The periplasmic domain of the barrel assembly machinery protein A (BamA) from Escherichia coli assists folding of outer membrane protein A

The assembly of outer membranes of the cell wall of Gram-negative bacteria and of various organelles of eukaryotic cells requires the evolutionarily conserved β-barrel-assembly machinery (BAM) complex. This thesis describes the biochemical and biophysical properties of the periplasmic domain of the β-barrel assembly machinery protein A (PD-BamA) of the E. coli BAM complex, its effect on insertion and folding of the Outer membrane protein A (OmpA) into lipid bilayers and the identification of regions of PD-BamA that may be involved in protein-protein interactions. The secondary structure of PD-BamA in mixed lipid bilayers, analyzed by Circular dichroism (CD) spectroscopy, contained less β-sheet at an increased content of phosphatidylglycerol (PG) in the lipid membrane. This result showed membrane binding, albeit only in the presence of negatively charged lipids. Fluorescence spectroscopy demonstrated that PD-BamA only binds to lipid bilayers containing the negatively charged DOPG, confirming the results of CD spectroscopy. PD-BamA did not bind to zwitterionic but overall neutral lipid bilayers. PD-BamA bound to OmpA at a stoichiometry of 1:1. PD-BamA strongly facilitated insertion and folding of OmpA into lipid membranes. Kinetics of PD-BamA mediated folding of OmpA was well described by two parallel folding processes, a fast folding process and a slow folding process, differing by 2-3 orders of magnitude in their rate constants. The folding yields of OmpA depended on the concentration of lipid membranes and also on the lipid head groups. The presence of PD-BamA resulted in increased folding yields of OmpA in negatively charged DOPG, but PD-BamA did not affect the folding kinetics of OmpA into bilayers of zwitterionic but overall neutral lipids. The efficiency of folding and insertion of OmpA into lipid bilayers strongly depended on the ratio PD-BamA/OmpA and was optimal at equimolar concentrations of PD-BamA and OmpA. To examine complexes of unfolded OmpA with PD-BamA in more detail, site-directed spectroscopy was used to explore contact regions in both, PD-BamA and OmpA. Similarly, contact regions were also investigated for another protein complex formed by PD-BamA and the lipoprotein BamD. The obtained data suggest, that the site of interaction on PD-BamA for OmpA might be oriented towards the exterior environment away from the preceding POTRA domains, but that PD-BamA is oriented with its short α-helix α1 of POTRA domain 5 towards the C-terminal end of BamD.

Engineered zeolitic materials: synthesis and application

Les zéolithes étant des matériaux cristallins microporeux ont démontré leurs potentiels et leur polyvalence dans un nombre très important d’applications. Les propriétés uniques des zéolithes ont poussé les chercheurs à leur trouver constamment de nouvelles utilités pour tirer le meilleur parti de ces matériaux extraordinaires. Modifier les caractéristiques des zéolithes classiques ou les combiner en synergie avec d’autres matériaux se trouvent être deux approches viables pour trouver encore de nouvelles applications. Dans ce travail de doctorat, ces deux approches ont été utilisées séparément, premièrement avec la modification morphologique de la ZSM-12 et deuxièmement lors de la formation des matériaux de type coeur/coquille (silice mésoporeuses@silicalite-1). La ZSM-12 est une zéolithe à haute teneur en silice qui a récemment attiré beaucoup l’attention par ses performances supérieures dans les domaines de l’adsorption et de la catalyse. Afin de synthétiser la ZSM-12 avec une pureté élevée et une morphologie contrôlée, la cristallisation de la zéolithe ZSM-12 a été étudiée en détail en fonction des différents réactifs chimiques disponibles (agent directeur de structure, types de silicium et source d’aluminium) et des paramètres réactionnels (l’alcalinité, ratio entre Na, Al et eau). Les résultats présentés dans cette étude ont montré que, contrairement à l’utilisation du structurant organique TEAOH, en utilisant un autre structurant, le MTEAOH, ainsi que le Al(o-i-Pr)3, cela a permis la formation de monocristaux ZSM-12 monodisperses dans un temps plus court. L’alcalinité et la teneur en Na jouent également des rôles déterminants lors de ces synthèses. Les structures de types coeur/coquille avec une zéolithe polycristalline silicalite-1 en tant que coquille, entourant un coeur formé par une microsphère de silice mésoporeuse (tailles de particules de 1,5, 3 et 20-45 μm) ont été synthétisés soit sous forme pure ou chargée avec des espèces hôtes métalliques. Des techniques de nucléations de la zéolithe sur le noyau ont été utilisées pour faire croitre la coquille de façon fiable et arriver à former ces matériaux. C’est la qualité des produits finaux en termes de connectivité des réseaux poreux et d’intégrité de la coquille, qui permet d’obtenir une stéréosélectivité. Ceci a été étudié en faisant varier les paramètres de synthèse, par exemple, lors de prétraitements qui comprennent ; la modification de surface, la nucléation, la calcination et le nombre d’étapes secondaires de cristallisation hydrothermale. En fonction de la taille du noyau mésoporeux et des espèces hôtes incorporées, l’efficacité de la nucléation se révèle être influencée par la technique de modification de surface choisie. En effet, les microsphères de silice mésoporeuses contenant des espèces métalliques nécessitent un traitement supplémentaire de fonctionnalisation chimique sur leur surface externe avec des précurseurs tels que le (3-aminopropyl) triéthoxysilane (APTES), plutôt que d’utiliser une modification de surface avec des polymères ioniques. Nous avons également montré que, selon la taille du noyau, de deux à quatre traitements hydrothermaux rapides sont nécessaires pour envelopper totalement le noyau sans aucune agrégation et sans dissoudre le noyau. De tels matériaux avec une enveloppe de tamis moléculaire cristallin peuvent être utilisés dans une grande variété d’applications, en particulier pour de l’adsorption et de la catalyse stéréo-sélective. Ce type de matériaux a été étudié lors d’une série d’expériences sur l’adsorption sélective du glycérol provenant de biodiesel brut avec des compositions différentes et à des températures différentes. Les résultats obtenus ont été comparés à ceux utilisant des adsorbants classiques comme par exemple du gel de sphères de silice mésoporeux, des zéolithes classiques, silicalite-1, Si-BEA et ZSM-5(H+), sous forment de cristaux, ainsi que le mélange physique de ces matériaux références, à savoir un mélange silicalite-1 et le gel de silice sphères. Bien que le gel de sphères de silice mésoporeux ait montré une capacité d’adsorption de glycérol un peu plus élevée, l’étude a révélé que les adsorbants mésoporeux ont tendance à piéger une quantité importante de molécules plus volumineuses, telles que les « fatty acid methyl ester » (FAME), dans leur vaste réseau de pores. Cependant, dans l’adsorbant à porosité hiérarchisée, la fine couche de zéolite silicalite-1 microporeuse joue un rôle de membrane empêchant la diffusion des molécules de FAME dans les mésopores composant le noyau/coeur de l’adsorbant composite, tandis que le volume des mésopores du noyau permet l’adsorption du glycérol sous forme de multicouches. Finalement, cette caractéristique du matériau coeur/coquille a sensiblement amélioré les performances en termes de rendement de purification et de capacité d’adsorption, par rapport à d’autres adsorbants classiques, y compris le gel de silice mésoporeuse et les zéolithes.

New dimeric supramolecular structure of mixed (phthalocyaninato)(porphyrinato)-europium(III) sandwiches : preparation and spectroscopic characteristics

The mixed double-decker Eu\[Pc(15C5)4](TPP) (1) was obtained by base-catalysed tetramerisation of 4,5-dicyanobenzo-15-crown-5 using the half-sandwich complex Eu(TPP)(acac) (acac = acetylacetonate), generated in situ, as the template. For comparative studies, the mixed triple-decker complexes Eu2\[Pc(15C5)4](TPP)2 (2) and Eu2\[Pc(15C5)4]2(TPP) (3) were also synthesised by the raise-by-one-story method. These mixed ring sandwich complexes were characterised by various spectroscopic methods. Up to four one-electron oxidations and two one-electron reductions were revealed by cyclic voltammetry (CV) and differential pulse voltammetry (DPV). As shown by electronic absorption and infrared spectroscopy, supramolecular dimers (SM1 and SM3) were formed from the corresponding double-decker 1 and triple-decker 3 in the presence of potassium ions in MeOH/CHCl3.

Raman spectroscopic characteristics of phthalocyanine and naphthalocyanine in sandwich-type phthalocyaninato and porphyrinato rare earth complexes Part 5. – Raman spectroscopic characteristics of naphthalocyanine in mixed [tetrakis(4-tert-butylphenyl)porphyrinato]-(naphthalocyaninato) rare earth double-deckers

Raman spectra were recorded in the range 400–1800 cm−1 for a series of 15 mixed \[tetrakis(4-tert-butylphenyl)porphyrinato](2,3-naphthalocyaninato) rare earth double-deckers M(TBPP)(Nc) (M = Y; La–Lu except Pm) using laser excitation at 632.8 and 785 nm. Comparisons with bis(naphthalocyaninato) rare earth counterparts reveal that the vibrations of the metallonaphthalocyanine M(Nc) fragment dominate the Raman features of M(TBPP)(Nc). When excited with radiation of 632.8 nm, the most intense vibration appears at about 1595 cm−1, due to the naphthalene stretching. These complexes exhibit the marker Raman band for Nc•− as a medium-intense band in the range 1496–1507 cm−1, attributed to the coupling of pyrrole and aza stretching, while the marker Raman band of Nc2− in intermediate-valence Ce(TBPP)(Nc) appears as a strong band at 1493 cm−1 and is due to the isoindole stretchings. By contrast, when excited with radiation of 785 nm that is in close resonance with the main Q absorption band of the naphthalocyanine ligand, the ring radial vibrations at ca 680 and 735 cm−1 for MIII(TBPP)(Nc) are selectively intensified and are the most intense bands. For the cerium double-decker, the most intense vibration also acting as the marker Raman band of Nc2− appears at 1497 cm−1 with contributions from both pyrrole CC and aza CN stretches. The same vibrational modes show weak to medium intensity scattering at 1506–1509 cm−1 for MIII(TBPP)(Nc) and this is the marker Raman band of Nc•− when thus excited. The scatterings due to the Nc breathings, ring radial vibration, aza group stretchings, naphthalene stretchings, benzoisoindole stretchings and the coupling of pyrrole CC and aza CN stretchings in MIII(TBPP)(Nc) are all slightly blue shifted along with the decrease in rare earth ionic radius, confirming the effects of increased ring–ring interactions on the Raman characteristics of naphthalocyanine in the mixed ring double-deckers.

Membrane associated transporter protein gene (SLC45A2) and the genetic basis of normal human pigmentation variation

This work is concerned with the genetic basis of normal human pigmentation variation. Specifically, the role of polymorphisms within the solute carrier family 45 member 2 (SLC45A2 or membrane associated transporter protein; MATP) gene were investigated with respect to variation in hair, skin and eye colour ― both between and within populations. SLC45A2 is an important regulator of melanin production and mutations in the gene underly the most recently identified form of oculocutaneous albinism. There is evidence to suggest that non-synonymous polymorphisms in SLC45A2 are associated with normal pigmentation variation between populations. Therefore, the underlying hypothesis of this thesis is that polymorphisms in SLC45A2 will alter the function or regulation of the protein, thereby altering the important role it plays in melanogenesis and providing a mechanism for normal pigmentation variation. In order to investigate the role that SLC45A2 polymorphisms play in human pigmentation variation, a DNA database was established which collected pigmentation phenotypic information and blood samples of more than 700 individuals. This database was used as the foundation for two association studies outlined in this thesis, the first of which involved genotyping two previously-described non-synonymous polymorphisms, p.Glu272Lys and p.Phe374Leu, in four different population groups. For both polymorphisms, allele frequencies were significantly different between population groups and the 272Lys and 374Leu alleles were strongly associated with black hair, brown eyes and olive skin colour in Caucasians. This was the first report to show that SLC45A2 polymorphisms were associated with normal human intra-population pigmentation variation. The second association study involved genotyping several SLC45A2 promoter polymorphisms to determine if they also played a role in pigmentation variation. Firstly, the transcription start site (TSS), and hence putative proximal promoter region, was identified using 5' RNA ligase mediated rapid amplification of cDNA ends (RLM-RACE). Two alternate TSSs were identified and the putative promoter region was screened for novel polymorphisms using denaturing high performance liquid chromatography (dHPLC). A novel duplication (c.–1176_–1174dupAAT) was identified along with other previously described single nucleotide polymorphisms (c.–1721C>G and c.–1169G>A). Strong linkage disequilibrium ensured that all three polymorphisms were associated with skin colour such that the –1721G, +dup and –1169A alleles were associated with olive skin in Caucasians. No linkage disequilibrium was observed between the promoter and coding region polymorphisms, suggesting independent effects. The association analyses were complemented with functional data, showing that the –1721G, +dup and –1169A alleles significantly decreased SLC45A2 transcriptional activity. Based on in silico bioinformatic analysis that showed these alleles remove a microphthalmia-associated transcription factor (MITF) binding site, and that MITF is a known regulator of SLC45A2 (Baxter and Pavan, 2002; Du and Fisher, 2002), it was postulated that SLC45A2 promoter polymorphisms could contribute to the regulation of pigmentation by altering MITF binding affinity. Further characterisation of the SLC45A2 promoter was carried out using luciferase reporter assays to determine the transcriptional activity of different regions of the promoter. Five constructs were designed of increasing length and their promoter activity evaluated. Constitutive promoter activity was observed within the first ~200 bp and promoter activity increased as the construct size increased. The functional impact of the –1721G, +dup and –1169A alleles, which removed a MITF consensus binding site, were assessed using electrophoretic mobility shift assays (EMSA) and expression analysis of genotyped melanoblast and melanocyte cell lines. EMSA results confirmed that the promoter polymorphisms affected DNA-protein binding. Interestingly, however, the protein/s involved were not MITF, or at least MITF was not the protein directly binding to the DNA. In an effort to more thoroughly characterise the functional consequences of SLC45A2 promoter polymorphisms, the mRNA expression levels of SLC45A2 and MITF were determined in melanocyte/melanoblast cell lines. Based on SLC45A2’s role in processing and trafficking TYRP1 from the trans-Golgi network to stage 2 melanosmes, the mRNA expression of TYRP1 was also investigated. Expression results suggested a coordinated expression of pigmentation genes. This thesis has substantially contributed to the field of pigmentation by showing that SLC45A2 polymorphisms not only show allele frequency differences between population groups, but also contribute to normal pigmentation variation within a Caucasian population. In addition, promoter polymorphisms have been shown to have functional consequences for SLC45A2 transcription and the expression of other pigmentation genes. Combined, the data presented in this work supports the notion that SLC45A2 is an important contributor to normal pigmentation variation and should be the target of further research to elucidate its role in determining pigmentation phenotypes. Understanding SLC45A2’s function may lead to the development of therapeutic interventions for oculocutaneous albinism and other disorders of pigmentation. It may also help in our understanding of skin cancer susceptibility and evolutionary adaptation to different UV environments, and contribute to the forensic application of pigmentation phenotype prediction.

Raman spectroscopic study of the mixed anion mineral Yecoraite Bi5Fe3O9(Te4+O3)(Te6+O4)2•9H2O

Tellurates are rare minerals as the tellurate anion is readily reduced to the tellurite ion. Often minerals with both tellurate and tellurite anions in the mineral are found. An example of such a mineral containing tellurate and tellurite is yecoraite. Raman spectroscopy has been used to study this mineral, the exact structure of which is unknown. Two Raman bands at 796 and 808 cm-1 are assigned to the ν1 (TeO4)2- symmetric and ν3 (TeO3)2- antisymmetric stretching modes and Raman bands at 699 cm-1 are attributed to the the ν3 (TeO4)2- antisymmetric stretching mode and the band at 690 cm-1 to the ν1 (TeO3)2- symmetric stretching mode. The intense band at 465 cm-1 with a shoulder at 470 cm-1 is assigned the (TeO4)2- and (TeO3)2- bending modes. Prominent Raman bands are observed at 2878, 2936, 3180 and 3400 cm-1. The band at 3936 cm-1 appears quite distinct and the observation of multiple bands indicates the water molecules in the yecoraite structure are not equivalent. The values for the OH stretching vibrations listed provide hydrogen bond distances of 2.625 Å (2878 cm-1), 2.636 Å (2936 cm-1), 2.697 Å (3180 cm-1) and 2.798 Å (3400 cm-1). This range of hydrogen bonding contributes to the stability of the mineral. A comparison of the Raman spectra of yecoraite with that of tellurate containing minerals kuranakhite, tlapallite and xocomecatlite is made.

Expression of Potato virus Y cytoplasmic inclusion protein in tobacco results in disorganization of parenchyma cells, distortion of epidermal cells, and induces mitochondrial and chloroplast abnormalities, formation of membrane whorls and atypical lipid accumulation

Infection of plant cells by potyviruses induces the formation of cytoplasmic inclusions ranging in size from 200 to 1000 nm. To determine if the ability to form these ordered, insoluble structures is intrinsic to the potyviral cytoplasmic inclusion protein, we have expressed the cytoplasmic inclusion protein from Potato virus Y in tobacco under the control of the chrysanthemum ribulose-1,5-bisphosphate carboxylase small subunit promoter, a highly active, green tissue promoter. No cytoplasmic inclusions were observed in the leaves of transgenic tobacco using transmission electron microscopy, despite being able to clearly visualize these inclusions in Potato virus Y infected tobacco leaves under the same conditions. However, we did observe a wide range of tissue and sub-cellular abnormalities associated with the expression of the Potato virus Y cytoplasmic inclusion protein. These changes included the disruption of normal cell morphology and organization in leaves, mitochondrial and chloroplast internal reorganization, and the formation of atypical lipid accumulations. Despite these significant structural changes, however, transgenic tobacco plants were viable and the results are discussed in the context of potyviral cytoplasmic inclusion protein function.

Difference-based meta-analytic procedures for between-participant and/or within-participant designs : a tutorial review for sports and exercise scientists

The aim of this paper is to provide a contemporary summary of statistical and non-statistical meta-analytic procedures that have relevance to the type of experimental designs often used by sport scientists when examining differences/change in dependent measure(s) as a result of one or more independent manipulation(s). Using worked examples from studies on observational learning in the motor behaviour literature, we adopt a random effects model and give a detailed explanation of the statistical procedures for the three types of raw score difference-based analyses applicable to between-participant, within-participant, and mixed-participant designs. Major merits and concerns associated with these quantitative procedures are identified and agreed methods are reported for minimizing biased outcomes, such as those for dealing with multiple dependent measures from single studies, design variation across studies, different metrics (i.e. raw scores and difference scores), and variations in sample size. To complement the worked examples, we summarize the general considerations required when conducting and reporting a meta-analysis, including how to deal with publication bias, what information to present regarding the primary studies, and approaches for dealing with outliers. By bringing together these statistical and non-statistical meta-analytic procedures, we provide the tools required to clarify understanding of key concepts and principles.

Kava Anxiety Depression Spectrum Study (KADSS): a mixed methods RCT using an aqueous extract of Piper methysticum

Objectives: To report on the design, significance and potential impacts of the first documented human clinical trial assessing the anxiolytic and thymoleptic efficacy of an aqueous monoextract of Piper methysticum (kava). The significance of the qualitative element of our clinical trial is also explored. The Kava Anxiety Depression Spectrum Study (KADSS) is a 3-week placebocontrolled, double-blind, cross-over trial involving 60 adult participants (18—65) with elevated stable anxiety and varying levels of depressive symptoms. Aims: The aims of KADSS are: (1) to determine whether an aqueous standardised extract of kava is effective for the treatment of anxiety; (2) to assess the effects of kava on differing levels of depression; and (3) to explore participants’ experience of taking kava via qualitative research. The study also provides preliminary assessment of the safety of an aqueous extract of kava in humans. Conclusion: If results reveal that the aqueous kava preparation exerts significant anxiolytic effects and appears safe, potentially beneficial impacts may occur. Data supporting a safe and effective kava extract may encourage a re-introduction of kava to Europe, UK and Canada. This may provide a major socioeconomic benefit to Pacific Island nations, and to sufferers of anxiety disorders.