Molecular architecture of fur binding to iron-induced and - repressed genes in Helicobacter pylori

The ferric uptake regulator protein Fur regulates iron-dependent gene expression in bacteria. In the human pathogen Helicobacter pylori, Fur has been shown to regulate iron-induced and iron-repressed genes. Herein we investigate the molecular mechanisms that control this differential iron-responsive Fur regulation. Hydroxyl radical footprinting showed that Fur has different binding architectures, which characterize distinct operator typologies. On operators recognized with higher affinity by holo-Fur, the protein binds to a continuous AT-rich stretch of about 20 bp, displaying an extended protection pattern. This is indicative of protein wrapping around the DNA helix. DNA binding interference assays with the minor groove binding drug distamycin A, point out that the recognition of the holo-operators occurs through the minor groove of the DNA. By contrast, on the apo-operators, Fur binds primarily to thymine dimers within a newly identified TCATTn10TT consensus element, indicative of Fur binding to one side of the DNA, in the major groove of the double helix. Reconstitution of the TCATTn10TT motif within a holo-operator results in a feature binding swap from an holo-Fur- to an apo-Fur-recognized operator, affecting both affinity and binding architecture of Fur, and conferring apo-Fur repression features in vivo. Size exclusion chromatography indicated that Fur is a dimer in solution. However, in the presence of divalent metal ions the protein is able to multimerize. Accordingly, apo-Fur binds DNA as a dimer in gel shift assays, while in presence of iron, higher order complexes are formed. Stoichiometric Ferguson analysis indicates that these complexes correspond to one or two Fur tetramers, each bound to an operator element. Together these data suggest that the apo- and holo-Fur repression mechanisms apparently rely on two distinctive modes of operator-recognition, involving respectively the readout of a specific nucleotide consensus motif in the major groove for apo-operators, and the recognition of AT-rich stretches in the minor groove for holo-operators, whereas the iron-responsive binding affinity is controlled through metal-dependent shaping of the protein structure in order to match preferentially the major or the minor groove.

Innovative architecture of on-board and on-ground radio systems for space communication

The radio communication system is one of the most critical system of the overall satellite platform: it often represents the only way of communication, between a spacecraft and the Ground Segment or among a constellation of satellites. This thesis focuses on specific innovative architectures for on-board and on-ground radio systems. In particular, this work is an integral part of a space program started in 2004 at the University of Bologna, Forlì campus, which led to the completion of the microsatellite ALMASat-1, successfully launched on-board the VEGA maiden flight. The success of this program led to the development of a second microsatellite, named ALMASat-EO, a three-axis stabilized microsatellite able to capture images of the Earth surface. Therefore, the first objective of this study was focused on the investigation of an innovative, efficient and low cost architecture for on-board radio communication systems. The TT&C system and the high data rate transmitter for images downlink design and realization are thoroughly described in this work, together with the development of the embedded hardware and the adopted antenna systems. Moreover, considering the increasing interest in the development of constellations of microsatellite, in particular those flying in close formations, a careful analysis has been carried out for the development of innovative communication protocols for inter-satellite links. Furthermore, in order to investigate the system aspects of space communications, a study has been carried out at ESOC having as objective the design, implementation and test of two experimental devices for the enhancement of the ESA GS. Thus, a significant portion of this thesis is dedicated to the description of the results of a method for improving the phase stability of GS radio frequency equipments by means of real-time phase compensation and a new way to perform two antennas arraying tracking using already existing ESA tracking stations facilities.

Spatio-temporal models of the functional architecture of the visual cortex

In this work I tried to explore many aspects of cognitive visual science, each one based on different academic fields, proposing mathematical models capable to reproduce both neuro-physiological and phenomenological results that were described in the recent literature. The structure of my thesis is mainly composed of three chapters, corresponding to the three main areas of research on which I focused my work. The results of each work put the basis for the following, and their ensemble form an homogeneous and large-scale survey on the spatio-temporal properties of the architecture of the visual cortex of mammals.

Geophysical Investigation of Subsurface Three-Dimensional Architecture of Icy Debris Fans With Ground Penetrating Radar in the Wrangell Mountains, Alaska

Icy debris fans have are newly-described landforms (Kochel and Trop, 2008 and 2012) as landforms developed immediately after deglaciation on Earth and similar features have been observed on Mars. Subsurface characteristics of Icy debris fans have not been previously investigated. Ground penetrating radar (GPR) was used to non-invasively investigate the subsurface characteristics of icy debris fans near McCarthy, Alaska, USA. The three fans investigated in Alaska are the East, West, and Middle fans (Kochel and Trop, 2008 and 2012) which below the Nabesna ice cap and on top of the McCarthy Creek Glacier. Icy debris fans in general are a largely unexplored suite of paraglacial landforms and processes in alpine regions. Recent field studies focused on direct observations and depositional processes. Their results showed that the fan's composition is primarily influenced by the type and frequency of depositional processes that supply the fan. Photographic studies show that the East Fan receives far more ice and snow avalanches whereas the Middle and West Fans receive fewer mass wasting events but more clastic debris is deposited on the Middle and West fan from rock falls and icy debris flows. GPR profiles and Wide-angle reflection and refraction (WARR) surveys consisting of both, common mid-point (CMP), and common shot-point (CSP) surveys investigated the subsurface geometry of the fans and the McCarthy Creek Glacier. All GPR surveys were collected in July of 2013 with 100MHz bi-static antennas. Four axial profiles and three cross-fan profiles were done on the West and Middle fans as well as the McCarthy Creek Glacier in order to investigate the relationship between the three features. GPR profiles yielded reflectors that were continuous for 10+ m and hyperbolic reflections in the subsurface. The depth to these reflections in the subsurface requires knowledge of the velocity of the subsurface. To find the velocity of the subsurface eight WARR surveys collected on the fans and on the McCarthy Creek glacier to provide information on variability of subsurface velocities. The profiles of the Middle and West fan have more reflections in their profiles compared to profiles done on the McCarthy Creek Glacier. Based on the WARR surveys, we interpret the lower energy return in the glacier to be caused by two reasons. 1) The increased attenuation due to wet ice versus drier ice and on the fan with GPR velocities >0.15m/ns. 2) Lack of interfaces in the glacier compared to those in the fans which are inferred to be produced by the alternating layers of stratified ice and lithic-rich layers. The GPR profiles on the West and Middle Fans show the shallow subsurface being dominated by lenticular reflections interpreted to be consistent with the shape of surficial deposits. The West Fan is distinguished from the Middle Fan by the nature of its reflections patterns and thicknesses of reflection packages that clearly shows the Middle fan with a greater thickness. The changes in subsurface reflections between the Middle and West Fans as well as the McCarthy Creek Glacier are thought to reflect the type and frequency of depositional processes and surrounding bedrock and talus slopes.

Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease

Crohn's disease and ulcerative colitis, the two common forms of inflammatory bowel disease (IBD), affect over 2.5 million people of European ancestry, with rising prevalence in other populations. Genome-wide association studies and subsequent meta-analyses of these two diseases as separate phenotypes have implicated previously unsuspected mechanisms, such as autophagy, in their pathogenesis and showed that some IBD loci are shared with other inflammatory diseases. Here we expand on the knowledge of relevant pathways by undertaking a meta-analysis of Crohn's disease and ulcerative colitis genome-wide association scans, followed by extensive validation of significant findings, with a combined total of more than 75,000 cases and controls. We identify 71 new associations, for a total of 163 IBD loci, that meet genome-wide significance thresholds. Most loci contribute to both phenotypes, and both directional (consistently favouring one allele over the course of human history) and balancing (favouring the retention of both alleles within populations) selection effects are evident. Many IBD loci are also implicated in other immune-mediated disorders, most notably with ankylosing spondylitis and psoriasis. We also observe considerable overlap between susceptibility loci for IBD and mycobacterial infection. Gene co-expression network analysis emphasizes this relationship, with pathways shared between host responses to mycobacteria and those predisposing to IBD.

The structural architecture of adult mammalian articular cartilage evolves by a synchronized process of tissue resorption and neoformation during postnatal development

OBJECTIVE: During postnatal development, mammalian articular cartilage acts as a surface growth plate for the underlying epiphyseal bone. Concomitantly, it undergoes a fundamental process of structural reorganization from an immature isotropic to a mature (adult) anisotropic architecture. However, the mechanism underlying this structural transformation is unknown. It could involve either an internal remodelling process, or complete resorption followed by tissue neoformation. The aim of this study was to establish which of these two alternative tissue reorganization mechanisms is physiologically operative. We also wished to pinpoint the articular cartilage source of the stem cells for clonal expansion and the zonal location of the chondrocyte pool with high proliferative activity. METHODS: The New Zealand white rabbit served as our animal model. The analysis was confined to the high-weight-bearing (central) areas of the medial and lateral femoral condyles. After birth, the articular cartilage layer was evaluated morphologically at monthly intervals from the first to the eighth postnatal month, when this species attains skeletal maturity. The overall height of the articular cartilage layer at each juncture was measured. The growth performance of the articular cartilage layer was assessed by calcein labelling, which permitted an estimation of the daily growth rate of the epiphyseal bone and its monthly length-gain. The slowly proliferating stem-cell pool was identified immunohistochemically (after labelling with bromodeoxyuridine), and the rapidly proliferating chondrocyte population by autoradiography (after labelling with (3)H-thymidine). RESULTS: The growth activity of the articular cartilage layer was highest 1 month after birth. It declined precipitously between the first and third months, and ceased between the third and fourth months, when the animal enters puberty. The structural maturation of the articular cartilage layer followed a corresponding temporal trend. During the first 3 months, when the articular cartilage layer is undergoing structural reorganization, the net length-gain in the epiphyseal bone exceeded the height of the articular cartilage layer. This finding indicates that the postnatal reorganization of articular cartilage from an immature isotropic to a mature anisotropic structure is not achieved by a process of internal remodelling, but by the resorption and neoformation of all zones except the most superficial (stem-cell) one. The superficial zone was found to consist of slowly dividing stem cells with bidirectional mitotic activity. In the horizontal direction, this zone furnishes new stem cells that replenish the pool and effect a lateral expansion of the articular cartilage layer. In the vertical direction, the superficial zone supplies the rapidly dividing, transit-amplifying daughter-cell pool that feeds the transitional and upper radial zones during the postnatal growth phase of the articular cartilage layer. CONCLUSIONS: During postnatal development, mammalian articular cartilage fulfils a dual function, viz., it acts not only as an articulating layer but also as a surface growth plate. In the lapine model, this growth activity ceases at puberty (3-4 months of age), whereas that of the true (metaphyseal) growth plate continues until the time of skeletal maturity (8 months). Hence, the two structures are regulated independently. The structural maturation of the articular cartilage layer coincides temporally with the cessation of its growth activity - for the radial expansion and remodelling of the epiphyseal bone - and with sexual maturation. That articular cartilage is physiologically reorganized by a process of tissue resorption and neoformation, rather than by one of internal remodelling, has important implications for the functional engineering and repair of articular cartilage tissue.

Architecture of European plastic surgery

The architecture of European Plastic Surgery was published in 1996 [Nicolai JPA, Scuderi N. Plastic surgical Europe in an organogram. Eur J Plast Surg 1996; 19: 253-256.] It is the objective of this paper to update information of that article. Continuing medical education (CME), science, training, examination, quality assurance and relations with the European Commission and Parliament all are aspects covered by the organisations to be discussed.

System Architecture of a Mixed Reality Framework

In this paper the software architecture of a framework which simplifies the development of applications in the area of Virtual and Augmented Reality is presented. It is based on VRML/X3D to enable rendering of audio-visual information. We extended our VRML rendering system by a device management system that is based on the concept of a data-flow graph. The aim of the system is to create Mixed Reality (MR) applications simply by plugging together small prefabricated software components, instead of compiling monolithic C++ applications. The flexibility and the advantages of the presented framework are explained on the basis of an exemplary implementation of a classic Augmented Realityapplication and its extension to a collaborative remote expert scenario.

Lessons from the Multilateral Trading System for Reforming the Architecture of the International Environmental Regime

Recent studies on environmental regimes suggest that important lessons and policy recommendations may be drawn from the functioning of the multilateral trading regime. This brief compares the needs and goals of the trade and environment regimes, and discusses how insights from over sixty years of experience of the multilateral trading system might provide ideas for redesigning the architecture of the international environmental regime. It further calls for a better dialogue and improved complementarities between the two fields in order to enhance coherence within international law.

Lake Floor Morphology and Sediment Architecture of Lake Torneträsk, Northern Sweden

ABSTRACT. Here we present datasets from a hydroacoustic survey in July 2011 at Lake Torneträsk, northern Sweden. Our hydroacoustic data exhibit lake floor morphologies formed by glacial erosion and accumulation processes, insights into lacustrine sediment accumulation since the beginning of deglaciation, and information on seismic activity along the Pärvie Fault. Features of glacial scouring with a high-energy relief, steep slopes, and relative reliefs of more than 50 m are observed in the large W-basin. The remainder of the lacustrine subsurface appears to host a broad variety of well preserved formations from glacial accumulation related to the last retreat of the Fennoscandian ice sheet. Deposition of glaciolacustrine and lacustrine sediments is focused in areas situated in proximity to major inlets. Sediment accumulation in distal areas of the lake seldom exceeds 2 m or is not observable. We assume that lack of sediment deposition in the lake is a result of different factors, including low rates of erosion in the catchment, a previously high lake level leading to deposition of sediments in higher elevated paleodeltas, tributaries carrying low suspension loads as a result of sedimentation in upstream lakes, and an overall low productivity in the lake. A clear off-shore trace of the Pärvie Fault could not be detected from our hydroacoustic data. However, an absence of sediment disturbance in close proximity to the presumed fault trace implies minimal seismic activity since deposition of the glaciolacustrine and lacustrine sediments.