OPUS 4 | Universitätspublikationen

Conformational dynamics of the tetracycline-binding aptamer (2011)

Ute Förster Julia E. Weigand Peter Trojanowski Beatrix Süß Josef Wachtveitl

The conformational dynamics induced by ligand binding to the tetracycline-binding aptamer is monitored via stopped-flow fluorescence spectroscopy and time-correlated single photon counting experiments. The fluorescence of the ligand is sensitive to changes within the tertiary structure of the aptamer during and after the binding process. In addition to the wild-type aptamer, the mutants A9G, A13U and A50U are examined, where bases important for regulation are changed to inhibit the aptamer’s function. Our results suggest a very fast two-step-mechanism for the binding of the ligand to the aptamer that can be interpreted as a binding step followed by a reorganization of the aptamer to accommodate the ligand. Binding to the two direct contact points A13 and A50 was found to occur in the first binding step. The exchange of the structurally important base A9 for guanine induces an enormous deceleration of the overall binding process, which is mainly rooted in an enhancement of the back reaction of the first binding step by several orders of magnitude. This indicates a significant loss of tertiary structure of the aptamer in the absence of the base A9, and underlines the importance of pre-organization on the overall binding process of the tetracycline-binding aptamer. Previous SectionNext Section

Functional characterization of NOSTRIN in signal transduction and vascular development (2011)

Igor Kovačević

NOSTRIN belongs to the recently defined F-BAR protein family. F-BAR proteins are multi-domain proteins, which serve as adaptors between plasma membrane and cytoskeleton components in processes such as membrane protrusion formation, endocytosis and migration. NOSTRIN encompasses a F-BAR domain at the N-terminus, which mediates membrane association, followed by a HR1 motif and an intermediate domain (ID) domain in the middle, and a SH3 domain at the C-terminus. The domain architecture and ability to form oligomers enable NOSTRIN to coordinate several interaction partners namely dynamin, caveolin, N-WASP and endothelial nitric oxide synthase (eNOS) in the process of eNOS trafficking. In this context NOSTRIN was originally identified and hence termed eNOS traffick inducer. NOSTRIN is expressed in vascularized tissues (e.g. liver and lung) and in primary endothelial cells. Aims of the present work were (1) to investigate if NOSTRIN is involved in other processes besides eNOS trafficking, (2) to analyse the function of NOSTRIN in vivo through knockdown of NOSTRIN in developing zebrafish and (3) to study the consequences of the loss of NOSTRIN on signal transduction in a primary cell culture model derived from NOSTRIN knockout mice. To study the possible involvement of NOSTRIN in other processes besides eNOS trafficking a yeast two-hybrid screen was performed in which fibroblast growth factor receptor 1 (FGFR1) was identified as a putative novel interaction partner of NOSTRIN. In a series of yeast two-hybrid, pulldown and co-immunoprecipitation experiments the interaction between NOSTRIN and FGFR1 was confirmed to occur between endogenously expressed proteins and determined to be direct and to depend on the ID domain of NOSTRIN and the 130 C-terminal amino acid residues of FGFR1. FGFR1 is activated by binding of fibroblast growth factors (FGFs) and induces several different signal transduction pathways (e.g. MAPK and Akt pathway). Overexpression of NOSTRIN in HeLa cells specifically enhanced FGF2-dependent MAPK activation. Accordingly, depletion of NOSTRIN attenuated FGF2-dependent MAPK activation and did not affect FGF2-induced Akt activation. In summary, NOSTRIN has been identified as a novel interaction partner of FGFR1 involved in FGF2-dependent signal transduction. The morpholino oligonucleotide-mediated knockdown of NOSTRIN in developing zebrafish caused vascular leakage and irregular vascular patterning e.g. a loss of the proper trajectory of intersegmental vessel and interruptions of the dorsal longitudinal anastomotic vessel. The vascular phenotype was consistent upon use of two different morpholinos and could be rescued in a dose dependent manner by the injection of zebrafish NOSTRIN mRNA. Detailed analysis involving confocal and time lapse microscopy in zebrafish with endothelial specific expression of EGFP revealed that the knockdown of NOSTRIN impacts in vivo on the migration and morphology of endothelial tip cells and leads to a reduction of filopodia number and length. Additionally a NOSTRIN knockout mouse was generated. The analysis of FGFR1 signal transduction in primary mouse lung endothelial cells (MLECs) from NOSTRIN knockout and wild type mice revealed that FGF2-dependent MAPK activation was attenuated in MLECs isolated from NOSTRIN knockout mice when compared to MLECs isolated from wild type mice. The effect of NOSTRIN on FGF2-dependent signal transduction seems to be specific, since VEGF-induced MAPK activation was not affected in NOSTRIN knockout MLECs. The importance of NOSTRIN for FGF2 signal transduction in vivo is demonstrated by the greatly impaired angiogenic response to FGF2 in NOSTRIN knockout mice in matrigel plug assay. In a detailed biochemical analysis it was discovered that NOSTRIN interacts with the activated small GTPase Rac1 and that overexpression of NOSTRIN enhances Rac1 activation. Furthermore, the interactions of NOSTRIN with both Rac1 and its GEF Sos1 are required for NOSTRIN-mediated activation of Rac1. In accordance, activation of Rac1 was not detected upon FGF2 stimulation in NOSTRIN knockout MLECs. In conclusion, the present work describes a novel function of the F-BAR protein NOSTRIN in FGFR1 signal transduction. Data presented in this work demonstrate that NOSTRIN is required for the assembly of a complex consisting of FGFR1, Sos1 and Rac1 and subsequently for the FGF2-dependent activation of Rac1 in endothelial cells.

Die Bedeutung von Zelltod-Prozessen während der Alterung des filamentösen Ascomyzeten Podospora anserina (2011)

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 125 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.

Improving L-arabinose utilization of pentose fermenting Saccharomyces cerevisiae cells by heterologous expression of L-arabinose transporting sugar transporters (2011)

Thorsten Subtil Eckhard Boles

Background: Hydrolysates of plant biomass used for the production of lignocellulosic biofuels typically contain sugar mixtures consisting mainly of D-glucose and D-xylose, and minor amounts of L-arabinose. The yeast Saccharomyces cerevisiae is the preferred microorganism for the fermentative production of ethanol but is not able to ferment pentose sugars. Although D-xylose and L-arabinose fermenting S. cerevisiae strains have been constructed recently, pentose uptake is still a limiting step in mixed sugar fermentations. Results: Here we described the cloning and characterization of two sugar transporters, AraT from the yeast Scheffersomyces stipitis and Stp2 from the plant Arabidopsis thaliana, which mediate the uptake of L-arabinose but not of D-glucose into S. cerevisiae cells. A yeast strain lacking all of its endogenous hexose transporter genes and expressing a bacterial L-arabinose utilization pathway could no longer take up and grow with L-arabinose as the only carbon source. Expression of the heterologous transporters supported uptake and utilization of L-arabinose especially at low L-arabinose concentrations but did not, or only very weakly, support D-glucose uptake and utilization. In contrast, the S. cerevisiae D-galactose transporter, Gal2, mediated uptake of both L-arabinose and D-glucose, especially at high concentrations. Conclusions: Using a newly developed screening system we have identified two heterologous sugar transporters from a yeast and a plant which can support uptake and utilization of L-arabinose in L-arabinose fermenting S. cerevisiae cells, especially at low L-arabinose concentrations.

PaCATB, a secreted catalase protecting Podospora anserina against exogenous oxidative stress (2011)

Sandra Zintel Dominik Bernhardt Adelina Rogowska-Wrzesinska Heinz D. Osiewacz

A differential mass spectrometry analysis of secreted proteins from juvenile and senescentPodospora anserina cultures revealed age-related differences in protein profiles. Among other proteins with decreased abundance in the secretome of senescent cultures a catalase, termed PaCATB, was identified. Genetic modulation of the abundance of PaCATB identified differential effects on the phenotype of the corresponding strains. Deletion of PaCatB resulted in decreased resistance, over-expression in increased resistance against hydrogen peroxide. While the lifespan of the genetically modified strains was found to be unaffected under standard growth conditions, increased exogenous hydrogen peroxide stress in the growth medium markedly reduced the lifespan of the PaCatB deletion strain but extended the lifespan of PaCatB over-expressors. Overall our data identify a component of the secretome of P. anserina as a new effective factor to cope with environmental stress, stress that under natural conditions is constantly applied on organisms and influences aging processes.

Influence of ground-state structure and Mg2+ binding on folding kinetics of the guanine-sensing riboswitch aptamer domain (2011)

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.

Strukturelle Organisation und Mobilisierung des Primaten-spezifischen Non-LTR-Retrotransposons SVA (2011)

Julija Raiz

SVA-Elemente repraesentieren die juengste Familie der Non-LTR-Retrotransposons, welche das humane Genom fortwaehrend modifizieren. SVA-Elemente zeichnen sich durch ihre Organisation aus zusammengesetzten repetitiven Elementen aus. Um Rueckschluesse auf den Assemblierungsprozess, der zur gegenwaertigen Organisation der SVA-Elemente fuehrte, und ueber transkriptionelle Regulation dieser Elemente zu ziehen, wurden Unterschiede in der Struktur der 116 SVA-Elemente, die auf humanem Chromosom 19 lokalisiert sind, detailliert untersucht. SVA-Elemente konnten in sieben unterschiedliche Strukturvarianten eingeteilt werden, einschliesslich neuer Varianten wie SVA2, 3`-verkuerzte Elemente und Elemente mit 5`- flankierenden Transduktionen. Ich habe auch eine extrem erfolgreiche human-spezifische 5`-Transduktionsgruppe identifiziert, SVA_F1, die trotz ihres jungen evolutionaeren Alters ca. 32% aller Mitglieder der SVA-Subfamilie SVA_F umfasst. Die transkriptionelle Kontrolle einer retrotransponierten und 5`-verkuerzten SVA_F-Kopie durch den Promotor des MAST2-Gens diente als urspruengliches Source-Element dieser umfangreichen 5`- Transduktionsgruppe, die mindestens 84 Elemente einschliesst. Die zusaetzlichen 5`- sowie 3`-Transduktionsereignisse der vollstaendigen Alu-Sequenzen bei Mitgliedern der SVA_F1-Transduktionsgruppe 4 weisen auf ihre wichtige Rolle in der erfolgreichen Expansion im humanen Genom hin. Diese nachtraeglich erworbenen Alu-Sequenzen machen SVA_F1-Familienmitglieder offensichtlich zum besseren Substrat fuer die Trans- Mobilisierung durch die L1-Proteinmaschinerie. Die unterschiedlichen konsekutiven 5`- Tansduktionsereignisse der SVA_F1-Familienmitglieder deuten auf transkriptionelle Kontrolle ihrer Source-Elemente durch eine Vielzahl externer zellulaerer Promotoren hin, die im Laufe der Evolution in Keimzellen aktiv waren. Ausserdem zeigt die Existenz von 5`-Transduktionen, dass SVA-Elemente sich die 5`-flankierenden Sequenzen aneignen koennen. Die Daten zeigen auch, dass SVA-vermittelte 5-Tansduktionsereignisse alternatives RNA-Spleissen an putativen Spleissstellen involvieren. Aus der EST- Datenbankanalyse ist ersichtlich, dass Mitglieder der SVA_F1-Subfamilie auch gegenwaertig transkribiert werden. SVA-Elemente sind hoch aktiv im humanen Genom, aber der Mechanismus ihrer Retrotransposition wurde bislang nicht aufgeklaert. Vorangehende Analysen genomischer SVA-Kopien liessen auf eine L1-vermittelte Mobilisierung schliessen; allerdings wurde der experimentelle Beweis dieser Hypothese bislang nicht geliefert. Mit Hilfe der Zellkultur-basierten Trans-Mobilisierungsassays wurde in dieser Arbeit zum ersten Mal experimentell bewiesen, dass SVA-Elemente tatsaechlich durch die L1-kodierten Proteine in trans mobilisiert werden. Zu diesem Zweck wurden HeLa-Zellen mit einem vollstaendigen oder mit einem 5`-verkuerzten SVA-Retrotranspositionsreporterkonstrukt sowie mit einem L1-Expressionsplasmid bzw. Leervektor kotransfiziert und dann die jeweiligen Raten der SVA-Retrotransposition anhand Neo-resistenter Kolonien, die mindestens ein de novo-Retrotranspositionsereignis widerspiegeln, bestimmt. Die Experimente zeigen, dass die Entstehung der Neo-resistenten Kolonien von der Koexpression L1-kodierter Proteine abhaengig ist. Ich konnte auch zeigen, dass das vollstaendige SVA-Testkonstrukt - im Gegensatz zum 5`-verkuerzten SVA-Konstrukt - mit einer signifikant hoeheren Retrotranspositionsrate als die Kontrollkonstrukte, die zur Generierung der prozessierten Pseudogenformation eingesetzt wurden, trans-mobilisiert wird. Die Ergebnisse der Trans-Mobilisierungsassays belegen, dass SVA-Elemente ein bevorzugtes Substrat fuer die L1-Proteinmaschinerie darstellen, und ihre 5`-Region einschliesslich der Alu-homologen Sequenz fuer die hohe Retrotranspositionsrate essentiell ist. Die elf analysierten SVA de novo-Integrationsereignisse weisen Merkmale der L1- vermittelten Retrotransposition auf, wie Poly(A)-Enden, L1-EN-spezifische Konsensus- Zielsequenz (NNAUNA), Zielsequenz-Verdoppelungen (TSDs), Mikrohomologien und zusaetzliche Guanosin-Nukleotide am 5`-UEbergang. Zusammenfassend demonstrieren die Ergebnisse dieser Studien, dass ein signifikanter Teil der Mitglieder der human-spezifischen SVA-Subfamilie aus transkriptioneller Kontrolle ihrer Source-Elemente durch externe Promotoren hervorgeht. Durch die in dieser Arbeit durchgefuehrten in silico-Analysen wurde auch gezeigt, dass SVA-vermittelte 5`- Transduktionsereignisse zur strukturellen Vielfalt der SVA-Elemente fuehren, und eine neue Art von genomischen Umstrukturierungen darstellen, die zur Plastizitaet des humanen Genoms beitragen. Ausserdem bestaetigen die Ergebnisse der Trans- Mobilisierungsassays die Hypothese, dass SVA-Elemente tatsaechlich durch die L1- kodierte Proteinmaschinerie trans-mobilisiert werden. Dabei sind Module am 5`-Ende der SVA-Elemente fuer diesen Prozess hoechst relevant. Die Ergebnisse der Dualen-Luciferase-Reportergen-Assays unterstuetzen die Hypothese, dass innerhalb der SINE-R-Sequenz von SVA H19_27 cis-aktive Elemente vorhanden sind, die auf aehnliche Weise wie die cis-aktiven Elemente innerhalb der 5`LTR von HERV-K reguliert werden. Ausserdem wurde in dieser Arbeit die Existenz interner reguatorischer Sequenzen innerhalb der SVA-Sequenz bestaetigt. Mit Hilfe der Dualen-Luciferase-Reportergen- Assays konnte zum ersten Mal gezeigt werden, dass SVA-Elemente cis-aktive Elemente enthalten, die hauptsaechlich in der SINE-R-Region lokalisiert sind. Diese cis-aktiven Elemente werden auf aehnliche Weise wie die cis-aktiven Elemente innerhalb der 5`LTR von HERV-K reguliert. Die starke transkriptionelle Aktivitaet des vollstaendigen SVA- Testelements und des L1RP-Promotors in den Teratokarzinom-Zelllinien bekraeftigen die Annahme, dass haeufige SVA-Mobilisierung in Keimzellen durch die gleichzeitig hochregulierte SVA- und L1-Transkription bedingt sein koennte. Es konnte gezeigt werden, dass SVA-Elemente cis-aktive Elemente enthalten, die hauptsaechlich in der SINE-R-Region lokalisiert sind, und auf aehnliche Weise wie die cis- aktiven Elemente innerhalb der 5`LTR von HERV-K reguliert werden. Die starke transkriptionelle Aktivitaet des vollstaendigen SVA-Testelements und des L1RP-Promotors in Teratokarzinom-Zelllinien bestaetigen die Annahme, dass haeufige SVA- Retrotransposition in Keimzellen durch die gleichzeitig hochregulierte SVA- und L1- Transkription bedingt sein koennte.

The sponges of the Chinese Yellow Sea (2011)

Daniela Henkel

Sponges are one of the major components of benthic communities and are considered to be a key role organism in marine ecosystems. In addition to their importance in terms of biodiversity, sponges are becoming increasingly attractive to the industry, as they themselves or associated symbionts, produce various kinds of secondary metabolites of pharmaceutical properties. Some of them have already been clinically applied. The taxonomic characters of Porifera are limited to only a few morphological and histological characters. In addition, sponges of the same species often show a wide morphological variability, whereas the latter depends on different ecological parameters such as water depth and current conditions. Thus, the taxonomic classification of sponges often becomes a scientific challenge. The fauna of the Yellow Sea rates among the least studied worldwide. At the same time, according to the UN Atlas of the Ocean, the Yellow Sea is one of the most intensively exploited marine areas in the world. This is not least due to the dense human population living in the entire catchment area of the Yellow Sea region. In order to compile medium- and longterm conclusions about the anthropogenic impact on biota of the Yellow Sea, the knowledge of species and their distribution is of crucial importance, as these data form the baseline for all future conservation efforts. Until now the sponge fauna of the Chinese Yellow Sea is insufficiently investigated. Thus, there is only one publication on sponges from this region that has been released hitherto. This paper is dealing with only a view species. However, there is no reference concerning the present location of the voucher material, on which this publication is based on. Consequently, no scientific collection on Porifera from the Chinese part of the Yellow Sea exists to date. In order to compile a documentation of the recent sponge community of the Chinese Yellow Sea, 12 study sites along the coast of the Liaoning Peninsula, China, Northeast Yellow Sea, were investigated with focus on sponge distribution. The corresponding habitats were characterized in regard to their topographical features, abiotic parameters, and common composition of benthic megafaunal and macroalgal assemblages. Due to the lack of comparable studies, a comprehensive literature research on sponges of the shallow Northwest Pacific Ocean was required. As a result the first compilation of publications is presented, dealing with sponges from shallow depths of the northwestern Pacific Ocean. Abstract 2 In the course of this study, 31 sponge species in total were recorded, which are scientifically processed. With the exception of four all specimens were determined to species- level. Twelve out of the total number of species are new to science and are described and classified according to the recent taxonomic system of the phylum Porifera. The results of this study indicate considerable differences in species composition between investigated sites. It is shown that physical factors (particularly current regime, sedimentation, seasonally related variations in temperatures), as well the availability of suitable substrates are directly related to the diversity and abundance of investigated sponge communities. In this context possible adaptation strategies of the corresponding sponges were discussed in detail. Two sponge species, Clathria (Clathria) asodes and Antho (Acarnia) lithophoenix, formerly known exclusively from the northeastern Pacific Ocean, are now recorded from the Northwest Pacific Ocean for the first time. Furthermore, Penares hongdoensis, Clathria (Clathria) hongdoensis and Celtodoryx girardae were synonymized with Penares cortius, Clathria (Clathria) acanthostyli, and Celtodoryx ciocalyptoides respectively. Moreover, the occurrence of eight sponge species, which were known from previous records from the Yellow Sea, could be confirmed. As a result of this study the Asian origin of a sponge species that is invasive to the French and Dutch coasts of the Northeast Atlantic Ocean since the 1990s could be established. Moreover, it is demonstrated that Celtodoryx girardae from the northeastern Atlantic is in fact conspecific with Cornulum ciocalyptoides described by Burton (1935) from the Posiet Bay, Sea of Japan. Apart from taxonomic remarks, variations between populations from both oceans are examined and discussed thoroughly in regard to possible ecological implications. The community of documented sponges shows overlapping with the one from the Sea of Japan. According to the results it is assumed that the endemic degree of the sponges from the Chinese Yellow Sea is rather low to moderate. The material obtained in the course of this study was integrated in the collection of the Senckenbergischen Naturforschenden Sammlungen. Therefore, it is the first scientific collection of sponges from the Chinese Yellow Sea that can be consulted as a basis for all further studies on sponges of this region. The present study is the only investigation of sponges from Dalian and adjacent waters before the spill occurred in the Dalian harbour in July 2010. Therefore, it provides an essential baseline needed to assess the impact of the oil spill on benthic communities.

Epigenetic regulation of innate immune responses (2011)

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.

Juvenile Neuronal Ceroid Lipofuscinosis: toponomics approach to identifying new drug targets / von Anna Pupu Ingeborg Krokfors (2011)

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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