Reasoners can be used to derive implicit consequences from an ontology. Sometimes unwanted consequences are revealed, indicating errors or privacy-sensitive information, and the ontology needs to be appropriately repaired. The classical approach is to remove just enough axioms such that the unwanted consequences vanish. However, this is often too rough since mere axiom deletion also erases many other consequences that might actually be desired. The goal should not be to remove a minimal number of axioms but to modify the ontology such that only a minimal number of consequences is removed, including the unwanted ones. Specifically, a repair should rather be logically entailed by the input ontology, instead of being a subset. To this end, we introduce a framework for computing fixed-premise repairs of $\mathcal{EL}$ TBoxes. In the first variant the conclusions must be generalizations of those in the input TBox, while in the second variant no such restriction is imposed. In both variants, every repair is entailed by an optimal one and, up to equivalence, the set of all optimal repairs can be computed in exponential time. A prototypical implementation is provided. In addition, we show new complexity results regarding gentle repairs. / This is an extended version of an article accepted at the 45th German Conference on Artificial Intelligence (KI 2022).

Ziel dieser Arbeit war die Entwicklung eines Twinribozyms, das durch zweifache Spaltung und anschließende zweifache Ligation den Fragmentaustausch innerhalb einer RNA-Substratsequenz katalysiert. Als Basis für dieses Konzept diente das Hairpinribozym, das durch die Einführung einer zusätzlichen Helix derart verändert wurde, dass die Verknüpfung zweier Einheiten in einem Twinribozym möglich wurde. Weitere Sequenz- und Strukturoptimierung führte zu zwei Einzelmotiven mit hoher Substratselektivität und verbesserter Kofaktorakzeptanz. Durch die Verwendung von 5-Benzylmercapto-1H-tetrazol als Aktivator beim Standard-Phosphoramidit-Verfahren konnte die chemische RNA-Synthese in einem Umfang verbessert werden, der die Synthese eines Twinribozyms mit einer Länge von 141 Nukleotiden und beidseitiger Spaltaktivität erlaubte. Auf enzymatischem Weg wurde ein Twinribozym HP-TW5 synthetisiert, das aus einem 45-mer RNA-Substrat ein 16-mer Fragment herausschneidet und durch ein 20-mer Reparaturfragment ersetzt. Das nach Ligation in bis zu 30 % Ausbeute entstandene 49-mer Produkt wurde durch Sequenzanalyse eindeutig nachgewiesen. Auf diese Weise konnte die Reparatur einer Deletionsmutation in einer Modellreaktion erfolgreich durchgeführt werden. Die Twinribozym-vermittelte RNA-Reparatur bietet damit einen neuartigen Zugang zu gentherapeutischen Anwendungen. / Aim of this work was the development of a twin ribozyme that catalyses the fragment exchange within a RNA substrate sequence by twofold cleavage and subsequent twofold ligation. The hairpin ribozyme, serving as basis for this concept, was changed by introduction of an additional helix in a way, that connection of two units in a twin ribozyme became possible. Further sequence and structure optimization led to two different motifs with high substrate selectivity and improved activity under different cofactor conditions. By application of 5-Benzylmercapto-1H-tetrazole as activator in the standard phosphoramidite method, chemical RNA synthesis could be highly improved, allowing synthesis of a Twinribozyme with a length of 141 nucleotides and cleavage activity of both units. The enzymatically synthesised twin ribozyme HP-TW5 was used to cut out a 16-mer fragment from a 45-mer RNA substrate and replace it with a 20-mer repair fragment. The chemical identity of the 49-mer repair product, resulting from ligation in up to 30 percent yield, was proven by sequence analysis. With this model reaction, the repair of a deletion mutation could be successfully demonstrated. Twin ribozyme-mediated RNA-repair offers access to new applications in gene therapy.

Biology has made great progress in identifying and measuring the building blocks of life. The availability of high-throughput methods in molecular biology has dramatically accelerated the growth of biological knowledge for various organisms. The advancements in genomic, proteomic and metabolomic technologies allow for constructing complex models of biological systems. An increasing number of biological repositories is available on the web, incorporating thousands of biochemical reactions and genetic regulations. Systems Biology is a recent research trend in life science, which fosters a systemic view on biology. In Systems Biology one is interested in integrating the knowledge from all these different sources into models that capture the interaction of these entities. By studying these models one wants to understand the emerging properties of the whole system, such as robustness. However, both measurements as well as biological networks are prone to considerable incompleteness, heterogeneity and mutual inconsistency, which makes it highly non-trivial to draw biologically meaningful conclusions in an automated way. Therefore, we want to promote Answer Set Programming (ASP) as a tool for discrete modeling in Systems Biology. ASP is a declarative problem solving paradigm, in which a problem is encoded as a logic program such that its answer sets represent solutions to the problem. ASP has intrinsic features to cope with incompleteness, offers a rich modeling language and highly efficient solving technology. We present ASP solutions, for the analysis of genetic regulatory networks, determining consistency with observed measurements and identifying minimal causes for inconsistency. We extend this approach for computing minimal repairs on model and data that restore consistency. This method allows for predicting unobserved data even in case of inconsistency. Further, we present an ASP approach to metabolic network expansion. This approach exploits the easy characterization of reachability in ASP and its various reasoning methods, to explore the biosynthetic capabilities of metabolic reaction networks and generate hypotheses for extending the network. Finally, we present the BioASP library, a Python library which encapsulates our ASP solutions into the imperative programming paradigm. The library allows for an easy integration of ASP solution into system rich environments, as they exist in Systems Biology. / In den letzten Jahren wurden große Fortschritte bei der Identifikation und Messung der Bausteine des Lebens gemacht. Die Verfügbarkeit von Hochdurchsatzverfahren in der Molekularbiology hat das Anwachsen unseres biologischen Wissens dramatisch beschleunigt. Durch die technische Fortschritte in Genomic, Proteomic und Metabolomic wurde die Konstruktion komplexer Modelle biologischer Systeme ermöglicht. Immer mehr biologische Datenbanken sind über das Internet verfügbar, sie enthalten tausende Daten biochemischer Reaktionen und genetischer Regulation. System Biologie ist ein junger Forschungszweig der Biologie, der versucht Biologische Systeme in ihrer Ganzheit zu erforschen. Dabei ist man daran interessiert möglichst viel Wissen aus den unterschiedlichsten Bereichen in ein Modell zu aggregieren, welches das Zusammenwirken der verschiedensten Komponenten nachbildet. Durch das Studium derartiger Modelle erhofft man sich ein Verständnis der aufbauenden Eigenschaften, wie zum Beispiel Robustheit, des Systems zu erlangen. Es stellt sich jedoch die Problematik, das sowohl die biologischen Modelle als auch die verfügbaren Messwerte, oft unvollständig, miteinander unvereinbar oder fehlerhaft sind. All dies macht es schwierig biologisch sinnvolle Schlussfolgerungen zu ziehen. Daher, möchten wir in dieser Arbeit Antwortmengen Programmierung (engl. Answer Set Programming; ASP) als Werkzeug zur diskreten Modellierung system biologischer Probleme vorschlagen. ASP verfügt über eingebaute Eigenschaften zum Umgang mit unvollständiger Information, eine reichhaltige Modellierungssprache und hocheffiziente Berechnungstechniken. Wir präsentieren ASP Lösungen zur Analyse von Netzwerken genetischer Regulierungen, zur Prüfung der Konsistenz mit gemessene Daten, und zur Identifikation von Gründen für Inkonsistenz. Diesen Ansatz erweitern wir um die Möglichkeit zur Berechnung minimaler Reparaturen an Modell und Daten, welche Konsistenz erzeugen. Mithilfe dieser Methode werden wir in die Lage versetzt, auch im Fall von Inkonsistenz, noch ungemessene Daten vorherzusagen. Weiterhin, präsentieren wir einen ASP Ansatz zur Analyse metabolischer Netzwerke. Bei diesem Ansatz, nutzen wir zum einen aus das sich Erreichbarkeit mit ASP leicht spezifizieren lässt und das ASP mehrere mächtige Methoden zur Schlussfolgerung bereitstellt, welche sich auch kombiniert lassen. Dadurch wird es möglich die Synthese Möglichkeiten eines Metabolischen Netzwerks zu erforschen und Hypothesen für Erweiterungen des metabolischen Netzwerks zu berechnen. Zu guter Letzt, präsentieren wir die BioASP Softwarebibliothek. Die BioASP-Bibliothek kapselt unsere ASP Lösungen in das imperative Programmierparadigma und vereinfacht eine Integration von ASP Lösungen in heterogene Betriebsumgebungen, wie sie in der System Biologie vorherrschen.

Loss of heterozygosity (LOH) is detectable in many forms of cancer including leukaemia. It contributes to tumorigenesis through the loss of one of the two alleles of one tumor suppressor gene at a given locus, caused by deletion or uniparental disomy (UPD). UPD can only be the result of homologous recombination. Little is known about the mechanisms of UPD and what connection this aberration has with the outcome of this disease. In this study, 146 patients with primary AML were analysed using a novel technique based on single nucleotide polymorphisms (SNPs). Leukaemic cells and healthy T-cells from each patient were obtained using FACS-Vantage cell sorting. In cases with very few sorted cells whole genome preamplification was done. Genome-wide SNP analysis was carried out according to the standard GeneChip Mapping Assay protocol (Affymetrix, USA) using the Human Mapping 10K Arrays. Moreover, the impact of the FLT3-ITD mutation on the homologous recombination using pmHPRT-DRGFP /pCbASce vectors system and yHA2x assay was investigated. Of 146 patients with normal karyotype LOH was found in 30 cases. The potential LOH regions, were confirmed by microsatellite analysis of short tandem repeat (STR) markers. In 21 of these cases STR-analysis of T-cells, representing the corresponding tumor-free material, confirmed the regions of partial UPD. This aberration affected different chromosomes, but most commonly chr. 2, 6, 11, 21, 13, and 7, and covered between 11.5 and 88 Mb. Interestingly, in 6 LOH cases, long stretches of homozygosity present at the same positions as in the healthy cells and in the blasts were found. The impact of this phenomenon is unknown. Additionally, chromosome losses were detected in 3 patients classified with normal karyotype according to current methods. These 9 cases were not included in the UPD positive group. No differences were observed regarding any clinical factors including age, WBC-counts and sex. The FAB M1 subtype was observed in 47.6% of the UPD positive patients, compared to only 19.2% of the UPD negative patients (P=0.04, n=146). In addition, no correlation between FLT3-ITD, MLL-PTD and NPM1 mutations in the UPD patients was found, but the data indicate that patients with UPD have a higher rate of treatment failure. Moreover, in this study the relationship between UPD and gene aberrations was able to be confirmed. In some cases, UPD found on chromosomes 21, 19 and 11 was correlated with mutations in the RUNX1, CEBPA and WT genes, respectively. Furthermore, AML cases with and without UPD showed different but specific gene expression profiles, revealing different expression levels for genes involved in double strand break repairs. Furthermore, it was found that different mutations could be responsible for the increase in efficiency of HR, such as FLT3-ITD or BCR-ABL. Moreover, cells with a FLT3-ITD mutation (without wt expression) rapidly increased the HR efficiency compared with heterozygous (FLT3-ITD/wt) cells. Preliminary results showed that the high repair efficiency was mainly dependent on the translocation of RAD51. In conclusion, SNP array technology allow the identification and mapping of LOH in AML patients with normal karyotype. The obtained data also point out the necessity of analysing tumour-free material to confirm the somatic origin of the alteration. Furthermore, the available results indicate that compared to patients without UPD, patients with UPD have a higher relapse rate, which might be used as a prognostic marker in the future. Also, it could be hypothesized that downregulation of RAD51 (for example by FLT3 inhibition) might be beneficial DNA damage occurs through the genotoxic agent by reducing the relapse risk of AML.

No description available.

Ontologies based on Description Logics may contain errors, which are usually detected when reasoning produces consequences that follow from the ontology, but do not hold in the modelled application domain. In previous work, we have introduced repair approaches for EL ontologies that are optimal in the sense that they preserve a maximal amount of consequences. In this paper, we will, on the one hand, review these approaches, but with an emphasis on motivation rather than on technical details. On the other hand, we will describe new results that address the problems that optimal repairs may become very large or need not even exist unless strong restrictions on the terminological part of the ontology apply. We will show how one can deal with these problems by introducing concise representations of optimal repairs.

Der erste Teil dieser Arbeit konzentriert sich auf die Mechanismen hormoninduzierter Ca2+-oszillationen, und wie diese von Konzentrationsschwankungen des Ca2+-freisetzenden Botenstoffes Inositol-1,4,5-trisphosphat (IP3) beinflusst werden. Wir konnten zeigen, dass IP3-Oszillationen die Frequenzkodierung des äußeren Stimulus durch Ca2+-Ozillationen deutlich verstärken. Zwei Mechanismen für das Entstehen der IP3-Oszillationen wurden untersucht: es zeigte sich, dass die Aktivierung der Phospholipase C durch Ca2+ der wahrscheinlichste Mechanismus ist. Um die Rolle der IP3-Oszillationen genauer zu verstehen, wurde ein Modell für den Stoffwechsel des IP3-Vorläufers Phosphatidylinositol-4,5-bisphosphat (PIP2) entwickelt. Es zeigt sich, dass die scheinbar nutzlosen Phosphorylierungs/Dephosphorylierungszyklen eine wichtige Rolle für den PIP2-Haushalt spielen. Durch Nachliefern von PIP2 während der Stimulierung ermöglichen sie anhaltende Ca2+-signale. Der zweite Teil der Arbeit beschäftigt sich mit einem DNS-Reparaturweg, der Reparatur mittels Entfernung von Nukleotiden (NER). Dieser Reparaturmechanismus ist äußerst vielseitig und entfernt Pyrimidinpaare, die durch UV-Strahlung erzeugt wurden, oder Schäden, die durch chemische Agentien erzeugt wurden. Es wurde ein mathematisches Model erarbeitet, das die Grundeigenschaften der NER beschreiben soll. Erstens wurde untersucht, wie die Bindungs- und Freisetzungskinetik der Reparaturfaktoren mit den strukturellen Eigenschaften des Systems, beispielsweise der Bindungsreihenfolge, zusammenhängt. Zweitens wurden anhand von in vivo gemessenen Rekrutierungskinetiken dreier Proteinfaktoren die Modellparameter bestimmt. Das so angepasste Modell sagt unter anderem eine Sättigung der NER durch den Verbrauch des Erkennungsfaktors vorher. Die theoretischen Untersuchungen deuten darauf hin, dass ein sequentieller Anlagerungsmechanismus im Hinblick auf Effizienz und auf Spezifität gegenüber den beschädigten Substrat große Vorteile bringen kann. / The first part of this thesis focuses on the mechanisms of hormone induced Ca2+ oscillations and how these depend on fluctuations in the concentration of the Ca2+-releasing messenger, inositol 1,4,5-trisphosphate (IP3). We were able to show that IP3 oscillations greatly enhances the ability to frequency encode the hormone stimulus by Ca2+ oscillations. Two mechanisms for the generation of IP3-oscillations have been investigated, we could show that Ca2+-activation of phospholipase C is the most probable mechanism. To better understand the role of IP3-oscillations a detailed model for the phosphoinositide pathway has been developed. The model illustrates the importance of futile (de)phosphorylation cycles for regenerating phosphatidylinositol-4,5-bisphophat during stimulation, an essential property to support long-lasting Ca2+ signals. The second part of the thesis is devoted to nucleotide excision repair (NER). It is a versatile DNA repair mechanism that can remove lesions such as UV light induced pyrimidine dimers and bulky adducts caused by chemical agents. To understand the mechanisms underlying the protein assembly during NER and the performance of repair, a mathematical model, delineating hallmarks and general characteristics of NER, has been developed. First, the binding and dissociation kinetics of repair factors are related to the structural properties of the system, such as the sequential order in which the factors enter repair. Second, using in vivo kinetic data for the recruitment of three different proteins at local damaged nuclei, the model parameters are determined and the dynamic behavior of the repair process is scrutinized in detail. The observed saturation of NER is predicted to rely on the high engagement of the recognition factor in repair. The theoretical analysis of repair performance indicates that a sequential assembly process is remarkably advantageous in terms of repair efficiency and can show a marked selectivity for the damaged substrate.

No description available.

No description available.

No description available.