Berlin, Techn. Univ., Diss., 2004. / Computerdatei im Fernzugriff.

This thesis focuses on searching for CpG islands of DNA sequences based on analysis of DNA spectrograms. The first part is theoretical and deals with the significance CpG island, and a description of the algorithms that are used or have been proposed for their search. The theoretical basis were implemented two algorithms based on the analysis of DNA spectrogram. One is based on the assumption that the region CpG islands has a higher content of guanine and cytosine than the region outside the CpG island and the other on the assumption of a higher frequency of occurrence of CG dinucleotides in the CpG island. The algorithms are implemented through MATLAB programming interface. For evaluation usefulness and effectiveness of solutions, results achieved on the selected DNA sequences implemented algorithms are compared with the results achieved by search engines CpG islands, which are freely available on the internet.

This thesis focuses on searching for CpG islands of DNA sequences based on analysis of DNA spectrograms. The first part is theoretical and deals with the significance CpG island, and a description of the algorithms that are used or have been proposed for their search. The theoretical basis were implemented two algorithms based on the analysis of DNA spectrogram. One is based on the assumption that the region CpG islands has a higher content of guanine and cytosine than the region outside the CpG island and the other on the assumption of a higher frequency of occurrence of CG dinucleotides in the CpG island. The algorithms are implemented through MATLAB programming interface. For evaluation usefulness and effectiveness of solutions, results achieved on the selected DNA sequences implemented algorithms are compared with the results achieved by search engines CpG islands, which are freely available on the internet.

No description available.

Bacterial DNA is immunostimulatory, and the motifs responsible for this activity are unmethylated CpG dinucleotides. Following cellular uptake, CpG-containing oligodeoxynucleotides (CpG ODN) are trafficked to the endosome where they bind Toll-like receptor 9 (TLR9) to initiate a signaling cascade that culminates in the release of numerous pro-inflammatory cytokines. Because of their immunostimulatory properties, CpG ODN are being clinically evaluated as treatments and vaccine adjuvants for infectious diseases, cancer, and allergic disorders. α2-Macroglobulin (α2M) is a human plasma protein that binds and modulates the activity of a variety of cytokines, growth factors, enzymes, and antigens. Upon proteolytic activation, α2M is converted to its receptor recognized form, α2M*, and rapidly binds to and is internalized by immune competent cells expressing the α2M* endocytic receptor, LRP, and is then trafficked to the endosome. Based on these interactions, α2M seems to play an important role at sites of infection and inflammation by controlling the level of proteinase activity, modulating cytokine signals, and enhancing antigen processing for the adaptive immune response. Here, we report the first evidence that α2M* binds and forms stable complexes with nucleic acids. We have characterized the mechanisms and stoichiometry of this interaction, examined the pH and temperature stability of these complexes, and identified structural variables in the nucleic acids, namely length, base composition, and chemical modifications, that affect the nature of this interaction. We hypothesized that CpG ODN incorporation into α2M* may alter their immunostimulatory properties. Murine macrophages (MΦs) treated with α2M*-ODN complexes respond more rapidly and produce a greater cytokine response than those treated with free CpG ODN alone. Treating human PBMCs with α2M*-ODN complexes likewise demonstrated their enhanced ability to elicit immune responses. This was due to more rapid uptake and CpG ODN protection from degradation by extracellular nucleases. Co-incorporation of both protein ligands and CpG ODN into α2M* yields ternary complexes; these may permit the simultaneous delivery of both protein antigens and adjuvants to immune competent cells, potentially greatly enhancing the adaptive immune response and protective immunity. Based on the findings that incorporation into α2M* confers enhanced immunostimulatory activity of CpG ODN, this technology may be exploited to improve CpG ODN-based therapeutics by increasing efficacy, minimizing side effects, reducing dosing requirements, and reducing cost. / Dissertation

Toll-like receptor 9 (TLR9) activates the innate immune system in response to microbial DNA or mimicking oligodeoxynucleotides. While the discrimination of host and microbial DNA is presumed to reflect TLR9-mediated recognition of CpG motifs, little information is available to verify this hypothesis. Cell stimulation experiments demonstrate preferential activation of TLR9 by CpG-containing nucleic acids, however direct binding investigations have reached contradictory conclusions with respect to the ability of TLR9 to bind nucleic acids in a sequence-specific fashion. Here we report expression of the soluble, ectodomain of human TLR9 with characterization of its ligand-binding properties. TLR9 has a high degree of ligand specificity in being able to discriminate not only CpG dinucleotides, but also higher order six nucleotide motifs that mediate species-specific activation. However, TLR9 ligand binding is also functionally influenced by nucleic acids in a sequence-independent manner both in vitro and in cell proliferation experiments. A model is proposed in which TLR9 activation is mediated specifically by CpG-containing ligands while sensitivity is mediated specifically by the absolute concentration of nucleic acids in a sequence-independent manner.<p>The bovine hsp70A promoter was used to direct the heat-regulated synthesis of the ectodomain of human TLR9 in transfected cultured bovine cells. The protein was efficiently secreted from transfected cells in a temperature-dependent manner and the recombinant receptor produced was found to be relatively pure. A stably transfected cell line with regulated expression of the protein was obtained and repeated thermal cycling of the cultures enabled high-yield production of the receptor in an active ligand-binding form. Using this recombinant receptor to study the ligand binding properties of TLR9, a model of positive cooperativity is proposed in which the sensitivity of TLR9 ligand binding is modulated by the absolute concentration of nucleic acids in a sequence-independent fashion, while activation of TLR9 is highly dependent on DNA sequence. That is to say that TLR9 is primed for activation by interaction with non-activating sequences but activation itself occurs in a sequence-specific fashion.

Toll-like receptor 9 (TLR9) activates the innate immune system in response to microbial DNA or mimicking oligodeoxynucleotides. While the discrimination of host and microbial DNA is presumed to reflect TLR9-mediated recognition of CpG motifs, little information is available to verify this hypothesis. Cell stimulation experiments demonstrate preferential activation of TLR9 by CpG-containing nucleic acids, however direct binding investigations have reached contradictory conclusions with respect to the ability of TLR9 to bind nucleic acids in a sequence-specific fashion. Here we report expression of the soluble, ectodomain of human TLR9 with characterization of its ligand-binding properties. TLR9 has a high degree of ligand specificity in being able to discriminate not only CpG dinucleotides, but also higher order six nucleotide motifs that mediate species-specific activation. However, TLR9 ligand binding is also functionally influenced by nucleic acids in a sequence-independent manner both in vitro and in cell proliferation experiments. A model is proposed in which TLR9 activation is mediated specifically by CpG-containing ligands while sensitivity is mediated specifically by the absolute concentration of nucleic acids in a sequence-independent manner.<p>The bovine hsp70A promoter was used to direct the heat-regulated synthesis of the ectodomain of human TLR9 in transfected cultured bovine cells. The protein was efficiently secreted from transfected cells in a temperature-dependent manner and the recombinant receptor produced was found to be relatively pure. A stably transfected cell line with regulated expression of the protein was obtained and repeated thermal cycling of the cultures enabled high-yield production of the receptor in an active ligand-binding form. Using this recombinant receptor to study the ligand binding properties of TLR9, a model of positive cooperativity is proposed in which the sensitivity of TLR9 ligand binding is modulated by the absolute concentration of nucleic acids in a sequence-independent fashion, while activation of TLR9 is highly dependent on DNA sequence. That is to say that TLR9 is primed for activation by interaction with non-activating sequences but activation itself occurs in a sequence-specific fashion.

Preventative immunotherapeutic treatments have been an area of great interest to combat infectious disease because of the ability to stimulate the hosts immune system which prepares the host to fight pathogenic microbes. The immunotherapeutic approach requires the use of an immune stimulating molecule that is able to boost the hosts immune response. A major problem exists that these immune stimulating molecules are often very expensive and require a large dose to be effective. To reduce the cost of using these molecules, a delivery system can be used which is able to lower the effective dose of the immune stimulant while not causing any toxic effects towards the hosts health. In this study, the immune stimulating molecules synthetic unmethylated cytidine-phosphate-guanosine oligodeoxynucleotides were attached non-covalently to multi-walled carbon nanotubes. The use of carbon nanotubes as a delivery mechanism could result in a lower effective dose able to stimulate a protective immune response in a chicken model. In this study, we first assessed which of the non-covalant linkages was ideal for linking the immune stimulant to the carbon nanotubes. This was conducted by looking at which method of linkage would allow the best cellular proliferation and transcriptional activation of selected innate immune genes. Once an appropriate linkage method had been selected, cellular uptake studies were conducted to establish that cytidine-phosphate-guanosine oligodeoxynucleotides were delivered to intracellular target receptors. After cellular uptake was demonstrated, it was important that the carbon nanotubes linked to the immune stimulant do not cause toxicity towards the host. To measure toxicity, in vitro studies were conducted to observe cell viability post treatment with carbon nanotube linked immune stimulant. Further studies were conducted on any alterations to the immune stimulants ability to activate immune cells by studying the pathway of macrophage activation. The protective ability of the molecules was then measured by the ability to protect chickens from a lethal challenge with S. typhimurium. Once the protective nature of the molecules was established, the mechanism of immune stimulation was examined by in vivo cell recruitment and in vitro cytokine production. These studies indicate that linking cytidine-phosphate-guanosine oligodeoxynucleotides to carbon nanotubes can lower the effective dose of the immune stimulant without altering the biological function of the molecule.

Escherichia coli ist eine der Hauptursachen von Meningitis und Meningoencephalitis in älteren und immunsupprimierten Patienten sowie von der durch Gram-negative Bakterien verursachten Meningitis bei Säuglingen. In der vorliegenden Arbeit untersuchten wir den Beitrag der neutrophilen Granulozyten und der TLR-Signalkaskade zur Resistenz adulter Mäuse gegen eine intrazerebrale Escherichia-coli-K1-Infektion, anhand von Mäusen, deren neutrophile Granulozyten durch den Anti-Ly-6G-Antikörper depletiert wurden sowie mit Hilfe von MyD88-defizienten und TRIF-defizienten Mäusen. Ein Mangel an MyD88-Adapter-Proteinen reduzierte dramatisch das Überleben der Tiere, während das Fehlen von TRIF-Adapter-Proteinen keine Einschränkung im Überleben nach sich zog im Vergleich zu den Wildtypmäusen. Die Depletion der neutrophilen CD11b+Ly-6G+Ly-6Cint-Granulozyten durch intraperitoneale Injektion des Anti-Ly-6G-Antikörpers führte zu höheren bakteriellen Titern im Kleinhirn und in der Milz und schließlich zu einer erhöhten Letalität im Vergleich zu den mit dem Isotyp behandelten Mäusen. Unsere Ergebnisse zeigen, dass der den Toll-like-Rezeptoren nachgeschaltete MyD88-Signalweg und die neutrophilen Granulozyten wichtige Elemente in der Immunabwehr während der Frühphase einer Escherichia-coli-Meningitis sind. Wie bereits in verschiedenen Experimenten gezeigt wurde, können CpG-ODNs Tiere vor verschiedenen Infektionen schützen (Elkins et al. 1999; Barrier et al.2006). Vor diesem Hintergrund prüften wir, ob eine prophylaktische Behandlung mit CpG-ODN ebenfalls vor einer experimentell erzeugten Infektion des Zentralen Nervensystems schützt. Dazu wurden Mäuse, denen mit Hilfe des Anti-Ly-6G-Antikörpers eine Neutropenie induziert wurde, sowie immunkompetente Mäuse und TLR9-defiziente Mäuse jeweils intrakraniell mit Escherichia coli K1 infiziert. Drei Tage vor der Infektion bekamen die Mäuse der CpG-Gruppen eine einmalige intraperitoneale Injektion von 100 μg CpG-ODN. Hierbei zeigte sich, dass die Behandlung mit CpG-ODN die Letalität nach einer intrazerebralen Infektion von 66 % auf 23 % bei den neutropenischen Mäusen senkte (P = 0,0002, Log-Rank-Test). Zusätzlich wiesen die mit CpG-ODN behandelten Mäuse 42 Stunden nach Infektion geringere bakterielle Titer im Kleinhirn und in der Milz auf, als es in den mit Puffer behandelten Tieren der Fall war (P = 0,01 und P = 0,04, Mann-Whitney-U-Test). In den immunkompetenten Mäusen war die Letalität der mit CpG-ODN behandelten Mäuse leicht niedriger im Vergleich zur Puffergruppe, es konnte jedoch kein statistisch signifikanter Unterschied gefunden werden. TLR9-defiziente Mäuse erhielten keinen schützenden Effekt durch die prophylaktische Behandlung mit CpG-ODN. Dies zeigt, dass die prophylaktische Behandlung mit CpG-ODN nicht nur während einer systemischen Infektion einen Vorteil bringt, sondern ebenfalls die Resistenz von neutropenischen Mäusen gegen eine ZNS-Infektion mit Escherichia coli erhöht. Somit könnte CpG-ODN in Zukunft ein Mittel bieten, um neutropenische Patienten prophylaktisch vor einer Escherichia-coli-K1-Meningitis zu schützen und ihnen somit schwere Verlaufsformen und Komplikationen der Krankheit zu ersparen.

Mit dieser Arbeit wird zum ersten Mal der therapeutische Einsatz von immunstimulativer DNA mit CpG-Motiv (CpG-ODN) bei einer akuten Virusinfektion beschrieben. Als experimentelles Modell wurde das Friend Virus (FV), ein muriner Retroviruskomplex, verwendet. Das FV kann in Mäusen eine tödlich verlaufende Erythroleukämie induzieren. Durch die Immuntherapie mit CpG-ODN in der akuten Phase einer FV-Infektion konnten 74% der Mäuse vor der Entstehung der Virus-induzierten Leukämie geschützt werden. Dieser Schutz ging einher mit der Reduktion der Viruslast im Blut und in der Milz der Tiere und wurde durch CpG-ODN induzierte FV-spezifische CD8+-Zellen vermittelt. FV-neutralisierende Antikörper und natürliche Killerzellen waren dagegen am CpG-ODN induzierten Schutz nicht beteiligt. Der Einsatz von CpG-ODN als Paraimmunisierung (unspezifische Immunisierung vor einer Infektion) verursachte hingegen einen schwereren FV-induzierten Leukämiever-lauf als in infizierten Mäusen ohne vorherige Behandlung. Die prophylaktische CpG-ODN Gabe führte sogar dazu, dass FV-resistente Mäuse empfänglich für eine FV-vermittelte Leukämie wurden. Der negative Effekt der prophylaktischen ODN-Behandlung wurde durch die CpG-ODN induzierte Proliferation der wichtigsten Ziel-zellen des FV (Ter119+- Erythrozytenvorläuferzellen und B-Zellen) verursacht. Durch die Stimulierung dieser Zellen konnte das Virus schneller replizieren, so dass das Immunsystem der Mäuse nicht mehr in der Lage war das Virus zu kontrollieren. Untersuchungen zum therapeutischen Einsatz von CpG-ODN in der späten, leukämi-schen Phase der Infektion zeigten, dass sich CpG-ODN auch für die Bekämpfung von FV-induzierten Tumorzellen einsetzen lassen. Das die CpG-ODN Behandlung von viralen Infektionen zu sehr unterschiedlichen Ergebnissen führen kann, konnte in der vorliegenden Arbeit gezeigt werden. Die CpG-ODN Behandlung stellte einerseits eine effektive Immuntherapie gegen die FV-induzierte Erkrankung dar, andererseits konnte sie die Viruserkrankung auch verstär-ken. Essentiell für den Erfolg der ODN-Behandlung war der richtige Behandlungs-zeitpunkt nach Infektion. Da viele Virusinfektionen durch eine CD8+ CTL-Aktivität kontrolliert werden und CpG-ODN Virus-spezifische CTL Antworten verstärken, ist der Einsatz von CpG-ODN für Behandlungen von Virusinfektionen im allgemeinen sehr interessant. Im zweiten Teil dieser Arbeit sollte eine transkutane Vakzinierung (Impfung über die Haut) gegen Retrovirus-induzierte Erkrankungen etabliert werden. CpG-ODN dienten dabei als starkes Adjuvants zur Induktion einer zellulären Immunantwort. Für die Imp-fung wurden FV-spezifische T-Zell-Epitope (CTL- und T-Helferzell-Peptide) als Anti-gene eingesetzt. Die transkutane Immunisierung schützte Mäuse vor einer FV-induzierten Leukämie. Der durch die Vakzine vermittelte Schutz reichte jedoch nicht aus, um eine persistierende Infektion mit FV zu verhindern. Die Ergebnisse der im-munologischen Untersuchungen zeigten, dass der Impfschutz von FV-spezifischen CD8+-Zellen vermittelt wurde. Die Studie belegt, daß eine nicht invasive Impfung durchaus in der Lage ist, einen Schutz gegen eine Retrovirus-induzierte Erkrankung zu vermitteln. / In this study immunstimulatory DNA containing unmethylated CpG motifs (CpG-ODN) was described as a new therapeutic approach against an acute virus infection. Friend virus (FV), a murine retrovirus complex, was used as experimental model. This virus can induce a lethal erythroleukemia in mice. The CpG-ODN therapy increased re-covery from FV-induced leukemia from 6% in the control group to 74% in the CpG-treated group. CpG-mediated recovery was associated with a significant reduction of viral loads in the blood and spleens of treated mice compared to those of control animals. The treatment promoted Th1-type cytokine production by splenocytes of FV-infected mice and augmented FV-specific cytotoxic T-cell responses but no influence on the virus-specific neutralizing antibody response or NK-cells were observed. FV-specific CD8+ T-cells were critical for effective treatment with CpG-ODN, since in vivo depletion of these cells from treated mice prevented their recovery. In stark contrast to the success of post-exposure treatments CpG-treatment of sus-ceptible mice prior to FV-infection accelerated the development of virus-induced erythroleukemia. Furthermore, 70,8% of mice that are resistant to FV-induced leuke-mia developed disease after inoculation of CpG-ODN before infection. The CpG pre-treatment of these mice enhanced viral loads in their spleens and blood compared to controls that received ODN without CpG motifs. The main target cells of Friend virus, erythroid precursor cells and B-cells, proliferated after CpG-ODN inoculation and provided an enlarged target population for viral infection. These findings demonstrate that CpG-ODN treatment of viral infections may be a double-edged swart that can result in an effective therapy but also in an acceleration of disease progression de-pending on the time point of treatment. Taken together, CpG-ODN therapy can significantly enhance virus-specific cellular immune responses and prevent retrovirus-induced disease, when given after virus infection. These findings may have implications for antiviral therapy in general. In ad-dition, successful CpG-treatment of mice with fully established, FV-induced erythro-leukemia implies that CpG-ODN are also interesting molecules for the therapy of vi-rus-induced cancers. The goal of the second part of this work was to establish a transcutan immunisation against retrovirus-induced disease. Here CpG-ODN were used as a strong adjuvants to induce a cellular immune response. As antigenes FV-specific T-cell epitops (CTL- and T-helper-cell-peptides) were utilized. The transcutan immunisation protected mice against FV-induced erythroleukemia. However, the vaccines were not protected from persistent FV infection. FV-specific CD8+ T-cells were induced by the transcutan immunisation. These findings demonstrate the potential of the bare skin immunisation (a non-invasive route) against retroviral infections.