Comparative analysis of midline guidance and axon pathfinding in the chelicerates Achaearanea tepidariorum and Cupiennius salei

Die Neurogenese und axonale Wegfindung sind in den vergangenen Jahrzehnten Thema einer Vielzahl wissenschaftlicher Untersuchungen in den verschiedensten Organismen gewesen. Die zusammengetragenen Daten in Insekten und Crustaceen geben eine gute Übersicht darüber, wie das Nervensystem in Arthropoden aufgebaut wird. Die entwicklungsbiologischen Prozesse, die daran beteiligt sind, sind in den beiden genannten Gruppen sehr gut verstanden. In den Gruppen der Cheliceraten und Myriapoden jedoch wurden ähnliche Analysen bisher kaum durchgeführt. Das Hauptanliegen dieser Arbeit war es daher, Mechanismen in den Spinnen Achaearanea tepidariorum und Cupiennius salei, zwei Vertretern der Cheliceraten, zu untersuchen, die eine Rolle im Leitsystem der ventralen Mittellinie und bei der axonalen Wegfindung spielen. Eine Vorraussetzung hierfür sind Kenntnisse über die Architektur des Zentralnervensystems. In einem ersten Schritt beschrieb ich daher grundlegend die Morphologie des Nervensystems im Verlauf der gesamten Embryoalentwicklung. Ich konnte zeigen, dass in Spinnen ein für Arthropoden typisches Strickleiternervensystem gebildet wird. Dieses wird von segmental angelegten Neuronen geformt, wobei sowohl Gruppen von Zellen als auch einzelne Neurone daran beteiligt sind, die primären axonalen Trakte zu etablieren. Im Besonderen konnte ich eine Zelle identifizieren, die in Position, Projektionsmuster und der Expression des Markergens even-skipped vergleichbar zum PR2 Neuron in Drosophila ist, welches die posteriore Wurzel des Segmentalnervs anlegt.rnrnIn einem zweiten Ansatz untersuchte ich die ventrale Mittellinie in Spinnen im Bezug auf ihre mögliche Funktion in der axonalen Wegfindung. Es konnte gezeigt werden, dass es sich beim Epithel der Mittellinie, das die Lücke zwischen beiden Keimstreifhälften während des gesamten Prozesses der Inversion überspannt, um eine transiente Struktur handelt, die keine neuralen Zellen hervorbringt. Es ist daher vergleichbar mit der so genannten Floor plate in Vertebraten, die ebenfalls nur vorübergehend existiert. Die Untersuchung von single minded (sim) zeigte, dass es, anders als in Drosophila, wo sim ein wichtiges regulatorisches Gen für die korrekte Spezifizierung von Mittellinienzellen ist, nicht in den Zellen der Mittellinie, sondern in diesen benachbarten Zellen, exprimiert wird. Das ist vergleichbar mit Vertebraten. Zusätzlich konnte ich Expression von sim an den Basen der Gliedmassen und im Kopf nachweisen. Wie in Vertebraten könnte sim an der Musterbildung dieser Gewebe beteiligt sein. Dennoch spielt die Mittellinie in Spinnen eine wichtige Rolle als Organisator für auswachsende, kommissurale Axone. Diese Funktion teilt sie mit anderen Invertebraten und Vertebraten.rnrnDie Signaltransduktionskaskade, die an der axonalen Wegfindung an der Mittellinie beteiligt ist, ist in den verschiedensten Organismen hoch konserviert. In der vorliegenden Arbeit konnte ich sowohl in Achaearanea als auch in Cupiennius ein netrin Homolog identifizieren und eine konservierte Funktion des Wegfindungsmoleküls während der Bildung der Kommissuren aufzeigen. RNAi Experimente belegen, dass, wird die Funktion von netrin herunterreguliert, das Strickleiternervensystem nicht korrekt gebildet wird, ins Besondere die kommissuralen Faszikel. Des Weiteren konnte ich eine neue Funktion von netrin, die bisher in anderen Organsimen noch nicht beschrieben wurde, identifizieren. Neben seiner Rolle in der axonalen Wegfindung, scheint netrin auch an der epithelialen Morphogenese im zentralen Nervensystem beteiligt zu sein. In dieser Funktion scheint netrin in Gliazellen, die die epithelialen Vesikel der Invaginationsgruppen umhüllen, wichtig zu sein, um neurale Vorläuferzellen in einem undifferenzierten Zustand zu halten. Der Abbau von netrin Transkript durch RNA Interferenz führt zu einer verfrühten Segregation neuraler Vorläuferzellen aus dem epithelialen Verband der Invaginationsgruppen und zu einer Zunahme an Zellen, die den frühen Differenzierungsmarker islet exprimieren.

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.

Analysis of the immunological and functional features of the Neisserial Heparin Binding Antigen (NHBA)

Neisserial Heparin Binding Antigen (NHBA) is a surface-exposed lipoprotein ubiquitously expressed by genetically diverse Neisseria meningitidis strains and is an antigen of the multicomponent protein-based 4CMenB vaccine, able to induce bactericidal antibodies in humans and to bind heparin-like molecules. The aim of this study is to characterize the immunological and functional properties of NHBA. To evaluate immunogenicity and the contribution of aminoacid sequence variability to vaccine coverage, we constructed recombinant isogenic strains that are susceptible to bactericidal killing only by anti-NHBA antibodies and engineered them to express equal levels of selected NHBA peptides. In these recombinant strains, we observed different titres associated with the different peptide variants. These recombinant strains were then further engineered to express NHBA chimeric proteins to investigate the regions important for immunogenicity. In natural strains, anti-NHBA antibodies were found to be cross-protective against strains expressing different peptides. To investigate the functional properties of this antigen, the recombinant purified NHBA protein was tested in in vitro binding studies and was found to be able to bind epithelial cells. The binding was abolished when cells were treated specifically with heparinase III, suggesting that the interaction with the cells is mediated by heparan sulfate proteoglycans (HSPG). Mutation of the Arg-rich tract of NHBA abrogated the binding, confirming the importance of this region in mediating the binding to heparin-like molecules. In a panel of N. meningitidis strains, the deletion of nhba resulted in a reduction of adhesion with respect to each isogenic wild type strain. Furthermore, the adhesion of the wild-type strain was prevented by using anti-NHBA polyclonal sera, demonstrating the specificity of the interaction. These results suggest that NHBA could be a novel meningococcal adhesin contributing to host-cell interaction. Moreover, we analysed NHBA NalP-mediated cleavage in different NHBA peptides and showed that not all NHBA peptides are cleaved.

Reparation and enforcement of judgments : a comparative analysis of the European and Inter-American human rights systems

The inter-American human rights system has been conceived following the example of the European system under the European Convention on Human Rights (ECHR) before it was modified by Protocol No 11. However, two important differences exist. First, the authority of the European Court of Human Rights (ECtHR) to order reparation has been strictly limited by the principle of subsidiarity. Thus, the ECtHR's main function is to determine whether the ECHR has been violated. Beyond the declaratory effect of its judgments, according to Article 41 ECHR, it may only "afford just satisfaction to the injured party". The powers of the Inter-American Court of Human Rights (IACtHR) were conceived in a much broader fashion in Article 63 of the American Convention on Human Rights (ACHR), giving the Court the authority to order a variety of individual and general measures aimed at obtaining restitutio in integrum. The first main part of this thesis shows how both Courts have developed their reparation practice and examines the advantages and disadvantages of each approach. Secondly, the ECtHR's rather limited reparation powers have, interestingly, been combined with an elaborate implementation system that includes several of the Council of Europe's organs, principally the Committee of Ministers. In the Inter-American System, no dedicated mechanism was implemented to oversee compliance with the IACtHR's judgments. The ACHR limits itself to inviting the Court to point out in its annual reports the cases that have not been complied with and to propose measures to be adopted by the General Assembly of the Organization of American States. The General Assembly, however, hardly ever took action. The IACtHR has therefore filled this gap by developing a proper procedure to oversee compliance with its judgments. Both the European and the American solutions to ensure compliance are presented and compared in the second main part of this thesis. Finally, based on the results of both main parts, a comparative analysis of the reparation practice and the execution results in both human rights systems is being provided, aimed at developing proposals for the improvement of the functioning of either human rights protection system.

Set up of a procedure for correlation analysis between current discharge and dose delivery in a pulsed power plasma device for medical application

This thesis work aims to find a procedure for isolating specific features of the current signal from a plasma focus for medical applications. The structure of the current signal inside a plasma focus is exclusive of this class of machines and a specific analysis procedure has to be developed. The hope is to find one or more features that shows a correlation with the dose erogated. The study of the correlation between the current discharge signal and the dose delivered by a plasma focus could be of some importance not only for the practical application of dose prediction but also for expanding the knowledge anbout the plasma focus physics. Vatious classes of time-frequency analysis tecniques are implemented in order to solve the problem.

Population-based trend analysis of laparoscopic Nissen and Toupet fundoplications for gastroesophageal reflux disease

The Nissen and Toupet fundoplications are the most commonly used techniques for surgical treatment of gastroesophageal reflux disease. To date, no population-based trend analysis has been reported examining the choice of procedure and short-term outcomes. This study was designed to analyze trends in the use of Nissen versus Toupet fundoplications, and corresponding short-term outcomes during a 10-year period between 1995 and 2004.

A navigation system for percutaneous needle interventions based on PET/CT images: design, workflow and error analysis of soft tissue and bone punctures

Percutaneous needle intervention based on PET/CT images is effective, but exposes the patient to unnecessary radiation due to the increased number of CT scans required. Computer assisted intervention can reduce the number of scans, but requires handling, matching and visualization of two different datasets. While one dataset is used for target definition according to metabolism, the other is used for instrument guidance according to anatomical structures. No navigation systems capable of handling such data and performing PET/CT image-based procedures while following clinically approved protocols for oncologic percutaneous interventions are available. The need for such systems is emphasized in scenarios where the target can be located in different types of tissue such as bone and soft tissue. These two tissues require different clinical protocols for puncturing and may therefore give rise to different problems during the navigated intervention. Studies comparing the performance of navigated needle interventions targeting lesions located in these two types of tissue are not often found in the literature. Hence, this paper presents an optical navigation system for percutaneous needle interventions based on PET/CT images. The system provides viewers for guiding the physician to the target with real-time visualization of PET/CT datasets, and is able to handle targets located in both bone and soft tissue. The navigation system and the required clinical workflow were designed taking into consideration clinical protocols and requirements, and the system is thus operable by a single person, even during transition to the sterile phase. Both the system and the workflow were evaluated in an initial set of experiments simulating 41 lesions (23 located in bone tissue and 18 in soft tissue) in swine cadavers. We also measured and decomposed the overall system error into distinct error sources, which allowed for the identification of particularities involved in the process as well as highlighting the differences between bone and soft tissue punctures. An overall average error of 4.23 mm and 3.07 mm for bone and soft tissue punctures, respectively, demonstrated the feasibility of using this system for such interventions. The proposed system workflow was shown to be effective in separating the preparation from the sterile phase, as well as in keeping the system manageable by a single operator. Among the distinct sources of error, the user error based on the system accuracy (defined as the distance from the planned target to the actual needle tip) appeared to be the most significant. Bone punctures showed higher user error, whereas soft tissue punctures showed higher tissue deformation error.

Serial analysis of the malapposed and uncovered struts of the new generation of everolimus-eluting bioresorbable scaffold with optical coherence tomography

The aim of this study is to assess the serial changes in strut apposition and coverage of the bioresorbable vascular scaffolds (BVS) and to relate this with the presence of intraluminal masses at 6 months with optical coherence tomography (OCT).

Mass Transport Perspective on an Accelerated Exclusion Process: Analysis of Augmented Current and Unit-Velocity Phases

In an accelerated exclusion process (AEP), each particle can "hop" to its adjacent site if empty as well as "kick" the frontmost particle when joining a cluster of size ℓ⩽ℓ_{max}. With various choices of the interaction range, ℓ_{max}, we find that the steady state of AEP can be found in a homogeneous phase with augmented currents (AC) or a segregated phase with holes moving at unit velocity (UV). Here we present a detailed study on the emergence of the novel phases, from two perspectives: the AEP and a mass transport process (MTP). In the latter picture, the system in the UV phase is composed of a condensate in coexistence with a fluid, while the transition from AC to UV can be regarded as condensation. Using Monte Carlo simulations, exact results for special cases, and analytic methods in a mean field approach (within the MTP), we focus on steady state currents and cluster sizes. Excellent agreement between data and theory is found, providing an insightful picture for understanding this model system.

Allogeneic stem cell transplant in adult patients with acute myelogenous leukemia: a systematic analysis of international guidelines and recommendations

In patients with acute myelogenous leukemia, published guidelines and treatment recommendations are usually the basis for starting the work-up process for allogeneic transplant. However, only consistent recommendations would allow a standardized clinical practice. We conducted a comprehensive systematic literature search to identify and evaluate the best available evidence from controlled clinical trials. In addition, recommendations given by leading organizations in the USA and Europe were analyzed. The following aspects were selected for systematic comparison: factors for risk assessment and categorization, role of type of donor, significance of allogeneic transplant in first or second complete remission and in relapse/progressive disease; and role of reduced intensity conditioning regimens. In conclusion, the recommendations for the use of allogeneic transplant given by the literature and by published guidelines are inconsistent and will need clarification.

Confirmation analysis of ethyl glucuronide and ethyl sulfate in human serum and urine by CZE-ESI-MS(n) after intake of alcoholic beverages

CZE coupled to sheath liquid-based electrospray ionization (ESI) and multiple-stage ion trap mass spectrometry (MS(n) ) was used for the confirmation analysis of ethyl glucuronide (EtG) and ethyl sulfate (EtS) in human serum and urine collected after intake of alcoholic beverages. Electrophoretic separations were performed in uncoated fused-silica capillaries using a pH 9.5 ammonium acetate background electrolyte and normal polarity. MS detection of EtG and EtS occurred after negative ionization using a spray liquid containing 0.5% v/v ammonia in isopropanol/water (60:40%, v/v). CZE-MS and CZE-MS² results obtained after injection of solid-phase extracts for EtG and EtS and of diluted urine confirmed the presence of EtG and EtS in samples whose levels were previously determined by CZE with indirect UV detection. Detection limits of each compound were estimated to be around 2.0 (injection of diluted urine) and 0.2 μg/mL (extracts).

Comparative analysis of canine monocyte- and bone-marrow-derived dendritic cells

Dendritic cells (DC) represent a heterogeneous cell family of major importance for innate immune responses against pathogens and antigen presentation during infection, cancer, allergy and autoimmunity. The aim of the present study was to characterize canine DC generated in vitro with respect to their phenotype, responsiveness to toll-like receptor (TLR) ligands and T-cell stimulatory capacity. DC were derived from monocytes (MoDC) and from bone marrow hematopoietic cells cultured with either Flt3-ligand (FL-BMDC) or with GM-CSF (GM-BMDC). All three methods generated cells with typical DC morphology that expressed CD1c, CD11c and CD14, similar to macrophages. However, CD40 was only found on DC, CD206 on MPhi and BMDC, but not on monocytes and MoDC. CD1c was not found on monocytes but on all in vitro differentiated cells. FL-BMDC and GM-BMDC were partially positive for CD4 and CD8. CD45RA was expressed on a subset of FL-BMDC but not on MoDC and GM-BMDC. MoDC and FL-DC responded well to TLR ligands including poly-IC (TLR2), Pam3Cys (TLR3), LPS (TLR4) and imiquimod (TLR7) by up-regulating MHC II and CD86. The generated DC and MPhi showed a stimulatory capacity for lymphocytes, which increased upon maturation with LPS. Taken together, our results are the basis for further characterization of canine DC subsets with respect to their role in inflammation and immune responses.