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The complex architecture of their structural elements and compartments is a hallmark of eukaryotic cells. The creation of high resolution models of whole cells has been limited by the relatively low resolution of conventional light microscopes and the requirement for ultrathin sections in transmission electron microscopy. We used soft x-ray tomography to study the 3D ultrastructural organization of whole cells of the unicellular green alga Chlamydomonas reinhardtii at unprecedented spatial resolution. Intact frozen hydrated cells were imaged using the natural x-ray absorption contrast of the sample without any staining. We applied different fiducial-based and fiducial-less alignment procedures for the 3D reconstructions. The reconstructed 3D volumes of the cells show features down to 30 nm in size. The whole cell tomograms reveal ultrastructural details such as nuclear envelope membranes, thylakoids, basal apparatus, and flagellar microtubule doublets. In addition, the x-ray tomograms provide quantitative data from the cell architecture. Therefore, nanoscale soft x-ray tomography is a new valuable tool for numerous qualitative and quantitative applications in plant cell biology.
Background: Purine nucleotides exhibit various functions in cellular metabolism. Besides serving as building blocks for nucleic acid synthesis, they participate in signaling pathways and energy metabolism. Further, IMP and GMP represent industrially relevant biotechnological products used as flavor enhancing additives in food industry. Therefore, this work aimed towards the accumulation of IMP applying targeted genetic engineering of Corynebacterium glutamicum.
Results: Blocking of the degrading reactions towards AMP and GMP lead to a 45-fold increased intracellular IMP pool of 22 mumol gCDW-1. Deletion of the pgi gene encoding glucose 6-phosphate isomerase in combination with the deactivated AMP and GMP generating reactions, however, resulted in significantly decreased IMP pools (13 mumol gCDW-1). Targeted metabolite profiling of the purine biosynthetic pathway further revealed a metabolite shift towards the formation of the corresponding nucleobase hypoxanthine (102 mumol gCDW-1) derived from IMP degradation.
Conclusions: The purine biosynthetic pathway is strongly interconnected with various parts of the central metabolism and therefore tightly controlled. However, deleting degrading reactions from IMP to AMP and GMP significantly increased intracellular IMP levels. Due to the complexity of this pathway further degradation from IMP to the corresponding nucleobase drastically increased suggesting additional targets for future strain optimization.
The ongoing debate on deforestation in the tropics usually points out agriculture and logging as the main causes. The two activities are often linked and the trails created by logging com-panies with their heavy machines are afterwards used by farmers to penetrate deep into the forest and cultivate. Shifting cultivation is a widespread agricultural practice in the tropics and its sustainability is often a matter of controversy. It is necessary to investigate forest recovery after shifting cultivation, analyze its succession stages for comparison with regeneration after natural disturbance, and evaluate its role for discussing the hazards of deforestation.
Background: In sequencing the genomes of two Xenorhabdus species, we encountered a large number of sequence repeats and assembly anomalies that stalled finishing efforts. This included a stretch of about 12 Kb that is over 99.9% identical between the plasmid and chromosome of X. nematophila.
Results: Whole genome restriction maps of the sequenced strains were produced through optical mapping technology. These maps allowed rapid resolution of sequence assembly problems, permitted closing of the genome, and allowed correction of a large inversion in a genome assembly that we had considered finished.
Conclusion: Our experience suggests that routine use of optical mapping in bacterial genome sequence finishing is warranted. When combined with data produced through 454 sequencing, an optical map can rapidly and inexpensively generate an ordered and oriented set of contigs to produce a nearly complete genome sequence assembly.
There is increasing evidence that climate change will have a severe impact on species’ distributions by altering the climatic conditions within their present ranges. Especially species inhabiting stream ecosystems are expected to be strongly affected due to warming temperatures and changes in precipitation patterns. The aim of this thesis was to
investigate how distributions of aquatic insects, i.e., benthic stream macroinvertebrates would be impacted by warming climates. The methods comprised of an ensemble forecasting technique based on species distribution models (SDMs) and climate change scenarios of the Intergovernmental Panel on Climate Change of the year 2080. Future model projections were generated for a wide variety of species from a number of taxonomic orders for two spatial scales: a stream network within the lower mountain ranges of Germany, and the entire territory across Europe. In addition, the effect of the modelling technique on habitat suitability projections was investigated by modifying the choice of study area (continuous area vs. stream network) and the choice of predictors (standard vs. corrected set).
Projections of future habitat suitability showed that potential climate-change impacts would be dependent on species’ thermal preferences, and with a similar pattern for both spatial scales. Future habitat suitability was projected to remain for most or all of the modelled species, and species were projected to track their climatically suitable conditions by shifting uphill along the river continuum within the lower mountain ranges, and into a north-easterly direction across Europe. Cold-adapted headwater and high-latitude species were projected to lose suitable habitats, whereas gains would be expected for warm-adapted river and low-latitude species along the river continuum and across Europe, respectively. Additionally, habitat specialist species in terms of endemics of the Iberian Peninsula were identified as potential climate-change losers, highlighting their restricted habitat availability and therefore vulnerability to warming climates.
The main findings of this thesis underline the high susceptibility of stream macroinvertebrates to ongoing climate change, and give insights into patterns of possible consequences due to changes in species’ habitat suitability. Concerning the methodology, a clear recommendation can be given for future modelling approaches of stream macroinvertebrates by building models within a stream network and with a careful choice of environmental predictors, to reduce uncertainties and thus to improve model projections.
All positive strand RNA viruses are known to replicate their genomes in close association with intracellular membranes. In case of the hepatitis C virus (HCV), a member of the family Flaviviridae, infected cells contain accumulations of vesicles forming a membranous web (MW) that is thought to be the site of viral RNA replication. However, little is known about the biogenesis and three-dimensional structure of the MW. In this study we used a combination of immunofluorescence- and electron microscopy (EM)-based methods to analyze the membranous structures induced by HCV in infected cells. We found that the MW is derived primarily from the endoplasmic reticulum (ER) and contains markers of rough ER as well as markers of early and late endosomes, COP vesicles, mitochondria and lipid droplets (LDs). The main constituents of the MW are single and double membrane vesicles (DMVs). The latter predominate and the kinetic of their appearance correlates with kinetics of viral RNA replication. DMVs are induced primarily by NS5A whereas NS4B induces single membrane vesicles arguing that MW formation requires the concerted action of several HCV replicase proteins. Three-dimensional reconstructions identify DMVs as protrusions from the ER membrane into the cytosol, frequently connected to the ER membrane via a neck-like structure. In addition, late in infection multi-membrane vesicles become evident, presumably as a result of a stress-induced reaction. Thus, the morphology of the membranous rearrangements induced in HCV-infected cells resemble those of the unrelated picorna-, corona- and arteriviruses, but are clearly distinct from those of the closely related flaviviruses. These results reveal unexpected similarities between HCV and distantly related positive-strand RNA viruses presumably reflecting similarities in cellular pathways exploited by these viruses to establish their membranous replication factories.
Ribosomal RNA undergoes various modifications to optimize ribosomal structure and expand the topological potential of RNA. The most common nucleotide modifications in ribosomal RNA (rRNA) are pseudouridylations and 2'-O methylations (Nm), performed by H/ACA box snoRNAs and C/D box snoRNAs, respectively. Furthermore, rRNAs of both ribosomal subunits also contain various base modifications, which are catalysed by specific enzymes. These modifications cluster in highly conserved areas of the ribosome. Although most enzymes catalysing 18S rRNA base modifications have been identified, little is known about the 25S rRNA base modifications. The m(1)A modification at position 645 in Helix 25.1 is highly conserved in eukaryotes. Helix formation in this region of the 25S rRNA might be a prerequisite for a correct topological framework for 5.8S rRNA to interact with 25S rRNA. Surprisingly, we have identified ribosomal RNA processing protein 8 (Rrp8), a nucleolar Rossman-fold like methyltransferase, to carry out the m(1)A base modification at position 645, although Rrp8 was previously shown to be involved in A2 cleavage and 40S biogenesis. In addition, we were able to identify specific point mutations in Rrp8, which show that a reduced S-adenosyl-methionine binding influences the quality of the 60S subunit. This highlights the dual functionality of Rrp8 in the biogenesis of both subunits.
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.
Zelluläre Immuntherapien mit hochaufgereinigten allogenen NK-Zellen sind eine mögliche Therapieoption um den GvL/T-Effekt nach haploidenter SZT bei pädiatrischen Hochrisikopatienten mit malignen Erkrankungen zu verstärken. Im Rahmen der in Frankfurt a. M. laufenden klinischen Phase I/II NK-Zell-Studie wurden 16 pädiatrische Patienten sowohl mit unstimulierten (NK-DLI(unstim), 9 Patienten) als auch mit zehn Tage ex vivo IL-2 (1000 U/ml) stimulierten Spender-NK-Zellen (NK DLI(IL-2 stim), 9 Patienten) an den Tagen (+3), +40 und +100 nach haploidenter SZT behandelt. Bisher gibt es kaum Daten über den Verbleib der transfundierten Zellen und den Einfluss der NK-DLI Immuntherapie auf sowohl zelluläre als auch humorale Komponenten des Immunsystems der Patienten. Da die Patienten zudem nach haploidenter SZT zur GvHD-Prophylaxe das immunsuppressive Medikament Mycophenolat-Mofetil (MMF) erhalten, sind Untersuchungen zum Einfluss von MMF auf die Funktionalität der Spender-NK-Zellen von großem Interesse. In der vorliegenden Arbeit wurde mit Hilfe eines studienbegleitenden, nichtinvasiven in vivo Immunmonitorings erstmalig ein unterschiedlicher Einfluss von NK-DLI(unstim) im Vergleich zu NK-DLI(IL-2 stim) auf zelluläre Bestandteile und auf die Zytokin/Chemokin-Spiegel des peripheren Blutes der Patienten vor und 10 min, 1 h, 4 h und 24 h nach der Zelltherapie beschrieben. Mittels durchflusszytometrischen single platform Analysen konnten sowohl Spender-NK-Zellen als auch patienteneigene NK-Zellen phänotypisch und funktionell charakterisiert und unterschieden werden. So wurden neben einer gesteigerten zytotoxischen Aktivität IL-2 stimulierter NK-Zellen auch Unterschiede hinsichtlich der Expression des Oberflächenmoleküls CD56, des Aktivierungsmarkers CD69, des Natürlichen Zytotoxizitäts-Rezeptors (NCR) NKp44 und des Lymphknoten Homing Moleküls CD62L beobachtet. Des Weiteren führte die Applikation von NK-DLI(IL-2 stim) zu einer signifikanten Zellmigration in der peripheren Blutzirkulation der Patienten. Während sich die Zahl der neutrophilen Granulozyten innerhalb von 4 h im peripheren Blut vervierfachte wurde unmittelbar 10 min nach NK-DLI(IL-2 stim) ein massiver Zellverlust von eosinophilen Granulozyten, Monozyten, dendritischen Zellen und vor allem der NK-Zellen beobachtet. Eine ausgeprägtere Reduktion der immunregulatorischen CD56(bright)CD16(dim/-) NK-Zellen hatte zudem eine Verschiebung in der prozentualen Verteilung der NK-Zell-Subpopulationen zur Folge. In den folgenden 24 h normalisierten sich alle Zellzahlen wieder zu den Werten vor NK-DLI. Anhand der beschriebenen phänotypischen Unterscheidungsmerkmale konnte gezeigt werden, dass dabei nur patienteneigene NK-Zellen in die periphere Blutbahn zurückkehrten. Die Zellmigration war zudem in vivo von einem signifikanten Anstieg der proinflammatorisch- und chemotaktisch-wirkenden Zytokine/Chemokine IL-2, IL-6, IL-8, IFN-γ, MCP-1 und MIP-1β im peripheren Blut der Patienten 10 min nach NK-DLI(IL-2 stim) Applikation begleitet. Die Applikationen von NK-DLI(unstim) zeigten im Gegensatz dazu keine vergleichbaren Effekte. Ein weiteres Ziel dieser Arbeit war herauszufinden, ob eine Therapie mit dem Immunsuppressivum MMF nach haploidenter SZT die Funktionalität dieser hochaktivierten Spender-NK-Zellen beeinträchtigt und somit die Effektivität der Immuntherapie gefährdet. Es konnten Einschränkungen in der ex vivo Funktionalität der NK-Zellen durch therapeutisch relevante Konzentrationen (1 bis 10 µM) des aktiven Metaboliten Mycophenolsäure (MPA) gezeigt werden. Die MPA-Inkubation führte zu einer dosisabhängigen aber reversiblen Inhibition der IL-2 bedingten ex vivo NK-Zell-Proliferation. Auch die während des ex vivo Expansionsprozesses induzierte Zytokin/Chemokin-Sekretion wurde signifikant gehemmt. Eine 24-stündige MPA-Inkubation der IL-2 stimulierten NK-Zellen führte zudem zu einer eingeschränkten Mobilität der NK-Zellen. Dies korrelierte mit einer signifikant reduzierten zytotoxischen Aktivität gegen K-562 Tumorzellen, was jedoch nicht mit einer Oberflächenreduktion der NCRs und des NKG2D Rezeptors assoziiert war. Auch die durch die IL-2 Stimulation verursachte Hochregulierung der in Aktivierung und Migration involvierten Oberflächenmoleküle CD25, LFA-1, ICAM-1, CCR5, CXCR7, DNAM-1 und CD62L wurde durch MPA inhibiert. Im Gegensatz dazu hatte eine 24-stündige oder 4-tägige MPA-Behandlung bereits vorstimulierter NK-Zellen keinen Einfluss. Zudem konnte im Rahmen dieser Arbeit erstmalig gezeigt werden, dass die IL-2 induzierte intrazelluläre Signaltransduktion durch MPA beeinflusst wird. Dies äußerte sich in einer partiell bis vollständig inhibierten Phosphorylierung zentraler Signalmoleküle wie STAT-3, -4 und -5, der MAP-Kinase ERK1/2 und der Proteinkinase AKT. Dadurch wurden die durch IL-2 geförderten Zellprozesse wie das Überleben, die Proliferation und die zytotoxische Aktivität der NK-Zellen drastisch gehemmt. Dies steht vermutlich im Zusammenhang mit einer reduzierten Expression der IL-2R Untereinheit (CD25), wodurch die Ausbildung des hochaffinen IL-2-Rezeptors auf der Zelloberfläche verhindert wurde. Demzufolge scheint die eingeschränkte NK-Zell-Effektorfunktion Ursache einer durch MPA gestörten IL-2 Signaltransduktion zu sein. Zusammenfassend scheinen NK-DLI(IL-2 stim) durch die gesteigerte Zytotoxizität, die geringere Sensitivität gegenüber der MPA-Exposition sowie durch die mutmaßliche Extravasation der stimulierten NK-Zellen aus der peripheren Blutbahn einen Vorteil gegenüber NK-DLI(unstim) zu haben. Ob dies auch in einer Steigerung der Effektivität der Immuntherapie resultiert und damit die Prognose der Patienten verbessert werden kann, werden jedoch erst zukünftige Studien mit größeren Patientenkohorten abschließend zeigen können.
Chemical contamination of the environment and thus of aquatic ecosystems is steadily increasing. Whenever environmental pollutants enter a water body, they affect not only the water, but also the sediment. Substances that bind to sediment particles can be stored for a long time, whereby sediments act as sinks for some contaminants. Therefore, sediment
assessments often more accurately describe the contamination of a water body than investigations of the water itself. Among environmental chemicals, endocrine disrupting compounds (EDCs) have gained more and more attention in recent years. Since they interfere with endocrine systems and may disturb reproduction, they endanger the survival of populations or even species. Hazardous substances enter the aquatic environment by different pathways, with sewage treatment plants (STPs) belonging to the most important contamination sources.The main objective of this work is a comprehensive sediment assessment of predominantly small surface waters in the German federal state of Hesse. The 50 study sites, located in 44 different creeks and small rivers, are situated in the densely populated and economically important Frankfurt/Rhine-Main area, as well as in rural and less urbanized regions.
Chemical analytical data, provided by the Hessian Agency for the Environment and Geology (HLUG), indicated different contamination levels of the study sites. In order to investigate the general toxicity of the sediment samples, the oligochaete Lumbriculus variegatus and the midge Chironomus riparius were exposed to whole sediments and apical endpoints regarding biomass, survival, and reproduction were determined. In further experiments, special attention was paid to the contamination with endocrine active compounds. For this purpose, the reproductive success of the New Zealand mudsnail Potamopyrgus antipodarum was analyzed after exposure to whole sediments. Additionally, a yeast-based reporter gene assay was applied with sediment eluates to assess the estrogenic and androgenic activity of the samples. Biotest results were compared with chemical analysis data to investigate whether the test organisms reflect the measured pollution of the study sites and if the observed effects can be explained by chemical contamination.
Five study sites, all located less than 1 km downstream of a STP discharger, were selected for further investigations based on the results of the sediment monitoring. The sediments from these sites were conspicuous due to their general toxic and/or estrogenic activity. In order to investigate whether the observed effects can be ascribed to the effluents, an active biomonitoring study was conducted with the mudsnail P. antipodarum and the zebra mussel Dreissena polymorpha, exposed at study sites located up- and downstream of the discharger.
In addition to endocrine activity, genotoxic effects were investigated using the comet assay and the micronucleus assay. Endocrine activity was examined based on the reproductive output of P. antipodarum and the content of vitellogenin-like proteins in D. polymorpha. Yeast-based reporter gene assays were used to estimate the endocrine potential (estrogen, anti-estrogen, anti-androgen, dioxin-like) of sediment and water samples.
22% of the 50 sediments showed ecologically relevant effects in the biotests with L. variegatus and C. riparius. Only one sediment caused a relevant effect on both test organisms, while the other ten positively tested sediments affected either L. variegatus or C. riparius, probably due to differences in inter-species sensitivities. This suggests that a combination of different biotests is necessary for a comprehensive evaluation of sediment toxicity. 78% of the sediments caused a significantly increased number of embryos in P. antipodarum, which could be ascribed to estrogenic contamination of the sediment samples. An increase in the number of embryos by 60%, as observed in this study, and an associated increase in population size may result in the displacement of other, less competitive species.
In the in vitro tests, 66% of the sediments showed estrogenic activity and 68% showed androgenic activity. Maximum observed values were 40.9 ng EEQ/kg sediment (EEQ = estradiol equivalent) for estrogenic and 93.4 ng TEQ/kg sediment (TEQ = testosterone equivalent) for androgenic activity. Natural and synthetic hormones as well as alkylphenols were the major contributors to the total estrogenicity of environmental samples in several other studies, and are likely responsible for a large part of the estrogenic activity in this case as well. Similarly, androgenic activity is mainly due to natural steroids and their metabolites.
Bioassay results reflect the analytically measured contamination levels at the study sites only very infrequently. This can be ascribed to the occurrence of integrated effects of chemical mixtures present in the sediments. Additionally, effects of substances not included in the analytical program or of substances present in concentrations below the detection limit of the chemical analytical investigations as well as varying bioavailabilities might be relevant. The fact that a large part of the observed effects cannot be explained by the chemical contamination demonstrates the need for effect studies in ecotoxicological sediment assessments.
In order to identify possible causes for the effects observed in the sediment monitoring, e.g. contamination sources, the area types (urban fabrics, arable lands, pasturages, etc.) of the catchment areas belonging to the study sites were analyzed. No significant differences were found between the area profiles of the sampling sites with and without effects in the biotests.
The results indicate that the contamination responsible for the observed effects can be ascribed to different sources. Furthermore, study sites whose sediments exerted significant effects in biotests were located in anthropogenic as well as in predominantly natural areas. The active biomonitoring study at STPs revealed genotoxic and endocrine effects only sporadically.
However, in the in vitro tests considerable endocrine activities of sediment and water samples were determined. No conclusive picture emerges as to whether the observed effects occur more frequently downstream of the dischargers, and thus could be attributed to a contamination by sewage. This indicates that contamination sources other than STP dischargers, for example agricultural runoff, may contribute to the observed effects. Weaker effects and biological activities downstream of a discharger compared to an upstream site might be ascribed to a dilution effect by the effluents. A comparison of the measured in vitro estrogenicity with exposure studies described in the literature shows that adverse effects in aquatic organisms can be expected at the EEQ concentrations determined in the present study.
The results of the sediment monitoring and the STP study revealed a widespread endocrine pollution of small surface waters in Hesse. The fact that the bioassay results only rarely reflect study site contamination as determined by chemical analysis demonstrates the need for effect studies in comprehensive sediment assessments. In some cases STP dischargers increased, in other cases they decreased the observed in vivo effects and in vitro activity of environmental samples. Transferring the results obtained in laboratory studies to the field, adverse effects on aquatic ecosystems can be expected. The study illustrates the need for restrictive measures that contribute to the removal or reduction of environmental pollutants.
For the identification of substances that have so far not been linked to adverse effects on the environment, methods such as effect-directed analyses (EDA) or toxicity identification evaluation (TIE) should be increasingly applied in future studies. Furthermore, bioassays for the assessment of endocrine activity should be implemented in standardized monitoring programs.
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.
The brain is characterized by its immune privileged state. However, recent studies suggest an extended contribution of hematopoietic cells to the brain. After transplantation of genetically labeled bone marrow into bone marrow depleted mice, not only labeled blood cells but also labeled neurons and other non-hematopoietic cells can be observed. Initially interpreted as transdifferentiated hematopoietic stem cells, this contribution later was identified as cell fusion of hematopoietic cells and neurons. Our lab previously addressed the question whether these fusion events also occur under non-invasive conditions. A Cre-LoxP based transgenic mouse line was used to irreversibly label all hematopoietic cells. In these mice, Cre expression is controlled by a hematopoietic promoter, thus causing recombination and subsequent marker gene expression restricted to blood cells. Interestingly, contribution of these hematopoietic cells to non-hematopoietic tissues was observed, but fusion could be excluded as the underlying mechanism. The Cre mRNA or protein seems to reach the non-hematopoietic cells from an external source. Extracellular vesicles, specifically exosomes, are increasingly recognized as a vehicle for the intercellular transfer of cellular components such as proteins or mRNAs. However, if they contribute to signaling between tissues in vivo is completely unknown and would represent a major paradigm shift for intercellular communication. Therefore, the aim of this PhD study is to investigate whether an exosomal transfer between the hematopoietic system and the brain exists. To confirm the previous results, a second Cre-LoxP mouse line that expresses the Cre recombinase under a different hematopoietic promoter is used additionally. Both mouse lines are screened for recombination and show comparable numbers and types of different non-hematopoietic cells. Besides hepatocytes and cells in lung and intestine, recombined Purkinje neurons in the cerebellum are detectable. To assess the influence of inflammation on these recombination events, different lesions such as peripheral tumors or peritonitis are applied to the mice. Inflammatory stimuli strongly increase the numbers of recombined Purkinje neurons. These neurons remain mononuclear, indicating that fusion does not occur. Also in human cerebellar material, no evidence for inflammation induced cell fusion is detectable. To screen for Cre recombinase containing exosomes, exosome purification protocols such as differential ultracentrifugation and sucrose gradient fractioning, are applied. The exosomal content is analyzed with nested PCR and western blot. Hematopoietically expressed Cre mRNA is detectable in blood plasma and hematopoietic cell culture conditioned medium. Further analysis reveals that this Cre mRNA but no Cre protein is contained in exosomes. The exosomal ability to induce recombination is investigated by injections into Cre reporter mice. After direct cerebellar injection, exosomes are sufficient to induce recombination of Purkinje neurons. Brain tissue of mice that received an inflammation is analyzed further to reveal other recombined cell types. The main immune cells of the brain, microglia, are not recombined. Mainly neuronal cell types are recombined in different areas of the brain. The observations made in this study are consistent with the hypothesis that a previously unrecognized way to communicate RNA based signals between the immune system and the brain exists. Specifically neurons are target cells for the uptake of hematopoietic exosomes and seem able to translate exosomal mRNA into functional protein. Microglial cells are neither involved as target cells, nor do they release Cre containing exosomes. By using the Cre-LoxP system, in vivo tracing of exosomes could be achieved for the first time. With this knowledge, other exosomal routes can be uncovered in future. The discovery of the exosomal transfer between the blood and the brain enables further research about the relevance of this signaling pathway. It will be important to investigate its role especially in the context of neural malfunctions and further studies might help to find new therapeutical approaches.
The regulation of cellular copper homeostasis is crucial in biology. Impairments lead to severe dysfunctions and are known to affect aging and development. Previously, a loss-of-function mutation in the gene encoding the copper-sensing and copper-regulated transcription factor GRISEA of the filamentous fungus Podospora anserina was reported to lead to cellular copper depletion and a pleiotropic phenotype with hypopigmentation of the mycelium and the ascospores, affected fertility and increased lifespan by approximately 60% when compared to the wild type. This phenotype is linked to a switch from a copper-dependent standard to an alternative respiration leading to both a reduced generation of reactive oxygen species (ROS) and of adenosine triphosphate (ATP). We performed a genome-wide comparative transcriptome analysis of a wild-type strain and the copper-depleted grisea mutant. We unambiguously assigned 9,700 sequences of the transcriptome in both strains to the more than 10,600 predicted and annotated open reading frames of the P. anserina genome indicating 90% coverage of the transcriptome. 4,752 of the transcripts differed significantly in abundance with 1,156 transcripts differing at least 3-fold. Selected genes were investigated by qRT-PCR analyses. Apart from this general characterization we analyzed the data with special emphasis on molecular pathways related to the grisea mutation taking advantage of the available complete genomic sequence of P. anserina. This analysis verified but also corrected conclusions from earlier data obtained by single gene analysis, identified new candidates of factors as part of the cellular copper homeostasis system including target genes of transcription factor GRISEA, and provides a rich reference source of quantitative data for further in detail investigations. Overall, the present study demonstrates the importance of systems biology approaches also in cases were mutations in single genes are analyzed to explain the underlying mechanisms controlling complex biological processes like aging and development.
Secretion in blowfly (Calliphora vicina) salivary glands is stimulated by the biogenic amine serotonin (5-hydroxytryptamine, 5-HT), which activates both inositol 1,4,5-trisphosphate (InsP3)/Ca2+ and cyclic adenosine 3′,5′-monophosphate (cAMP) signalling pathways in the secretory cells. In order to characterize the signal-inducing 5-HT receptors, we cloned two cDNAs (Cv5-ht2α, Cv5-ht7) that share high similarity with mammalian 5-HT2 and 5-HT7 receptor genes, respectively. RT-PCR demonstrated that both receptors are expressed in the salivary glands and brain. Stimulation of Cv5-ht2α-transfected mammalian cells with 5-HT elevates cytosolic [Ca2+] in a dose-dependent manner (EC50 = 24 nM). In Cv5-ht7-transfected cells, 5-HT produces a dose-dependent increase in [cAMP]i (EC50 = 4 nM). We studied the pharmacological profile for both receptors. Substances that appear to act as specific ligands of either Cv5-HT2α or Cv5-HT7 in the heterologous expression system were also tested in intact blowfly salivary gland preparations. We observed that 5-methoxytryptamine (100 nM) activates only the Cv5-HT2α receptor, 5-carboxamidotryptamine (300 nM) activates only the Cv5-HT7 receptor, and clozapine (1 µM) antagonizes the effects of 5-HT via Cv5-HT7 in blowfly salivary glands, providing means for the selective activation of each of the two 5-HT receptor subtypes. This study represents the first comprehensive molecular and pharmacological characterization of two 5-HT receptors in the blowfly and permits the analysis of the physiological role of these receptors, even when co-expressed in cells, and of the modes of interaction between the Ca2+- and cAMP-signalling cascades.
The tumour suppressor p53 controls transcription of various genes involved in apoptosis, cell-cycle arrest, DNA repair and metabolism. However, its DNA-recognition specificity is not nearly sufficient to explain binding to specific locations in vivo. Here, we present evidence that KLF4 increases the DNA-binding affinity of p53 through the formation of a loosely arranged ternary complex on DNA. This effect depends on the distance between the response elements of KLF4 and p53. Using nuclear magnetic resonance and fluorescence techniques, we found that the amino-terminal domain of p53 interacts with the KLF4 zinc fingers and mapped the interaction site. The strength of this interaction was increased by phosphorylation of the p53 N-terminus, particularly on residues associated with regulation of cell-cycle arrest genes. Taken together, the cooperative binding of KLF4 and p53 to DNA exemplifies a regulatory mechanism that contributes to p53 target selectivity.
Global climate change and land use change will not only alter entire ecosystems and biodiversity patterns, but also the supply of ecosystem services. A better understanding of the consequences is particularly needed in under-investigated regions, such as West Africa. The projected environmental changes suggest negative impacts on nature, thus representing a threat to the human well-being. However, many effects caused by climate and land use change are poorly understood so far. Thus, the main objective of this thesis was to investigate the impact of climate and land use change on vegetation patterns, plant diversity and important provisioning ecosystem services in West Africa. The three different aspects are separately explored and build the chapters of this thesis. The findings help to improve our understanding of the effects of environmental change on ecosystems and human well-being. In the first study, the main objectives were to model trends and the extent of future biome shifts in West Africa that may occur by 2050. Also, I modelled a trend in West African tree cover change, while accounting for human impact. Additionally, uncertainty in future climate projections was evaluated to identify regions with reliable trends and regions where the impacts remain uncertain. The potential future spatial distributions of desert, grassland, savanna, deciduous and evergreen forest were modelled in West Africa, using six bioclimatic models. Future tree cover change was analysed with generalized additive models (GAMs). I used climate data from 17 general circulation models (GCMs) and included human population density and fire intensity to model tree cover. Consensus projections were derived via weighted averages to: 1) reduce inter-model variability, and 2) describe trends extracted from different GCM projections. The strongest predicted effect of climate change was on desert and grasslands, where the bioclimatic envelope of grassland is projected to expand into the Sahara desert by an area of 2 million km2. While savannas are predicted to contract in the south (by 54 ± 22 × 104 km2), deciduous and evergreen forest biomes are expected to expand (64 ± 13 × 104 km2 and 77 ± 26 × 104 km2). However, uncertainty due to different GCMs was particularly high for the grassland and the evergreen forest biome shift. Increasing tree cover (1–10%) was projected for large parts of Benin, Burkina Faso, Côte d’Ivoire, Ghana and Togo, but a decrease was projected for coastal areas (1–20%). Furthermore, human impact negatively affected tree cover and partly changed the direction of the projected climate-driven tendency from increase to decrease. Considering climate change alone, the model results of potential vegetation (biomes) showed a ‘greening’ trend by 2050. However, the modelled effects of human impact suggest future forest degradation. Thus, it is essential to consider both climate change and human impact in order to generate realistic future projections on woody cover. The second study focused on the impact and the interplay of future (2050) climate and land use change on the plant diversity of the West African country Burkina Faso. Synergistic forecasts for this country are lacking to date. Burkina Faso covers a broad bioclimatic gradient which causes a similar gradient in plant diversity. Thus, the impact of climate and land use change can be investigated in regions with different levels of species richness. The LandSHIFT model from the Centre of Environmental System research CESR (Kassel, Germany) was adapted for this study to derive novel regional, spatially explicit future (2050) land use simulations for Burkina Faso. Additionally, the simulations include different assumptions on the technological developments in the agricultural sector. Oneclass support vector machines (SVMs), a machine learning method, were performed with these land use simulations together with current and future (2050) climate projections at a 0.1° resolution (cell: ~ 10 × 10 km). The modelling results showed that the flora of Burkina Faso will be primarily negatively impacted by future climate and land use changes. The species richness will be significantly reduced by 2050 (P < 0.001, paired Wilcoxon signed-rank test). However, contrasting latitudinal patterns were found. Although climate change is predicted to cause species loss in the more humid regions in Southern Burkina Faso (~ 200 species per cell), the model projects an increase of species richness in the Sahel. However, land use change is expected to suppress this increase to the current species diversity level, depending on the technological developments. Climate change is a more important threat to the plant diversity than land use change under the assumption of technological stagnation in the agricultural sector. Overall, the study highlights the impact and interplay of future climate and land use change on plant diversity along a broad bioclimatic gradient in West Africa.Furthermore, the results suggest that plant diversity in dry and humid regions of the tropics might generally respond differently to climate and land use change. This pattern has not been detected by global studies so far. Several of the plant species in West Africa significantly contribute to the livelihoods of the population. The plants provide so-called non-timber forest products (NTFPs), which are important provisioning ecosystem services. However, these services are also threatened by environmental change. Thus, the third study aimed at developing a novel approach to assess the impacts of climate and land use change on the economic benefits derived from NTFPs. This project was carried out in cooperation with Katja Heubach (BiK-F) who provided data on household economics. These data include 60 interviews that were conducted in Northern Benin on annual quantities and revenues of collected NTFPs from the three most important savanna tree species: Adansonia digitata, Parkia biglobosa and Vitellaria paradoxa. The current market prices of the NTFPs were derived from respective local markets. To assess current and future (2050) occurrence probabilities of the three species, I calibrated niche-based models with climate data (from Miroc3.2medres) and land use data (LandSHIFT) at a 0.1° resolution (cell: ~ 10 × 10 km). Land use simulations were taken from the previous study on plant diversity. Three different niche-based models were used: 1) generalized additive models (regression method), 2) generalized boosting models (machine learning method), and 3) flexible discriminant analysis (classification method). The three model simulations were averaged (ensemble forecasting) to increase the robustness of the predictions. To assess future economic gains and losses, respectively, the modelled species’ occurrence probabilities were linked with the spatially assigned monetary values. Highest current annual benefits are obtained from V. paradoxa (54,111 ± 28,126 US$/cell), followed by P. biglobosa (32,246 ± 16,526 US$/cell) and A. digitata (9,514 ± 6,243 US$/cell). However, in the prediction large areas will lose up to 50% of their current economic value by 2050. Vitellaria paradoxa and Parkia biglobosa, which currently reveal the highest economic benefits, are heavily affected. Adansonia digitata is negatively affected less strongly by environmental change and might regionally even supply increasing economic benefits, in particular in the west and east of the investigation area. We conclude that adaptive strategies are needed to create alternative income opportunities, in particular for women that are responsible for collecting the NTFPs. The findings provide a benchmark for local policy-makers to economically compare different land use options and adjust existing management strategies for the near future. Overall, this thesis improves our understanding of the impacts of climate and land use changes on West African vegetation patterns, plant diversity and provisioning ecosystem services. Climate change had spatially varying impacts (positive and negative effects) on the vegetation cover and plant diversity, while predominantly negative effects resulted from human pressure. Regional contrasting impacts of environmental change were also found considering the provisioning ecosystem services.
The TATA Box Binding Protein (TBP) is a 20 kD protein that is essential and universally conserved in eucarya and archaea. Especially among archaea, organisms can be found that live below 0°C as well as organisms that grow above 100°C. The archaeal TBPs show a high sequence identity and a similar structure consisting of α-helices and β-sheets that are arranged in a saddle-shape 2-symmetric fold. In previous studies, we have characterized the thermal stability of thermophilic and mesophilic archaeal TBPs by infrared spectroscopy and showed the correlation between the transition temperature (Tm) and the optimal growth temperature (OGT) of the respective donor organism. In this study, a “new” mutant TBP has been constructed, produced, purified and analyzed for a deeper understanding of the molecular mechanisms of thermoadaptation. The β-sheet part of the mutant consists of the TBP from Methanothermobacter thermoautotrophicus (OGT 65°C, MtTBP65) whose α-helices have been exchanged by those of Methanosarcina mazei (OGT 37°C, MmTBP37). The Hybrid-TBP irreversibly aggregates after thermal unfolding just like MmTBP37 and MtTBP65, but the Tm lies between that of MmTBP37 and MtTBP65 indicating that the interaction between the α-helical and β-sheet part of the TBP is crucial for the thermal stability. The temperature stability is probably encoded in the variable α-helices that interact with the highly conserved and DNA binding β-sheets.
The estimation model PhytoCalc allows a non-destructive quantification of dry weight and nutrient pools of understorey plants in forests by using the relationship between species biomass, cover and mean shoot length. The model has been validated with independent samples in several German forest types and can be a useful tool in forest monitoring. However, in open areas within forests (e.g. clearcuts), the current model version underestimates biomass and produces unreliable nutrient pool estimations. Thus, tissue density, as approximated by leaf dry matter content (LDMC), is systematically higher under high light compared to low light conditions. We demonstrate that the ratio of LDMC under clearcut conditions to LDMC under forest conditions can be used to adjust the PhytoCalc model to clearcut conditions. We investigated the LDMC ratio of five exemplary species commonly occurring on clearcuts. Integrating the square of the ratio as a correction factor improved estimates of biomass to more than 70% fit between observations and predictions. Results also suggest this ratio can be used to correct nutrient concentrations modelled in PhytoCalc, which tend to be overestimated in clearcuts. As morphological groups of plant species exhibit significantly different ratios, we advise using group-specific correction factors for clearcut adjustments in the future.
The magnetic compass of a migratory bird, the European robin (Erithacus rubecula), was shown to be lateralized in favour of the right eye/left brain hemisphere. However, this seems to be a property of the avian magnetic compass that is not present from the beginning, but develops only as the birds grow older. During first migration in autumn, juvenile robins can orient by their magnetic compass with their right as well as with their left eye. In the following spring, however, the magnetic compass is already lateralized, but this lateralization is still flexible: it could be removed by covering the right eye for 6 h. During the following autumn migration, the lateralization becomes more strongly fixed, with a 6 h occlusion of the right eye no longer having an effect. This change from a bilateral to a lateralized magnetic compass appears to be a maturation process, the first such case known so far in birds. Because both eyes mediate identical information about the geomagnetic field, brain asymmetry for the magnetic compass could increase efficiency by setting the other hemisphere free for other processes.
Background: The genome of the carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii, Order: Dasyuromorphia), was sequenced in the hopes of finding a cure for or gaining a better understanding of the contagious devil facial tumor disease that is threatening the species’ survival. To better understand the Tasmanian devil genome, we screened it for transposable elements and investigated the dynamics of short interspersed element (SINE) retroposons.
Results: The temporal history of Tasmanian devil SINEs, elucidated using a transposition in transposition analysis, indicates that WSINE1, a CORE-SINE present in around 200,000 copies, is the most recently active element. Moreover, we discovered a new subtype of WSINE1 (WSINE1b) that comprises at least 90% of all Tasmanian devil WSINE1s. The frequencies of WSINE1 subtypes differ in the genomes of two of the other Australian marsupial orders. A co-segregation analysis indicated that at least 66 subfamilies of WSINE1 evolved during the evolution of Dasyuromorphia. Using a substitution rate derived from WSINE1 insertions, the ages of the subfamilies were estimated and correlated with a newly established phylogeny of Dasyuromorphia. Phylogenetic analyses and divergence time estimates of mitochondrial genome data indicate a rapid radiation of the Tasmanian devil and the closest relative the quolls (Dasyurus) around 14 million years ago.
Conclusions: The radiation and abundance of CORE-SINEs in marsupial genomes indicates that they may be a major player in the evolution of marsupials. It is evident that the early phases of evolution of the carnivorous marsupial order Dasyuromorphia was characterized by a burst of SINE activity. A correlation between a speciation event and a major burst of retroposon activity is for the first time shown in a marsupial genome.
Mitochondria form a dynamic tubular reticulum within eukaryotic cells. Currently, quantitative understanding of its morphological characteristics is largely absent, despite major progress in deciphering the molecular fission and fusion machineries shaping its structure. Here we address the principles of formation and the large-scale organization of the cell-wide network of mitochondria. On the basis of experimentally determined structural features we establish the tip-to-tip and tip-to-side fission and fusion events as dominant reactions in the motility of this organelle. Subsequently, we introduce a graph-based model of the chondriome able to encompass its inherent variability in a single framework. Using both mean-field deterministic and explicit stochastic mathematical methods we establish a relationship between the chondriome structural network characteristics and underlying kinetic rate parameters. The computational analysis indicates that mitochondrial networks exhibit a percolation threshold. Intrinsic morphological instability of the mitochondrial reticulum resulting from its vicinity to the percolation transition is proposed as a novel mechanism that can be utilized by cells for optimizing their functional competence via dynamic remodeling of the chondriome. The detailed size distribution of the network components predicted by the dynamic graph representation introduces a relationship between chondriome characteristics and cell function. It forms a basis for understanding the architecture of mitochondria as a cell-wide but inhomogeneous organelle. Analysis of the reticulum adaptive configuration offers a direct clarification for its impact on numerous physiological processes strongly dependent on mitochondrial dynamics and organization, such as efficiency of cellular metabolism, tissue differentiation and aging.
The C. elegans nervous system is particularly well suited for optogenetic analyses of circuit function: Essentially all connections have been mapped, and light can be directed at the neuron of interest in the freely moving, transparent animals, while behavior is observed. Thus, different nodes of a neuronal network can be probed for their role in controlling a particular behavior, using different optogenetic tools for photo-activation or –inhibition, which respond to different colors of light. As neurons may act in concert or in opposing ways to affect a behavior, one would further like to excite these neurons concomitantly, yet independent of each other. In addition to the blue-light activated Channelrhodopsin-2 (ChR2), spectrally red-shifted ChR variants have been explored recently. Here, we establish the green-light activated ChR chimera C1V1 (from Chlamydomonas and Volvox ChR1′s) for use in C. elegans. We surveyed a number of red-shifted ChRs, and found that C1V1-ET/ET (E122T; E162T) works most reliable in C. elegans, with 540–580 nm excitation, which leaves ChR2 silent. However, as C1V1-ET/ET is very light sensitive, it still becomes activated when ChR2 is stimulated, even at 400 nm. Thus, we generated a highly efficient blue ChR2, the H134R; T159C double mutant (ChR2-HR/TC). Both proteins can be used in the same animal, in different neurons, to independently control each cell type with light, enabling a further level of complexity in circuit analyses.
Background: The branched chain alcohol isobutanol exhibits superior physicochemical properties as an alternative biofuel. The yeast Saccharomyces cerevisiae naturally produces low amounts of isobutanol as a by-product during fermentations, resulting from the catabolism of valine. As S. cerevisiae is widely used in industrial applications and can easily be modified by genetic engineering, this microorganism is a promising host for the fermentative production of higher amounts of isobutanol.
Results: Isobutanol production could be improved by re-locating the valine biosynthesis enzymes Ilv2, Ilv5 and Ilv3 from the mitochondrial matrix into the cytosol. To prevent the import of the three enzymes into yeast mitochondria, N-terminally shortened Ilv2, Ilv5 and Ilv3 versions were constructed lacking their mitochondrial targeting sequences. SDS-PAGE and immunofluorescence analyses confirmed expression and re-localization of the truncated enzymes. Growth tests or enzyme assays confirmed enzymatic activities. Isobutanol production was only increased in the absence of valine and the simultaneous blockage of the mitochondrial valine synthesis pathway. Isobutanol production could be even more enhanced after adapting the codon usage of the truncated valine biosynthesis genes to the codon usage of highly expressed glycolytic genes. Finally, a suitable ketoisovalerate decarboxylase, Aro10, and alcohol dehydrogenase, Adh2, were selected and overexpressed. The highest isobutanol titer was 0.63 g/L at a yield of nearly 15 mg per g glucose.
Conclusion: A cytosolic isobutanol production pathway was successfully established in yeast by re-localization and optimization of mitochondrial valine synthesis enzymes together with overexpression of Aro10 decarboxylase and Adh2 alcohol dehydrogenase. Driving forces were generated by blocking competition with the mitochondrial valine pathway and by omitting valine from the fermentation medium. Additional deletion of pyruvate decarboxylase genes and engineering of co-factor imbalances should lead to even higher isobutanol production.
Riboswitches reflect a novel concept in gene regulation that is particularly suited for technological adaptation. Therefore, we characterized thermodynamically the ligand binding properties of a synthetic, tetracycline (tc)-binding RNA aptamer, which regulates gene expression in a dose-dependent manner when inserted into the untranslated region of an mRNA. In vitro, one molecule of tc is bound by one molecule of partially pre-structured and conformationally homogeneous apo-RNA. The dissociation constant of 770 pM, as determined by fluorimetry, is the lowest reported so far for a small molecule-binding RNA aptamer. Additional calorimetric analysis of RNA point mutants and tc derivatives identifies functional groups crucial for the interaction and including their respective enthalpic and entropic contributions we can propose detailed structural and functional roles for certain groups. The conclusions are consistent with mutational analyses in vivo and support the hypothesis that tc-binding reinforces the structure of the RNA aptamer, preventing the scanning ribosome from melting it efficiently.
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.
The importance of RNA in molecular and cell biology has long been underestimated. Besides transmitting genetic information, studies of recent years have revealed crucial tasks of RNA especially in gene regulation. Riboswitches are natural RNA-based genetic switches and known only for ten years. They directly sense small-molecule metabolites and regulate in response the expression of the corresponding metabolic genes. Within recent years, artificial riboswitches have been developed that operate according to user-defined demands. Hence, they represent powerful tools for synthetic biology.
This study focused on the development of engineered catalytic riboswitches for conditional gene expression in eukaryotes. A self-cleaving hammerhead ribozyme was linked to a tetracycline binding aptamer in order to regulate ribozyme cleavage allosterically with tetracycline. By integrating such a hybrid molecule into a gene of interest, mRNA cleavage and thereby gene expression is controllable in a ligand dependent manner. The linking domain between ribozyme and aptamer was randomised. Tetracycline inducible ribozymes were isolated after eleven cycles of in vitro selection (SELEX). 80% of the analysed ribozymes show cleavage that strongly depends on tetracycline. In the presence of 1 μM tetracycline, their cleavage rates are comparable to that of the parental hammerhead ribozyme. In the absence of tetracycline, cleavage rates are inhibited up to 333-fold. The allosteric ribozymes bind tetracycline with similar affinity and specificity as the parental aptamer. Ribozyme cleavage is fully induced within minutes after addition of tetracycline. Interestingly, the isolated linker domains exhibit structural consensus motives rather than consensus sequences.
When transferred to yeast, three switches reduced reporter gene expression by 30 - 60% in the presence of tetracycline; none of them controlled gene expression in mammalian cells. In vitro selected molecules do not necessarily retain their characteristics when applied in a cellular context. Therefore, high throughput screening and selection systems have been developed in mammalian cells. The screening system is based on two fluorescent reporter proteins (GFP and mCherry). 1152 individual constructs of the selected ribozyme pool were tested, but none of them reduced reporter gene expression significantly in the presence of tetracycline. The selection system employs a fusion peptide encoding two selection markers (Hygromycin B phosphotransferase and HSV thymidine kinase) facilitating both negative and positive selection. 6.5 x 104 individual constructs of the selected ribozyme pool are currently under investigation.
This study presents the development and mapping of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in chickpea. The mapping population is based on an inter-specific cross between domesticated and non-domesticated genotypes of chickpea (Cicer arietinum ICC 4958 × C. reticulatum PI 489777). This same population has been the focus of previous studies, permitting integration of new and legacy genetic markers into a single genetic map. We report a set of 311 novel SSR markers (designated ICCM—ICRISAT chickpea microsatellite), obtained from an SSR-enriched genomic library of ICC 4958. Screening of these SSR markers on a diverse panel of 48 chickpea accessions provided 147 polymorphic markers with 2–21 alleles and polymorphic information content value 0.04–0.92. Fifty-two of these markers were polymorphic between parental genotypes of the inter-specific population. We also analyzed 233 previously published (H-series) SSR markers that provided another set of 52 polymorphic markers. An additional 71 gene-based SNP markers were developed from transcript sequences that are highly conserved between chickpea and its near relative Medicago truncatula. By using these three approaches, 175 new marker loci along with 407 previously reported marker loci were integrated to yield an improved genetic map of chickpea. The integrated map contains 521 loci organized into eight linkage groups that span 2,602 cM, with an average inter-marker distance of 4.99 cM. Gene-based markers provide anchor points for comparing the genomes of Medicago and chickpea, and reveal extended synteny between these two species. The combined set of genetic markers and their integration into an improved genetic map should facilitate chickpea genetics and breeding, as well as translational studies between chickpea and Medicago.
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.
Analysis of photosystem I (PSI) complexes from Cyclotella meneghiniana cultured under different growth conditions led to the identification of three groups of antenna proteins, having molecular weights of around 19, 18, and 17 kDa. The 19-kDa proteins have earlier been demonstrated to be more peripherally bound to PSI, and their amount in the PSI complexes was significantly reduced when the iron supply in the growth medium was lowered. This polypeptide was almost missing, and thus the total amount of fucoxanthin-chlorophyll proteins (Fcps) bound to PSI was reduced as well. When treating cells with high light in addition, no further changes in antenna polypeptide composition were detected. Xanthophyll cycle pigments were found to be bound to all Fcps of PSI. However, PSI of high light cultures had a significantly higher diatoxanthin to diadinoxanthin ratio, which is assumed to protect against a surplus of excitation energy. PSI complexes from the double-stressed cultures (high light plus reduced iron supply) were slightly more sensitive against destruction by the detergent treatment. This could be seen as a higher 674-nm emission at 77 K in comparison to the PSI complexes isolated from other growth conditions. Two major emission bands of the Fcps bound to PSI at 77 K could be identified, whereby chlorophyll a fluorescing at 697 nm was more strongly coupled to the PSI core than those fluorescing at 685 nm. Thus, the build up of the PSI antenna of several Fcp components enables variable reactions to several stress factors commonly experienced by the diatoms in vivo, in particular diatoxanthin enrichment under high light and reduction of antenna size under reduced iron conditions.
Xenorhabdus and Photorhabdus spp. are bacterial symbionts of entomopathogenic nematodes (EPNs). In this study, we isolated and characterized Xenorhabdus and Photorhabdus spp. from across Thailand together with their associated nematode symbionts, and characterized their phylogenetic diversity. EPNs were isolated from soil samples using a Galleria-baiting technique. Bacteria from EPNs were cultured and genotyped based on recA sequence. The nematodes were identified based on sequences of 28S rDNA and internal transcribed spacer regions. A total of 795 soil samples were collected from 159 sites in 13 provinces across Thailand. A total of 126 EPNs isolated from samples taken from 10 provinces were positive for Xenorhabdus (n = 69) or Photorhabdus spp. (n = 57). Phylogenetic analysis separated the 69 Xenorhabdus isolates into 4 groups. Groups 1, 2 and 3 consisting of 52, 13 and 1 isolates related to X. stockiae, and group 4 consisting of 3 isolates related to X. miraniensis. The EPN host for isolates related to X. stockiae was S. websteri, and for X. miraniensis was S. khoisanae. The Photorhabdus species were identified as P. luminescens (n = 56) and P. asymbiotica (n = 1). Phylogenenic analysis divided P. luminescens into five groups. Groups 1 and 2 consisted of 45 and 8 isolates defined as subspecies hainanensis and akhurstii, respectively. One isolate was related to hainanensis and akhurstii, two isolates were related to laumondii, and one isolate was the pathogenic species P. asymbiotica subsp. australis. H. indica was the major EPN host for Photorhabdus. This study reveals the genetic diversity of Xenorhabdus and Photorhabdus spp. and describes new associations between EPNs and their bacterial symbionts in Thailand.
EGFL7 regulates adult neural stem cell maintenance and differentiation by inhibition of Notch1
(2010)
In neurobiology the preexisting dogma on the unchangeability of the adult mammalian brain and its inability to give rise to new neurons has been challenged since the early nineties. Generally, it is now accepted that neurogenesis persists in adults. Progress in developmental and stem cell biology in recent years led to an increasing interest in regeneration-based treatment strategies for damaged tissue of the central nervous system. Thus, the enhancement of the endogenous potential of the brain to repair itself is potentially a feasible therapeutic strategy to treat various types of brain damage. Therefore, it is of great interest to understand the molecular mechanism that regulate adult neurogenesis. One of the prominent pathways suggested to be involved here is the Notch signaling cascade. Previously, it has been shown that various components of Notch signaling are expressed in the stem cell niche of the adult subventricular zone (SVZ) in vivo. Interestingly, a recent study demonstrated that the self-renewal potential of adult neural stem cells (NSCs) isolated from the SVZ depend on Notch signaling in vitro.
Recently, we identified a novel non-canonical Notch ligand termed epidermal growth factor-like domain 7 (EGFL7), which was originally described as a protein secreted by endothelial cells and functionally implicated in cellular responses of the vascular system such as cell migration and blood vessel formation. We were able to show that secreted EGFL7 binds to a region in Notch that is involved in ligand-mediated receptor activation, thus acting as an antagonist of Notch signaling.
The present study identifies neurons of the human and murine brain as a novel source of EGFL7, which suggests functions of EGFL7 in the neural system. Expression analyses by quantitative RT-PCR (qRT-PCR) revealed EGFL7 is down regulated in the adult SVZ, which suggests that endogenous EGFL7 may act as a Notch modulator of NSCs. We assessed the expression of Notch pathway components in adult NSCs isolated from the SVZ of adult mice and demonstrated that inhibition of Notch activity by the γ-secretase inhibitor DAPT reduced the self-renewal potential of NSCs. Accordingly, adenoviral-mediated expression of EGFL7 in vitro decreased Notch-specific signaling and reduced proliferation and self-renewal of NSCs. Conversely, activation of Notch by a constitutive active form of Notch (NICD) rescued the EGFL7-mediated reduction of NSC self-renewal verifying that this effect was directly linked to Notch signaling. Congruent to the reduced proliferation rate measured in vitro, induced expression of EGFL7 in vivo significantly reduced the number of Ki-67 positive cells within the SVZ upon cerebroventricular injection of EGFL7 adenovirus.
Expression analyses in the developing brain showed single EGFL7-positive cells within the marginal zone of the neocortex as measured by in situ hybridization. These cells might be Cajal-Retzius cells, specialized neurons, which specifically express Reelin, which is a protein of the extracellular matrix known to control neuronal migration and differentiation. Interstingly, we could show that Reelin and EGFL7 are expressed in a subtype of neurons of the adult mouse cortex. This implied an interaction of both proteins and was verified by co-immunoprecipitation assays, suggesting an additional role for EGFL7 in neuronal maintenance. QRT-PCR based expression analyses in vitro comparing differentiated and non-differentiated NSCs displayed an increase in EGFL7 expression during the differentiation process, which was paralled by reduced Notch signaling. NSCs differentiated on coverslips coated with EGFL7 differentiated into all three cell types - neurons, oligodendrocytes and astrocytes. EGFL7 favored the formation of neurons as compared to control comparable to the effect of the Notch-inhibitor DAPT. Furthermore, additional oligodendrocytes were formed. These cells displayed a mature morphology with distinct sprouts and branches in contrast to the small and round oligodendrocytes that formed on control coverslips, which resembled us of precursor cells. Neurons and oligodendrocytes were formed at the expense of astrocytes. Congruently to the effect observed in vitro, adenoviral-based expression of EGFL7 in the SVZ yielded a slight induction of neuronal differentiation in vivo. Taken together, these results show for the first time a previously unrecognized role for EGFL7 in the brain by modulation of the Notch pathway in adult NSCs, which changes the proliferation and differentiation potential of adult NSCs in vitro and in vivo.
Protein translocation across the chloroplast membrane is mediated by molecular machinery composed of protein complexes termed the TOC/TIC (the outer/inner envelope chloroplasts translocases). This translocation process is regulated by metabolic energy in form of GTP and ATP and is influenced by the lipid composition of the membrane. The ability to study the function of a single complex “TOC” in vitro using purified protein or purified chloroplast outer envelope vesicles has been instrumental for our understanding of the mechanism underlying this process.
Indeed, the TOC complex has been purified by previously established procedures. However its functional and structural analyses are impaired by the limited yield of purified protein. Therefore, protocols for native TOC complex purification are described here. The complex isolation is achieved by direct biochemical treatment of biological membrane hosting this complex or by tandem affinity purification of modified protein complex components from generated transgenic plants.
Furthermore, in this thesis, radioactive based in vitro import assays are described, namely those that allow monitoring translocation activity across the outer envelope of chloroplast. Based on the analysis of knock-out plants and isolated complexes it was previously suggested that lipid dependence of protein translocation might exist. Thus, the question was raised whether the lipid composition of the membrane has a direct influence on the behavior and functionality of the TOC translocon, or whether additional components of the chloroplast membrane account for the observed effect in vivo. To answer this question, a technique for vesicle fusion was developed. The principal aim was to explore the effect of an exchange of the lipid environment surrounding the complex translocon. This method helped to demonstrate that the SQDG and PI act stimulatory on the translocation across the outer envelope of chloroplast, whereas DGDG exhibits an inhibitory effect on TOC complex functionality.
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.
Strukturelle Organisation und Mobilisierung des Primaten-spezifischen Non-LTR-Retrotransposons SVA
(2011)
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.
PaCATB : a secreted catalase protecting Podospora anserina against exogenous oxidative stress
(2011)
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.
A decade since the availability of Mycobacterium tuberculosis (Mtb) genome sequence, no promising drug has seen the light of the day. This not only indicates the challenges in discovering new drugs but also suggests a gap in our current understanding of Mtb biology. We attempt to bridge this gap by carrying out extensive re-annotation and constructing a systems level protein interaction map of Mtb with an objective of finding novel drug target candidates. Towards this, we synergized crowd sourcing and social networking methods through an initiative ‘Connect to Decode’ (C2D) to generate the first and largest manually curated interactome of Mtb termed ‘interactome pathway’ (IPW), encompassing a total of 1434 proteins connected through 2575 functional relationships. Interactions leading to gene regulation, signal transduction, metabolism, structural complex formation have been catalogued. In the process, we have functionally annotated 87% of the Mtb genome in context of gene products. We further combine IPW with STRING based network to report central proteins, which may be assessed as potential drug targets for development of drugs with least possible side effects. The fact that five of the 17 predicted drug targets are already experimentally validated either genetically or biochemically lends credence to our unique approach.
We describe and analyze a Neandertal postcranial skeleton and dentition, which together show unambiguous signs of right-handedness. Asymmetries between the left and right upper arm in Regourdou 1 were identified nearly 20 years ago, then confirmed by more detailed analyses of the inner bone structure for the clavicle, humerus, radius and ulna. The total pattern of all bones in the shoulder and arm reveals that Regourdou 1 was a right-hander. Confirmatory evidence comes from the mandibular incisors, which display a distinct pattern of right oblique scratches, typical of right-handed manipulations performed at the front of the mouth. Regourdou's right handedness is consistent with the strong pattern of manual lateralization in Neandertals and further confirms a modern pattern of left brain dominance, presumably signally linguistic competence. These observations along with cultural, genetic and morphological evidence indicate language competence in Neandertals and their European precursors.
Background: Cyanobacteria possess several cytochrome P450s, but very little is known about their catalytic functions. CYP110 genes unique to cyanaobacteria are widely distributed in heterocyst-forming cyanobacteria including nitrogen-fixing genera Nostoc and Anabaena. We screened the biocatalytic functions of all P450s from three cyanobacterial strains of genus Nostoc or Anabaena using a series of small molecules that contain flavonoids, sesquiterpenes, low-molecular-weight drugs, and other aromatic compounds.
Results: Escherichia coli cells carrying each P450 gene that was inserted into the pRED vector, containing the RhFRed reductase domain sequence from Rhodococcus sp. NCIMB 9784 P450RhF (CYP116B2), were co-cultured with substrates and products were identified when bioconversion reactions proceeded. Consequently, CYP110E1 of Nostoc sp. strain PCC 7120, located in close proximity to the first branch point in the phylogenetic tree of the CYP110 family, was found to be promiscuous for the substrate range mediating the biotransformation of various small molecules. Naringenin and (hydroxyl) flavanones were respectively converted to apigenin and (hydroxyl) flavones, by functioning as a flavone synthase. Such an activity is reported for the first time in prokaryotic P450s. Additionally, CYP110E1 biotransformed the notable sesquiterpene zerumbone, anti-inflammatory drugs ibuprofen and flurbiprofen (methylester forms), and some aryl compounds such as 1-methoxy and 1-ethoxy naphthalene to produce hydroxylated compounds that are difficult to synthesize chemically, including novel compounds.
Conclusion: We elucidated that the CYP110E1 gene, C-terminally fused to the P450RhF RhFRed reductase domain sequence, is functionally expressed in E. coli to synthesize a robust monooxygenase, which shows promiscuous substrate specificity (affinity) for various small molecules, allowing the biosynthesis of not only flavones (from flavanones) but also a variety of hydroxyl-small molecules that may span pharmaceutical and nutraceutical industries.
The biosynthesis pathway to diadinoxanthin and fucoxanthin was elucidated in Phaeodactylum tricornutum by a combined approach involving metabolite analysis identification of gene function. For the initial steps leading to β-carotene, putative genes were selected from the genomic database and the function of several of them identified by genetic pathway complementation in Escherichia coli. They included genes encoding a phytoene synthase, a phytoene desaturase, a ζ-carotene desaturase, and a lycopene β-cyclase. Intermediates of the pathway beyond β-carotene, present in trace amounts, were separated by TLC and identified as violaxanthin and neoxanthin in the enriched fraction. Neoxanthin is a branching point for the synthesis of both diadinoxanthin and fucoxanthin and the mechanisms for their formation were proposed. A single isomerization of one of the allenic double bounds in neoxanthin yields diadinoxanhin. Two reactions, hydroxylation at C8 in combination with a keto-enol tautomerization and acetylation of the 3′-HO group results in the formation of fucoxanthin.
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.
Amino acids can induce yeast cell adhesion but how amino acids are sensed and signal the modulation of the FLO adhesion genes is not clear. We discovered that the budding yeast Saccharomyces cerevisiae CEN.PK evolved invasive growth ability under prolonged nitrogen limitation. Such invasive mutants were used to identify amino acid transporters as regulators of FLO11 and invasive growth. One invasive mutant had elevated levels of FLO11 mRNA and a Q320STOP mutation in the SFL1 gene that encodes a protein kinase A pathway regulated repressor of FLO11. Glutamine-transporter genes DIP5 and GNP1 were essential for FLO11 expression, invasive growth and biofilm formation in this mutant. Invasive growth relied on known regulators of FLO11 and the Ssy1-Ptr3-Ssy5 complex that controls DIP5 and GNP1, suggesting that Dip5 and Gnp1 operates downstream of the Ssy1-Ptr3-Ssy5 complex for regulation of FLO11 expression in a protein kinase A dependent manner. The role of Dip5 and Gnp1 appears to be conserved in the S. cerevisiae strain ∑1278b since the dip5 gnp1 ∑1278b mutant showed no invasive phenotype.
Secondly, the amino acid transporter gene GAP1 was found to influence invasive growth through FLO11 as well as other FLO genes. Cells carrying a dominant loss-of-function PTR3647::CWNKNPLSSIN allele had increased transcription of the adhesion genes FLO1, 5, 9, 10, 11 and the amino acid transporter gene GAP1. Deletion of GAP1 caused loss of FLO11 expression and invasive growth. However, deletions of FLO11 and genes encoding components of the mitogen-activated protein kinase pathway or the protein kinase A pathway were not sufficient to abolish invasive growth, suggesting involvement of other FLO genes and alternative pathways. Increased intracellular amino acid pools in the PTR3647::CWNKNPLSSIN-containing strain opens the possibility that Gap1 regulates the FLO genes through alteration of the amino acid pool sizes.
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 Makrophytenvegetation eines stillgelegten Kanalabschnittes ("Alte Fahrt") bei Senden in Westfalen hat sich seit Beginn der 90er Jahre drastisch verändert. Aus einem typischen Potamogetonetum lucentis sind Reinbestände von Myriophyllum spicatum geworden, denen stellenweise Ceratophyllum demersum beigemischt ist. Die Ursachen für diese gravierenden Vegetationsveränderungen sind nicht klar. Da es sich um einen der bedeutendsten westfälischen Standorte des Potamogetonetum lucentis, einer in Nordrhein-Westfalen stark gefährdeten Pflanzengesellschaft, handelte, sind weiterführende Untersuchungen und Versuche zur Wiederansiedlung zu fordern.
Mitochondrial dynamics and mitophagy play a key role in ensuring mitochondrial quality control. Impairment thereof was proposed to be causative to neurodegenerative diseases, diabetes, and cancer. Accumulation of mitochondrial dysfunction was further linked to aging. Here we applied a probabilistic modeling approach integrating our current knowledge on mitochondrial biology allowing us to simulate mitochondrial function and quality control during aging in silico. We demonstrate that cycles of fusion and fission and mitophagy indeed are essential for ensuring a high average quality of mitochondria, even under conditions in which random molecular damage is present. Prompted by earlier observations that mitochondrial fission itself can cause a partial drop in mitochondrial membrane potential, we tested the consequences of mitochondrial dynamics being harmful on its own. Next to directly impairing mitochondrial function, pre-existing molecular damage may be propagated and enhanced across the mitochondrial population by content mixing. In this situation, such an infection-like phenomenon impairs mitochondrial quality control progressively. However, when imposing an age-dependent deceleration of cycles of fusion and fission, we observe a delay in the loss of average quality of mitochondria. This provides a rational why fusion and fission rates are reduced during aging and why loss of a mitochondrial fission factor can extend life span in fungi. We propose the ‘mitochondrial infectious damage adaptation’ (MIDA) model according to which a deceleration of fusion–fission cycles reflects a systemic adaptation increasing life span.