66 search hits
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Juvenile Neuronal Ceroid Lipofuscinosis: toponomics approach to identifying new drug targets / von Anna Pupu Ingeborg Krokfors
(2011)
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Anna Krokfors
- Juvenile Neuronal Ceroid Lipofuscinosis (JNCL) is a rare inherited childhood neurodegenerative disease that is caused by a mutation in the gene CLN3. The function of the protein produced by the gene has remained elusive, and therefore the disease mechanism of JNCL is as of yet unknown. The disease is fatal, and no cure is currently available. We believe that simvastatin shows promise as a possible treatment. Simvastatin is well tolerated in children, and as currently no other viable, less invasive treatment for JNCL exists, at least pilot-scale clinical trials for this new off-label use of simvastatin are warranted.
The protein CLN3 has been indicated to have several different subcellular localizations and functions, but conclusive evidence about its role in cellular metabolism is lacking. It is also unclear why the mutation causes the distinct phenotype of the JNCL disease. In order to bring lucidity to the issue, we set out to identify metabolic pathways related to the phenotype of JNCL by using Multi-Epitope Ligand Cartography (MELC) and the related field of toponomics. Toponomic methods are required to process the massive amount of data generated by the MELC runs in order to extract information from them.
Our disease model of choice was the CLN3Δex7/8 knock-in mouse. To separate cause from effect, we compared embryonal wild type and mutant mouse brains to their adult counterparts. The first analyses revealed progressively abnormal Combinatorial Molecular Patterns (CMPs, an unit of toponomic data) related to cholera toxin/ganglioside 1 (Ctx/GM1), which is a membrane microdomain marker.
Cholesterol is an essential part of microdomains, so we utilized filipin staining to see if there were actual changes in cholesterol concentration and localization between healthy and diseased animals. After the disturbance in cholesterol metabolism was verified, we investigated the metabolic pathway that synthesizes cholesterol, the mevalonate pathway. Simvastatin is a drug that specifically down-regulates the mevalonate pathway. Fish oil affects lipid homeostasis and has some effects similar to those of simvastatin, and both of these drugs have previously been studied for their effects on neurodegenerative diseases. After treatment of mice with these drugs, highperformance liquid chromatography (HPLC) measurements on the brain homogenate showed a decrease in levels of farnesyl pyrophosphate (FPP) and geranyl-geranyl pyrophosphate (GGPP), products of the mevalonate pathway, confirming the effect of these drugs on the brains of the animals. Analyses of motor function of the mice further supported the notion that simvastatin had a positive effect on the condition of the diseased animals.
CMP analyses from the simvastatin treated mice showed a rescue of the Ctx/GM1 CMPs, suggesting at least a partial restoration of membrane microdomain homeostasis. Filipin staining revealed reversion of the apparent cholesterol depletion in the adult mutant mouse hippocampus by simvastatin. Interestingly, an additional effect of the treatment was found: simvastatin also affected glutamate receptor homeostasis, especially as regarding to N-methyl-D-aspartate (NMDA) and alphaamino-3-hydroxyl-5-methyl-4-isoxazole-propionate (AMPA) receptors. This finding suggested that excitotoxicity could be a part of the disease process, and pointed towards glutamate receptors as possible therapy targets. This is in line with previous studies that have shown that attenuation of AMPA receptors and L voltage-dependent channels improve the phenotype of a JNCL mouse and cell model, respectively.
Simvastatin mediates many of its effects via downregulation of the mevalonate pathway products, such as isoprenoids and cholesterol. However, simvastatin also has multiple pleiotropic effects that include suppression of excitotoxicity and granting neuroprotection. It is apparent that simvastatin treatment has a positive effect on JNCL mice, but if its effects are mediated via cholesterol (and membrane microdomains), isoprenoids (and isoprenylated proteins) or via a fully cholesterol independent mechanism remains to be solved.
In this study we have shown that with the MELC method and toponomics it is possible to approach rare diseases with confounded disease mechanisms with a hypothesis-free approach, to identify possible drug targets, and to monitor the effects of the drugs on treated individuals. This should open up a new avenue in the research of the many diseases that so far have avoided all attempts at discerning their nature.
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Ordnung der Johann Wolfgang Goethe–Universität Frankfurt am Main für den Bachelorstudiengang Bioinformatik vom 16.11.2009 : genehmigt durch das Präsidium der Johann Wolfgang Goethe-Universität am 15.02.2011
(2011)
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Ordnung der Johann Wolfgang Goethe-Universität Frankfurt am Main für den Masterstudiengang Bioinformatik in der Fassung vom 06.12.2010 : vorläufig genehmigt mit Beschluss des Präsidiums vom 01.02.2011
(2011)
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Ordnung des Fachbereichs Biowissenschaften der Johann Wolfgang Goethe-Universität für den Masterstudiengang Molekulare Biowissenschaften mit dem Abschluss "Master of Science" (M.Sc.) vom 21. Februar 2011 : genehmigt vom Präsidium der Johann Wolfgang Goethe–Universität Frankfurt am Main am 27. September 2011
(2011)
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Ordnung der Fachbereiche Medizin, Biowissenschaften, Biochemie, Chemie und Pharmazie sowie Psychologie und Sportwissenschaften der Johann Wolfgang Goethe-Universität für den Masterstudiengang Interdisciplinary Neuroscience mit dem Abschluss "Master of Science" (M.Sc.) vom 30. März 2009 in der Fassung vom 22. April 2009 : genehmigt durch das Präsidium am 11. Oktober 2011
(2011)
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Ordnung des Fachbereichs Biowissenschaften der Johann Wolfgang Goethe-Universität für den Masterstudiengang Cell Biology and Physiology mit dem Abschluss Master of Science (M.Sc.) vom 18. Oktober 2011 : genehmigt durch das Präsidium am 29. November 2011
(2011)
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Epigenetic regulation of innate immune responses
(2011)
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Uwe Schaefer
- We found that the HMTase G9a, that catalyzes H3K9me2 in euchromatin, plays
a key modulatory role in type I IFN expression. This finding raises the possibility
of targeted intervention with type I IFN expression by using small synthetic
inhibitors of G9a. Given the overall minimal negative effect of G9a-deficiency on
differentiated cells, the short-term suppression of G9a could be used to
potentiate type I IFN expression during chronic viral diseases such as
hepatitis C.
Accordingly, pharmacological enhancement of methylation, for example by
inhibition of the H3K9me2 specific demethylases, could be potentially used to
attenuate type I IFN expression and help to control chronic inflammatory and
autoimmune conditions. The mechanism responsible for canvassing the
epigenetic profile of type I IFN expressing cells are not known. It is plausible, that
similar to neurons, where G9a is targeted to specific loci with the help of noncoding
RNAs, IFN expressing cells possess similar mechanisms to target
H3K9me2 demethylating enzymes to type I IFN loci, thus keeping these loci
accessible for IFN-inducing transcription factors. Identification of non-coding
RNAs that may contribute to the establishment of the epigenetic state of IFN
producing cells will provide a further opportunity for targeted manipulation of IFN
expression.
In my thesis, I describe the collaborative experiments that show the ability of
synthetic compounds that interfere with the histone readers to suppress
inflammation. Our results present a novel concept for the regulation of
inflammatory gene expression. The diversity of histone readers and the
combinatorial nature of regulation of gene transcription may provide an
opportunity for highly selective interference with disease associated
transcriptional programs by interfering with specific readers. In the future we plan
to address the therapeutic potential of BET antagonists in autoimmune and
chronic inflammatory conditions.In summary, the experiments described in my thesis provide an example of how
the understanding of the basic mechanisms of chromatin control of gene
expression can facilitate novel therapeutic approaches that target chromatin.
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Die Bedeutung von Zelltod-Prozessen während der Alterung des filamentösen Ascomyzeten Podospora anserina
(2011)
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Diana Brust
- Die im Rahmen dieser Arbeit durchgeführten Untersuchungen führten zu folgenden Ergebnissen:
1. In-silico Analysen von putativen Apoptose-Faktoren im Genom von P. anserina
Es konnten mehrere Gene, die in einer Apoptose-Maschinerie involviert sein könnten, im Genom von P. anserina identifiziert werden. Diese Homologen wurden in zwei Ka-tegorien unterteilt: (i) die nicht-mitochondrialen Proteine PaMCA1, PaMCA2 und PaPARP und (ii) die Homologen des Apoptose-induzierenden Faktors AIF.
2. Einfluss der Metacaspase-Aktivität auf programmierte Zelltodprozesse
Mithilfe von Aktivitätsmessungen konnte eine Arginin-spezifische Aktivität der Meta-caspasen nachgewiesen werden. Diese Metacaspase-Aktivität nimmt in seneszenten Kulturen und nach H2O2-Behandlung signifikant zu. Diese Ergebnisse unterstützen die Hypothese eines programmierten, ROS-induzierten Zelltods im letzten Entwicklungs-stadium des Alternsmodell P. anserina.
3. Die Rolle von AIF-Homologen in der Entwicklung von P. anserina
GFP-Fusionsproteine identifizierten eine mitochondriale Lokalisation der AIF-Homologen PaAIF2, PaAMID2 und PaPRG3. Desweiteren konnte eine altersabhängige PaAIF2-Translokation von den Mitochondrien zum Zellkern gezeigt werden, ähnlich der Apoptose-induzierenden Translokation von humanem AIF. Die Deletion von PaAif2 und PaAmid2 führte zu einer signifikanten Resistenz gegenüber oxidativem Stress und zu einer Verlängerung der Lebensspanne. Diese Befunde weisen auf einen ROS-induzierten, AIF-vermittelten Zelltod hin, der an der Lebensspannen-Kontrolle von P. anserina beteiligt ist.
4. Die Funktion des Proteins PaCYPD bei Seneszenz und programmiertem Zelltod
Membranpotential-Messungen konnten einen Rückgang des mitochondrialen Memb-ranpotentials von 21 % bei den PaCYPD-Überexpressionsstämmen nachweisen. Durch die Behandlung mit dem spezifischen PaCYPD-Inhibitor CSA konnte das Membranpo-tential wieder normalisiert werden. Zusammen mit dem detektierten Verlust von
7 Zusammenfassung
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Cytochrom c in den Mitochondrien der Überexpressionsstämme wird durch diese Studi-en die Vermutung einer PaCYPD-abhängigen Öffnung der mPTP untermauert. Die Pa-PaCypD-Deletion führte zu einer signifikanten Resistenz gegenüber mitochondrial-abhängigem, oxidativem Stress und gegenüber verschiedenen Apoptose-Induktoren. Die Überexpression von PaCypD hingegen führte zu einem beschleunigten Alterungspro-zess (Präseneszenz), einem verschlechterten Resistenzverhalten gegenüber Stress- und Apoptose-Induktoren und zu einer massiven Verkürzung der Lebensspanne. Die Le-bensspanne konnte aber durch die Behandlung mit CSA wieder auf Wildtyp-Niveau verbessert werden. Dies weist auf einen PaCYPD-vermittelte Zelltod hin. Interessan-terweise konnte durch das Wachstum auf CSA-haltigem Medium auch die Lebensspanne des Wildtyps verlängert werden. Um die hier nachgewiesene, lebensver-längernde Wirkung von CSA zu verifizieren, könnte diese Studie leicht auf andere Modellorganismen übertragen werden.
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Functional genomic and advanced genetic studies reveal novel insights into the metabolism, regulation, and biology of Haloferax volcanii
(2011)
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Jörg Soppa
- The genome sequence of Haloferax volcanii is available and several comparative genomic in silico studies were performed that yielded novel insight for example into protein export, RNA modifications, small non-coding RNAs, and ubiquitin-like Small Archaeal Modifier Proteins. The full range of functional genomic methods has been established and results from transcriptomic, proteomic and metabolomic studies are discussed. Notably, Hfx. volcanii is together with Halobacterium salinarum the only prokaryotic species for which a translatome analysis has been performed. The results revealed that the fraction of translationally-regulated genes in haloarchaea is as high as in eukaryotes. A highly efficient genetic system has been established that enables the application of libraries as well as the parallel generation of genomic deletion mutants. Facile mutant generation is complemented by the possibility to culture Hfx. volcanii in microtiter plates, allowing the phenotyping of mutant collections. Genetic approaches are currently used to study diverse biological questions–from replication to posttranslational modification—and selected results are discussed. Taken together, the wealth of functional genomic and genetic tools make Hfx. volcanii a bona fide archaeal model species, which has enabled the generation of important results in recent years and will most likely generate further breakthroughs in the future.
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Influence of ground-state structure and Mg2+ binding on folding kinetics of the guanine-sensing riboswitch aptamer domain
(2011)
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Janina Buck
Anna Wacker
Eberhart Warkentin
Jens Wöhnert
Julia Wirmer-Bartoschek
Harald Schwalbe
- Riboswitch RNAs fold into complex tertiary structures upon binding to their cognate ligand. Ligand recognition is accomplished by key residues in the binding pocket. In addition, it often crucially depends on the stability of peripheral structural elements. The ligand-bound complex of the guanine-sensing riboswitch from Bacillus subtilis, for example, is stabilized by extensive interactions between apical loop regions of the aptamer domain. Previously, we have shown that destabilization of this tertiary loop–loop interaction abrogates ligand binding of the G37A/C61U-mutant aptamer domain (Gswloop) in the absence of Mg2+. However, if Mg2+ is available, ligand-binding capability is restored by a population shift of the ground-state RNA ensemble toward RNA conformations with pre-formed loop–loop interactions. Here, we characterize the striking influence of long-range tertiary structure on RNA folding kinetics and on ligand-bound complex structure, both by X-ray crystallography and time-resolved NMR. The X-ray structure of the ligand-bound complex reveals that the global architecture is almost identical to the wild-type aptamer domain. The population of ligand-binding competent conformations in the ground-state ensemble of Gswloop is tunable through variation of the Mg2+ concentration. We quantitatively describe the influence of distinct Mg2+ concentrations on ligand-induced folding trajectories both by equilibrium and time-resolved NMR spectroscopy at single-residue resolution.
