<p>Early processes following photon absorption by the photosynthetic pigment-protein complex photosystem I (PS I) have been the subject of decades of research, yet many questions remain in this area of study. Among the trickiest to investigate is the role of the PS I reaction center’s (RC’s) two accessory (A_‑1) chlorophyll (Chl) cofactors as primary electron donors or acceptors, oxidizing the special pair (P₇₀₀) of Chls or reducing a nominal primary electron acceptor (A₀) Chl in the first electron transfer step. Such processes, which occur on a picosecond timescale, have long been studied via ultrafast spectroscopy, though difficulty lies in distinguishing among signals from early processes, which have similar lifetimes and involve many identical pigments. In this work, we used steady-state and ultrafast optical pump-probe spectroscopies on PS I trimers from wildtype and mutant strains of the cyanobacterium <i>Synechocystis</i> sp. PCC 6803 in which an asparagine amino acid residue near A_‑1 had been replaced with methionine on one or both sides of the RC. We also conducted an identical set of experiments on mutants in which A₀ was similarly targeted, as well as studied the effects on the A₀ absorption spectrum of a third category of mutations in which a peripheral H‑bond to A₀ was lost. Steady-state absorption spectroscopy revealed that many of these mutations caused mild Chl deficiencies in the light-capturing antenna of PS I without necessarily preventing organisms’ growth. More importantly, we determined that contrary to certain hypotheses, A_‑1 is the most likely true first electron acceptor, as reasoned from observing rapid triplet state formation in double A_‑1 mutants. We also concluded from non-additive detrimental effects of single-side mutations that if one RC branch is damaged at the level of A₀ or A_‑1, electron transfer may be redirected along the intact branch. This may help explain the conservation of two functional RC branches in PS I over many generations of natural selection, despite the additional cost to organisms of manufacturing both.</p>

Thesis (MScMedSc)--Stellenbosch University, 2001. / ENGLISH ABSTRACT: The plasmid pAL5000 is a mycobacterial plasmid isolated from Mycobacterium fortuitum. It is a low copy number plasmid, which replicates in both fast growing (e.g. M. smegmatis) and slow growing (e.g. M. bovis BCG) mycobacteria. Most mycobacterial-E. coli shuttle vectors utilise the pAL5000 origin of replication. The minimum replicon consists of ORF1 (RepA), ORF2 (RepB) and the origin of replication. Dr W.R. Bourn created an E. coli-mycobacterial vector based on the pAL5000 origin of replication (pORI) and then subjected it to semi-random mutagenesis. A high copy number mutant was identified (pHIGH) and the causative mutation was tentatively identified as a 3bp deletion situated just upstream of repB. This work describes the further characterisation of the mutant plasmid. Firstly, it was shown by retransforming M. smegmatis with both the original and mutant plasmids (pORI and pHIGH), that the mutation causing the increased copy number was plasmid-encoded and not on the chromosome. Following this, it was demonstrated by simple subcloning of the region that carries the 3 bp deletion, that other pAL5000-based vectors could be converted to high copy number. In addition to this, the subcloned region was sequenced and the nature of the mutations was confirmed. The subcloning experiment confirmed that the 3bp deletion caused the high copy number phenotype. Following this, the exact copy number of pHIGH and the relative increase in copy number was determined. From this, the copy number of pORI could also be determined. The plasmid pHIGH has a copy number of approximately 54, compared to the 8 of pORI (a relative increase by a factor of 7). Because it is important for researchers to know the characteristics of the vectors that they use, especially the influence it will have on its host, stability tests and growth curves were also performed. It was seen that the higher copy number did not markedly increase the stability, however, this is because pORI is already extremely, and unexpectedly, stable in the host M. smegmatis. According to the growth curves, the increased copy number has little effect on the growth of the host M. smegmatis. Possible mechanisms for the increased copy number were then investigated. By using a promoter probe vector, the possible existence of a promoter situated between the two open reading frames of pAL5000 (repA and repB) was investigated. It was thought that the mutation might have created, or changed an existing promoter, situated between repA and repB. The results showed, however, that in both pORI and pHIGH there might be a very weak promoter upstream of repB, but the mutation did not cause any change that was measurable by the method that was used. A further possibility was that the mutation caused a change in the RNA secondary structure, which might then have an effect on the translational efficiency of RepB. It was found that the 3bp deletion in pHIGH causes a change in the local RNA secondary structure around the ribosomal binding site and the start codon, when compared to pORI (wild type). This change may cause the translation initiation rate of RepB to be different between pHIGH and pORI. Ultimately it would lead to a different ratio of RepA and RepB in the cell. / AFRIKAANSE OPSOMMING: Die plasmied pAL5000 is ‘n mikobakteriele plasmied wat vanuit Mycobacterium fortuitum gei'soleer is. Dit is ‘n lae kopie-getal plasmied wat in beide vinnig groeiende (bv. M. smegmatis) en stadig groeiende (bv. M. bovis BCG) mikobakteriee kan repliseer. Die meeste mikobakteriele-E. coli shuttle vektore gebruik die pAL5000 oorsprong van replisering. Die minimum replikon bestaan uit ORF1 (RepA), ORF2 (RepB) en die oorsprong van replisering. Dr. W.R. Bourn het ‘n E. coli-mikobakteriele vektor gemaak wat gebaseer is op die pAL5000 oorsprong van replisering (pORI), en dit onderwerp aan semi-random mutagenese. ‘n Hoë kopie-getal mutant is gei'dentifiseer (pHIGH) en die mutasie hiervoor verantwoordelik was tentatief gei'dentifiseer as ‘n 3bp delesie, net stroomop van repB. Die projek beskryf die verdere karakterisering van die mutante plasmied. Eerstens, deur M. smegmatis te hertransformeer met die plasmied DNA (pORI en pHIGH), is dit bewys dat dit mutasie wat die toename in kopie-getal veroorsaak, deur die plasmied gekodeer word, en dat dit nie ‘n mutasie op die chromosoom is nie. Hierna is dit deur eenvoudige subklonering bewys dat die gedeelte wat die 3bp delesie dra, ander pAL5000-gebaseerde vektore ook kan verander in ‘n hoër kopie-getal. Die sub-klonerings eksperiment het ook bewys dat die 3 bp delesie die oorsaak is vir die hoë kopie-getal fenotipe. Volgende is die presiese kopie-getal van pHIGH en die relatiewe toename in kopiegetal bepaal. Die kopie-getal van pORI kon vanaf hierdie data bepaal word. Die plasmied pHIGH het ‘n kopie-getal van ongeveer 54 in M. smegmatis, in vergelyking met die 8 van pORI (‘n relatiewe toename met ‘n faktor van 7). Aangesien dit vir navorsers belangrik is om die eienskappe van die vektore wat hulle gebruik, te ken, en veral die invloed wat dit op die gasheer sal hê, is stabiliteits toetse, en groeikurwes gedoen. Die hoër kopie-getal het nie die stabiliteit werklik verbeter nie, maar dit is omdat pORI alreeds uiters stabiel is in die gasheer M. smegmatis. Volgens die groeikurwes het die toename in kopie-getal ‘n minimale effek op die groei van die gasheer M. smegmatis. Moontlike meganismes vir die hoër kopie-getal is ook ondersoek. Die moontlike bestaan van ‘n promoter tussen die twee oop-leesrame van pAL5000 (repA en repB) is ondersoek deur gebruik te maak van ‘n “promoter probe” vektor. Die mutasie kon moontlik ‘n promoter geskep het, of ‘n bestaande een tussen repA en repB verander het. Die resultate het gewys dat daar in beide pORI en pHIGH moontlik ‘n baie swak promoter stroomop van repB is, maar die mutasie het nie enige veranderinge veroorsaak wat meetbaar was met die metode wat gebruik is nie. ‘n Verdere moontlikheid was dat die mutasie ‘n verandering in die RNA sekondere struktuur kon veroorsaak het, en dit mag ‘n effek hê op die translasie effektiwiteit van RepB. Daar is gevind dat, in vergelyking met pORI, het die 3bp delesie in pHIGH ‘n verandering in die lokale RNA sekondere struktuur rondom die ribosomale bindings posisie en die begin-kodon veroorsaak. Die verandering mag veroorsaak dat die translasie inisiasie tempo van RepB verskillend is vir pORI en pHIGH. Uiteindelik sal dit lei tot ‘n heeltemal ander verhouding van RepA en RepB in die sel.

<p>Evolution of enzymes with novel functional properties has gained much attention in recent years. Naturally evolved enzymes are adapted to work in living cells under physiological conditions, circumstances that are not always available for industrial processes calling for novel and better catalysts. Furthermore, altering enzyme function also affords insight into how enzymes work and how natural evolution operates. </p><p>Previous investigations have explored catalytic properties in the directed evolution of mutant libraries with high sequence variation. Before this study was initiated, functional analysis of mutant libraries was, to a large extent, restricted to uni- or bivariate methods. Consequently, there was a need to apply multivariate data analysis (MVA) techniques in this context. Directed evolution was approached by DNA shuffling of glutathione transferases (GSTs) in this thesis. GSTs are multifarious enzymes that have detoxication of both exo- and endogenous compounds as their primary function. They catalyze the nucleophilic attack by the tripeptide glutathione on many different electrophilic substrates. </p><p>Several multivariate analysis tools, <i>e.g.</i> principal component (PC), hierarchical cluster, and K-means cluster analyses, were applied to large mutant libraries assayed with a battery of GST substrates. By this approach, evolvable units (quasi-species) fit for further evolution were identified. It was clear that different substrates undergoing different kinds of chemical transformation can group together in a multi-dimensional substrate-activity space, thus being responsible for a certain quasi-species cluster. Furthermore, the importance of the chemical environment, or substrate matrix, in enzyme evolution was recognized. Diverging substrate selectivity profiles among homologous enzymes acting on substrates performing the same kind of chemistry were identified by MVA. Important structure-function activity relationships with the prodrug azathioprine were elucidated by segment analysis of a shuffled GST mutant library. Together, these results illustrate important methods applied to molecular enzyme evolution.</p>

<p>The study evaluated the Mutant Prevention Concentration (MPC) of Pradofloxacin on three Escherichia coli (E.coli) strains, 2 wildtypes and one first-step gyrA resistant mutant. We also measured the value of AUC (Under the Concentration)/MPC that prevents growth of resistant mutants. It is of importance to reach a concentration above MPC that prevent E.coli from developing resistance against the antibiotic.</p><p>We used an in vitro kinetic model where we added bacteria? and antibiotic. The culture flask was attached to a pump with an adjustable pump-speed. This made it possible to dilute the antibiotics in a satisfying elimination half-life (t1/2= 7 hours) pace. Samples were removed with a syringe at different times in the study. The samples where then cultured on agar- plates to enable counting of the viable colonies after incubation.</p><p>The optimal concentration to completely eradicate both E.coli wildtypes Nu14 and MG1655 with Pradofloxacin was Cmax ≥8 times MPC and AUC/MPC then became73. Additional experiments needs to be done on the resistant mutant LM378 before we can determine the optimal concentration. But results so far indicate that the concentration of Cmax would be about 8-12 timesMPC to completely eradicate that mutant.</p>

Head and neck squamous cell carcinoma (HNSCC) is the 6th most common type of cancer in the western hemisphere with a five-year survival rate of only 50% for patients with a localized tumor, which decreases significantly to as low as 5% for those patients with tumors that have metastasized to distant sites of the body. It has been found that both mutant p53 and epidermal growth factor receptor (EGFR) signaling pathways function to increase the expression of CXCL5, which has been identified as a key mediator in the process of tumor metastasis. Previous data from our lab suggested that the p53 homolog, p63, may function as a negative regulator of CXCL5 and that mutant p53 may inhibit this molecule to elevate CXCL5 expression levels. In the current study we utilized an model system in which the H179L p53 mutant was expressed in HN4 cells to investigate the hypothesis that mutant p53 enhances expression of CXCL5 by both interfering with p63 function and cooperating with EGFR/EPS8 signaling, leading to increased cell proliferation and motility. The results of the current study indicate a role for mutant p53 in head and neck squamous cell carcinoma proliferation, migration and tumorigenicity, possibly through enhancement of CXCL5 expression. We were able to show that mutant p53 expression caused an increase in the expression of this chemokine in addition to increasing proliferation and migration of the cells compared to the vector control. Additionally, we showed that p63 protein is a negative regulator of CXCL5 that is downregulated in the cells expressing mutant p53, which suggests that through direct interaction, mutant p53 may function to inhibit p63 function as well as target it for degradation. These results support the hypothesis that GOF mutant p53 enhances expression of CXCL5 by interfering with p63 function in cancer cells. The results of the current study results also showed that upon treatment with EGF, HN4 cells expressing mutant p53 express elevated levels of CXCL5; and that the mutant p53-expressing HN4 cells cooperate with EGFR/EPS8 signaling to further deregulate chemokine expression. These data taken together suggest there are complex interactions taking place between mutant p53, p63, EGFR signaling, and CXCL5 to regulate the biological processes that promote tumor progression that could lead to metastasis. Additional studies are needed to further elucidate the molecules involved in the mutant p53 mechanism that promotes tumorigenesis.

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

La souris "dystoniamusculorum" (Dstdt-j) résulte d'une mutation spontanée autosomale récessive d'un gène codant pour la dystonine, protéine du cytosquelette qui s'exprime normalement dans les neurones sensitifs du système nerveux périphérique, mais aussi dans de nombreuses structures du système nerveux central. Elle est caractérisée par une dégénérescence des fibres nerveuses affectant principalement les voies afférentes sensitives du système nerveux périphérique et les afférences secondaires cérébelleuses et thalamiques. Des troubles posturaux et une sévère ataxie apparaissent avec les dégénérescences. Une altération des muscles squelettiques est associée. Afin d'étudier l'incidence des troubles du transport axonal sur l'activité métabolique de la fibre nerveuse et l'impact de la dégénérescence sensitive sur les fonctions motrices, une analyse histopathologique et biochimique comparative du système nerveux central et des muscles squelettiques est effectuée sur des souris de souche B6C3Fea /a-Dstdt-j, âgées de 42 à 54 jours réparties un groupe de souris homozygotes Dstdt-j et un groupe contrôle, formé de souris homozygotes normales et hétérozygotes. En plus des dégénérescences afférentes périphériques, l'étude histopathologique montre des altérations centrales au niveau de centres segmentaires et de différentes structures du système extra-pyramidal comme le cervelet, le noyau rouge et les noyaux du pont. Une évaluation quantitative de l'activité métabolique régionale par marquage histochimique de la cytochrome oxydase (enzyme du complexe IV de la phosphorylation oxydative) est effectuée sur l'ensemble de l'encéphale et de la moelle épinière cervicale. Elle met en évidence une hyperactivité métabolique des voies de la proprioception inconsciente, affectant principalement les structures du tronc cérébral et du cervelet, et plus spécifiquement des structures motrices impliquées dans l'équilibre, le tonus musculaire et les réflexes posturaux. Une étude de l'innervation cholinergique est effectuée par marquage histochimique de l'acétylcholinestérase (AChE). Des augmentations importantes de l'activité AChE sont observées dans les structures cibles du noyau cholinergique tegmental pontique, à savoir le thalamus servant à l'activation corticale, le striatum et certains noyaux mésencéphaliques connectés au striatum, impliqués dans le contrôle des mouvements. Des altérations structuro-fonctionnelles des trois muscles observés (langue, muscle masséter et flexordigitorumsuperficialis) illustrent un tableau clinique d'hypotonicité et d'hypoactivité musculaire. Une dégénérescence partielle des fibres musculaires semble indiquer que ces modifications sont conséquentes de la lésion nerveuse plutôt que d'une atteinte intrinsèque des fibres musculaires. La présente étude sert à comprendre la physiopathologie 1) des neuropathies sensitives humaines présentant des atteintes similaires comme l'ataxie de Friedreich, ou la forme infantile de l'ataxie spino-cérébélleuse, 2) de déafférentations trigéminales pouvant survenir par compressions iatrogènes lors d'actes chirurgicaux / The "dystoniamusculorum" (Dstdt-J) mouse is the result of a recessive autosomal mutation of the dystonin (dst) gene responsible for the expression of a protein of the cytoskeleton, normally present in sensory peripheral neurons and numerous central nervous structures. The mutation is characterised by primary degeneration of peripheral afferent fibers followed by degenerative processes in secondary cerebellar and thalamic afferents. Postural reflex dysfunction and a severe ataxia occurat the same time as peripheral neurodegenerative processes. To study the impact of axonal transport alteration on neuronal activity as well as sensory degeneration on motorfunctions, histopathatological and biochemical studies have were performed on brain and skeletal muscles of B6C3Fea /a-Dstdt-j mice displayed in two groups, homozygotes Dstdt-J and controls. In addition to sensory defects, histopathological evaluation showed central alterations affecting the segmentar nuclei and motor control regions, such as cerebellum, red nucleus, and pontine nuclei. Regional metabolism assessed by cytochrome oxidase histochemistry showed hypermetabolic activity in cerebellum and motor regions of the brain stem involved in equilibrium, muscle tonicity, and postural reflexes. Brain cholinergic innervation was performed by histochemical labelling of acetylcholinesterase (AChE) activity. Enzymatic hyperactivity was observed in target structures of the cholinergic pedunculo-pontine tegmental nucleus, the thalamus, and the basal ganglia. The morphological and functional alterations observed in the three skeletal muscles (masseteric, flexor digitorum superficialis and tongue) were characterized by muscle hypotonicity and hypoactivity. A partial muscular fiber degeneration was observed, probably as a result of sensory denervation rather than an intrinsic defect of muscle fibers. Several sensory neuropathies (Friedreich's ataxia or infant-onset spinocerebellar ataxia) have similar clinicopathological features. The present studies are of interest in understanding the physiopathology of these lesions. They can also contribute in the study of the pathological effects of trigeminal deafferentation induced by compression

Estudos empíricos têm mostrado que a Análise de Mutantes – um dos critérios de teste baseado em erros – é bastante eficaz em revelar a presença de erros. Entretanto, seu alto custo, decorrente principalmente do grande número de mutantes gerados, tem motivado a proposição de diversas abordagens alternativas para a sua aplicação. Um estudo relevante nesse sentido resultou na determinação de um conjunto essencial de operadores de mutação para a linguagem Fortran, mostrando-se que é possível reduzir o custo de aplicação do critério, preservando um alto grau de adequação em relação à Análise de Mutantes. Alguns estudos também têm demonstrado que a redução da eficácia não é significativa. Este trabalho tem como objetivo investigar alternativas pragmáticas para a aplicação do critério Análise de Mutantes e, nesse contexto, é proposto um procedimento para a determinação de um conjunto essencial de operadores de mutação para a linguagem C, a partir dos operadores implementados na ferramenta Proteum. Procurando aplicar e validar o procedimento proposto, dois grupos distintos de programas são utilizados. Para ambos os grupos, o conjunto essencial obtido apresenta resultados bastante significativos quanto à redução de custo, com um decréscimo muito pequeno no grau de adequação em relação à Análise de Mutantes. Estratégias para evoluir e refinar um conjunto essencial para diferentes domínios de aplicação também são investigadas. / Mutation Analysis – one of the error based criteria – has been found to be effective on revealing faults. However, its high cost, due to the high number of mutants created, has motivated the proposition of many alternative approaches for its application. In this perspective, a relevant study resulted on the determination of a sufficient mutant operator set for Fortran, indicating that it is possible to have a large cost reduction of mutation testing, preserving a high mutation score. Some studies have also shown that the reduction on the effectiveness is not significant. This work aims to investigate pragmatic alternatives for mutation analysis application and, in this context, a procedure for the determination of a sufficient mutant operators set for C is proposed, using Proteum testing tool. Aiming to apply and validate the proposed procedure, two different groups of programs are used. For both of them, the sufficient mutant operator set presents very significant results in terms of cost reduction, with a very small reduction on the mutation score. Strategies to evolve and refine an essential mutant operator set to different application domains are also investigated.

A conjuntura tecnológica atual confere profundas mudanças na política, na economia e nas relações sociais, sendo a ubiquidade da informática um dos principais vetores de difusão dessa transformação. O design gráfico, evidentemente, está sujeito a essa interferência, e as marcas mutantes, que são identidades visuais que alteram de modo sistemático sua forma, cor ou tipografia, parecem ser uma expressão dessa modificação. O escopo deste trabalho consiste na investigação da percepção de pesquisadores, profissionais e clientes do design gráfico acerca das oportunidades e dos riscos da escolha por essas identidades visuais mutantes. Para tanto, foi realizada uma pesquisa bibliográfica com vistas a se compreender a história e o contexto atual das identidades visuais, além de uma análise qualitativa, por meio de entrevistas, para tentar entender em que medida as identidades visuais mutantes conseguem transmitir, com clareza, a essência das organizações que as utilizam e identificar para quais setores econômicos esse tipo de marca é mais indicado. / The current technological environment confers profound changes in politics, economics and social relations, being the ubiquity of computing one of the main vectors of dissemination of this transformation. The graphic design is, of course, subject to this interference, and the mutant brands, which are visual identities that systematically alter its shape, color and typography, seem to be an expression of this change. The scope of this work consists on the investigation of the perceptions of researchers, professionals and clients of graphic design related to the opportunities and risks of choice for these mutants visual identities. Therefore, a literature review with a view to understand the history and current context of visual identities was performed, and a qualitative analysis, through interviews, to try to understand to what extent the changing visual identity can convey, with clarity, the essence of the organizations that use them and to identify to which economic sectors this kind of brand is most appropriate.

Rett syndrome (RTT) is a severe neurological disorder that affects approximately 1:10000 girls. Classical RTT is defined by a developmental regression phase and subsequent stabilisation of diagnostic criteria, which include partial or complete loss of spoken language, dyspraxic gait and stereotypic hand movements such as hand mouthing. RTT is a monogenic disorder, with the majority of cases being due to loss-of-function mutations in MeCP2 (methyl-CpG binding protein 2). Due to this clear genotype-phenotype link multiple RTT mouse models have been used to elucidate the molecular details, and consequent neuropathogenesis, of this complex neurological disease, as well as for the development of potential therapeutics for RTT. However, as the molecular details become clearer, the need for a simpler model system becomes evident. Human induced pluripotent stem cells (hiPSCs) generated from RTT patient fibroblasts are an option; however the handling of these cells is laborious, time-consuming and expensive and they often differentiate into a heterogeneous population of cells. To explore an alternative human model system I have been genetically engineering and experimenting with the human dopaminergic LUHMES cell line. LUHMES cells are an immortalised pre-neuronal cell line derived from an 8-week old, female foetus and can readily be differentiated into a homogeneous population of mature, electrically active neurons in just one week. In this thesis I have assessed the phenotypic properties of the wild-type cell line, demonstrated the ease of genetic manipulation of LUHMES cells by CRISPR/Cas9 approaches, generated seven mutant MECP2 LUHMES cell lines and explored the potential of protein therapy as a therapeutic approach for RTT. The LUHMES cell line proves to be extremely easy to handle and robust and has yielded novel molecular insights into the function of MeCP2 in human neurons. In particular, MeCP2-null cells show a striking relationship between the level of gene body methylation and the extent of transcriptional upregulation when compared to wild-type neurons. In contrast neurons that express a form of MeCP2 that can bind to DNA but cannot recruit a transcriptional corepressor complex (the R306C mutant) do not exhibit substantial gene expression alterations, yet do display a consistent decrease in total RNA amount. This decrease in total RNA is recapitulated in MeCP2-null LUHMES-derived neurons and in brain regions from MeCP2-R306C mice. The requirement for functional DNA binding for normal gene-body methylation dependent gene repression is demonstrated by assessing LUHMES cells that overexpress MeCP2-R111G, a protein that cannot bind to DNA. Furthermore, overexpression of the MeCP2-R306C protein highlights the importance of NCoR binding for normal gene repression, but also demonstrates that MeCP2-R306C protein retains some gene repression activity. Thinking more broadly, this cell line also has applications as a model system for a variety of other neurological disorders; as a simplified model system to elucidate molecular and neurological phenotypes, and as a relevant human system that can be cultured in a high-throughput manner for testing therapeutic strategies.