3D-electron microscopy of different conformations of cephalopod hemocyanins

Die Hämocyanine der Cephalopoden Nautilus pompilius und Sepia officinalis sorgen für den Sauerstofftransport zwischen den Kiemen und den Geweben. Sie bestehen aus einem zylindrischen Dekamer mit interner Kragenstruktur. Während eine Untereinheit (also eine Polypeptidkette) bei NpH aus sieben paralogen funktionellen Domänen (FU-a bis FU-g) besteht, führte ein Genduplikationsereignis der FU-d zu acht FUs in SoH (a, b, c, d, d´, e, f, g). In allen Mollusken Hämocyaninen bilden sechs dieser FUs den äußeren Ring und die restlichen die interne Kragenstruktur. rnrnIn dieser Arbeit wurde ein dreidimensionales Modell des Hämocyanins von Sepia officinalis (SoH) erstellt. Die Rekonstruktion, mit einer Auflösung von 8,8Å (FSC=0,5), erlaubt das Einpassen von Homolologiemodellen und somit das Erstellen eines molekularen Modells mit pseudo atomarer Auflösung. Des Weiteren wurden zwei Rekonstruktionen des Hämocyanins von Nautilus pompilius (NpH) in verschiedenen Oxygenierungszuständen erstellt. Die auf 10 und 8,1Å aufgelösten Modelle zeigen zwei verschiedene Konformationen des Proteins. Daraus ließ sich eine Modellvorstellung über die allosterische Funktionsweise ableiten. Die hier erreichte Auflösung von 8Å ist die momentan höchste eines Molluskenhämocyanins. rnAuf Grundlage des molekularen Modells von SoH konnte die Topologie des Proteins aufgeklärt werden. Es wurde gezeigt, dass die zusätzliche FU-d´ in den Kragen integriert ist und somit die prinzipielle Wandarchitektur aller Mollusken Hämocyanine identisch ist. Wie die Analyse des erstellten molekularen Modells zeigt werden sind die beiden Isoformen (SoH1 und SoH2) in den Bereichen der Interfaces nahezu identisch; auch der Vergleich mit NpH zeigt grosse Übereinstimmungen. Des weiteren konnte eine Fülle von Informationen bezüglich der allosterischen Signalübertragung innerhalb des Moleküls gewonnen werden. rnDer Versuch, NpH in verschiedenen Oxygenierungszuständen zu zeigen, war erfolgreich. Die Datensätze, die unter zwei atmosphärischen Bedingungen präpariert wurden, führten reproduzierbar zu zwei unterschiedlichen Rekonstruktionen. Dies zeigt, daß der hier entwickelte experimentelle Ansatz funktioniert. Er kann nun routinemäßig auf andere Proteine angewandt werden. Wie der strukturelle Vergleich zeigte, verändert sich die Orientierung der FUs durch die Oxygenierung leicht. Dies wiederum beeinflusst die Anordnung innerhalb der Interfaces sowie die Abstände zwischen den beteiligten Aminosäuren. Aus dieser Analyse konnte eine Modellvorstellung zum allosterischen Signaltransfer innerhalb des Moleküls abgeleitet werden, die auf einer Umordnung von Salzbrücken basiert.

Influence of defects and disorder on anomalous Hall effect and spin Seebeck effect on permalloy and Heusler compounds

In dieser Arbeit wurden dünne Schichten von Heusler-Verbindungen hergestellt und auf ihre Transporteigenschaften hin untersucht.rnDer Anomale Hall-Effekt (AHE) ist dabei von besonderem Interesse. Er ist ein seit langer Zeit bekannter, jedoch noch nicht vollständig verstandener Transport-Effekt. Die meisten Veröffentlichungen theoretischer Arbeiten konzentrieren sich auf den Einfluss eines bestimmten Beitrags zum AHE. Tatsächlich gemessene experimentelle Daten können jedoch oft nicht in Einklang mit idealisierten Annahmen gebracht werden. rnDie vorliegende Arbeit diskutiert die Ergebnisse, welche aus Messungen von Materialien mit niedrigem Restwiderstand erhalten wurden. rnrnAls prototypische Materialien wurden hier hyphenation Heusler-Verbindungen untersucht. Als Material mit einer komplexen Topologie der Fermi-Fläche zeichnet sich dort der Einfluss von Defekten und der Unordnung der Kristallstruktur deutlich ab.rnrnDurch Verwendung von Filmen mit unterschiedlichem Grad der Unordnung können verschiedene Streumechanismen unterschieden werden. Für Co$_{2}$FeSi$_{0.6}$Al$_{0.4}$ and Co$_{2}$FeGa$_{0.5}$Ge$_{0.5}$ zeigt sich ein positiver AHE bei einer Unordnung vom Typ B2 und bei einer induzierten temperaturabh"angigen Streuung, wo hingegen eine Typ DO$_{3}$-Unordnung zusammen mit anderen möglichen intrinsischen Beiträgen einen negativen Effekt hervorruft.rnrnDarüber hinaus wurden die magneto-optische Kerr-Effekte (MOKE) dieser Verbindungen untersucht. Hierfür wurden Beiträge erster Ordnung als Funktion der intrinsischen und extrinsischen Parameter qualitativ analysiert. Auf den Einfluss der kristallinen Ordnung auf Beiträge zweiter Ordnung des MOKE-Signals wird ebenfalls eingegangen.rnrnDes Weiteren wurden dünne Schichten der Heusler-Verbindung Co$_{2}$MnAl auf MgO- und Si-Subs-traten (beide (100)) mit Hochfrequenz-Mag-netron-Sputtern erzeugt. Die zusammensetzung sowie die magnetischen und Transport-Eigenschaften wurden hinsichtlich unterschiedlicher Abscheidebedingungen systematisch untersucht.rnrnInsbesondere zeigt der AHE-Widerstand ein außerordentliches temperaturunabhängiges Verhalten in einem Bereich moderater Magnetfeldstärken von 0 bis 0.6,T. Hierf"ur wurde der nicht-diagonale Transport bei Temperaturen bis zu 300,$^{circ}$C analysiert. Die Daten zeigen die Eignung des Materials für Hall-Sensoren auch oberhalb der Raumtemperatur.rnrnJüngst wurde der Spin Seebeck-Effekt (SSE) entdeckt. Der Effekt aus dem Bereich der Spin-Kaloritronik erzeugt eine Spin-Spannung'' aufgrund eines Temperaturgradienten in magnetischen Materialien. Hier werden vorläufige Messungen des SSE in Ni$_{80}$Fe$_{20}$ und in Heusler-Verbindungen präsentiert.rn

Formation of DNA complexes in aqueous and organic solvents

From a physical-chemical point of view, it is challenging to form complexes with polyelectrolytes, consisting of only molecule of the largest component, i.e. the component with the highest number of charges. In this study, complexes are formed with DNA because of its potential applications as an artificial vector for gene delivery. The aim of this work is to prepare complexes in aqueous solutions as well as in organic solvents containing only one DNA molecule. For this purpose, the topology, equilibrium and conformation of complexes between a supercoiled DNA pUC19 (2686 base pairs) and spermine containing hydrophilic and/or hydrophobic moieties or a polylysine with a hydrophilic block are determined by means of dynamic (DLS) and static light scattering (SLS), atomic force microscopy (AFM), and circular dichroism (CD) spectroscopy. It is demonstrated that all of these complexes consisted of only one molecule of the polyanion. Only the polylysine-b-polyethylene glycol copolymer satisfied the conditions: 1) 100% neutralization of DNA charges and with a small excess of the cation (lower than 30%) and 2) form stable complexes at every charge ratio. rnDNA complex formation is also investigated in organic solvents. Precipitation is induced by neutralizing the charge of the supercoiled DNA pUC19 with the surfactants dodecyltrimethylammonium bromide (DTAB) and tetradecyltrimethylammonium bromide (TTAB). After isolation and drying of the solids, the complexes are dissolved in organic solvents. DNA-TTA complexes are only soluble in methanol and DNA-DTA in DMF. The complexes again consisted of only one DNA molecule. The final topology of the complexes is different in methanol than in DMF. In the former case, DNA seems to be compacted whereas in the latter case, the DNA-DTA complexes seem to have an expanded conformation. Upon complex formation with polycations in organic solvents (with polyvilylpyridine brush (b-PVP) in methanol and with a protected polylysine in DMF), DNA aggregates and precipitates. rnDNA is linearized with an enzyme (SmaI) to investigate the influence of the initial topology of the polyanion on the final conformation of the complexes in organic solvents. Two main differences are evidenced: 1. Complexes in organic solvents formed with linear DNA have in general a more expanded conformation and a higher tendency to aggregate. 2. If a polycation, i.e. the b-PVP, is added to the linear DNA-TTA complexes in methanol, complexes with the polycation are formed at a higher charge ratio. In DMF, the addition of the same b-PVP and of b-PLL did not lead to the formation of complexes.rn

EPR spectroscopy as a tool for the elucidation of non-covalent structuring principles in complex soft matter

This thesis aims at connecting structural and functional changes of complex soft matter systems due to external stimuli with non-covalent molecular interaction profiles. It addresses the problem of elucidating non-covalent forces as structuring principle of mainly polymer-based systems in solution. The structuring principles of a wide variety of complex soft matter types are analyzed. In many cases this is done by exploring conformational changes upon the exertion of external stimuli. The central question throughout this thesis is how a certain non-covalent interaction profile leads to solution condition-dependent structuring of a polymeric system.rnTo answer this question, electron paramagnetic resonance (EPR) spectroscopy is chosen as the main experimental method for the investigation of the structure principles of polymers. With EPR one detects only the local surroundings or environments of molecules that carry an unpaired electron. Non-covalent forces are normally effective on length scales of a few nanometers and below. Thus, EPR is excellently suited for their investigations. It allows for detection of interactions on length scales ranging from approx. 0.1 nm up to 10 nm. However, restriction to only one experimental technique likely leads to only incomplete pictures of complex systems. Therefore, the presented studies are frequently augmented with further experimental and computational methods in order to yield more comprehensive descriptions of the systems chosen for investigation.rnElectrostatic correlation effects in non-covalent interaction profiles as structuring principles in colloid-like ionic clusters and DNA condensation are investigated first. Building on this it is shown how electrostatic structuring principles can be combined with hydrophobic ones, at the example of host-guest interactions in so-called dendronized polymers (denpols).rnSubsequently, the focus is shifted from electrostatics in dendronized polymers to thermoresponsive alkylene oxide-based materials, whose structuring principles are based on hydrogen bonds and counteracting hydrophobic interactions. The collapse mechanism in dependence of hydrophilic-hydrophobic balance and topology of these polymers is elucidated. Complementarily the temperature-dependent phase behavior of elastin-like polypeptides (ELPs) is investigated. ELPs are the first (and so far only) class of compounds that is shown to feature a first-order inverse phase transition on nanoscopic length scales.rnFinally, this thesis addresses complex biological systems, namely intrinsically disordered proteins (IDPs). It is shown that the conformational space of the IDPs Osteopontin (OPN), a cytokine involved in metastasis of several kinds of cancer, and BASP1 (brain acid soluble protein one), a protein associated with neurite outgrowth, is governed by a subtle interplay between electrostatic forces, hydrophobic interaction, system entropy and hydrogen bonds. Such, IDPs can even sample cooperatively folded structures, which have so far only been associated with globular proteins.

REGULATION OF WHOLE-BODY ENERGY HOMEOSTASIS WITH GROWTH HORMONE REPLACEMENT THERAPY AND ENDURANCE EXERCISE

We hypothesized that network analysis is useful to expose coordination between whole body and myocellular levels of energy metabolism and can identify entities that underlie skeletal muscle's contribution to growth hormone-stimulated lipid handling and metabolic fitness. We assessed 112 metabolic parameters characterizing metabolic rate and substrate handling in tibialis anterior muscle and vascular compartment at rest, after a meal and exercise with growth hormone replacement therapy (GH-RT) of hypopituitary patients (n = 11). The topology of linear relationships (| r | ≥ 0.7, P ≤ 0.01) and mutual dependencies exposed the organization of metabolic relationships in three entities reflecting basal and exercise-induced metabolic rate, triglyceride handling, and substrate utilization in the pre- and postprandial state, respectively. GH-RT improved aerobic performance (+5%), lean-to-fat mass (+19%), and muscle area of tibialis anterior (+2%) but did not alter its mitochondrial and capillary content. Concomitantly, connectivity was established between myocellular parameters of mitochondrial lipid metabolism and meal-induced triglyceride handling in serum. This was mediated via the recruitment of transcripts of muscle lipid mobilization (LIPE, FABP3, and FABP4) and fatty acid-sensitive transcription factors (PPARA, PPARG) to the metabolic network. The interdependence of gene regulatory elements of muscle lipid metabolism reflected the norm in healthy subjects (n = 12) and distinguished the regulation of the mitochondrial respiration factor COX1 by GH and endurance exercise. Our observations validate the use of network analysis for systems medicine and highlight the notion that an improved stochiometry between muscle and whole body lipid metabolism, rather than alterations of single bottlenecks, contributes to GH-driven elevations in metabolic fitness.

Influence of Smoothing on Voxel-Based Mesh Accuracy in Micro-Finite Element

The interest in automatic volume meshing for finite element analysis (FEA) has grown more since the appearance of microfocus CT (μCT), due to its high resolution, which allows for the assessment of mechanical behaviour at a high precision. Nevertheless, the basic meshing approach of generating one hexahedron per voxel produces jagged edges. To prevent this effect, smoothing algorithms have been introduced to enhance the topology of the mesh. However, whether smoothing also improves the accuracy of voxel-based meshes in clinical applications is still under question. There is a trade-off between smoothing and quality of elements in the mesh. Distorted elements may be produced by excessive smoothing and reduce accuracy of the mesh. In the present work, influence of smoothing on the accuracy of voxel-based meshes in micro-FE was assessed. An accurate 3D model of a trabecular structure with known apparent mechanical properties was used as a reference model. Virtual CT scans of this reference model (with resolutions of 16, 32 and 64 μm) were then created and used to build voxel-based meshes of the microarchitecture. Effects of smoothing on the apparent mechanical properties of the voxel-based meshes as compared to the reference model were evaluated. Apparent Young’s moduli of the smooth voxel-based mesh were significantly closer to those of the reference model for the 16 and 32 μm resolutions. Improvements were not significant for the 64 μm, due to loss of trabecular connectivity in the model. This study shows that smoothing offers a real benefit to voxel-based meshes used in micro-FE. It might also broaden voxel-based meshing to other biomechanical domains where it was not used previously due to lack of accuracy. As an example, this work will be used in the framework of the European project ContraCancrum, which aims at providing a patient-specific simulation of tumour development in brain and lungs for oncologists. For this type of clinical application, such a fast, automatic, and accurate generation of the mesh is of great benefit.

A Social Network Analysis Of Hamadryas Baboons

The study of animal sociality investigates the immediate and long-term consequences that a social structure has on its group members. Typically, social behavior is observed from interactions between two individuals at the dyadic level. However, a new framework for studying social behavior has emerged that allows the researcher to assess social complexity at multiple scales. Social Network Analysis has been recently applied in the field of ethology, and this novel tool enables an approach of focusing on social behavior in context of the global network rather than limited to dyadic interactions. This new technique was applied to a group of captive hamadryas baboons (Papio hamadryas hamadryas) in order to assess how overall network topology of the social group changes over time with the decline of an aging leader male. Observations on aggressive, grooming, and proximity spatial interactions were collected from three separate years in order to serve as `snapshots¿ of the current state of the group. Data on social behavior were collected from the group when the male was in prime health, when the male was at an old age, and after the male¿s death. A set of metrics was obtained from each time period for each type of social behavior and quantified a change in the patterns of interactions. The results suggest that baboon social behavior varies across context, and changes with the attributes of its individual members. Possible mechanisms for adapting to a changing social environment were also explored.

Crystal structure of the platelet glycoprotein Ib(alpha) N-terminal domain reveals an unmasking mechanism for receptor activation

Glycoprotein Ib (GPIb) is a platelet receptor with a critical role in mediating the arrest of platelets at sites of vascular damage. GPIb binds to the A1 domain of von Willebrand factor (vWF-A1) at high blood shear, initiating platelet adhesion and contributing to the formation of a thrombus. To investigate the molecular basis of GPIb regulation and ligand binding, we have determined the structure of the N-terminal domain of the GPIb(alpha) chain (residues 1-279). This structure is the first determined from the cell adhesion/signaling class of leucine-rich repeat (LRR) proteins and reveals the topology of the characteristic disulfide-bonded flanking regions. The fold consists of an N-terminal beta-hairpin, eight leucine-rich repeats, a disulfide-bonded loop, and a C-terminal anionic region. The structure also demonstrates a novel LRR motif in the form of an M-shaped arrangement of three tandem beta-turns. Negatively charged binding surfaces on the LRR concave face and anionic region indicate two-step binding kinetics to vWF-A1, which can be regulated by an unmasking mechanism involving conformational change of a key loop. Using molecular docking of the GPIb and vWF-A1 crystal structures, we were also able to model the GPIb.vWF-A1 complex.

Algorithms For Automatic And Robust Registration Of 3D Head Scans

wo methods for registering laser-scans of human heads and transforming them to a new semantically consistent topology defined by a user-provided template mesh are described. Both algorithms are stated within the Iterative Closest Point framework. The first method is based on finding landmark correspondences by iteratively registering the vicinity of a landmark with a re-weighted error function. Thin-plate spline interpolation is then used to deform the template mesh and finally the scan is resampled in the topology of the deformed template. The second algorithm employs a morphable shape model, which can be computed from a database of laser-scans using the first algorithm. It directly optimizes pose and shape of the morphable model. The use of the algorithm with PCA mixture models, where the shape is split up into regions each described by an individual subspace, is addressed. Mixture models require either blending or regularization strategies, both of which are described in detail. For both algorithms, strategies for filling in missing geometry for incomplete laser-scans are described. While an interpolation-based approach can be used to fill in small or smooth regions, the model-driven algorithm is capable of fitting a plausible complete head mesh to arbitrarily small geometry, which is known as "shape completion". The importance of regularization in the case of extreme shape completion is shown.

Structure and function study of prostaglandin H synthase

Prostaglandin H synthase (PGHS) is a key enzyme in biosynthesis of prostaglandins, thromboxane, and prostacyclin. It has two activities, cyclooxygenase and peroxidase. "PGHS" means PGHS-1. A current hypothesis considers the cyclooxygenase reaction to be a free radical chain reaction, initiated by interaction of the synthase peroxidase with hydroperoxides leading to the production of a tyrosyl free radical. According to this hypothesis, tyrosyl residue(s) may play a key role in the cyclooxygenase reaction. Tetranitromethane (TNM) can relatively selectively nitrate tyrosines at pH 8.0. The effect of TNM on both cyclooxygenase activity and peroxidase activity has been examined: reaction of the synthase holoenzyme with TNM at pH 8.0 led to inactivation of both activities, with the cyclooxygenase activity being lost rapidly and completely, while the peroxidase activity was lost more slowly. Indomethacin, a non-steroidal anti-inflammatory agent, can protect the synthase from the inactivation of TNM. Amino acid analyses indicated that a loss of tyrosine and formation of nitrotyrosine residues occurred during reaction with TNM, and that TNM-reacted holoenzyme with $<$10% residual cyclooxygenase activity had about 2.0 nitrotyrosine/subunit.^ PGH synthase is known to be an endoplasmic reticulum membrane-associated protein. Antibodies directed at particular PGHS peptide segments and indirect immunofluorescence have been used to characterize the membrane topology of crucial portions of PGHS. PGHS was expressed in COS-1 cells transfected with the appropriate cDNA. Stably-transfected human endothelial cells were also used for the topology study. The cells were treated with streptolysin-O, which selectively permeabilizes the plasma membrane, or with saponin to achieve general membrane disruption, before incubation with the antipeptide antibodies. Bound antipeptide antibody was stained by FITC-labelled secondary antibody and visualized by fluorescence microscopy. With the antipeptide antibodies against residues 51-66, 156-170 or 377-390, there was a significant reticular and perinuclear pattern of staining in cells permeabilized with saponin but not in cells permeabilized with SLO alone. Antibodies directed against the endogenous C-terminal peptide or against residues 271-284 produced staining in cells permeabilized with saponin, and also in a lower, but significant fraction of cells permeabilized with SLO. Similar results were obtained when COS-1 cells expressing recombinant PGHS with a viral reporter peptide inserted at the C-terminus were stained with antibody against the reporter epitope.^ The PGHS C-terminal sequence is similar to that of the consensus KDEL ER retention signal. The potential function of the PGHS C-terminus segment in ER retention was examined by mutating this segment and analyzing the subcellular distribution of the mutants expressed in COS-1 cells. None of the mutants had an altered subcellular distribution, although some had greatly diminished the enzyme activities. (Abstract shortened by UMI.) ^

Role of phosphatidylethanolamine in the function and assembly of phenylalanine-specific permease of Escherichia coli

Transmembrane segments of polytopic membrane proteins once inserted are generally considered stably oriented due to the large free energy barrier for topological reorientation of adjacent extra-membrane domains. However, proper topology and function of the polytopic membrane protein lactose permease (LacY) of Escherichia coli is dependent on the membrane phospholipid composition revealing topological dynamics of transmembrane domains (Bogdanov, M., Heacock, P. N., and Dowhan, W. (2002) EMBO J. 21, 2107–2116). The high affinity phenylalanine permease PheP shares many topological similarities with LacY. In this study, mutant E. coli cells lacking phosphatidylethanolamine (PE) as a membrane component were used to evaluate the role of PE in the function and assembly of PheP. Active transport of phenylalanine by cells lacking PE was severely inhibited (both Vmax and Km were altered), whereas the PheP protein level in membranes was unaffected. Cysteine residues were introduced into predicted periplasmic or cytoplasmic segments of cysteine-less PheP, and the topology of the protein was explored using a membrane-impermeable thiol-specific biotinylated probe. Based on the biotinylation patterns of PheP in whole cells, the N-terminus and adjoining transmembrane hairpin of PheP adopted an inverted topological orientation in PE-lacking cells. Introduction of PE following the assembly of PheP triggered a reorientation of the N-terminus and adjacent hairpin to their native orientation associated with regain of wild type transport function. These results coupled with the results for LacY support a specific role for membrane lipid composition in determining topological organization and function of membrane proteins. Several other secondary symporters are compromised for activity in PE-lacking cells suggesting that lipid-assisted topogenesis is a general property of such transporters. The reversible orientation of these secondary transport proteins in response to a change of phospholipid composition might be a result of inherent conformational flexibility necessary for transport function or during protein assembly. ^

Lipid-dependent topogenesis and function of membrane proteins

Membranes are essential for the integrity and function of the cell. The collective property of the lipid bilayer is critical in providing an optimal functioning environment for membrane proteins. The simple yet well-characterized bacterium Escherichia coli serves an ideal model system to study the function of specific lipids since its lipid content can be easily manipulated. The most abundant lipid in E. coli membrane is phosphatidylethanolamine (PE, 70-80%). A PE-lacking E. coli mutant displays a complex mixture of deficient phenotypes, suggesting a profound role for PE in different aspects of cell function. A novel role of PE as a topological and functional determinant for membrane proteins has been established using lactose permease (LacY) as a model protein. PE is found to be required for energy-dependent uphill transport process of LacY. In PE-lacking membranes, LacY undergoes a dramatic conformational change, and the first half of the protein adopts an inverted topology with respect to the bilayer plane. ^ The work reported here was initiated to understand the molecular properties of lipids that enable their function as topological and functional determinants for membrane proteins. A glycolipid, monoglucosyldiacylglycerol (MGlcDAG) which shares physicochemical similarities with PE, was introduced to PE-lacking E. coli membranes. The introduction of MGlcDAG suppresses many of the PE-deficient phenotypes, and in particular supports the function and native topology of LacY. ^ The lipid-sensitive topogenic signals encoded in the amino acid sequence of LacY were also identified. Native LacY adopts an inverted topology when synthesized without PE, but mutation of specific acidic residues in the cytoplasmic extra-membrane domains can prevent this inversion and supports a native topological organization of LacY in PE-lacking membranes. These results suggest that it is the interplay between the collective charge properties of the lipid bilayer and extra-membrane loops of protein that determines the final orientation of transmembrane domains. By comparing the similarities as well as differences between these two lipids, we established how specific physical and chemical properties of lipids influence various cell functions and elucidated the molecular basis for the novel role of lipids in determining membrane protein topology. ^

Analysis of VirB4, a membrane-associated ATPase subunit essential for T -complex transport in Agrobacterium tumefaciens

Agrobacterium tumefaciens is a plant pathogen with the unique ability to export oncogenic DNA-protein complexes (T-complexes) to susceptible plant cells and cause crown gall tumors. Delivery of the T-complexes across the bacterial membranes requires eleven VirB proteins and VirD4, which are postulated to form a transmembrane transporter. This thesis examines the subcellular localization and oligomeric structure of the 87-kDa VirB4 protein, which is one of three essential ATPases proposed to energize T-complex transport and/or assembly. Results of subcellular localization studies showed that VirB4 is tightly associated with the cytoplasmic membrane, suggesting that it is a membrane-spanning protein. The membrane topology of VirB4 was determined by using a nested deletion strategy to generate random fusions between virB4 and the periplasmically-active alkaline phosphatase, $\sp\prime phoA$. Analysis of PhoA and complementary $\beta$-galactosidase reporter fusions identified two putative periplasmically-exposed regions in VirB4. A periplasmic exposure of one of these regions was further confirmed by protease susceptibility assays using A. tumefaciens spheroplasts. To gain insight into the structure of the transporter, the topological configurations of other VirB proteins were also examined. Results from hydropathy analyses, subcellular localization, protease susceptibility, and PhoA reporter fusion studies support a model that all of the VirB proteins localize at one or both of the bacterial membranes. Immunoprecipitation and Co$\sp{2+}$ affinity chromatography studies demonstrated that native VirB4 (87-kDa) and a functional N-terminally tagged HIS-VirB4 derivative (89-kDa) interact and that the interaction is independent of other VirB proteins. A $\lambda$ cI repressor fusion assay supplied further evidence for VirB4 dimer formation. A VirB4 dimerization domain was localized to the N-terminal third of the protein, as judged by: (i) transdominance of an allele that codes for this region of VirB4; (ii) co-retention of a His-tagged N-terminal truncation derivative and native VirB4 on Co$\sp{2+}$ affinity columns; and (iii) dimer formation of the N-terminal third of VirB4 fused to the cI repressor protein. Taken together, these findings are consistent with a model that VirB4 is topologically configured as an integral cytoplasmic membrane protein with two periplasmic domains and that VirB4 assembles as homodimers via an N-terminal dimerization domain. Dimer formation is postulated to be essential for stabilization of VirB4 monomers during T-complex transporter assembly. ^

Evolution and breakup of viscous rotating drops

We study the evolution of a viscous fluid drop rotating about a fixed axis at constant angular velocity $Omega$ or constant angular momentum L surrounded by another viscous fluid. The problem is considered in the limit of large Ekman number and small Reynolds number. The analysis is carried out by combining asymptotic analysis and full numerical simulation by means of the boundary element method. We pay special attention to the stability/instability of equilibrium shapes and the possible formation of singularities representing a change in the topology of the fluid domain. When the evolution is at constant $Omega$, depending on its value, drops can take the form of a flat film whose thickness goes to zero in finite time or an elongated filament that extends indefinitely. When evolution takes place at constant L and axial symmetry is imposed, thin films surrounded by a toroidal rim can develop, but the film thickness does not vanish in finite time. When axial symmetry is not imposed and L is sufficiently large, drops break axial symmetry and, depending on the value of L, reach an equilibrium configuration with a 2-fold symmetry or break up into several drops with a 2- or 3-fold symmetry. The mechanism of breakup is also described

Pressure measurements of the detachment bubble on the Bolund Island

Pressure measurements on the surface of a 1:230 scale model of Bolund Island are presented. The model is smooth and no boundary layer generation has been considered since the experiment is designed as the simplest possible reference case. Measurement have been taken for a range of Reynolds numbers based on the average undisturbed wind speed U∞ and the maximum height of the island, h [1.7×104, 8.5×104], and for a range of wind directions. Four minutes time series of pressure in more than 400 points have been acquired and analysed to obtain the spatial distribution of both the time average and the variance of the pressure signal. The horizontal extension of the detachment bubble for the different Reynolds numbers and wind directions is identified by isobars and curves of constant value of pressure variance. The applicability of this technique for evaluating the horizontal topology of high turbulence regions associated to detachment bubbles after escarpments in potential wind farm sites is analysed. The results obtained shows that the behaviour of the mean pressure coefficient, Cp, the std. pressure coefficient, Cp, and the skewness of the pressure, Sp can be used to study the bubble over the island to a certain extent. This experiment is part of the set of different analysis on the Bolund test case that is being undertaken within WAUDIT project by the different scientific groups.