@phdthesis{Pleines2009,
  author    = {Pleines, Irina},
  title     = {The role of the Rho GTPases Rac1 and Cdc42 for platelet function and formation},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-48572},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2009},
  abstract  = {Platelet activation induces cytoskeletal rearrangements involving a change from discoid to spheric shape, secretion, and eventually adhesion and spreading on immobilized ligands. Small GTPases of the Rho family, such as Rac1 and Cdc42, are known to be involved in these processes by facilitating the formation of lamellipodia and filopodia, respectively. This thesis focuses on the role Rac1 and Cdc42 for platelet function and formation from their precursor cells, the megakaryocytes (MKs), using conditional knock-out mice. In the first part of the work, the involvement of Rac1 in the activation of the enzyme phospholipase (PL) C2 in the signaling pathway of the major platelet collagen receptor glycoprotein (GP) VI was investigated. It was found that Rac1 is essential for PLC2 activation independently of tyrosine phosphorylation of the enzyme, resulting in a specific platelet activation defect downstream of GPVI, whereas signaling of other activating receptors remains unaffected. Since Rac1-deficient mice were protected from arterial thrombosis in two different in vivo models, the GTPase might serve as a potential target for the development of new drugs for the treatment and prophylaxis of cardio- and cerebrovascular diseases. The second part of the thesis deals with the first characterization of MK- and platelet-specific Cdc42 knock-out mice. Cdc42-deficient mice displayed mild thrombo-cytopenia and platelet production from mutant MKs was markedly reduced. Unexpectedly, Cdc42-deficient platelets showed increased granule content and release upon activation, leading to accelerated thrombus formation in vitro and in vivo. Furthermore, Cdc42 was not generally required for filopodia formation upon platelet activation. Thus, these results indicate that Cdc42, unlike Rac1, is involved in multiple signaling pathways essential for proper platelet formation and function. Finally, the outcome of combined deletion of Rac1 and Cdc42 was studied. In contrast to single deficiency of either GTPase, platelet production from double-deficient MKs was virtually abrogated, resulting in dramatic macrothrombocytopenia in the animals. Formed platelets were largely non-functional leading to a severe hemostatic defect and defective thrombus formation in double-deficient mice in vivo. These results demonstrate for the first time a functional redundancy of Rac1 and Cdc42 in the hematopoietic system.},
  subject      = {Thrombose},
  language  = {en}
}
@phdthesis{Muhammad2009,
  author    = {Muhammad, Khalid},
  title     = {Longterm impact of anti-CD20 mediated transient B cell depletion on memory B cells in patients with rheumatoid arthritis},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-36319},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2009},
  abstract  = {B-Lymphozyten leisten unterschiedliche Beitr{\"a}ge zur Pathophysiologie der Rheumatoiden Arthritis. Sie produzieren Autoantik{\"o}rper, pr{\"a}sentieren Autoantigene und sch{\"u}tten verschiedene Zytokine, die am proinflammatorischen Prozess beteiligt sind, aus. Aufbauend auf diesen Ergebnissen wurden in den letzten Jahren Therapien entwickelt, die gezielt B-Lymphozyten ansteuern um direkt oder indirekt in den autoimmunen Krankheitsverlauf einzugreifen. Die zeitlich begrenzte B-Zell-Depletion mit Rituximab (anti CD20-Antik{\"o}rper) hat dabei in den letzten Jahren einen hohen Stellenwert erlangt und wird im klinischen Alltag insbesondere bei der Behandlung von Patienten mit rheumatoider Arthritis angewandt. Rituximab induziert im peripheren Blut bemerkenswerte Ver{\"a}nderungen in der Hom{\"o}ostase der B-Zell-Subpopulationen. Nach Therapie mit dem anti-CD20 Antik{\"o}rper Rituximab beginnt die Repletionsphase mit der peripheren Aussaat von transitionalen unreifen B-Zellen. Im weiteren Verlauf kommt es zu einer Normalisierung des naiven B-Zell-Pools. Das B-Zell Ged{\"a}chtnis und in besonderem Maße die IgD+CD27+ Ged{\"a}chtniszellen erholen sich nach Therapie nur langsam. In einer prospektiven klinischen Studie hat unsere Arbeitsgruppe gezeigt, dass die Gesamtzahl der Ged{\"a}chtniszellen gut mit der Dauer der klinischen Antwort auf Rituximab korreliert. Es ist wenig {\"u}ber die speziellen molekularen Ver{\"a}nderungen innerhalb der Ged{\"a}chtnis B-Zellen nach Rituximab Therapie bekannt. Um die Ver{\"a}nderungen im peripheren Blut zu verstehen untersuchten wir die somatische Mutationsfrequenz und das Muster der Ig-VH3 Gen Rearrangements, indem wir pr{\"a}- und posttherapeutisch bei 18 Patienten einzelne B-Zellen isolierten und den individuellen B-Zellrezeptor durch eine Einzelzell RT-PCR amplifizierten und sequenzierten. Wir verglichen das Mutationsmuster nach erfolgreicher B-Zelldepletion in den neu rezirkulierenden Ged{\"a}chtnis B-Zellen mit dem Mutationsmuster von vier Gesunden Blutspendern und sechs nicht-RA Patienten, die eine Hochdosis Chemotherapie mit anschließender autologer oder allogener Stammzelltransplantation erhalten hatten. Zun{\"a}chst haben wir die Zusammensetzung der Ged{\"a}chtniszellen im peripheren Blut analysiert. Der Ph{\"a}notyp der peripheren pr{\"a}-switch (IgD+CD27+) und post-switch (IgD-CD27+) Ged{\"a}chtniszellen zeigte keine quantitativen Unterschiede in RA-Patienten im Vergleich zu Gesunden. Bei der direkten Analyse des B-Zell Immunglobulin Rezeptors fanden sich jedoch zwischen klassengeswitchten und ungeswitchten Ged{\"a}chtnis B-Zellen signifikante Unterschiede in der Anzahl der Mutationen in der variablen Region der Ig Rezeptors. Die Population der IgD+CD27+ Ged{\"a}chtniszellen beinhaltete sowohl nicht mutierte, wenig mutierte und stark mutierte (Median= 9 Mutationen pro Sequenz) rearrangierte Ig- Rezeptoren, wohingegen die IgD-CD27+ Ged{\"a}chtniszellen einen durchgehend hoch mutierten (Median = 18 Mutationen pro Sequenz) Rezeptor aufwiesen. Der Unterschied zwischen beiden Gruppen war signifikant (Mutationsfrequenzen 3.83±0.19\% vs. 7.1±0.53\%; P=0.0001). Grundlegende Ver{\"a}nderungen wurden bei den rezirkulierenden ungeswitchten Ged{\"a}chtniszellen (IgD+CD27+) nach vor{\"u}bergehender B-Zell Depletion mit Rituximab festgestellt. Diese Zellen wurden bis 6 Jahre nach Rituximab beobachtet und zeigten eine stark verz{\"o}gerte Zunahme an Mutationen im Ig-Rezeptor. Ein Jahr nach einmaliger Gabe von Rituximab waren 84\% der einzelnen zirkulierenden IgD+/CD27+ B-Zellen unmutiert. Zu diesem Zeitpunkt fanden sich keine stark mutierten Ig-VH3 Gen Rearrangements (P=0.0001). Mit zunehmendem Abstand zur B-Zell depletierenden Therapie konnten in der Repopulationsphase zunehmende Zahlen an Mutationen in den B-Zell Ig Rezeptoren festgestellt werden. Beispielsweise waren w{\"a}hrend des 2. Jahres der Regeneration (P=0.0001) 7.8\%, sowie nach 4 Jahren nur 14\% der Ig Rezeptoren mutiert. Sogar 6 Jahre nach Behandlung, waren VH Mutationen in IgD+ Ged{\"a}chtniszellen noch deutlich vermindert. Selbst nach dieser Zeit fanden sich in der pr{\"a}-switch Ged{\"a}chtnispopulation nur 27\% hochmutierte Sequenzen w{\"a}hrend vor der passageren B-Zelldepletion 52\% ein hohe Zahl an Mutationen trugen (P=0.0001). Die posttherapeutische Analyse der CDR3 L{\"a}nge der regenerierten IgD+ Ged{\"a}chtniszellen ergab eine erh{\"o}hte CDR3 L{\"a}nge, die signifikant mit der Anzahl der nicht mutierten VH Genrearrangements w{\"a}hrend der Repletionsphase korreliert. Interessanterweise regenerierten Patienten nach Hochdosis Chemotherapie und allogener Stammzelltransplantation ihre IgD+ Ged{\"a}chtniszellen mit einer deutlich h{\"o}heren Anzahl an Mutationen. Ein Jahr nach Transplantation zeigten die Ig Rezeptoren schon 22\% hoch mutierte und 42\% unmutierte VH Rearrangements. Das zeigt, dass eine gegen CD20 gerichtete Behandlung nicht nur eine Verz{\"o}gerung der Produktion der ungeswitchten Ged{\"a}chtniszellen zur Folge hat, sondern dar{\"u}ber hinaus einen signifikanten Effekt auf die Mutationsrate im pr{\"a}switch Ged{\"a}chtnis B-Zellpool besitzt. Im Gegensatz zum Mutationsmuster der IgD+ Ged{\"a}chtniszellen regenerierten die klassengeswitchten Ged{\"a}chtniszellen nach anti-CD20 Depletion im peripheren Blut mit quantitativ normalen Mutationen im Ig Rezeptor. Interessanterweise fand sich allerdings eine {\"A}nderung der exprimierten Isotypen mit deutlicher Dominanz IgA exprimierender B Zellen. Weitere Analysen der klassengeswitchten Ged{\"a}chtnis B-Zellen zeigen außerdem eine Therapie induzierte qualitative Ver{\"a}nderung dieses B-Zellpools. So waren posttherapeutisch die Mutationen in bestimmten T-Zell abh{\"a}ngigen Mutationshotspots, dem RGYW/WRCY Motiv, signifikant vermehrt (Mutationstargeting vor Therapie 27\% vs. 43\% nach Rituximab, P=0.0003). Dies weist darauf hin, dass die Mechanismen der Affinit{\"a}tsreifung im klassengeswitchten B-Zellged{\"a}chtnis vor und nach B-Zelldepletion unterschiedlich funktionieren. Der Mutationsmechanismus selbst ist allerdings in diesen Zellen quantitativ nicht eingeschr{\"a}nkt. Zusammenfassend zeigt unsere Arbeit zum erstem mal, dass es nach einer passageren B-Zelldepletion mit anti-CD20 Antik{\"o}rpern zu einer {\"u}ber Jahre hinweg nachweisbaren ausgepr{\"a}gten Verz{\"o}gerung in der Aquisition von somatischen Mutationen in rearrangierten VH Genen der IgD+ Ged{\"a}chtniszellen kommt. Demgegen{\"u}ber erholt sich das klassengeswitchte B-Zellged{\"a}chtnis mit uneingeschr{\"a}nkter Zahl von Mutationen im Ig Rezeptor. Diese Resultate zeigen, dass anti-CD20 gerichtete Therapien in besonderem Maße IgD+ Ged{\"a}chtniszellen beeinflussen. Der Selektionsdruck durch Antigene und/oder die Selektion der Ig Rezeptoren erscheint unter diesen Bedingungen speziell bei IgD-Ged{\"a}chtnis B-Zellen reduziert. Die Daten unterst{\"u}tzen die Hypothese, dass pr{\"a}-switch Ged{\"a}chtnis B-Zellen im Vergleich zu post-switch Ged{\"a}chtnis B-Zellen andere Bedingungen f{\"u}r die Aktivierung der Mutationsmaschinerie ben{\"o}tigen. Die Resultate er{\"o}ffnen neue Wege f{\"u}r das Verst{\"a}ndnis der Pathophysiologie der B-Zell Ged{\"a}chtnisentwicklung und k{\"o}nnen helfen neue zielgerichtete Therapien zur Behandlung von Autoimmunerkrankungen zu konzipieren.},
  subject      = {Rheumatoider arthritis},
  language  = {en}
}
@phdthesis{Erro2009,
  author    = {Erro, Alejandro Berna},
  title     = {Generation and Characterization of Stromal Interaction Molecule 2 (STIM2)-deficient Mice},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-47301},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2009},
  abstract  = {An increase in cytosolic Ca2+ levels ([Ca2+]i) is a key event that occurs downstream of many signaling cascades in response to an external stimulus and regulates a wide range of cellular processes, including platelet activation. Eukaryotic cells increase their basal [Ca2+]i allowing extracellular Ca2+ influx into the cell, which involves different mechanisms. Store-operated Ca2+ entry (SOCE) is considered the main mechanism of extracellular Ca2+ influx in electrically non-excitable cells and platelets, and comprises an initial Ca2+ depletion from intracellular Ca2+ stores prior to activation of extracellular Ca2+ influx. Although the close relation between Ca2+ release from intracellular stores and extracellular Ca2+ influx was clear, the nature of the signal that linked both events remained elusive until 2005, when Stromal Interaction Molecule 1 (STIM1) was identified as an endoplasmic reticulum (ER) Ca2+ sensor essential for inositol (1,4,5)-trisphosphate (IP3)-mediated SOCE in vitro. However, the function of its homologue STIM2 in Ca2+ homeostasis was in general unknown. Therefore, mice lacking STIM2 (Stim2-/-) were generated in this work to study initially STIM2 function in platelets and in cells of the immune system. Stim2-/- mice developed normally in size and weight to adulthood and were fertile. However, for unknown reasons, they started to die spontaneously at the age of 8 weeks. Unexpectedly, Stim2-/- mice did not show relevant differences in platelets, revealing that STIM2 function is not essential in these cells. However, STIM2 seems to be involved in mammary gland development during pregnancy and is essential for mammary gland function during lactation. CD4+ T cells lacking STIM2 showed decreased SOCE. Our data suggest that STIM2 has a very specific function in the immune system and is involved in Experimental Autoimmune Encephalomyelitis (EAE) at early stages of the disease progression. Stim2-/- neurons were also defective in SOCE. Surprisingly, our results evidenced that STIM2 participates in mechanisms of neuronal damage after ischemic events in brain. This is the first time that the involvement of SOCE in ischemic neuronal damage has been reported. This finding may serve as a basis for the development of novel neuroprotective agents for the treatment of ischemic stroke, and possibly other neurodegenerative disorders in which disturbances in cellular Ca2+ homeostasis are considered a major pathophysiological component.},
  subject      = {Calcium-bindende Proteine},
  language  = {en}
}
@phdthesis{Nekhoroshkova2009,
  author    = {Nekhoroshkova, Elena},
  title     = {A-RAF kinase functions in ARF6 regulated endocytic membrane traffic},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-44566},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2009},
  abstract  = {Extracellular signals are translated and amplified via cascades of serially switched protein kinases, MAP kinases (MAPKs). One of the MAP pathways, the classical RAS/RAF/MEK/ERK pathway, transduces signals from receptor tyrosine kinases and plays a central role in regulation of cell proliferation. RAF kinases (A-, B- and C-RAF) function atop of this cascade and convert signals emanating from conformational change of RAS GTPases into their kinase activity, which in turn phosphorylates their immediate substrate, MEK. Disregulated kinase activity of RAF can result in tumor formation, as documented for many types of cancer, predominantly melanomas and thyroid carcinomas (B-RAF). A-RAF is the least characterized RAF, possibly due to its low intrinsic kinase activity and comparatively mild phenotype of A-RAF knockout mice. Nevertheless, the unique phenotype of araf -/- mice, showed predominantly neurological abnormalities such as cerebellum disorders, suggesting that A-RAF participates in a specific process not complemented by activities of B- and CRAF. Here we describe the role of A-RAF in membrane trafficking and identify its function in a specific step of endocytosis. This work led to the discovery of a C-terminally truncated version of A-RAF, AR149 that strongly interfered with cell growth and polarization in yeast and with endocytosis and actin polymerization in mammalian cells. As this work was in progress two splicing isoforms of ARAF, termed DA-RAF1 and DA-RAF2 were described that act as natural inhibitors of RAS-ERK signaling during myogenic differentiation (Yokoyama et al., 2007). DA-RAF2 contains the first 153 aa of A-RAF and thus is nearly identical with AR149. AR149 localized specifically to the recycling endosomal compartments as confirmed by colocalization and coimmunoprecipitation with ARF6. Expression of AR149 interferes with recycling of endocytosed transferrin (Tfn) and with actin polymerization. The endocytic compartment, where internalized Tfn is trapped, was identified as ARF6- and RAB11- positive endocytic vesicles. We conclude that the inhibition of Tfn trafficking in the absence of A-RAF or under overexpression of AR149 occurs between tubular- and TGNassociated recycling endosomal compartments. siRNA-mediated depletion of endogenous A-RAF or inhibition of MEK by U0126 mimic the AR149 overexpression phenotype, supporting a role of ARAF regulated ERK signalling at endosomes that is controlled by AR149 and targets ARF6. Our data additionally suggest EFA6 as a partner of A-RAF during activation of ARF6. The novel findings on the A-RAF localization and the interaction with ARF6 have led to a new model of ARAF function were A-RAF via activation of ARF6 controls the recycling of endocytic vesicles.Endocytosis and rapid recycling of synaptic vesicles is critically important for the physiological function of neurons. The finding, that A-RAF regulates endocytic recycling open a new perspective for investigation of the role of A-RAF in the nervous system.},
  subject      = {Raf-Kinasen},
  language  = {en}
}
@phdthesis{Filatova2009,
  author    = {Filatova, Alina},
  title     = {Mechanism and Control of Nuclear-Cytoplasmic Translocation of the Transporter Regulator RS1},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-38512},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2009},
  abstract  = {Das RS1 Protein (Gen RSC1A1) beteiligt sich an der Regulation des Na+-D-Glukose-kotransporters SGLT1 und einiger anderer Transporter. In subkonfluenten LLC-PK1 Zellen hemmt RS1 die Freisetzung von SGLT1 aus dem trans-Golgi-Netzwerk und die Transkription von SGLT1. W{\"a}hrend es sich in konfluenten Zellen haupts{\"a}chlich im Zytoplasma befindet, ist RS1 in subkonfluenten Zellen im Kern und im Zytoplasma lokalisiert. In der vorliegenden Arbeit wurden Mechanismus und Regulation der konfluenzabh{\"a}ngigen Kernlokalisation von RS1 untersucht. Dabel konnte gezeigt werden, dass die von Konfluenz abh{\"a}ngige Kernlokalisation von RS1 durch den Zellzyklus reguliert wird. In RS1 aus Sus scrofa (pRS1) wurde eine Sequenz identifiziert („nuclear shuttling signal", NS), die f{\"u}r die konfluenzabh{\"a}ngige Verteilung von RS1 verantwortlich ist und sowohl das Signal f{\"u}r die Kernlokalisation (NLS) als auch das Signal f{\"u}r den Export aus dem Kern (NES) beinhaltet. Die NLS und NES Signale von RS1 vermitteln die Translokation des Proteins in den Kern und aus dem Kern mit Hilfe von Importin \&\#946;1 bzw. CRM1, wobei die Verteilung von RS1 zwischen Kern und Zytoplasma durch die Aktivit{\"a}t des Exportsystems bestimmt wird. Es wurde gezeigt, dass die benachbarte Proteinkinase C (PKC) Phosphorylierungsstelle an Serin 370 von pRS1 die NS-gesteuerte Kernlokalisierung kontrolliert und f{\"u}r die vom Zellzyklus abh{\"a}ngige Kernlokalisation notwendig ist. Aufgrund der Ergebnisse der ortsgerichteten Mutagenese, PKC-Aktivierungsexperimenten und Massenspektrometrie-Analyse des Phosphorylierungsmusters von RS1 wurde ein Modell vorgeschlagen, das die Regulation der Kernlokalisation des RS1 Proteins in LLC-PK1 Zellen beschreibt. Dem Modell zufolge wird RS1 in subkonfluenten Zellen stark in den Kern bef{\"o}rdert, w{\"a}hrend der Export von RS1 aus dem Kern nicht stattfindet. Das f{\"u}hrt zur Anreicherung von RS1 im Kern. Nach Konfluenz wird Serin 370 durch PKC phosphoryliert, was die Steigerung des RS1-Exports aus dem Kern beg{\"u}nstigt und die {\"u}berwiegend zytoplasmatische Lokalisation des Proteins in konfluenten Zellen hervorruft. Die konfluenzabh{\"a}ngige Regulation der Lokalisation von RS1 kann die Expression von SGLT1 w{\"a}hrend der Regeneration von Enterozyten im D{\"u}nndarm und der Regeneration von Zellen der Nierentubuli nach hypox{\"a}mischem Stress kontrollieren. Außerdem deutet die Analyse der Genexpression in embryonalen Fibroblasten der RS-/- M{\"a}use deutet darauf hin, dass die transkriptionale Regulation durch RS1 im Zellzyklus und bei der Zellteilung eine wichtige Rolle spielen kann. Da die Lokalisation von RS1 zellzyklusabh{\"a}ngig ist, kann RS1 f{\"u}r die Regulation der Transporter in spezifischen Phasen des Zellzyklus wichtig sein.},
  subject      = {RS1},
  language  = {en}
}
@phdthesis{Friedrich2009,
  author    = {Friedrich, Torben},
  title     = {New statistical Methods of Genome-Scale Data Analysis in Life Science - Applications to enterobacterial Diagnostics, Meta-Analysis of Arabidopsis thaliana Gene Expression and functional Sequence Annotation},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-39858},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2009},
  abstract  = {Recent progresses and developments in molecular biology provide a wealth of new but insufficiently characterised data. This fund comprises amongst others biological data of genomic DNA, protein sequences, 3-dimensional protein structures as well as profiles of gene expression. In the present work, this information is used to develop new methods for the characterisation and classification of organisms and whole groups of organisms as well as to enhance the automated gain and transfer of information. The first two presented approaches (chapters 4 und 5) focus on the medically and scientifically important enterobacteria. Its impact in medicine and molecular biology is founded in versatile mechanisms of infection, their fundamental function as a commensal inhabitant of the intestinal tract and their use as model organisms as they are easy to cultivate. Despite many studies on single pathogroups with clinical distinguishable pathologies, the genotypic factors that contribute to their diversity are still partially unknown. The comprehensive genome comparison described in Chapter 4 was conducted with numerous enterobacterial strains, which cover nearly the whole range of clinically relevant diversity. The genome comparison constitutes the basis of a characterisation of the enterobacterial gene pool, of a reconstruction of evolutionary processes and of comprehensive analysis of specific protein families in enterobacterial subgroups. Correspondence analysis, which is applied for the first time in this context, yields qualitative statements to bacterial subgroups and the respective, exclusively present protein families. Specific protein families were identified for the three major subgroups of enterobacteria namely the genera Yersinia and Salmonella as well as to the group of Shigella and E. coli by applying statistical tests. In conclusion, the genome comparison-based methods provide new starting points to infer specific genotypic traits of bacterial groups from the transfer of functional annotation. Due to the high medical importance of enterobacterial isolates their classification according to pathogenicity has been in focus of many studies. The microarray technology offers a fast, reproducible and standardisable means of bacterial typing and has been proved in bacterial diagnostics, risk assessment and surveillance. The design of the diagnostic microarray of enterobacteria described in chapter 5 is based on the availability of numerous enterobacterial genome sequences. A novel probe selection strategy based on the highly efficient algorithm of string search, which considers both coding and non-coding regions of genomic DNA, enhances pathogroup detection. This principle reduces the risk of incorrect typing due to restrictions to virulence-associated capture probes. Additional capture probes extend the spectrum of applications of the microarray to simultaneous diagnostic or surveillance of antimicrobial resistance. Comprehensive test hybridisations largely confirm the reliability of the selected capture probes and its ability to robustly classify enterobacterial strains according to pathogenicity. Moreover, the tests constitute the basis of the training of a regression model for the classification of pathogroups and hybridised amounts of DNA. The regression model features a continuous learning capacity leading to an enhancement of the prediction accuracy in the process of its application. A fraction of the capture probes represents intergenic DNA and hence confirms the relevance of the underlying strategy. Interestingly, a large part of the capture probes represents poorly annotated genes suggesting the existence of yet unconsidered factors with importance to the formation of respective virulence phenotypes. Another major field of microarray applications is gene expression analysis. The size of gene expression databases rapidly increased in recent years. Although they provide a wealth of expression data, it remains challenging to integrate results from different studies. In chapter 6 the methodology of an unsupervised meta-analysis of genome-wide A. thaliana gene expression data sets is presented, which yields novel insights in function and regulation of genes. The application of kernel-based principal component analysis in combination with hierarchical clustering identified three major groups of contrasts each sharing overlapping expression profiles. Genes associated with two groups are known to play important roles in Indol-3 acetic acid (IAA) mediated plant growth and development as well as in pathogen defence. Yet uncharacterised serine-threonine kinases could be assigned to novel functions in pathogen defence by meta-analysis. In general, hidden interrelation between genes regulated under different conditions could be unravelled by the described approach. HMMs are applied to the functional characterisation of proteins or the detection of genes in genome sequences. Although HMMs are technically mature and widely applied in computational biology, I demonstrate the methodical optimisation with respect to the modelling accuracy on biological data with various distributions of sequence lengths. The subunits of these models, the states, are associated with a certain holding time being the link to length distributions of represented sequences. An adaptation of simple HMM topologies to bell-shaped length distributions described in chapter 7 was achieved by serial chain-linking of single states, while residing in the class of conventional HMMs. The impact of an optimisation of HMM topologies was underlined by performance evaluations with differently adjusted HMM topologies. In summary, a general methodology was introduced to improve the modelling behaviour of HMMs by topological optimisation with maximum likelihood and a fast and easily implementable moment estimator. Chapter 8 describes the application of HMMs to the prediction of interaction sites in protein domains. As previously demonstrated, these sites are not trivial to predict because of varying degree in conservation of their location and type within the domain family. The prediction of interaction sites in protein domains is achieved by a newly defined HMM topology, which incorporates both sequence and structure information. Posterior decoding is applied to the prediction of interaction sites providing additional information of the probability of an interaction for all sequence positions. The implementation of interaction profile HMMs (ipHMMs) is based on the well established profile HMMs and inherits its known efficiency and sensitivity. The large-scale prediction of interaction sites by ipHMMs explained protein dysfunctions caused by mutations that are associated to inheritable diseases like different types of cancer or muscular dystrophy. As already demonstrated by profile HMMs, the ipHMMs are suitable for large-scale applications. Overall, the HMM-based method enhances the prediction quality of interaction sites and improves the understanding of the molecular background of inheritable diseases. With respect to current and future requirements I provide large-scale solutions for the characterisation of biological data in this work. All described methods feature a highly portable character, which allows for the transfer to related topics or organisms, respectively. Special emphasis was put on the knowledge transfer facilitated by a steadily increasing wealth of biological information. The applied and developed statistical methods largely provide learning capacities and hence benefit from the gain of knowledge resulting in increased prediction accuracies and reliability.},
  subject      = {Genomik},
  language  = {en}
}
@phdthesis{Luckner2009,
  author    = {Luckner, Sylvia},
  title     = {Towards the development of high affinity InhA and KasA inhibitors with activity against drug-resistant strains of Mycobacterium tuberculosis},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-43621},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2009},
  abstract  = {Mycobacterium tuberculosis is the causative agent of tuberculosis and responsible for more than eight million new infections and about two million deaths each year. Novel chemotherapeutics are urgently needed to treat the emerging threat of multi drug resistant and extensively drug resistant strains. Cell wall biosynthesis is a widely used target for chemotherapeutic intervention in bacterial infections. In mycobacteria, the cell wall is comprised of mycolic acids, very long chain fatty acids that provide protection and allow the bacteria to persist in the human macrophage. The type II fatty acid biosynthesis pathway in Mycobacterium tuberculosis synthesizes fatty acids with a length of up to 56 carbon atoms that are the precursors of the critical mycobacterial cell wall components mycolic acids. KasA, the mycobacterial ß-ketoacyl synthase and InhA, the mycobacterial enoyl reductase, are essential enzymes in the fatty acid biosynthesis pathway and validated drug targets. In this work, KasA was expressed in Mycobacterium smegmatis, purified and co-crystallized in complex with the natural thiolactone antibiotic thiolactomycin (TLM). High-resolution crystal structures of KasA and the C171Q KasA variant, which mimics the acyl enzyme intermediate of the enzyme, were solved in absence and presence of bound TLM. The crystal structures reveal how the inhibitor is coordinated by the enzyme and thus specifically pinpoint towards possible modifications to increase the affinity of the compound and develop potent new drugs against tuberculosis. Comparisons between the TLM bound crystal structures explain the preferential binding of TLM to the acylated form of KasA. Furthermore, long polyethylene glycol molecules are bound to KasA that mimic a fatty acid substrate of approximately 40 carbon atoms length. These structures thus provide the first insights into the molecular mechanism of substrate recognition and reveal how a wax-like substance can be accommodated in a cytosolic environment. InhA was purified and co-crystallized in complex with the slow, tight binding inhibitor 2-(o-tolyloxy)-5-hexylphenol (PT70). Two crystal structures of the ternary InhA-NAD+-PT70 were solved and reveal how the inhibitor is bound to the substrate binding pocket. Both structures display an ordered substrate binding loop and corroborate the hypothesis that slow onset inhibition is coupled to loop ordering. Upon loop ordering, the active site entrance is more restricted and the inhibitor is kept inside more tightly. These studies provide additional information on the mechanistic imperatives for slow onset inhibition of enoyl ACP reductases.},
  subject      = {Tuberkelbakterium},
  language  = {en}
}
@phdthesis{Bender2009,
  author    = {Bender, Markus},
  title     = {Studies on platelet cytoskeletal dynamics and receptor regulation in genetically modified mice},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-48390},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2009},
  abstract  = {Blutpl{\"a}ttchen werden von Megakaryozyten im Knochenmark in einem Prozess produziert, an dem Aktin beteiligt ist. Aktin-Depolymerisierungsfaktor (ADF) und Cofilin sind Aktin-bindende Proteine, die als entscheidende Regulatoren im Aktinumsatz agieren, indem sie das Schneiden und Depolymerisieren von Filamenten unterst{\"u}tzen. Die Bedeutung von ADF/Cofilin und des Aktinumsatzes in der Bildung von Blutpl{\"a}ttchen ist gegenw{\"a}rtig nicht bekannt. In der vorliegenden Arbeit wurden M{\"a}use untersucht, die eine konstitutive ADF-Defizienz und/oder die eine konditionale n-Cofilin Defizienz (Cre/loxP) aufweisen. Um Cofilin nur in Megakaryozyten und Blutpl{\"a}ttchen auszuschalten, wurden Cofilinfl/fl M{\"a}use mit PF4-Cre M{\"a}usen verpaart. ADF- oder n-Cofilin-defiziente M{\"a}use hatten keinen oder nur einen geringen Ph{\"a}notyp in Blutpl{\"a}ttchen. Eine Defizienz von ADF und n-Cofilin f{\"u}hrte hingegen zu einem beinahe kompletten Verlust der Blutpl{\"a}ttchen, was mit Defekten in der Bildung von Pl{\"a}ttchenzonen in Knochenmark-Megakaryozyten einherging. Weitere Untersuchungen an in vitro und ex vivo kultivierten Megakaryozyten zeigten eine Reduzierung der Bildung von Propl{\"a}ttchen und das Fehlen der typischen Verdickungen der Propl{\"a}ttchen. Diese Daten zeigen redundante aber essentielle Funktionen von ADF und n-Cofilin im terminalen Schritt der Pl{\"a}ttchenbildung in vitro und in vivo, und belegen erstmals eine wichtige Rolle des Aktinumsatzes in diesem Prozess. Im zweiten Teil dieser Dissertation wurden die Mechanismen untersucht, die f{\"u}r die zellul{\"a}re Regulierung des Hauptkollagenrezeptors auf Blutpl{\"a}ttchen, Glykoprotein VI (GPVI), verantwortlich sind. Nach einer Gef{\"a}ßwandverletzung wird subendotheliales Kollagen freigelegt, wodurch GPVI die Aktivierung von Blutpl{\"a}ttchen vermittelt, und damit zur Blutstillung (H{\"a}mostase), aber auch zum Verschluss eines verletzten Gef{\"a}ßes beitragen kann, was letztendlich zu einem Myokardinfarkt oder einem Schlaganfall f{\"u}hren kann. Deshalb ist GPVI ein attraktives Zielprotein f{\"u}r eine anti-thrombotische Therapie, insbesondere weil fr{\"u}here Studien gezeigt haben, dass anti-GPVI Antik{\"o}rper eine irreversible Herunterregulierung des Rezeptors auf zirkulierenden Blutpl{\"a}ttchen mittels Internalisierung und Abspaltung induzieren. Es wird vermutet, dass Metalloproteinasen der ADAM (a disintegrin and metalloproteinase domain) - Familie das Abspalten vermitteln, jedoch fehlt in vivo der Beweis daf{\"u}r. Um die Mechanismen des Abspaltungsprozesses des GPVI Rezeptors in vivo besser verstehen zu k{\"o}nnen, wurden zwei Mauslinien, GPVI- und konditionale ADAM10-defiziente M{\"a}use, generiert und zus{\"a}tzlich sogenannte „low TACE (TNFalpha converting enzyme)" M{\"a}use analysiert. Es konnte gezeigt werden, dass GPVI in vitro von ADAM10 oder TACE in Abh{\"a}ngigkeit der Signalwege, die zum Abspalten des Rezeptors f{\"u}hren, geschnitten werden kann. Dar{\"u}berhinaus wurde GPVI in vivo nach Antik{\"o}rperverabreichung in ADAM10-defizienten M{\"a}usen und „low TACE" M{\"a}usen herunterreguliert, was vermuten l{\"a}sst, dass entweder beide Metalloproteinasen an diesem Prozess beteiligt sind oder noch eine zus{\"a}tzliche Metalloproteinase f{\"u}r die GPVI Regulation in vivo verantwortlich ist.},
  subject      = {Zellskelett},
  language  = {en}
}