The fetomaternal interface in the placenta of three species of armadillos (Eutheria, Xenarthra, Dasypodidae)

Background: Placental characters vary among Xenarthra, one of four supraordinal clades of Eutheria. Armadillos are known for villous, haemochorial placentas similar to humans. Only the nine-banded armadillo has been well studied so far. Methods: Placentas of three species of armadillos were investigated by means of histology, immunohistochemistry including proliferation marker, and transmission and scanning electron microscopy. Results: The gross anatomy differed: Euphractus sexcinctus and Chaetophractus villosus had extended, zonary placentas, whereas Chaetophractus vellerosus had a disk. All taxa had complex villous areas within the maternal blood sinuses of the endometrium. Immunohistochemistry indicated the validity of former interpretations that the endothelium of the sinuses was largely intact. Tips of the villi and the columns entering the maternal tissue possessed trophoblast cell clusters with proliferation activity. Elsewhere, the feto-maternal barrier was syncytial haemochorial with fetal vessels near the surface. Conclusions: Differences among armadillos occurred in regard to the extension of the placenta, whereas the fine structure was similar. Parallels to the human suggest that armadillos are likely to be useful animal models for human placentation.

Numerical assessment of stability of interface discontinuous finite element pressure spaces

The stability of two recently developed pressure spaces has been assessed numerically: The space proposed by Ausas et al. [R.F. Ausas, F.S. Sousa, G.C. Buscaglia, An improved finite element space for discontinuous pressures, Comput. Methods Appl. Mech. Engrg. 199 (2010) 1019-1031], which is capable of representing discontinuous pressures, and the space proposed by Coppola-Owen and Codina [A.H. Coppola-Owen, R. Codina, Improving Eulerian two-phase flow finite element approximation with discontinuous gradient pressure shape functions, Int. J. Numer. Methods Fluids, 49 (2005) 1287-1304], which can represent discontinuities in pressure gradients. We assess the stability of these spaces by numerically computing the inf-sup constants of several meshes. The inf-sup constant results as the solution of a generalized eigenvalue problems. Both spaces are in this way confirmed to be stable in their original form. An application of the same numerical assessment tool to the stabilized equal-order P-1/P-1 formulation is then reported. An interesting finding is that the stabilization coefficient can be safely set to zero in an arbitrary band of elements without compromising the formulation's stability. An analogous result is also reported for the mini-element P-1(+)/P-1 when the velocity bubbles are removed in an arbitrary band of elements. (C) 2012 Elsevier B.V. All rights reserved.

Molecular Dynamics Investigations of PRODAN in a DLPC Bilayer

Molecular dynamics computer simulations have been performed to identify preferred positions of the fluorescent probe PRODAN in a fully hydrated DLPC bilayer in the fluid phase. In addition to the intramolecular charge-transfer first vertical excited state, we considered different charge distributions for the electronic ground state of the PRODAN molecule by distinct atomic charge models corresponding to the probe molecule in vacuum as well as polarized in a weak and a strong dielectric solvent (cyclohexane and water). Independent on the charge distribution model of PRODAN, we observed a preferential orientation of this molecule in the bilayer with the dimethylamino group pointing toward the membrane's center and the carbonyl oxygen toward the membrane's interface. However, changing the charge distribution model of PRODAN, independent of its initial position in the equilibrated DLPC membrane, we observed different preferential positions. For the ground state representation without polarization and the in-cyclohexane polarization, the probe maintains its position close to the membrane's center. Considering the in-water polarization model, the probe approaches more of the polar headgroup region of the bilayer, with a strong structural correlation with the choline group, exposing its oxygen atom to water molecules. PRODAN's representation of the first vertical excited state with the in-water polarization also approaches the polar region of the membrane with the oxygen atom exposed to the bilayer's hydration shell. However, this model presents a stronger structural correlation with the phosphate groups than the ground state. Therefore, we conclude that the orientation of the PRODAN molecule inside the DLPC membrane is well-defined, but its position is very sensitive to the effect of the medium polarization included here by different models for the atomic charge distribution of the probe.

The immediate effects of local and adjacent acupuncture on the tibialis anterior muscle: a human study

Abstract Background This study compares the immediate effects of local and adjacent acupuncture on the tibialis anterior muscle and the amount of force generated or strength in Kilogram Force (KGF) evaluated by a surface electromyography. Methods The study consisted of a single blinded trial of 30 subjects assigned to two groups: local acupoint (ST36) and adjacent acupoint (SP9). Bipolar surface electrodes were placed on the tibialis anterior muscle, while a force transducer was attached to the foot of the subject and to the floor. An electromyograph (EMG) connected to a computer registered the KGF and root mean square (RMS) before and after acupuncture at maximum isometric contraction. The RMS values and surface electrodes were analyzed with Student's t-test. Results Thirty subjects were selected from a total of 56 volunteers according to specific inclusion and exclusion criteria and were assigned to one of the two groups for acupuncture. A significant decrease in the RMS values was observed in both ST36 (t = -3.80, P = 0,001) and SP9 (t = 6.24, P = 0.001) groups after acupuncture. There was a decrease in force in the ST36 group after acupuncture (t = -2.98, P = 0.006). The RMS values did not have a significant difference (t = 0.36, P = 0.71); however, there was a significant decrease in strength after acupuncture in the ST36 group compared to the SP9 group (t = 2.51, P = 0.01). No adverse events were found. Conclusion Acupuncture at the local acupoint ST36 or adjacent acupoints SP9 reduced the tibialis anterior electromyography muscle activity. However, acupuncture at SP9 did not decrease muscle strength while acupuncture at ST36 did.

New functional and biomechanical assessments for the improvement of the surgical navigation systems for joint replacement in the human lower limb

In case of severe osteoarthritis at the knee causing pain, deformity, and loss of stability and mobility, the clinicians consider that the substitution of these surfaces by means of joint prostheses. The objectives to be pursued by this surgery are: complete pain elimination, restoration of the normal physiological mobility and joint stability, correction of all deformities and, thus, of limping. The knee surgical navigation systems have bee developed in computer-aided surgery in order to improve the surgical final outcome in total knee arthroplasty. These systems provide the surgeon with quantitative and real-time information about each surgical action, like bone cut executions and prosthesis component alignment, by mean of tracking tools rigidly fixed onto the femur and the tibia. Nevertheless, there is still a margin of error due to the incorrect surgical procedures and to the still limited number of kinematic information provided by the current systems. Particularly, patello-femoral joint kinematics is not considered in knee surgical navigation. It is also unclear and, thus, a source of misunderstanding, what the most appropriate methodology is to study the patellar motion. In addition, also the knee ligamentous apparatus is superficially considered in navigated total knee arthroplasty, without taking into account how their physiological behavior is altered by this surgery. The aim of the present research work was to provide new functional and biomechanical assessments for the improvement of the surgical navigation systems for joint replacement in the human lower limb. This was mainly realized by means of the identification and development of new techniques that allow a thorough comprehension of the functioning of the knee joint, with particular attention to the patello-femoral joint and to the main knee soft tissues. A knee surgical navigation system with active markers was used in all research activities presented in this research work. Particularly, preliminary test were performed in order to assess the system accuracy and the robustness of a number of navigation procedures. Four studies were performed in-vivo on patients requiring total knee arthroplasty and randomly implanted by means of traditional and navigated procedures in order to check for the real efficacy of the latter with respect to the former. In order to cope with assessment of patello-femoral joint kinematics in the intact and replaced knees, twenty in-vitro tests were performed by using a prototypal tracking tool also for the patella. In addition to standard anatomical and articular recommendations, original proposals for defining the patellar anatomical-based reference frame and for studying the patello-femoral joint kinematics were reported and used in these tests. These definitions were applied to two further in-vitro tests in which, for the first time, also the implant of patellar component insert was fully navigated. In addition, an original technique to analyze the main knee soft tissues by means of anatomical-based fiber mappings was also reported and used in the same tests. The preliminary instrumental tests revealed a system accuracy within the millimeter and a good inter- and intra-observer repeatability in defining all anatomical reference frames. In in-vivo studies, the general alignments of femoral and tibial prosthesis components and of the lower limb mechanical axis, as measured on radiographs, was more satisfactory, i.e. within ±3°, in those patient in which total knee arthroplasty was performed by navigated procedures. As for in-vitro tests, consistent patello-femoral joint kinematic patterns were observed over specimens throughout the knee flexion arc. Generally, the physiological intact knee patellar motion was not restored after the implant. This restoration was successfully achieved in the two further tests where all component implants, included the patellar insert, were fully navigated, i.e. by means of intra-operative assessment of also patellar component positioning and general tibio-femoral and patello-femoral joint assessment. The tests for assessing the behavior of the main knee ligaments revealed the complexity of the latter and the different functional roles played by the several sub-bundles compounding each ligament. Also in this case, total knee arthroplasty altered the physiological behavior of these knee soft tissues. These results reveal in-vitro the relevance and the feasibility of the applications of new techniques for accurate knee soft tissues monitoring, patellar tracking assessment and navigated patellar resurfacing intra-operatively in the contest of the most modern operative techniques. This present research work gives a contribution to the much controversial knowledge on the normal and replaced of knee kinematics by testing the reported new methodologies. The consistence of these results provides fundamental information for the comprehension and improvements of knee orthopedic treatments. In the future, the reported new techniques can be safely applied in-vivo and also adopted in other joint replacements.

Spatial mechanisms for modelling the human ankle passive motion

Knowledge on how ligaments and articular surfaces guide passive motion at the human ankle joint complex is fundamental for the design of relevant surgical treatments. The dissertation presents a possible improvement of this knowledge by a new kinematic model of the tibiotalar articulation. In this dissertation two one-DOF spatial equivalent mechanisms are presented for the simulation of the passive motion of the human ankle joint: the 5-5 fully parallel mechanism and the fully parallel spherical wrist mechanism. These mechanisms are based on the main anatomical structures of the ankle joint, namely the talus/calcaneus and the tibio/fibula bones at their interface, and the TiCaL and CaFiL ligaments. In order to show the accuracy of the models and the efficiency of the proposed procedure, these mechanisms are synthesized from experimental data and the results are compared with those obtained both during experimental sessions and with data published in the literature. Experimental results proved the efficiency of the proposed new mechanisms to simulate the ankle passive motion and, at the same time, the potentiality of the mechanism to replicate the ankle’s main anatomical structures quite well. The new mechanisms represent a powerful tool for both pre-operation planning and new prosthesis design.

Computer simulation of ordering and dynamics in liquid crystals in the bulk and close to the surface

The aim of this PhD thesis is to investigate the orientational and dynamical properties of liquid crystalline systems, at molecular level and using atomistic computer simulations, to reach a better understanding of material behavior from a microscopic point view. In perspective this should allow to clarify the relation between the micro and macroscopic properties with the objective of predicting or confirming experimental results on these systems. In this context, we developed four different lines of work in the thesis. The first one concerns the orientational order and alignment mechanism of rigid solutes of small dimensions dissolved in a nematic phase formed by the 4-pentyl,4 cyanobiphenyl (5CB) nematic liquid crystal. The orientational distribution of solutes have been obtained with Molecular Dynamics Simulation (MD) and have been compared with experimental data reported in literature. we have also verified the agreement between order parameters and dipolar coupling values measured in NMR experiments. The MD determined effective orientational potentials have been compared with the predictions of Maier­Saupe and Surface tensor models. The second line concerns the development of a correct parametrization able to reproduce the phase transition properties of a prototype of the oligothiophene semiconductor family: sexithiophene (T6). T6 forms two crystalline polymorphs largely studied, and possesses liquid crystalline phases still not well characterized, From simulations we detected a phase transition from crystal to liquid crystal at about 580 K, in agreement with available experiments, and in particular we found two LC phases, smectic and nematic. The crystal­smectic transition is associated to a relevant density variation and to strong conformational changes of T6, namely the molecules in the liquid crystal phase easily assume a bent shape, deviating from the planar structure typical of the crystal. The third line explores a new approach for calculating the viscosity in a nematic through a virtual exper- iment resembling the classical falling sphere experiment. The falling sphere is replaced by an hydrogenated silicon nanoparticle of spherical shape suspended in 5CB, and gravity effects are replaced by a constant force applied to the nanoparticle in a selected direction. Once the nanoparticle reaches a constant velocity, the viscosity of the medium can be evaluated using Stokes' law. With this method we successfully reproduced experimental viscosities and viscosity anisotropy for the solvent 5CB. The last line deals with the study of order induction on nematic molecules by an hydrogenated silicon surface. Gaining predicting power for the anchoring behavior of liquid crystals at surfaces will be a very desirable capability, as many properties related to devices depend on molecular organization close to surfaces. Here we studied, by means of atomistic MD simulations, the flat interface between an hydrogenated (001) silicon surface in contact with a sample of 5CB molecules. We found a planar anchoring of the first layers of 5CB where surface interactions are dominating with respect to the mesogen intermolecular interactions. We also analyzed the interface 5CB­vacuum, finding a homeotropic orientation of the nematic at this interface.

Use of computer algebra in the calculation of Feynman diagrams

The increasing precision of current and future experiments in high-energy physics requires a likewise increase in the accuracy of the calculation of theoretical predictions, in order to find evidence for possible deviations of the generally accepted Standard Model of elementary particles and interactions. Calculating the experimentally measurable cross sections of scattering and decay processes to a higher accuracy directly translates into including higher order radiative corrections in the calculation. The large number of particles and interactions in the full Standard Model results in an exponentially growing number of Feynman diagrams contributing to any given process in higher orders. Additionally, the appearance of multiple independent mass scales makes even the calculation of single diagrams non-trivial. For over two decades now, the only way to cope with these issues has been to rely on the assistance of computers. The aim of the xloops project is to provide the necessary tools to automate the calculation procedures as far as possible, including the generation of the contributing diagrams and the evaluation of the resulting Feynman integrals. The latter is based on the techniques developed in Mainz for solving one- and two-loop diagrams in a general and systematic way using parallel/orthogonal space methods. These techniques involve a considerable amount of symbolic computations. During the development of xloops it was found that conventional computer algebra systems were not a suitable implementation environment. For this reason, a new system called GiNaC has been created, which allows the development of large-scale symbolic applications in an object-oriented fashion within the C++ programming language. This system, which is now also in use for other projects besides xloops, is the main focus of this thesis. The implementation of GiNaC as a C++ library sets it apart from other algebraic systems. Our results prove that a highly efficient symbolic manipulator can be designed in an object-oriented way, and that having a very fine granularity of objects is also feasible. The xloops-related parts of this work consist of a new implementation, based on GiNaC, of functions for calculating one-loop Feynman integrals that already existed in the original xloops program, as well as the addition of supplementary modules belonging to the interface between the library of integral functions and the diagram generator.

Computer simulations of two-dimensional colloidal crystals in confinement

Monte Carlo simulations are used to study the effect of confinement on a crystal of point particles interacting with an inverse power law potential in d=2 dimensions. This system can describe colloidal particles at the air-water interface, a model system for experimental study of two-dimensional melting. It is shown that the state of the system (a strip of width D) depends very sensitively on the precise boundary conditions at the two ``walls'' providing the confinement. If one uses a corrugated boundary commensurate with the order of the bulk triangular crystalline structure, both orientational order and positional order is enhanced, and such surface-induced order persists near the boundaries also at temperatures where the system in the bulk is in its fluid state. However, using smooth repulsive boundaries as walls providing the confinement, only the orientational order is enhanced, but positional (quasi-) long range order is destroyed: The mean-square displacement of two particles n lattice parameters apart in the y-direction along the walls then crosses over from the logarithmic increase (characteristic for $d=2$) to a linear increase (characteristic for d=1). The strip then exhibits a vanishing shear modulus. These results are interpreted in terms of a phenomenological harmonic theory. Also the effect of incommensurability of the strip width D with the triangular lattice structure is discussed, and a comparison with surface effects on phase transitions in simple Ising- and XY-models is made

Computer simulations of microstructures related to the olivine spinel transition

Tiefherd-Beben, die im oberen Erdmantel in einer Tiefe von ca. 400 km auftreten, werden gewöhnlich mit dem in gleicher Tiefe auftretenden druckabhängigen, polymorphen Phasenübergang von Olivine (α-Phase) zu Spinel (β-Phase) in Verbindung gebracht. Es ist jedoch nach wie vor unklar, wie der Phasenübergang mit dem mechanischen Versagen des Mantelmaterials zusammenhängt. Zur Zeit werden im Wesentlichen zwei Modelle diskutiert, die entweder Mikrostrukturen, die durch den Phasenübergang entstehen, oder aber die rheologischen Veränderungen des Mantelgesteins durch den Phasenübergang dafür verantwortlich machen. Dabei sind Untersuchungen der Olivin→Spinel Umwandlung durch die Unzugänglichkeit des natürlichen Materials vollständig auf theoretische Überlegungen sowie Hochdruck-Experimente und Numerische Simulationen beschränkt. Das zentrale Thema dieser Dissertation war es, ein funktionierendes Computermodell zur Simulation der Mikrostrukturen zu entwickeln, die durch den Phasenübergang entstehen. Des Weiteren wurde das Computer Modell angewandt um die mikrostrukturelle Entwicklung von Spinelkörnern und die Kontrollparameter zu untersuchen. Die Arbeit ist daher in zwei Teile unterteilt: Der erste Teil (Kap. 2 und 3) behandelt die physikalischen Gesetzmäßigkeiten und die prinzipielle Funktionsweise des Computer Modells, das auf der Kombination von Gleichungen zur Errechnung der kinetischen Reaktionsgeschwindigkeit mit Gesetzen der Nichtgleichgewichtsthermodynamik unter nicht-hydostatischen Bedingungen beruht. Das Computermodell erweitert ein Federnetzwerk der Software latte aus dem Programmpaket elle. Der wichtigste Parameter ist dabei die Normalspannung auf der Kornoberfläche von Spinel. Darüber hinaus berücksichtigt das Programm die Latenzwärme der Reaktion, die Oberflächenenergie und die geringe Viskosität von Mantelmaterial als weitere wesentliche Parameter in der Berechnung der Reaktionskinetic. Das Wachstumsverhalten und die fraktale Dimension von errechneten Spinelkörnern ist dabei in guter Übereinstimmung mit Spinelstrukturen aus Hochdruckexperimenten. Im zweiten Teil der Arbeit wird das Computermodell angewandt, um die Entwicklung der Oberflächenstruktur von Spinelkörnern unter verschiedenen Bedigungen zu eruieren. Die sogenannte ’anticrack theory of faulting’, die den katastrophalen Verlauf der Olivine→Spinel Umwandlung in olivinhaltigem Material unter differentieller Spannung durch Spannungskonzentrationen erklärt, wurde anhand des Computermodells untersucht. Der entsprechende Mechanismus konnte dabei nicht bestätigt werden. Stattdessen können Oberflächenstrukturen, die Ähnlichkeiten zu Anticracks aufweisen, durch Unreinheiten des Materials erklärt werden (Kap. 4). Eine Reihe von Simulationen wurde der Herleitung der wichtigsten Kontrollparameter der Reaktion in monomineralischem Olivin gewidmet (Kap. 5 and Kap. 6). Als wichtigste Einflüsse auf die Kornform von Spinel stellten sich dabei die Hauptnormalspannungen auf dem System sowie Heterogenitäten im Wirtsminerals und die Viskosität heraus. Im weiteren Verlauf wurden die Nukleierung und das Wachstum von Spinel in polymineralischen Mineralparagenesen untersucht (Kap. 7). Die Reaktionsgeschwindigkeit der Olivine→Spinel Umwandlung und die Entwicklung von Spinelnetzwerken und Clustern wird durch die Gegenwart nicht-reaktiver Minerale wie Granat oder Pyroxen erheblich beschleunigt. Die Bildung von Spinelnetzwerken hat das Potential, die mechanischen Eigenschaften von Mantelgestein erheblich zu beeinflussen, sei es durch die Bildung potentieller Scherzonen oder durch Gerüstbildung. Dieser Lokalisierungprozess des Spinelwachstums in Mantelgesteinen kann daher ein neues Erklärungsmuster für Tiefbeben darstellen.

Engineering Agent-Oriented Technologies and Programming Languages for Computer Programming and Software Development

Mainstream hardware is becoming parallel, heterogeneous, and distributed on every desk, every home and in every pocket. As a consequence, in the last years software is having an epochal turn toward concurrency, distribution, interaction which is pushed by the evolution of hardware architectures and the growing of network availability. This calls for introducing further abstraction layers on top of those provided by classical mainstream programming paradigms, to tackle more effectively the new complexities that developers have to face in everyday programming. A convergence it is recognizable in the mainstream toward the adoption of the actor paradigm as a mean to unite object-oriented programming and concurrency. Nevertheless, we argue that the actor paradigm can only be considered a good starting point to provide a more comprehensive response to such a fundamental and radical change in software development. Accordingly, the main objective of this thesis is to propose Agent-Oriented Programming (AOP) as a high-level general purpose programming paradigm, natural evolution of actors and objects, introducing a further level of human-inspired concepts for programming software systems, meant to simplify the design and programming of concurrent, distributed, reactive/interactive programs. To this end, in the dissertation first we construct the required background by studying the state-of-the-art of both actor-oriented and agent-oriented programming, and then we focus on the engineering of integrated programming technologies for developing agent-based systems in their classical application domains: artificial intelligence and distributed artificial intelligence. Then, we shift the perspective moving from the development of intelligent software systems, toward general purpose software development. Using the expertise maturated during the phase of background construction, we introduce a general-purpose programming language named simpAL, which founds its roots on general principles and practices of software development, and at the same time provides an agent-oriented level of abstraction for the engineering of general purpose software systems.

New computational biology tools for the systematic analysis of the structure and expression of human genes

From the late 1980s, the automation of sequencing techniques and the computer spread gave rise to a flourishing number of new molecular structures and sequences and to proliferation of new databases in which to store them. Here are presented three computational approaches able to analyse the massive amount of publicly avalilable data in order to answer to important biological questions. The first strategy studies the incorrect assignment of the first AUG codon in a messenger RNA (mRNA), due to the incomplete determination of its 5' end sequence. An extension of the mRNA 5' coding region was identified in 477 in human loci, out of all human known mRNAs analysed, using an automated expressed sequence tag (EST)-based approach. Proof-of-concept confirmation was obtained by in vitro cloning and sequencing for GNB2L1, QARS and TDP2 and the consequences for the functional studies are discussed. The second approach analyses the codon bias, the phenomenon in which distinct synonymous codons are used with different frequencies, and, following integration with a gene expression profile, estimates the total number of codons present across all the expressed mRNAs (named here "codonome value") in a given biological condition. Systematic analyses across different pathological and normal human tissues and multiple species shows a surprisingly tight correlation between the codon bias and the codonome bias. The third approach is useful to studies the expression of human autism spectrum disorder (ASD) implicated genes. ASD implicated genes sharing microRNA response elements (MREs) for the same microRNA are co-expressed in brain samples from healthy and ASD affected individuals. The different expression of a recently identified long non coding RNA which have four MREs for the same microRNA could disrupt the equilibrium in this network, but further analyses and experiments are needed.

Simulations of amphiphilic peptides at the air-water interface

Amphiphile Peptide, Pro-Glu-(Phe-Glu)n-Pro, Pro-Asp-(Phe-Asp)n-Pro, und Phe-Glu-(Phe-Glu)n-Phe, können so aus n alternierenden Sequenzen von hydrophoben und hydrophilen Aminosäuren konstruiert werden, dass sie sich in Monolagen an der Luft-Wasser Grenzfläche anordnen. In biologischen Systemen können Strukturen an der organisch-wässrigen Grenzfläche als Matrix für die Kristallisation von Hydroxyapatit dienen, ein Vorgang der für die Behandlung von Osteoporose verwendet werden kann. In der vorliegenden Arbeit wurden Computersimulationenrneingesetzt, um die Strukturen und die zugrunde liegenden Wechselwirkungen welche die Aggregation der Peptide auf mikroskopischer Ebene steuern, zu untersuchen. Atomistische Molekulardynamik-Simulationen von einzelnen Peptidsträngen zeigen, dass sie sich leicht an der Luft-Wasser Grenzfläche anordnen und die Fähigkeit haben, sich in β-Schleifen zu falten, selbst für relativ kurze Peptidlängen (n = 2). Seltene Ereignisse wie diese (i.e. Konformationsänderungen) erfordern den Einsatz fortgeschrittener Sampling-Techniken. Hier wurde “Replica Exchange” Molekulardynamik verwendet um den Einfluss der Peptidsequenzen zu untersuchen. Die Simulationsergebnisse zeigten, dass Peptide mit kürzeren azidischen Seitenketten (Asp vs. Glu) gestrecktere Konformationen aufwiesen als die mit längeren Seitenketten, die in der Lage waren die Prolin-Termini zu erreichen. Darüber hinaus zeigte sich, dass die Prolin-Termini (Pro vs. Phe) notwendig sind, um eine 2D-Ordnung innerhalb derrnAggregate zu erhalten. Das Peptid Pro-Asp-(Phe-Asp)n-Pro, das beide dieser Eigenschaften enthält, zeigt das geordnetste Verhalten, eine geringe Verdrehung der Hauptkette, und ist in der Lage die gebildeten Aggregate durch Wasserstoffbrücken zwischen den sauren Seitenketten zu stabilisieren. Somit ist dieses Peptid am besten zur Aggregation geeignet. Dies wurde auch durch die Beurteilung der Stabilität von experimentnah-aufgesetzten Peptidaggregaten, sowie der Neigung einzelner Peptide zur Selbstorganisation von anfänglich ungeordneten Konfigurationen unterstützt. Da atomistische Simulationen nur auf kleine Systemgrößen und relativ kurze Zeitskalen begrenzt sind, wird ein vergröbertes Modell entwickelt damit die Selbstorganisation auf einem größeren Maßstab studiert werden kann. Da die Selbstorganisation an der Grenzfläche vonrnInteresse ist, wurden existierenden Vergröberungsmethoden erweitert, um nicht-gebundene Potentiale für inhomogene Systeme zu bestimmen. Die entwickelte Methode ist analog zur iterativen Boltzmann Inversion, bildet aber das Update für das Interaktionspotential basierend auf der radialen Verteilungsfunktion in einer Slab-Geometrie und den Breiten des Slabs und der Grenzfläche. Somit kann ein Kompromiss zwischen der lokalen Flüssigketsstruktur und den thermodynamischen Eigenschaften der Grenzfläche erreicht werden. Die neue Methode wurde für einen Wasser- und einen Methanol-Slab im Vakuum demonstriert, sowie für ein einzelnes Benzolmolekül an der Vakuum-Wasser Grenzfläche, eine Anwendung die von besonderer Bedeutung in der Biologie ist, in der oft das thermodynamische/Grenzflächenpolymerisations-Verhalten zusätzlich der strukturellen Eigenschaften des Systems erhalten werden müssen. Daraufrnbasierend wurde ein vergröbertes Modell über einen Fragment-Ansatz parametrisiert und die Affinität des Peptids zur Vakuum-Wasser Grenzfläche getestet. Obwohl die einzelnen Fragmente sowohl die Struktur als auch die Wahrscheinlichkeitsverteilungen an der Grenzfläche reproduzierten, diffundierte das Peptid als Ganzes von der Grenzfläche weg. Jedoch führte eine Reparametrisierung der nicht-gebundenen Wechselwirkungen für eines der Fragmente der Hauptkette in einem Trimer dazu, dass das Peptid an der Grenzfläche blieb. Dies deutet darauf hin, dass die Kettenkonnektivität eine wichtige Rolle im Verhalten des Petpids an der Grenzfläche spielt.

Exploring host-pathogen interactions through protein microarray. Large-scale protein microarray analysis revealed novel human receptors for the staphylococcal immune evasion protein FLIPr and for the neisserial adhesin NadA

Adhesion, immune evasion and invasion are key determinants during bacterial pathogenesis. Pathogenic bacteria possess a wide variety of surface exposed and secreted proteins which allow them to adhere to tissues, escape the immune system and spread throughout the human body. Therefore, extensive contacts between the human and the bacterial extracellular proteomes take place at the host-pathogen interface at the protein level. Recent researches emphasized the importance of a global and deeper understanding of the molecular mechanisms which underlie bacterial immune evasion and pathogenesis. Through the use of a large-scale, unbiased, protein microarray-based approach and of wide libraries of human and bacterial purified proteins, novel host-pathogen interactions were identified. This approach was first applied to Staphylococcus aureus, cause of a wide variety of diseases ranging from skin infections to endocarditis and sepsis. The screening led to the identification of several novel interactions between the human and the S. aureus extracellular proteomes. The interaction between the S. aureus immune evasion protein FLIPr (formyl-peptide receptor like-1 inhibitory protein) and the human complement component C1q, key players of the offense-defense fighting, was characterized using label-free techniques and functional assays. The same approach was also applied to Neisseria meningitidis, major cause of bacterial meningitis and fulminant sepsis worldwide. The screening led to the identification of several potential human receptors for the neisserial adhesin A (NadA), an important adhesion protein and key determinant of meningococcal interactions with the human host at various stages. The interaction between NadA and human LOX-1 (low-density oxidized lipoprotein receptor) was confirmed using label-free technologies and cell binding experiments in vitro. Taken together, these two examples provided concrete insights into S. aureus and N. meningitidis pathogenesis, and identified protein microarray coupled with appropriate validation methodologies as a powerful large scale tool for host-pathogen interactions studies.

Neonatal plasmacytoid dendritic cells at the interface of innate and adaptive immunity = Neonatale plasmazytoide dendritische Zellen - an der Schnittstelle zwischen angeborener und adaptiver Immunität

Human cord blood plasmacytoid dendritic cells (PDC) react to stimulation with CPG A and CPG B with an increase in cell surface activation and maturation markers and cytokine production, similar to adult PDC. Intracellular phosphorylation in neonatal PDC did not benefit from CPG stimulation, in contrast to adult PDC. Cord blood PDC primed with CPG A, CPG B and CD40L do not promote division of autologous T cells contrary to adult PDC. Priming of neonatal PDC with CPG A or CPG B does not induce a clear bias in T helper cell response towards Th1 or Th2 while adult PDC trend towards a Th2 response.