Membranproteine spielen eine wichtige Rolle in vielen biochemischen Prozessen der Zelle, wie zum Beispiel der Signaltransduktion, der Zelladhesion oder auch der Erkennung von Krankheitserregern. Viele dieser Proteine sind von Bedeutung für die Entwicklung neuer innovativer Medikamente. Somit hat auch die Entwicklung von Sensoren, die die Untersuchung von Membranproteinen in ihrer natürlichen Umgebung erlauben an Bedeutung gewonnen [1]. Thema dieser Doktorarbeit war die Entwicklung von Analysekonzepten die es ermöglichen unterschiedliche Aspekte von Membraninteraktionen zu untersuchen und zu quantifizieren. Als Analysemethode wurde dafür reflektometrische Interferenz Spektroskopie (RIfS) eine markierungsfreie, optische Methode verwendet. RIfS erlaubt es die Höhe dünner transparenter Filme zu bestimmen, indem das Weißlicht-Reflexionspektrum eines solchen Films aufgezeichnet wird. Durch die Überlagerung der in dem Film mehrfach reflektierten Teilstrahlen entsteht ein Interferenzmuster im Reflexionsspektrum, welches Aufschluß gibt über die Schichtdicke und den Brechungsindex des transparenten Films. Es wurde bereits gezeigt, dass RIfS eine geeignete Methode zur Untersuchung von Protein-ProteinWechselwirkungen ist [2]. Aus diesem Grund wurde RIfS als Detektionsverfahren für die Entwicklung eines Membransensors gewählt. Im Laufe dieser Arbeit entstanden zwei Aufbauten für reflektometrische Messungen. Ein Standard RIfS Aufbau und ein Instrument das die Methode mit Fluoreszenz-Mikroskopie kombiniert. Um dieWechselwirkung von Proteinen selbst und Proteinen mit Membranbestandteilen wie Lipiden zu untersuchen, wurde ein Konzept basierend auf festkörperunterstützten Membranen entwickelt. Dieses Experiment erlaubt es die Wechselwirkungen auf artifiziellen Membranen, sowie auf rekonstituierten Zellmembranen zu untersuchen. Zudem wurde ein Analysekonzept mit Nano-BLMs entwickelt, dass es erlaubt den simultanen Transport von Molekülen in ein membranverschlossenes Kompartiment hinein als auch heraus zu beobachten. Neben diesen membranbasierten Experimenten wurde auch ein Konzept entwickelt, welches es erlaubt die molekulare Erkennungsreaktion von sehr kleiner Analyten direkt zu messen. Dieses Messkonzept erlaubt es die Bindung von Molekülen mit sehr kleinem Molekulargewicht an einen auf dem Sensor immobilisierten Partner direkt zu quantifizieren.

Energy-Coupling-Factor (ECF)-Transporter sind Aufnahmesysteme für Vitamine und Übergangsmetallkationen in Prokaryoten. Sie bestehen aus den zwei unverwandten Membranproteinen S und T sowie einem Paar ABC-ATPasen (A). Die S-Einheit vermittelt die Substratspezifität. Die Kombination aus der T- und den A-Einheiten wird als ECF bezeichnet. In dieser Arbeit wurden Fragen zur kontrovers diskutierten Stöchiometrie der Untereinheiten von ECF-Transportern sowie zur zuvor postulierten Substrattransport-Funktion einzelner S-Komponenten auch ohne ECF untersucht. Dazu wurden der ECF-Biotintransporter BioMNY, mehrere natürlicherweise in Organismen ohne ECF existierende biotinspezifische S Einheiten (BioY) sowie zwei Vertreter der metallspezifischen ECF-Systeme genutzt. Die S-Einheit BioY des dreiteiligen Biotinimporters lag in vitro als Monomer und Dimer vor. Oligomeres BioY wurde außerdem in lebenden Bakterienzellen beobachtet. „Pull-down“-Experimente zeigten, dass die T Komponente BioN im BioMNY-Komplex zum Teil als Dimer vorlag. Wachstumsuntersuchungen bestätigten die Transportfunktion von acht solitär vorkommenden BioY. Die in vitro auch für diese BioY-Proteine nachgewiesene Dimerisierung könnte die Transportfunktion von BioY ohne ECF erklären. Die metallspezifischen S Einheiten CbiM/NikM interagieren mit für die Transportfunktion essentiellen, zusätzlichen Transmembranproteinen (N) und zeichnen sich durch eine Topologie mit sieben Transmembranhelices und einem extrem konservierten, weit in das Proteininnere hineinragenden N-Terminus aus. Die Metallbindestelle besteht aus vier Stickstoffatomen von Met1, His2 und His67 und wird durch ein Netz aus Wasserstoffbrückenbindungen stabilisiert. Die Transport¬funktion von CbiMN bzw. Nik(MN) ohne ECF wurde in vivo mittels des nickelabhängigen Enzyms Urease als Indikator für die intrazelluläre Nickelkonzentration verifiziert. Zum gegenwärtigen Zeitpunkt ist die Funktion der für den Transport essentiellen N-Komponente jedoch noch unklar. / Energy-coupling factor (ECF) transporters are uptake systems for vitamins and transition metal cations in prokaryotes. They consist of the two unrelated membrane proteins S and T, and a pair of ABC ATPases (A). The S unit mediates substrate specificity. The combination of the T and the A units is called ECF. In this thesis the controversially discussed stoichiometry of the subunits of ECF transporters and the postulated substrate transport function of solitary S units without ECF were analysed. For this purpose, the biotin-specific ECF transporter BioMNY, several biotin-specific S units (BioY) encoded in organisms lacking any recognizable ECF and two metal-specific ECF transporters were used. The S unit BioY of the tripartite biotin importer existed in vitro as monomer and dimer. Furthermore, oligomeric BioY was observed in living bacterial cells. Oligomerisation of a part of the T unit BioN in the BioMNY complex was shown by “pull-down”- experiments. Growth analyses confirmed the transport function of eight solitary BioY proteins. The dimerisation, also proved for these solitary BioY proteins in vitro, could be an explanation for the transport function of BioY without ECF. The metal-specific S units CbiM/NikM interact with additional and for the transport function essential transmembrane proteins (N). The S units consist of seven transmembrane helices and an extremely conserved N-terminus, which extends deeply into the protein. The metal-binding site consists of four nitrogen atoms from Met1, His2 and His67 and is stabilised by a series of hydrogen bonds. The transport function of CbiMN and Nik(MN) without ECF was verified respectively in vivo using the nickel-depending enzyme urease as an indicator for intracellular nickel concentration, respectively. However, the role of the N component, which is essential for transport activity, is currently under investigation.

Um Prozesse in biologischen Systemen auf molekularer Ebene zu untersuchen, haben sich vor allem fluoreszenzspektroskopische Methoden bewährt. Die Möglichkeit, einzelne Moleküle zu beobachten, hat zu einem deutlichen Fortschritt im Verständnis von elementaren biochemischen Prozessen geführt. Zu einer der bekanntesten Methoden der Einzelmolekülspektroskopie zählt die Fluoreszenz-Korrelations-Spektroskopie (FCS), mit deren Hilfe intramolekulare und diffusionsgesteuerte Prozesse in einem Zeitbereich von µs bis ms untersucht werden können. Durch die Verwendung von sog. Fluoreszenzsonden können Informationen über deren molekulare Mikroumgebung erhalten werden. Insbesondere für die konfokale Mikroskopie und die Einzelmolekülspektroskopie werden Fluoreszenzfarbstoffe mit einer hohen Photostabilität und hohen Fluoreszenzquantenausbeute benötigt. Aufgrund ihrer hohen Fluoreszenzquantenausbeute und der Möglichkeit, maßgeschneiderte“ Farbstoffe in einem breiten Spektralbereich für die Absorption und Fluoreszenz zu entwickeln, sind Cyaninfarbstoffe von besonderem Interesse für bioanalytische Anwendungen. Als Fluoreszenzmarker finden diese Farbstoffe insbesondere in der klinischen Diagnostik und den Lebenswissenschaften Verwendung. Die in dieser Arbeit verwendeten Farbstoffe DY-635 und DY-647 sind zwei typische Vertreter dieser Farbstoffklasse. Durch Modifizierung können die Farbstoffe kovalent an biologisch relevante Moleküle gebunden werden. Aufgrund ihres Absorptionsmaximums oberhalb von 630nm werden sie insbesondere in der Bioanalytik eingesetzt. In der vorliegenden Arbeit wurden die spektroskopischen Eigenschaften der Cyaninfarbstoffe DY-635 und DY-647 in biomimetischen und biologischen Modellsystemen untersucht. Zur Charakterisierung wurden dabei neben der Absorptionsspektroskopie insbesondere fluoreszenzspektroskopische Methoden verwendet. Dazu zählen die zeitkorrelierte Einzelphotonenzählung zur Ermittlung des Fluoreszenzabklingverhaltens, Fluoreszenz-Korrelations-Spektroskopie (FCS) zur Beobachtung von Diffusions- und photophysikalischen Desaktivierungsprozessen und die zeitaufgelöste Fluoreszenzanisotropie zur Untersuchung der Rotationsdynamik und Beweglichkeit der Farbstoffe im jeweiligen Modellsystem. Das Biotin-Streptavidin-System wurde als Modellsystem für die Untersuchung von Protein-Ligand-Wechselwirkungen verwendet, da der Bindungsmechanismus weitgehend aufgeklärt ist. Nach Bindung der Farbstoffe an Streptavidin wurde eine erhebliche Veränderung in den Absorptions- und Fluoreszenzeigenschaften beobachtet. Es wird angenommen, dass diese spektralen Veränderungen durch Wechselwirkung von benachbarten, an ein Streptavidintetramer gebundenen Farbstoffmolekülen und Bildung von H-Dimeren verursacht wird. Für das System Biotin-Streptavidin ist bekannt, dass während der Bindung des Liganden (Biotin) an das Protein eine Konformationsänderung auftritt. Anhand von zeitaufgelösten Fluoreszenzanisotropieuntersuchungen konnte in dieser Arbeit gezeigt werden, dass diese strukturellen Veränderungen zu einer starken Einschränkung der Beweglichkeit des Farbstoffes DY-635B führen. Liegt eine Mischung von ungebundenem und Streptavidin-gebundenem Farbstoff vor, können die Anisotropieabklingkurven nicht nach einem exponentiellen Verlauf angepasst werden. Es konnte im Rahmen dieser Arbeit gezeigt werden, dass in diesem Fall die Auswertung mit Hilfe des Assoziativen Anisotropiemodells möglich ist, welches eine Unterscheidung der Beiträge aus den zwei verschiedenen Mikroumgebungen ermöglicht. Als zweites Modellsystem dieser Arbeit wurden Mizellen des nichtionischen Tensids Tween-20 eingesetzt. Mizellen bilden eines der einfachsten Systeme, um die Mikroumgebung einer biologischen Membran nachzuahmen. Sind die Farbstoffe in den Mizellen eingelagert, so kommt es zu keiner Veränderung der Mizellgröße. Die ermittelten Werte des Diffusionskoeffizienten der mizellar eingelagerten Farbstoffe spiegeln demzufolge die Translationsbewegung der Tween-20-Mizellen wider. Die Beweglichkeit der Farbstoffe innerhalb der Tween-20-Mizellen wurde durch zeitaufgelöste Fluoreszenzanisotropiemessungen untersucht. Neben der „Wackelbewegung“, entsprechend dem wobble-in-a-cone-Modell, wird zusätzlich noch die laterale Diffusion der Farbstoffe entlang der Mizelloberfläche beschrieben. / To investigate processes in biological systems on a molecular level, particularly fluorescence spectroscopic methods have proven. The possibility to observe single molecules led to significant progress in the understanding of basic biochemical processes. Fluorescence correlation spectroscopy (FCS) is one of the most popular methods of single molecule spectroscopy and is a powerful technique for the investigation of intramolecular and diffusion-controlled processes on a µs to ms time scale. The photophysical characteristics of fluorescent probes are often strongly influenced by their microenvironment. For confocal microscopy and single molecule detection applications fluorescent dyes with properties, such as high photostability and high fluorescence efficiency are highly needed. Due to the high fluorescence efficiency and the high potential to design tailor-made fluorescence probes covering a wide spectral range in absorption and fluorescence, cyanine dyes are highly attractive as fluorescence probes for bioanalytical applications, such as clinical diagnostics and life sciences. The dyes DY-635 and DY-647 are two typical representatives of this class of dyes and can be covalently attached to biologically relevant molecules. Because of their excitation wavelength above 630nm these dyes are especially suited for bioanalytical applications. In this work the spectroscopic properties of DY-635 and DY-647 in biomimetic and biological model systems were studied by absorption and fluorescence spectroscopy techniques: time-correlated single photon counting to determine fluorescence decay behavior, fluorescence correlation spectroscopy (FCS) to observe diffusion and photophysical deactivation processes, and fluorescence anisotropy to study the mobility and rotational behavior of the dyes in the respective model system. The well characterized system biotin-streptavidin was used as a model system for protein-ligand interactions. Binding to streptavidin resulted in significant changes in the steady-state photophysical characteristics of DY-635B and DY-647. These spectral changes are attributed to dye-dye interactions and the formation of H-dimers. Previous studies have demonstrated, that binding of biotin alters the conformation of streptavidin. Based on the evaluation of time-resolved anisotropy data in this study it was shown that these structural changes result in strong hindrance of the rotational freedom of DY-635B. For mixtures of unbound and streptavidin-bound dyes the fluorescence anisotropy decay curves are found to be nonexponential. In this case the concept of an associated anisotropy were applied which allowed discrimination between contributions from different microenvironments. As a second model system, micelles of the nonionic surfactant Tween-20 were used. Micelles are one of the simplest systems to mimic the microenvironment of a biological membrane. Incorporation of the dyes had no effect on the micelle size. The diffusion coefficient of the dyes, obtained by fluorescence correlation spectroscopy (FCS), reflects the translational behavior of Tween-20 micelles. The mobility of the dyes in the Tween-20 micelles was studied by time-resolved fluorescence anisotropy. In addition to a „wobbling“ motion ccording to the wobble-in-a-cone model, a lateral diffusion of the dyes along the micelle surface is described.

Biotin Protein Ligase (BPL) is an essential enzyme responsible for the covalent attachment of biotin to a specific lysine residue of biotin-dependent carboxylases, transcarboxylases and decarboxylases. Due to the fundamental processes that these enzymes are involved in such as lipogenesis, amino acid catabolism and gluconeogenesis, much research has been conducted on these enzymes. Studies encompassing structural, mutational and catalytic functions of these enzymes have lead to novel drug developments for the treatment of obesity, diabetes, metabolic syndrome, bacterial and fungal infections. As BPL is required for activation of these enzymes by biotinylation, it is believed that it too could be targeted in a similar way to produce novel therapeutics. To date, the most characterised BPLs are from the Gramnegative bacteria Escherichia coli and the archea Pyrococcus hirokoshii. However minimal information is known about other forms of clinically important bacterial species or eukaryotic forms of this important enzyme. Through my candidature I have compiled a thorough literature review summarised as chapter 1: Introduction. Furthering this literature analysis, a human BPL model was generated with aid of BPL structural co-ordinates already deposited in the protein data bank (PDB), thus allowing focus on human BPL mutations that cause multiple carboxylase deficiency (chapter 2). I have solved the structure of BPL from the clinically important pathogenic bacteria Staphylococcus aureus. This was performed in several ligand-bound and non-bound states (chapters 3 and 4). A novel high-throughput assay was developed to test BPL activity. This assay allow testing of compounds that could potentially inhibit the BPL from Candida albicans (a species responsible for invasive fungal infections) (chapter 5). Large amounts of highly purified BPL from Saccharomyces cerevisiae allowed for the first structural analysis of a eukaryotic BPL (Chapter 6). The work has been summarised by a general discussion and future directions for the project (Chapter 7). / Thesis (Ph.D.) -- University of Adelaide, School of Molecular and Biomedical Science, 2009

The design of versatile biohybrid nanosized materials has revealed itself as a promising avenue towards biomedical applications in today´s life sciences. In this regard the combination of components of synthetic and natural origin facilitates an applicability which is supposed to be far beyond the sum of their single components. These biohybrid structures (BHS) can be built by a huge variety of building blocks including solid or soft nanoparticles, peptides/proteins, polynucleotides or low molecular weight drugs. Along with the latter the attachment of biologically active entities or imaging moieties, e. g. enzymes, fluorescence markers or targeting motifs display thereby a key step towards the development of carrier systems for drug delivery purposes. Among the soft nanoparticles especially dendritic polymers such as perfectly branched dendrimers or hyperbranched polymers are considered as ideal building blocks, since they allow an easy tailoring of crucial properties such as solubility, biocompatibility or bioactivity by means of surface functionalization. Especially in the field of targeted drug delivery the crucial role of sizes and size distributions of carriers has been highlighted recently, since it critically influences important factors such as circulation time or biodistribution within the body. The ability of avidin to form high molecular weight associates with biotinylated macromolecules as well as its inherent properties makes it a suitable candidate for passive and active targeting in combination with biotinylated (bio-)polymers. Furthermore, along with the covalent attachment of bioactive moieties, non-covalent attachment is a frequently used approach, because it is assumed to only require stoichiometric mixing. In context of the latter molecular recognition processes such as the avidin-biotin, β-cyclodextrin-adamantane or Ni(II)-NTA-histidine-tag interactions have shown to be fruitful strategies for the attachment of bioactive entities. The overall aim of this work was to fabricate BHS based on dendritic glycopolymers with varied sizes in the nano- and micrometer range as models for biomedical applications e. g. carriers for drug delivery. Therefore the molecular recognition of avidin with biotin derivatives and β-cyclodextrin with adamantane derivatives was utilized in order to tailor final sizes, functionality or catalytic activity of those BHS.

Thesis (MscAgric (Animal Sciences))--University of Stellenbosch, 2006. / Six non-lactating, ruminally cannulated Holstein cows were used in a three part study to determine the effect of biotin supplementation to dairy cows on forage fermentation characteristics. Cows were randomly assigned to two groups in a 2 x 3 change-over experiment. All cows received oat hay ad libitum and one of two concentrate feeds, fed twice daily at 2 kg per feeding as a top dressing. The concentrates were identical in composition, except for a premix that was included to provide either 0 or 40 mg supplemental biotin/cow per day when the concentrate was fed at a rate of 4 kg/cow. Cows received the respective treatments for 28 days before being changed over to the other treatment. All cows therefore received both treatments. The first 21 days in each period were used for adaptation, while the last 7 days of the period were used for an in sacco trial, as well as for the collection of rumen liquor for two in vitro studies. The in vitro studies were a gas production trial and an in vitro digestibility trial. Forages differing in neutral detergent fibre (NDF) content were used as substrates in the study. Lucerne hay (440 g NDF/kg DM), oat hay (680 g NDF/kg DM), and wheat straw (798 g NDF/kg DM) were chosen to represent high, medium and low quality forages. In the gas production study, samples (0.5 g) of the three forages were incubated at 39ºC in buffered rumen liquor (obtained from cows in the different treatments) in glass vials. Pressure readings were taken after 12, 18, 24, 30 and 48 hours incubation using a digital pressure gauge fitted with a 21 gauge needle. Pressure readings were converted to gas volumes with the aid of a predetermined regression equation. In the in vitro digestibility trial, forage samples (0.25 g) were weighed into Ankom F57 filter bags and incubated at 39ºC in an Ankom Daisy II incubator in buffered rumen liquor. Three bags of each substrate were removed from the incubation jars after 18, 24 and 30 h incubation. Bag residues were analyzed for dry matter, organic matter and NDF. In the in sacco degradability trial, forage samples (5 g) were weighed into 100 x 200 mm Ankom Forage Bags and inserted into the rumina of the respective cow simultaneously. One bag per substrate was removed from each cow at after 4, 8, 18, 24, 30 and 48 h incubation, while two bags per substrate were removed after 72 and 96 h to ensure enough residue for subsequent chemical analysis. Samples of rumen liquor were taken at each of the mentioned incubation times for VFA analysis, while rumen pH was also measured at these times. All the data collected were subjected to a one-way ANOVA, least square means were determined and significance was declared at P<0.05. Biotin supplementation increased the rate of gas production (0-12 h) of all three substrates, as well as cumulative gas production at 48 h. No treatment effects were observed in the in vitro digestion study. Biotin supplementation increased the rate of in sacco NDF disappearance and calculated effective NDF degradability in oat hay and wheat straw, but not in lucerne hay. The rumen pH curve appeared higher for the biotin treatment than for the control and the value at the 72 h sampling time was significantly higher for the biotin treatment than for the control treatment (6.13 vs 5.94). Rumen pH tended to be higher (P<0.10) at 18 h (6.44 vs 6.23), 48 h (6.13 vs 6.00) and 96 h (6.14 vs 6.04). There was also a tendency (P<0.10) for the mean pH over the total 96 h period to be higher for the biotin treatment than for the control (6.09 vs 5.97), while the maximum and minimum pH values did not differ between treatments. Molar proportions of volatile fatty acids did not differ between treatments and the acetic acid proportion was relatively high (acetic:propionic = 74:15), which was probably because the cows were not on a very high concentrate diet. It was concluded that biotin supplementation to dairy cows may improve fermentation rates and NDF digestibility of certain forages.

<p>This thesis describes recombinant proteins that have been generated by rational and combinatorial protein engineering strategies for use in subunit vaccine delivery and tumor targeting.</p><p>In a first series of studies, recombinant methods for incorporating immunogens into an adjuvant formulation, e.g. immunostimulating complexes (iscoms), were evaluated. Protein immunogens, which are not typically immunogenic in themselves, are normally administered with an adjuvant to improve their immunogenicity. To accomplish iscom incorporation of a <i>Toxoplasma gondii</i> surface antigen through hydrophobic interaction, lipids were added either <i>in vivo</i> via <i>E. coli</i> expression, or <i>in vitro</i> via interaction of an introduced hexahistidyl (His6) peptide and a chelating lipid. The possibility of exploiting the strong interaction between biotin and streptavidin was also explored, in order to couple a<i> Neospora caninum</i> surface antigen to iscom matrix, i.e. iscom particles without any antigen. Subsequent analyses confirmed that the immunogens were successfully incorporated into iscoms by the investigated strategies. In addition, immunization of mice with the recombinant Neospora antigen NcSRS2, associated with iscoms through the biotin-streptavidin interaction, induced specific antibodies to native NcSRS2 and reduced clinical symptoms following challenge infection. The systems described in this thesis might offer convenient and efficient methods for incorporating recombinant immunogens into adjuvant formulations that might be considered for the generation of future recombinant subunit vaccines.</p><p>In a second series of studies, Affibody® (affibody) ligands directed to the extracellular domain of human epidermal growth factor receptor 2 (HER2/neu), which is known to be overexpressed in ∼ 20-30% of breast cancers, were isolated by phage display <i>in vitro</i> selection from a combinatorial protein library based on the 58 amino acid residue staphylococcal protein A-derived Z domain. Biosensor analyses demonstrated that one of the variants from the phage selection, denoted His₆-Z_HER2/neu:4, selectively bound with nanomolar affinity (KD ≈ 50 nM) to the extracellular domain of HER2/neu (HER2-ECD) at a different site than the monoclonal antibody trastuzumab. In order to exploit avidity effects, a bivalent affibody ligand was constructed by head-to-tail dimerization, resulting in a 15.6 kDa affibody ligand, termed His₆-(Z_HER2/neu:4)₂, that was shown to have an improved apparent affinity to HER2-ECD (KD ≈ 3 nM) compared to the monovalent affibody. Moreover, radiolabeled monovalent and bivalent affibody ligands showed specific binding in vitro to native HER2/neu molecules expressed in human cancer cells. Biodistribution studies in mice carrying SKOV-3 xenografted tumors revealed that significant amounts of radioactivity were specifically targeted to the tumors <i>in vivo</i>, and the tumors could easily be visualized with a gamma camera. These results suggest that affibody ligands would be interesting candidates for specific tumor targeting in clinical applications, such as <i>in vivo</i> imaging and radiotherapy.</p>

The development of improved sequencing technologies hasenabled the field of genomics to evolve. Handling andsequencing of large numbers of samples require an increasedlevel of automation in order to obtain high throughput andconsistent quality. Improved performance has lead to thesequencing of numerous microbial genomes and a few genomes fromhigher eukaryotes and the benefits of comparing sequences bothwithin and between species are now becoming apparent. Thisthesis describes both the development of automated purificationmethods for DNA, mainly sequencing products, and a comparativesequencing project. The initially developed purification technique is dedicatedto single stranded DNA containing vector specific sequences,exemplified by sequencing products. Specific capture probescoupled to paramagnetic beads together with stabilizing modularprobes hybridize to the single stranded target. After washing,the purified DNA can be released using water. When sequencingproducts are purified they can be directly loaded onto acapillary sequencer after elution. Since this approach isspecific it can be applied to multiplex sequencing products.Different probe sets are used for each sequencing product andthe purifications are performed iteratively. The second purification approach, which can be applied to anumber of different targets, involves biotinylated PCR productsor sequencing products that are captured using streptavidinbeads. This has been described previously, buthere theinteraction between streptavidin and biotin can be disruptedwithout denaturing the streptavidin, enabling the re-use of thebeads. The relatively mild elution conditions also enable therelease of sensitive biotinylated molecules. Another project described in this thesis is the comparativesequencing of the 40 kbcagpathogenicity island (PAI) in fourHelicobacter pyloristrains. The results included thediscovery of a novel gene, present in approximately half of theSwedish strains tested. In addition, one of the strainscontained a major rearrangement dividing thecagPAI into two parts. Further, information about thevariability of different genes could be obtained. Keywords:DNA sequencing, DNA purification, automation,solid-phase, streptavidin, biotin, modular probes,Helicobacter pylori,cagPAI. / <p>NR 20140805</p>

Made available in DSpace on 2014-06-11T19:22:18Z (GMT). No. of bitstreams: 0 Previous issue date: 2010-12-20Bitstream added on 2014-06-13T20:28:32Z : No. of bitstreams: 1 goncalves_gs_me_arafcf.pdf: 376750 bytes, checksum: d261fb301fa1b4c966236fbf2eb5c9d0 (MD5) / Universidade Estadual Paulista (UNESP) / O presente trabalho consiste no desenvolvimento de um método analítico para determinação de biotina, utilizando-se a potenciometria indireta. O objetivo é apresentar a validação de método analítico como um processo que estime a eficiência do método proposto na rotina do laboratório para garantia da qualidade total. É um método que envolve equipamento simples e pouco dispendioso como o potenciômetro, que possibilita medir com precisão o valor da concentração de biotina. O doseamento quantitativo de biotina baseia-se no estudo das reações oscilantes do analito perante as análises da titulação indireta utilizando potenciômetro automático. A concentração de biotina foi determinada com massa adicionada conhecida numa matriz que simula uma cápsula, contendo aerosil (1%), estearato de magnésio (1%), celulose microcristalina (20%), amido (40%) e lactose q.s.p. Os resultados mostraram um valor médio de biotina (massa adicionada de aproximadamente 25 mg) determinada de 99,4% com desvio-padrão de 0,0345. As condições experimentais como temperatura, vidraria e concentração dos reagentes foram otimizadas. Os parâmetros investigados no processo de validação para demonstrar o desempenho do método foram: especificidade, linearidade, intervalo, precisão tanto repetitividade, quanto intermediária, exatidão e robustez. O tratamento estatístico dos dados da validação do método analítico envolveu a determinação da média, do desvio padrão e do coeficiente de variação. Para obtenção da curva de calibração se fez necessária a determinação da equação da reta, regressão linear e coeficiente de correlação linear. Este método apresenta grande aplicabilidade em soluções turvas, fluorescentes, opacas ou coradas, ou quando não existem, ou não podem aplicar-se indicadores visuais apropriados. Há possibilidade de determinação... / The present work shows the development of an analytical method for the determination of biotin by using indirect potentiometry. The main goal is to present the validation of analytical methods as a process to estimate the efficiency of the proposed methodology in the laboratory routine for the guaranty of total quality. This method involves simple and low cost devices as the potentiometer, which allows the precise measurement of biotin concentration. The quantitative dosing of biotin is based on the study of the oscillating chemical reactions with the analyte by performing the analysis of the indirect titration with an automatic potentiometer. Biotin concentration was determined by adding a known mass to a matrix that simulates a capsule containing aerosol (1%), estearato de magnésio (1%), celulose microcristalina (20%), amido (40%) e lactose q.s.p. The results showed an average value for the determination of biotin (added mass was ca. 25 mg) of 99.4% with a standard deviation of 0.0345. The experimental conditions as temperature, glassware, and concentration of the chemicals were optimized. The investigated parameters of the validation procedure to demonstrate the performance of the method were: specificity, linearity, interval, precision (repeatability and intermediate), exactness and robustness. The statistical treatment of the data for the validation of the analytical method involved the determination of the average value, standard deviation, and the variation coefficient. In order to obtain the calibration curve, the line´s equation, the linear regression and the coefficient of linear correlation were determined. This method shows great applicability for turbid, fluorescent, opaque or color solutions, or if an appropriate visual indicator is not available or cannot be applied. The method also shows the possibility for the determination of a sequence of equivalence... (Complete abstract click electronic access below)

Biotin is an essential vitamin in plants and mammals functioning as the carbon dioxide carrier within central lipid metabolism. Biotin is composed of a fused bicylic ring system and a five carbon, carboxylic acid chain. Biotin biosynthesis in bacteria is catalysed by a series of enzymes that use fatty acid, amino acid and sulfur-containing substrates. In Bacillus subtilis, pimeloyl-CoA synthetase (PCAS, EC 6.2.1.14, UNIPROT code: P53559, 29.6 kDa) is the first enzyme in the biotin biosynthetic pathway and acts as a highly specific substrate selection gate ensuring the integrity of the carbon chain in biotin synthesis. PCAS catalyses the synthesis of the key acyl-thioester, pimeloyl-CoA in two steps; the first involves activation of pimelic acid (C7 dicarboxylic acid) using ATP to give an acyl-adenylate, enzyme-bound intermediate and pyrophosphate (PPi), and in the second step, this pimeloyl-adenylate reacts with coenzyme A (CoASH) to form the pimeloyl-CoA thioester. This thesis describes the results of biochemical, structural and mechanistic studies of B. subtilis PCAS. Recombinant PCAS was prepared by expressing the B. subtilis BioW gene in E. coli in various hexa-histidine affinity-tagged forms and the enzyme purified in high purity and yield. Enzyme activity and kinetic constants were measured using reverse-phase HPLC and enzyme coupled spectroscopic assays. These revealed the enzyme to have a strict carboxylic acid specificity. In collaboration with colleagues at the University of St. Andrews various commercial and in-house screens were used to obtain diffraction-quality crystals suitable for X-ray crystallography. This also included the generation of seleno-methionine (SeMet) labelled PCAS, as well as heavy-metal derivatives. Structures of B. subtilis PCAS in complex with the substrate pimelic acid and the pimeloyl-adenylate intermediate and product PPi were determined at 2.04 Å and 2.34 Å resolution respectively. The B. subtilis PCAS displays a novel 3D fold and defines a new class (Class IV) in the ANL superfamily of adenylate forming enzymes. The enzyme is a homodimer composed of two domains, a short N-terminus and a large C-terminal domain and the ligand-bound structures revealed the residues potentially involved in substrate specificity and enzyme catalysis. The enzyme uses an internal ruler composed of a number of conserved arginine residues (Arg213, Arg227 and Arg170) to select the correct dicarboxylic acid substrate. The X-ray structures guided the production of a number of site directed mutants to identify residues involved in the catalytic mechanism and stabilising the acyl-adenylate intermediate. This also allowed rational engineering of the PCAS active site to generate mutants with altered substrate specificity. Mutant PCAS Y211F was shown to synthesise both heptanoyl (C7) and octanoyl (C8) mono carboxylic acid-CoA and C8 dicarboxylic-CoA thioester products, highlighting the synthetic potential of PCAS. The PCAS pimeloyl-CoA product is the substrate for the next enzyme in the biotin pathway, a pyridoxal 5'phosphate (PLP)-dependent 8-amino 7-oxononanoate synthase (AONS). AONS catalyses the condensation of pimeloyl-CoA with L-alanine to give AON which is converted to biotin by the action of three other enzymes. We used genome mining to identify a putative ~66 kDa, bi-functional PCAS/AONS enzyme with an N-terminal PCAS domain fused to C-terminal AONS domain in the organism Corynebacterium amycolatum. A recombinant C. amycolatum PCAS/AONS fusion protein was expressed and purified from E. coli and initial studies suggest that it forms a functional, fused, dimeric enzyme.