la pesticine par sa protéine d’immunité, grâce à des données biochimiques et structurales, mais aussi d’apporter des solutions pour contourner ce problème de résistance. La structure de la pesticine révèle des homologies structurales avec le T4 lysozyme du bactériophage T4. Pour contourner le problème de la résistance bactérienne liée à la protéine d’immunité, une solution a été de fusionner le domaine de réception/translocation de la pesticine avec le T4 lysozyme. Nous avons ainsi pu créer et résoudre la structure tridimensionnelle d’une protéine chimère fonctionnelle, capable de se fixer sur FyuA (récepteur de la pesticine) et tuer une souche exprimant ce récepteur et dont l’activité létale n’est pas inhibée par Pim. / In Gram-negative bacteria, two essential systems for cell survival have been characterized: the Tol and TonB system. Both Ton and Tol systems are very well conserved in Gram-negative bacteria and coupled to the proton motive force across the inner membrane, acting as energy transducers for active transport (Ton) or maintenance of outer envelope integrity (Tol). Both systems have been embezzled from their primary function and hijacked by colicins as part of the colicin killing pathway. Colicin is a bacteriocin (toxin) produced by and toxic to some strains of Escherichia coli. Colicins are highly effective toxins. However E.coli could develop protective mechanisms to resist to colicin cytotoxic effect. These mechanisms essentially consist to produce an immunity protein. These proteins bind to colicin catalytic domain and inhibit its lethal activity. Yersinia pestis, plague agent, possesses its own colicin-like bacteriocin, Pesticin, which degrades murein. Pesticin activity is inhibited by an immunity protein, Pim, localized in the periplasm. The main goal of this project is to understand inhibition mechanisms between Pim and Pesticin by biochemical and structural data and to provide solution to overcome the resistance issue, since Pesticin was thought to be used as antimicrobial agent. The Pesticin structure has revealed that Pesticin share structural homologies with the T4 lysozyme from the bacteriophage T4. To overcome the resistance issue due to the immunity protein, one solution has been to fuse the Pesticin binding/translocation domain with the T4 lysozyme. Thus, we could engineered and solved the three-dimensional structure of a chimera protein, able to bind FyuA (Pesticin physiological receptor) and kill a FyuA expressing strain, in which the lethal activity is not affected by Pim.

Cellular therapy is emerging as a clinically viable strategy in the field of solid organ transplantation, where it is expected to reduce the dependency on conventional immunosuppression. This has produced a demand for highly sensitive methods to monitor the persistence and tissue distribution of administered cells in vivo. However, tracking cells presents significant challenges. In many cases transplanted cells are autologous with the immune system of the transplant recipient, and hence are invisible to typical methods of detection. To enable their differentiation, the cells must be labelled with a suitable, non-toxic and long lifetime label, prior to their administration to patients. In addition, administered cells represent only a small fraction of the recipient's endogenous cells, which necessitates the use of an extremely sensitive detection method. Laser ablation – inductively coupled plasma – mass spectrometry (LA-ICP-MS) is an exquisitely sensitive analytical technique, capable of imaging trace elements in complex samples, at high spatial resolution.

ENGLISH: This study looks at the bereavement of adolescents left orphaned by and vulnerable to the HIV and Aids crisis that is crippling the continent of Africa. Their bereavement and the psycho-spiritual issues relating to this bereavement are examined by means of postfoundationalism as an approach to practical theology along with the narrative approach to research and therapy. This is done by integrating these approaches with the art of storytelling within the unique African context. By listening to the stories of ten adolescents under the care of PEN, a Non Governmental Organisation (NGO), this research gives them the opportunity to express their own unique stories of bereavement. Stories that would otherwise have been silenced by the wave of bereavement in the wake of countless deaths worldwide due to the HIV and Aids infection. It looks holistically at the multiple losses these adolescents have suffered and consequently how this has affected them not only physically, but also especially emotionally and spiritually. In light of the above, this research attempts to show how these adolescents are in the process of – by means of storytelling – reformulating the story of their lives and the lives of those they care about in the true spirit of Ubuntu to find hope anew in the proverbial pot of gold at the end of the rainbow. AFRIKAANS: Hierdie studie fokus op die verlies wat tieners ervaar wat wees gelaat is deur die MIV en Vigs pandemie wat besig is om die vasteland van Afrika te verlam. Hulle rousmart en die gepaardgaande psigies-spirituele aangeleenthede word ondersoek deur middel van die postfondamentele benadering tot praktiese teologie in samehang met die narratiewe benadering tot navorsing en terapie. Dit word gedoen deur die integrasie van hierdie benaderings met die vertelkuns binne die unieke Afrika konteks. Deur te luister na die stories van tien tieners onder die sorg van PEN, ‘n Nie- Regeringsorganisasie (NRO), gun hierdie navorsing hulle die geleentheid om hul eie unieke stories van smart te vertel. Stories wat andersins verlore sou gegaan het in die golf van verlies wat volg op die ontelbare getal sterftes wêreldwyd as gevolg van MIV en Vigs besetting. Daar word holisties gekyk na die veelvoudige verliese wat hierdie tieners beleef het en gevolglik hoe dit hulle nie net fisies nie, maar ook emosioneel en geestelik beïnvloed. Asook hoe hulle in staat is om – deur die gebruikmaking van stories – hul lewensstorie te hervertel asook die lewens van diegene naby aan hulle, in die ware gees van Ubuntu, om nuwe hoop in die spreekwoordelike pot goud aan die einde van die reënboog te vind. SEPEDI: Dinyakišišo tše di lebelela go hlokofalelwa ga bana ba mahlalagading bao ba tlogetšwego e le ditšhiwana le go ba kotsing ya mathata a HIV le Aids yeo e golofatšago khonthinente ya Afrika. Go hlokofalelwa le ditaba tša bona tša monagano le tša semoya tše di amanago le go hlokofalelwa mo di hlahlobja ka go šomiša post-foundationalism bjalo ka mokgwa wa Tiragatšo ya Thutabodumedi gammogo le mokgwakanegelo wa dinyakišišo le kalafo. Se se dirwa ka go kopanya mekgwa ye ka bokgabo bja go anega kanegelo ka tikologong ya Seafrika ye e swanago e nnoši. Ka go theeletša dikanegelo tša bana ba mahlalagading ba lesome bao ba lego ka fase ga tlhokomelo ya PEN, Mokgatlo wo e Sego wa Semmušo (NGO), dinyakišišo tše di ba fa sebaka sa go anega dikanegelo tša bona tša go hlokofalelwa tše di swanago di nnoši. Dikanegelo tše di ka bego di ile tša homotšwa ke leuba la go hlokofalelwa ka lebaka la mahu a mantši lefaseng ka bophara ka lebaka la bolwetši bja HIV le Aids. Di lebelela ka botlalo go hlokofala ga batho ba bantši mo go dirilego gore bana ba ba mahlalagading ba be le mathata le ka moo se se ba amilego e sego fela mmeleng, eupša maikutlong le meboyeng ya bona. Ka lebaka le, dinyakišišo tše di leka go bontšha ka moo bana ba ba mahlalagading ba lego gare ka tshepedišo ya – ka go šomiša go anega dikanegelo – go beakanya lefsa kanegelo ya maphelo a bona le maphelo a bao ba kgathalago ka bona ka moya wa mmakgonthe wa Botho (Ubuntu) go hwetša kholofelo ye mpsha ka pitšeng ya gauta ye e lego mafelelong a molalatladi ye go bolelwago ka yona ka se. / AFRIKAANS: Hierdie studie fokus op die verlies wat tieners ervaar wat wees gelaat is deur die MIV en Vigs pandemie wat besig is om die vasteland van Afrika te verlam. Hulle rousmart en die gepaardgaande psigies-spirituele aangeleenthede word ondersoek deur middel van die postfondamentele benadering tot praktiese teologie in samehang met die narratiewe benadering tot navorsing en terapie. Dit word gedoen deur die integrasie van hierdie benaderings met die vertelkuns binne die unieke Afrika konteks. Deur te luister na die stories van tien tieners onder die sorg van PEN, ‘n Nie- Regeringsorganisasie (NRO), gun hierdie navorsing hulle die geleentheid om hul eie unieke stories van smart te vertel. Stories wat andersins verlore sou gegaan het in die golf van verlies wat volg op die ontelbare getal sterftes wêreldwyd as gevolg van MIV en Vigs besetting. Daar word holisties gekyk na die veelvoudige verliese wat hierdie tieners beleef het en gevolglik hoe dit hulle nie net fisies nie, maar ook emosioneel en geestelik beïnvloed. Asook hoe hulle in staat is om – deur die gebruikmaking van stories – hul lewensstorie te hervertel asook die lewens van diegene naby aan hulle, in die ware gees van Ubuntu, om nuwe hoop in die spreekwoordelike pot goud aan die einde van die reënboog te vind. SEPEDI: Dinyakišišo tše di lebelela go hlokofalelwa ga bana ba mahlalagading bao ba tlogetšwego e le ditšhiwana le go ba kotsing ya mathata a HIV le Aids yeo e golofatšago khonthinente ya Afrika. Go hlokofalelwa le ditaba tša bona tša monagano le tša semoya tše di amanago le go hlokofalelwa mo di hlahlobja ka go šomiša post-foundationalism bjalo ka mokgwa wa Tiragatšo ya Thutabodumedi gammogo le mokgwakanegelo wa dinyakišišo le kalafo. Se se dirwa ka go kopanya mekgwa ye ka bokgabo bja go anega kanegelo ka tikologong ya Seafrika ye e swanago e nnoši. Ka go theeletša dikanegelo tša bana ba mahlalagading ba lesome bao ba lego ka fase ga tlhokomelo ya PEN, Mokgatlo wo e Sego wa Semmušo (NGO), dinyakišišo tše di ba fa sebaka sa go anega dikanegelo tša bona tša go hlokofalelwa tše di swanago di nnoši. Dikanegelo tše di ka bego di ile tša homotšwa ke leuba la go hlokofalelwa ka lebaka la mahu a mantši lefaseng ka bophara ka lebaka la bolwetši bja HIV le Aids. Di lebelela ka botlalo go hlokofala ga batho ba bantši mo go dirilego gore bana ba ba mahlalagading ba be le mathata le ka moo se se ba amilego e sego fela mmeleng, eupša maikutlong le meboyeng ya bona. Ka lebaka le, dinyakišišo tše di leka go bontšha ka moo bana ba ba mahlalagading ba lego gare ka tshepedišo ya – ka go šomiša go anega dikanegelo – go beakanya lefsa kanegelo ya maphelo a bona le maphelo a bao ba kgathalago ka bona ka moya wa mmakgonthe wa Botho (Ubuntu) go hwetša kholofelo ye mpsha ka pitšeng ya gauta ye e lego mafelelong a molalatladi ye go bolelwago ka yona ka se. / SEPEDI: Dinyakišišo tše di lebelela go hlokofalelwa ga bana ba mahlalagading bao ba tlogetšwego e le ditšhiwana le go ba kotsing ya mathata a HIV le Aids yeo e golofatšago khonthinente ya Afrika. Go hlokofalelwa le ditaba tša bona tša monagano le tša semoya tše di amanago le go hlokofalelwa mo di hlahlobja ka go šomiša post-foundationalism bjalo ka mokgwa wa Tiragatšo ya Thutabodumedi gammogo le mokgwakanegelo wa dinyakišišo le kalafo. Se se dirwa ka go kopanya mekgwa ye ka bokgabo bja go anega kanegelo ka tikologong ya Seafrika ye e swanago e nnoši. Ka go theeletša dikanegelo tša bana ba mahlalagading ba lesome bao ba lego ka fase ga tlhokomelo ya PEN, Mokgatlo wo e Sego wa Semmušo (NGO), dinyakišišo tše di ba fa sebaka sa go anega dikanegelo tša bona tša go hlokofalelwa tše di swanago di nnoši. Dikanegelo tše di ka bego di ile tša homotšwa ke leuba la go hlokofalelwa ka lebaka la mahu a mantši lefaseng ka bophara ka lebaka la bolwetši bja HIV le Aids. Di lebelela ka botlalo go hlokofala ga batho ba bantši mo go dirilego gore bana ba ba mahlalagading ba be le mathata le ka moo se se ba amilego e sego fela mmeleng, eupša maikutlong le meboyeng ya bona. Ka lebaka le, dinyakišišo tše di leka go bontšha ka moo bana ba ba mahlalagading ba lego gare ka tshepedišo ya – ka go šomiša go anega dikanegelo – go beakanya lefsa kanegelo ya maphelo a bona le maphelo a bao ba kgathalago ka bona ka moya wa mmakgonthe wa Botho (Ubuntu) go hwetša kholofelo ye mpsha ka pitšeng ya gauta ye e lego mafelelong a molalatladi ye go bolelwago ka yona ka se. / Thesis (PhD)--University of Pretoria, 2010. / Practical Theology / unrestricted