<p>Members of the Transforming Growth factor-β (TGF-β) superfamily and its subclass Bone Morphogenetic Proteins (BMP) play important roles for nervous system development. </p><p>In order to study the BMP role for catecholaminergic neurons <i>in vivo</i>, we generated three knock-in mice, expressing the transgenes specifically in the targeting cells. </p><p>Two genetic modifications result in expression of dominant negative (dn) BMP receptors (BMPRII and ALK2). The tissue-specific expression was achieved by the transgene insertion into 3’- untranslated region of the endogenous gene for tyrosine hydroxylase (TH), the first enzyme in catecholamine biosynthesis. An Internal Ribosome Entry site (IRES) preceded inserted cDNAs, allowing for functional bicistronic mRNA production. While almost no defects in Th-IRES-dnALK2, the Th-IRES-dnBMPRII mouse demonstrated declined levels of catecholamines, including dopamine in the striatum. Losses of midbrain dopaminergic neurons (MDN) might cause the effect. Additionally, intermediate lines of these mice, preserving a neo-cassette, oriented opposite to the locus transcription, demonstrate dramatic decrease of catecholamine level, hence, represent models for rare catecholamine-deficiency diseases, including L-DOPA-responsive dystonia.</p><p>The third mouse, expressing in the same way Cre-recombinase (Th-IRES-Cre), represents a tool for catecholaminergic cell-limited deletion of any gene, which has to be flanked by loxP sites. Besides TH-positive areas, unexpected sites of Cre-recombination were identified, indicating regions of transient TH expression. Surprising recombination in oocytes opens a possibility to use our mouse as a general Cre-deletor.</p><p>Using TH-IRES-Cre mouse we generated tissue-specific knockout mice for two BMP signal transducers: Smad1 and Smad4 (also crucial for TGF-β). While no phenotype in Smad1 knockout, TH-IRES-Cre/Smad4 mouse revealed several defects including decreased level of striatal dopamine. </p><p>These results demonstrate a positive role of BMPs for MDN fate<i> in vivo</i>. Generated mice represent a tool-box for comprehensive study of the BMP function in catecholaminergic neurons. This study is of potential interest for understanding some aspects of Parkinson’s disease.</p>

Members of the Transforming Growth factor-β (TGF-β) superfamily and its subclass Bone Morphogenetic Proteins (BMP) play important roles for nervous system development. In order to study the BMP role for catecholaminergic neurons in vivo, we generated three knock-in mice, expressing the transgenes specifically in the targeting cells. Two genetic modifications result in expression of dominant negative (dn) BMP receptors (BMPRII and ALK2). The tissue-specific expression was achieved by the transgene insertion into 3’- untranslated region of the endogenous gene for tyrosine hydroxylase (TH), the first enzyme in catecholamine biosynthesis. An Internal Ribosome Entry site (IRES) preceded inserted cDNAs, allowing for functional bicistronic mRNA production. While almost no defects in Th-IRES-dnALK2, the Th-IRES-dnBMPRII mouse demonstrated declined levels of catecholamines, including dopamine in the striatum. Losses of midbrain dopaminergic neurons (MDN) might cause the effect. Additionally, intermediate lines of these mice, preserving a neo-cassette, oriented opposite to the locus transcription, demonstrate dramatic decrease of catecholamine level, hence, represent models for rare catecholamine-deficiency diseases, including L-DOPA-responsive dystonia. The third mouse, expressing in the same way Cre-recombinase (Th-IRES-Cre), represents a tool for catecholaminergic cell-limited deletion of any gene, which has to be flanked by loxP sites. Besides TH-positive areas, unexpected sites of Cre-recombination were identified, indicating regions of transient TH expression. Surprising recombination in oocytes opens a possibility to use our mouse as a general Cre-deletor. Using TH-IRES-Cre mouse we generated tissue-specific knockout mice for two BMP signal transducers: Smad1 and Smad4 (also crucial for TGF-β). While no phenotype in Smad1 knockout, TH-IRES-Cre/Smad4 mouse revealed several defects including decreased level of striatal dopamine. These results demonstrate a positive role of BMPs for MDN fate in vivo. Generated mice represent a tool-box for comprehensive study of the BMP function in catecholaminergic neurons. This study is of potential interest for understanding some aspects of Parkinson’s disease.

The DDT metabolite 3-methylsulphonyl-DDE (3-MeSO2-DDE) induces cell death specifically in the adrenal cortex of mice after a cytochrome P45011B1 (CYP11B1)-catalysed bioactivation. This substance is not only an environmental pollutant, but also a suggested lead compound for an improved chemotherapy of adrenocortical carcinoma (ACC). The aim of the thesis was to further investigate this compound in terms of kinetics, cell death mechanisms and species differences. The pharmacokinetics of 3-MeSO2-DDE and the current drug for ACC, o,p’-DDD, was studied during 6 months following a single dose in minipigs. The elimination was slower for 3-MeSO2-DDE than for o,p’-DDD, indicated by a lower clearance and longer t½ in plasma and subcutaneous fat. Both substances remained in fat tissue during the whole study period. Unlike o,p’-DDD, 3-MeSO2-DDE was retained also in liver. The adequacy of the murine adrenocortical cell line Y-1 was evaluated for studies of adrenotoxic compounds. The Y-1 cells proved to be an appropriate test system for future mechanism studies, since CYP-catalysed irreversible binding, inhibited corticosterone production induced by 3-MeSO2-DDE and o,p’-DDD were successfully demonstrated. Cell death of 3-MeSO2-DDE in the mouse adrenal cortex was implied to be necrotic. Early apoptotic signalling (i.e. up-regulation of caspase-9) was observed, although it seemed to be interrupted by ATP-depletion and anti-apoptotic actions by heat shock protein 70, resulting in lack of activation of caspase-3. Using cultured adrenal tissue slices, two not previously studied species were examined ex vivo regarding adrenal binding of 3-MeSO2-[14C]DDE. Binding was found in the hamster adrenal cortex and in assumed cortical cells in the medulla, while the guinea pig adrenal was devoid of binding. This emphasises the species specificity in bioactivation of 3-MeSO2-DDE. The thesis forms a basis for further investigations in the human adrenocortical cell line H295R and provides new knowledge of importance for toxicological risk assessment of 3-MeSO2-DDE.

This thesis performs de novo predictions for functionally significant sequence motifs in the Arabidopsis genome under two separate contexts. Each study applies the use of genomic positional information, statistical over-representation and several biologically contextual filters to maximize the visibility of biological signal in prediction results. Numerous literature supported motifs are prevalent in the results of both studies and a number of novel motif patterns possess a strong potential for in planta significance. The first study examines the statistical over-representation of C-terminal tripeptides as a means for identifying eukaryotic conserved protein targetting signatures. Comparative genomics is applied to the analysis of tripeptide frequencies in the C-terminus of 7 eukaryotic proteomes. While biological signal is maximized through the filtering of both simple sequences and homologous sequences present across protein families. The second study introduces a methodology for the effective prediction of transcription factor binding sites in Arabidopsis. A collection of motif prediction algorithms and a novel enumerative strategy are applied to the prediction of cis-acting regulatory elements within the promoters of genes found coexpressed within distinct tissues and under specific abiotic stress treatments. Overall, the analysis identifies 4 known motifs in expected contexts, 5 known motifs in novel contexts and 7 novel motifs with a high potential for biological function.

This thesis performs de novo predictions for functionally significant sequence motifs in the Arabidopsis genome under two separate contexts. Each study applies the use of genomic positional information, statistical over-representation and several biologically contextual filters to maximize the visibility of biological signal in prediction results. Numerous literature supported motifs are prevalent in the results of both studies and a number of novel motif patterns possess a strong potential for in planta significance. The first study examines the statistical over-representation of C-terminal tripeptides as a means for identifying eukaryotic conserved protein targetting signatures. Comparative genomics is applied to the analysis of tripeptide frequencies in the C-terminus of 7 eukaryotic proteomes. While biological signal is maximized through the filtering of both simple sequences and homologous sequences present across protein families. The second study introduces a methodology for the effective prediction of transcription factor binding sites in Arabidopsis. A collection of motif prediction algorithms and a novel enumerative strategy are applied to the prediction of cis-acting regulatory elements within the promoters of genes found coexpressed within distinct tissues and under specific abiotic stress treatments. Overall, the analysis identifies 4 known motifs in expected contexts, 5 known motifs in novel contexts and 7 novel motifs with a high potential for biological function.

No description available.

No description available.

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<p><strong> </strong>Comparison of tissue-specific gene expression profiles between sibling species and their F1 interspecific hybrids are expected to reveal important information about the mechanisms involved in speciation and species divergence. In the present study, the expression of 40 candidate genes were analyzed using qRT-PCR in the testis, ovary and head tissues (both male and female) among the hybrids and their parental species. The expression patterns of these genes were profiled via quantification of misexpression (both over- and under-expression) relative to that of their parents as well as across tissues. We set out to answer several questions as well as test the following hypotheses: (1) Do <em>Drosophila</em> sibling species differ in tissue-specific distribution of gene expression? (2) Do males and females differ in tissue specific distribution of expression? (3) Do reciprocal crosses differ in patterns of gene misexpression suggesting X-effect? (4) Do sex and non-sex genes differ in extent of gene misexpression? The results of this study gave rise to two important findings. First, it was found that while the majority of genes showed head and testis expression in <em>Drosophila melanogaster</em>, more genes showed head and ovary expression in <em>D. sechellia</em>. Second, we observed differences in gene misexpression between reciprocal <em>D. simulans </em>and <em>D. sechellia</em> hybrid females, suggesting the role of maternal effect. Thus, these findings supply a wealth of data regarding tissue-specific expression in both fertile females and sterile male hybrids, the former of which have largely been ignored, as well as advance our understanding of the process of species divergence and speciation. Ultimately, this thesis will provide a contribution to the field of gene regulatory evolution.</p> / Master of Science (MSc)

Bei der adjuvanten Immuntherapie soll das Immunsystem von Tumorpatienten gezielt gegen Mikrometastasen aktiviert werden, die nach der operativen Entfernung des Primärtumors im Körper verbleiben. Tumor-assoziierte Antigene (TAA) spielen dabei die zentrale Rolle. Um der Heterogenität eines Tumors in der Expression einzelner TAAs Rechnung zu tragen, werden in modernen Vakzinierungsstrategien Pools von verschiedenen TAAs eingesetzt. Für das Mammakarzinom sind aber bislang nur wenige TAAs bekannt. Auf der Suche nach unbekannten Genen mit Mamma- bzw. Mammakarzinom-restringierter Expression in der Transkriptomdatenbank GeneExpress® wurde ein EST gefunden, das nur in 2 % der getesteten weibl. Normalgewebe ohne Mamma mit einer marginalen mittleren Expression von 16 FE (Fluoreszenzeinheit) detektiert wurde, aber in 63 % der Mammanormalgewebe (159 FE) und in 61 % der Mammakarzinome (339 FE) exprimiert wurde. Das korrespondierende UniGene-Cluster gab erste Hinweise auf die Zugehörigkeit dieses neuen Gens zu der Cytochrom P450 (CYP) Familie. Durch computergestützte Homologievergleiche mit verwandten Mitgliedern dieser Familie in Kombination mit RT-PCR konnte die cDNA-Sequenz dieses neuen CYP ermittelt werden: Durch Amplifikation der Gesamtlängen-cDNA wurden drei Transkripte in der Mammakarzinomzelllinie SK-BR-3 gefunden, die von zwei neuen CYP Genen stammen, CYP4Z1 und dem Pseudogen CYP4Z2P. Die cDNA von CYP4Z1 kodiert für ein 505 As großes Protein, das aufgrund von Homologien einer neuen Subfamilie innerhalb der CYP4 Familie zugeordnet werden kann. Sowohl die Sequenz als auch die vorhergesagte Sekundärstruktur zeigen alle charakteristischen Merkmale eines funktionellen Mitglieds dieser Familie. Aufgrund einer Nonsensemutation in Exon 8 kodiert die cDNA von CYP4Z2P (1436 bp) für ein verkürztes, nichtfunktionelles P450 von 340 As, das zu 96% identisch mit P450 4Z1 ist. Außerdem wurde in SK-BR-3 eine Spleißvariante von CYP4Z1 identifiziert. CYP4Z1 (50,8 kb) und CYP4Z2P (57,3 kb) liegen auf Chromosom 1p33-p34.1 und bestehen aus 12 Exons mit konservierten Exon-Intron-Grenzen. CYP4Z2P ist aus einer inversen Duplikation von CYP4Z1 hervorgegangen. Mittels Realtime RT-PCR mit cDNA von 17 Normalgeweben von gepoolten Spendern und von Mammakarzinomen konnte die auf Brustdrüsengewebe restringierte Expression beider Gene demonstriert werden: Die Expression von CYP4Z1 war in Mammakarzinomgewebe 3,6-mal höher als in Mammanormalgewebe, 60-mal höher als in Lunge und 84-mal höher als in Leber. Alle anderen getesteten weibl. Normalgewebe zeigten eine noch geringere Expression. Ein ähnlich stringentes Expressionsprofil ergab die Analyse von CYP4Z2P, allerdings mit einer deutlich niedrigeren Expressionsstärke. Das Mamma-restringierte Expressionsverhalten von CYP4Z1 wurde durch einen ?Cancer-Profiling-Array? (241 Tumor-/Normalgewebepaare von 13 Gewebetypen) bestätigt. Damit konnte gezeigt werden, dass CYP4Z1 bei 52 % der getesteten 50 Brustkrebspatientinnen im Tumor versus peritumoralem Normalgewebe überexprimiert war. Mit einem spezifischen Kaninchen-Antiserum konnte die Expression von P450 4Z1 Protein sowohl in CYP4Z1-transduzierten Zelllinien als auch in Mammagewebeproben mittels Western-Blot nachgewiesen werden. Konfokale Laser-Scanning Mikroskopie von MCF-7 Zellen, die das Fusionsprotein CYP4Z1-EGFP exprimierten, und die subzelluläre Fraktionierung der CYP4Z1-Transduktanten zeigten P450 4Z1 als integrales Membranprotein des endoplasmatischen Retikulums (ER). Für die Lokalisation und die Zurückhaltung im ER ohne Recycling aus dem Prä-Golgiapparat sind die ersten 32 As erforderlich, was Studien mit unterschiedlichen Deletionsmutanten aus der N-terminalen Sequenz von 4Z1 zeigten. Die Entdeckung eines neuen Mamma-spezifisch exprimierten P450 Enzyms eröffnet neue Möglichkeiten sowohl in Hinsicht auf eine Immuntherapie von Brustkrebs als auch für die Entwicklung neuer Chemotherapeutika, die spezifisch durch P450 4Z1 am Tumorort umgesetzt werden können.