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In den letzten 20 Jahren hat sich der Maiszünsler (Ostrinia nubilalis HÜBNER), aus der Schmetterlingsfamilie der Pyralidae oder Zünsler, zum bedeutendsten tierischen Schädling des Maises (Zea mays) entwickelt. Eine Möglichkeit den Befall des Maiszünslers abzuwenden, bietet der Anbau von Bacillus thuringiensis-Mais (Bt-Mais). Mit Hilfe der Gentechnik wurden Gene des Bakteriums Bacillus thuringiensis übertragen, die einen für Fraßinsekten giftigen Wirkstoff bilden, wodurch die Pflanzen während der kompletten Vegetation vor den Larven des Maiszünslers geschützt sind. Ziel des vorliegenden Projektes war es, in einer 3-jährigen Studie die Auswirkungen des großflächigen Anbaus von Bt-Mais auf die ökologische Situation und den Handlungsrahmen des integrierten Pflanzenschutzes komplex zu untersuchen. Dazu wurden in Betrieben im Oderbruch, das als permanentes Befallsgebiet des Maiszünslers gilt, in den Jahren 2002 bis 2004 jährlich zwei Felder mit jeweils einer Bt-Sorte und einer konventionellen Sorte angelegt. Zusätzlich wurden biologische und chemische Maiszünsler-Bekämpfungsvarianten geprüft. Durch verschiedene Methoden wie Bonituren, Ganzpflanzenernten, Bodenfallenfänge und Beobachtungen des Wahlverhaltens von (Flug-)insekten konnten Aussagen zum Vorkommen von Insekten und Spinnentieren getroffen werden, wobei hierfür Daten aus Untersuchungen der Jahre 2000 und 2001 im Oderbruch ergänzend herangezogen werden konnten. Durch Ertragsmessungen, Energie- und Qualitätsermittlungen, sowie Fusarium- und Mykotoxinanalysen konnte der Anbau von Bt-Mais als neue Alternative zur Bekämpfung des Maiszünslers bewertet werden. Bezüglich des Auftretens von Insekten und Spinnentieren wurden im Mittel der fünfjährigen Datenerhebung beim Vergleich der Bt-Sorte zur konventionellen Sorte, mit Ausnahme der fast 100 %igen Bekämpfung des Maiszünslers, keine signifikanten Unterschiede festgestellt. Hierfür wurde ein besonderes Augenmerk auf Thripse, Wanzen, Blattläuse und deren Fraßfeinde, sowie mittels Bodenfallenfängen auf Laufkäfer und Spinnen gerichtet. Die erwarteten ökonomischen Vorteile wie etwa Ertragsplus oder bessere Nährstoff- und Energiegehalte durch geringeren Schaden beim Anbau von Bt-Mais als Silomais blieben in den Untersuchungsjahren aus. Allerdings zeigten Fusarium- und Mykotoxinanalysen eine geringere Belastung des Bt-Maises, was möglicherweise auf den geringeren Schaden zurückzuführen ist, da beschädigte Pflanzen für Fusarium und Mykotoxine anfälliger sind. Desweiteren konnten erste methodische Ansätze für ein auf EU-Ebene gefordertes, den Anbau von Bt-Mais begleitendes Monitoring, erarbeitet werden. So konnten Vorschläge für geeignete Methoden, deren Umfang sowie des Zeitpunktes der Durchführungen gemacht werden.
In dieser Arbeit wurden die Möglichkeiten und Grenzen für Zirkulardichroismus-Messungen mit Synchrotronstrahlung untersucht. Dazu wurde ein Messaufbau für Zirkulardichroismus-Messungen an zwei Strahlrohren am Berliner Elektronenspeicherring für Synchrotronstrahlung eingesetzt, die für Messungen im Bereich des ultravioletten Lichts geeignet sind. Eigenschaften der Strahlrohre und des Messaufbau wurden in einigen wichtigen Punkten mit kommerziellen Zirkulardichroismus-Spektrometern verglichen. Der Schwerpunkt lag auf der Ausdehnung des zugänglichen Wellenlängenbereichs unterhalb von 180 nm zur Untersuchung des Zirkulardichroismus von Proteinen in diesem Bereich. In diesem Bereich ist es nicht nur die Lichtquelle sondern vor allem die Absorption des Lichts durch Wasser, die den Messbereich bei der Messung biologischer Proben in wässriger Lösung einschränkt. Es wurden Bedingungen gefunden, unter denen der Messbereich auf etwa 160 nm, in einigen Fällen bis auf 130 nm ausgedehnt werden konnte. Dazu musste die Pfadlänge deutlich reduziert werden und verschieden Probenküvetten wurden getestet. Der Einfluss der dabei auftretenden Spannungsdoppelbrechung in den Probenküvetten auf das Messsignal konnte mit einem alternativen Messaufbau deutlich reduziert werden. Systematische Fehler im Messsignal und auftretende Strahlenschäden begrenzen jedoch die Zuverlässigkeit der gemessenen Spektren. Bei Proteinfilmen schränkt die Absorption von Wasser den Messbereich kaum ein. Es wurden jedoch meist deutliche Unterschiede zwischen den Spektren von Proteinfilmen und den Spektren von Proteinen in wässriger Lösung festgestellt. Solange diese Unterschiede nicht minimiert werden können, stellen Proteinfilme keine praktikable Alternative zu Messungen in wässriger Lösung dar.
Im ersten Teil der Arbeit wurden Strategien zur Analyse von Transkripten erarbeitet. Die ersten Versuche zielten darauf ab, in mit Glaskapillaren genommenen Einzelzellproben verschiedener Gewebeschichten RT-PCR durchzuführen, um spezifische Transkripte nachweisen zu können. Dies gelang für eine Reihe von Genen aus verschiedenen Pflanzenspezies. Dabei konnten sowohl Transkripte stark wie auch schwach exprimierter Gene nachgewiesen werden. Für die Erstellung von Gewebe-spezifischen Expressionsprofilen war es notwendig, die in vereinigten Zellproben enthaltene mRNA zunächst zu amplifizieren, um eine ausreichende Menge für Arrayhybridisierungen zu erhalten. Vor der Vermehrung wurde die mRNA revers transkribiert. Es wurden daran anschließend verschiedene Amplifikationsstrategien getestet: Die neben Tailing, Adapterligation und anderen PCR-basierenden Protokollen getestete Arbitrary-PCR hat sich in dieser Arbeit als einfache und einzige Methode herausgestellt, die mit so geringen cDNA-Mengen reproduzierbar arbeitet. Durch Gewebe-spezifische Array-hybridisierungen mit der so amplifizierten RNA konnten schon bekannte Expressionsmuster verschiedener Gene, vornehmlich solcher, die an der Photosynthese beteiligt sind, beobachtet werden. Es wurden aber auch eine ganze Reihe neuer offensichtlich Gewebe-spezifisch exprimierter Gene gefunden. Exemplarisch für die differentiell exprimierten Gene konnte das durch Arrayhybridisierungen gefundene Expressionsmuster der kleinen Untereinheit von Rubisco verifiziert werden. Hierzu wurden Methoden zum Gewebe-spezifischen Northernblot sowie semiquantitativer und Echtzeit-Einzelzell-RT-PCR entwickelt. Im zweiten Teil der Arbeit wurden Methoden zur Analyse von Metaboliten einschließlich anorganischer Ionen verwendet. Es stellte sich heraus, daß die multiparallele Methode der Gaschromatographie-Massenspektrometrie keine geeignete Methode für die Analyse selbst vieler vereinigter Zellinhalte ist. Daher wurde auf Kapillarelektrophorese zurückgegriffen. Eine Methode, die mit sehr kleinen Probenvolumina auskommt, eine hohe Trennung erzielt und zudem extrem geringe Detektionslimits besitzt. Die Analyse von Kohlenhydraten und Anionen erfordert eine weitere Optimierung. Über UV-Detektion konnte die K+-Konzentration in verschiedenen Geweben von A. thaliana bestimmt werden. Sie lag in Epidermis und Mesophyll mit ca. 25 mM unterhalb der für andere Pflanzenspezies (Solanum tuberosum und Hordeum vulgare) publizierten Konzentration. Weiter konnte gezeigt werden, daß zwölf freie Aminosäuren mittels einer auf Kapillarelektrophorese basierenden Methode in vereinigten Zellproben von Cucurbita maxima identifiziert werden konnten. Die Übertragung der Methode auf A. thaliana-Proben muß jedoch weiter optimiert werden, da die Sensitivität selbst bei Laser induzierter Fluoreszenz-Detektion nicht ausreichte. Im dritten und letzten Teil der Arbeit wurde eine Methode entwickelt, die die Analyse bekannter wie unbekannter Proteine in Gewebe-spezifischen Proben ermöglicht. Hierzu wurde zur Probennahme mittels mechanischer Mikrodissektion eine alternative Methode zur Laser Capture Microdissection verwendet, um aus eingebetteten Gewebeschnitten distinkte Bereiche herauszuschneiden und somit homogenes Gewebe anzureichern. Aus diesem konnten die Proteine extrahiert und über Polyacrylamidgelelektrophorese separariert werden. Banden konnten ausgeschnitten, tryptisch verdaut und massenspektrometrisch die Primärsequenz der Peptidfragmente bestimmt werden. So konnten als Hauptproteine im Mesophyll die große Untereinheit von Rubisco sowie ein Chlorophyll bindendes Protein gefunden werden. Die in dieser Arbeit entwickelten und auf die Modellpflanze Arabidopsis thaliana angewandten Einzelzellanalysetechniken erlauben es in Zukunft, physiologische Prozesse besser sowohl räumlich als auch zeitlich aufzulösen. Dies wird zu einem detaillierteren Verständnis mannigfaltiger Vorgänge wie Zell-Zell-Kommunikation, Signalweiterleitung oder Pflanzen-Pathogen-Interaktionen führen.
Im Rahmen dieser Arbeit wurden zwei humane Varianten des von Wang et al., 1999, erstmals beschriebenen muskelspezifischen Proteins Xin (Huhn und Maus) über Sequenzanalyse, Immunofluoreszenzmikroskopie, Transfektionsstudien und biochemischer Analyse näher charakterisiert. Die Proteine wurden mit human Xin related proteins 1 und 2 – hXirp1 und 2 –bezeichnet. Die Xin-Proteine enthielten bisher unbekannte, sowie spezifische, repetitive Motive, die aus jeweils mindestens 16 Aminosäuren bestanden. Ihre Aminosäuresequenz, mit einer Vielzahl weiterer putativer Motivsequenzen, verwies auf eine potentielle Funktion von hXirp als Adapterprotein in Muskelzellen. Das hier näher untersuchte hXirp1 lokalisierte an den Zell-Matrix-Verbindungen der Muskel-Sehnen-Übergangszone im Skelettmuskel, sowie an den Zell-Zell-Verbindungen der Glanzstreifen im Herzmuskel. Während der Muskelentwicklung zeigte hXirp1 eine sehr frühe Expression, zusammen mit einer prägnanten Lokalisation an den Prämyofibrillen und deren Verankerungsstrukturen, die auf eine Funktion des Proteins in der Myofibrillogenese deuten. Ektopische Expressionen von hXirp1 in einer Vielzahl von Nichtmuskel-Kulturzellen zeigten wiederum eine Lokalisation des Proteins an den Zell-Matrix-Kontakten dieser Zellen. Am Beispiel von hXirp1 und 2 wurde stellvertretend für die Familie der Xin-Proteine gezeigt, daß es sich bei den repetitiven Motiven um neuartige, F-Aktin bindende Sequenzmotive handelte. Die Xin-Proteine können somit als muskelspezifische, aktinbindende, potentielle Adapterproteine bezeichnet werden, denen eine strukturelle und funktionelle Beteiligung an der Verankerung der Myofibrillen im adulten Muskel, wie auch während der Myofibrillogenese zukommt.
In der vorliegenden Arbeit habe ich wichtige Teilmechanismen der Erregungs-Sekretionskopplung in der Speicheldrüse der Schabe Periplaneta americana (L.) untersucht. Die Speicheldrüse ist von dopaminergen und serotonergen Fasern innerviert (Baumann et al., 2002). Beide Transmitter stimulieren eine unterschiedliche Reaktion der Drüse: Dopamin (DA) stimuliert die P-Zellen der Acini und die Ausführgangzellen, während Serotonin (5-HT) die P- und C-Zellen der Acini stimuliert, nicht jedoch die Ausführgangzellen. Der Endspeichel ist nach einer DA-Stimulierung proteinfrei. Dagegen enthält er nach einer 5-HT-Stimulierung Proteine, die von den C-Zellen sezerniert werden (Just & Walz, 1996). Im ersten Teil meiner Arbeit habe ich mittels Kapillarelektrophoretischer Analyse (CE-Analyse) die Elektrolytkonzentrationen im Endspeichel untersucht sowie die Raten der Flüssigkeitssekretion gemessen. Damit wollte ich klären, welche Transporter an der Sekretion des Primärspeichels und an dessen Modifikation beteiligt sind. Ausserdem wollte ich die Rolle der transportaktiven Epithelzellen der Ausführgänge für die Modifikation des Primärspeichels untersuchen. Dafür habe ich einen Vergleich der Elektrolytkonzentrationen im DA- und 5-HT-stimulierten Endspeichel durchgeführt. Der Elektrolytgehalt des DA- und 5-HT-stimulierten Endspeichels unterscheidet sich nicht signifikant voneinander. Er ist nach beiden Stimulierungen hypoosmotisch zum verwendeten Ringer. Die Ausführgangzellen werden durch DA stimuliert und modifizieren den Primärspeichel durch eine netto-Ionenreabsorption. Meine Versuche zeigen jedoch, dass auch die während einer 5-HT-Stimulierung der Drüse unstimulierten Ausführgangzellen den Primärspeichel modifizieren. In einer nachfolgenden Versuchsreihe habe ich den Einfluss von Ouabain, einem Hemmstoff der Na+-K+-ATPase, und Bumetanid, einem Hemmstoff des NKCC, auf die Raten der Flüssigkeitssekretion sowie den Elektrolytgehalt des Endspeichels untersucht. Ich habe gefunden, dass die Aktivität der Na+-K+-ATPase wichtig für die Modifikation des DA-stimulierten Primärspeichels ist. Im Gegensatz dazu ist sie für die Modifikation des 5-HT-stimulierten Primärspeichels nicht von Bedeutung. Bezüglich der Flüssigkeitssekretion habe ich keinen Einfluss der Na+-K+-ATPase-Aktivität auf die DA-stimulierten Sekretionsraten gefunden, dagegen ist die 5-HT-stimulierte Sekretionsrate in Anwesenheit von Ouabain gesteigert. Die Aktivität des NKCC ist für beide sekretorische Prozesse, die Ionen- und die Flüssigkeitssekretion, wichtig. Eine Hemmung des NKCC bewirkt eine signifikante Verringerung der Raten der Flüssigkeitssekretion nach DA- und 5-HT-Stimulierung sowie in beiden Fällen einen signifikanten Abfall der Ionenkonzentrationen im Endspeichel. Im zweiten Teil meiner Arbeit habe ich versucht, Änderungen der intrazellulären Ionenkonzentrationen in den Acinuszellen während einer DA- oder 5-HT-Stimulierung zu messen. Diese Experimente sollten mit der Methode des "ratiometric imaging" durchgeführt werden. Messungen mit dem Ca2+-sensitiven Fluoreszenzfarbstoff Fura-2 zeigten keinen globalen Anstieg in der intrazellulären Ca2+-Konzentration der P-Zellen. Aufgrund von Problemen mit einer schlechten Beladung der Zellen, einer starken und sich während der Stimulierung ändernden Autofluoreszenz der Zellen sowie Änderungen im Zellvolumen wurden keine Messungen mit Na+- und K+-sensitiven Fluoreszenzfarbstoffen durchgeführt. Im dritten Teil dieser Arbeit habe ich die intrazellulären Signalwege untersucht, die zwischen einer 5-HT-Stimulierung der Drüse und der Proteinsekretion vermitteln. Dazu wurde der Proteingehalt im Endspeichel biochemisch mittels eines modifizierten Bradford Assay gemessen. Eine erstellte Dosis-Wirkungskurve zeigt, dass die Rate der Proteinsekretion von der zur Stimulierung verwendeten 5-HT-Konzentration abhängt. In einer Serie von Experimenten habe ich die intrazellulären Konzentrationen von Ca2+, cAMP und / oder cGMP erhöht und anschließend den Proteingehalt im Endspeichel gemessen. Ein Anstieg der intrazellulären Ca2+-Konzentration aktiviert nur eine geringe Rate der Proteinsekretion. Dagegen kann die Steigerung der intrazellulären cAMP-Konzentration eine stärkere Proteinsekretion aktivieren, die sich nicht signifikant von der nach 5-HT-Stimulierung unterscheidet. Die cAMP-stimulierte Proteinsekretion kann durch gleichzeitige Erhöhung der intrazellulären Ca2+-Konzentration weiter gesteigert werden. Dagegen aktivierte eine Erhöhung der intrazellulären cGMP-Konzentration die Proteinsekretion nicht. Aufgrund dieser Ergebnisse postuliere ich die Existenz eines die Adenylatcyclase aktivierenden 5-HT-Rezeptors in der Basolateralmembran der C-Zellen.
Dispersal behavior plays an important role for the geographical distribution and population structure of any given species. Individual’s fitness, reproductive and competitive ability, and dispersal behavior can be determined by the age of the individual. Age-dependent as well as density-dependent dispersal patterns are common in many bird species. In this thesis, I first present age-dependent breeding ability and natal site fidelity in white storks (Ciconia ciconia); migratory birds breeding in large parts of Europe. I predicted that both the proportion of breeding birds and natal site fidelity increase with the age. After the seventies of the last century, following a steep population decline, a recovery of the white stork population has been observed in many regions in Europe. Increasing population density in the white stork population in Eastern Germany especially after 1983 allowed examining density- as well as age-dependent breeding dispersal patterns. Therefore second, I present whether: young birds show more often and longer breeding dispersal than old birds, and frequency of dispersal events increase with the population density increase, especially in the young storks. Third, I present age- and density-dependent dispersal direction preferences in the give population. I asked whether and how the major spring migration direction interacts with dispersal directions of white storks: in different age, and under different population densities. The proportion of breeding individuals increased in the first 22 years of life and then decreased suggesting, the senescent decay in aging storks. Young storks were more faithful to their natal sites than old storks probably due to their innate migratory direction and distance. Young storks dispersed more frequently than old storks in general, but not for longer distance. Proportion of dispersing individuals increased significantly with increasing population densities indicating, density- dependent dispersal behavior in white storks. Moreover, the finding of a significant interaction effects between the age of dispersing birds and year (1980–2006) suggesting, older birds dispersed more from their previous nest sites over time due to increased competition. Both young and old storks dispersed along their spring migration direction; however, directional preferences were different in young storks and old storks. Young storks tended to settle down before reaching their previous nest sites (leading to the south-eastward dispersal) while old birds tended to keep migrating along the migration direction after reaching their previous nest sites (leading to the north-westward dispersal). Cues triggering dispersal events may be age-dependent. Changes in the dispersal direction over time were observed. Dispersal direction became obscured during the second half of the observation period (1993–2006). Increase in competition may affect dispersal behavior in storks. I discuss the potential role of: age for the observed age-dependent dispersal behavior, and competition for the density dependent dispersal behavior. This Ph.D. thesis contributes significantly to the understanding of population structure and geographical distribution of white storks. Moreover, presented age- and density (competition)-dependent dispersal behavior helps understanding underpinning mechanisms of dispersal behavior in bird species.
Das Centrosom von Dictyostelium ist acentriolär aufgebaut, misst ca. 500 nm und besteht aus einer dreischichten Core-Struktur mit umgebender Corona, an der Mikrotubuli nukleieren. In dieser Arbeit wurden das centrosomale Protein Cep192 und mögliche Interaktionspartner am Centrosom eingehend untersucht. Die einleitende Lokalisationsuntersuchung von Cep192 ergab, dass es während der gesamten Mitose an den Spindelpolen lokalisiert und im Vergleich zu den anderen Strukturproteinen der Core-Struktur am stärksten exprimiert ist. Die dauerhafte Lokalisation an den Spindelpolen während der Mitose wird für Proteine angenommen, die in den beiden identisch aufgebauten äußeren Core-Schichten lokalisieren, die das mitotische Centrosom formen. Ein Knockdown von Cep192 führte zur Ausbildung von überzähligen Mikrotubuli-organisierenden Zentren (MTOC) sowie zu einer leicht erhöhten Ploidie. Deshalb wird eine Destabilisierung des Centrosoms durch die verminderte Cep192-Expression angenommen. An Cep192 wurden zwei kleine Tags, der SpotH6- und BioH6-Tag, etabliert, die mit kleinen fluoreszierenden Nachweiskonjugaten markiert werden konnten. Mit den so getagten Proteinen konnte die hochauflösende Expansion Microscopy für das Centrosom optimiert werden und die Core-Struktur erstmals proteinspezifisch in der Fluoreszenzmikroskopie dargestellt werden. Cep192 lokalisiert dabei in den äußeren Core-Schichten. Die kombinierte Markierung von Cep192 und den centrosomalen Proteinen CP39 und CP91 in der Expansion Microscopy erlaubte die Darstellung des dreischichtigen Aufbaus der centrosomalen Core-Struktur, wobei CP39 und CP91 zwischen Cep192 in der inneren Core-Schicht lokalisieren. Auch die Corona wurde in der Expansion Microscopy untersucht: Das Corona-Protein CDK5RAP2 lokalisiert in räumlicher Nähe zu Cep192 in der inneren Corona. Ein Vergleich der Corona-Proteine CDK5RAP2, CP148 und CP224 in der Expansion Microscopy ergab unterscheidbare Sublokalisationen der Proteine innerhalb der Corona und relativ zur Core-Struktur. In Biotinylierungsassays mit den centrosomalen Core-Proteinen CP39 und CP91 sowie des Corona-Proteins CDK5RAP2 konnte Cep192 als möglicher Interaktionspartner identifiziert werden.
Die Ergebnisse dieser Arbeit zeigen die wichtige Funktion des Proteins Cep192 im Dictyostelium-Centrosom und ermöglichen durch die Kombination aus Biotinylierungsassays und Expansion Microscopy der untersuchten Proteine ein verbessertes Verständnis der Topologie des Centrosoms.
Die vorliegende Arbeit wurde im Zeitraum von Oktober 2002 bis November 2005 an dem Institut für Biochemie und Biologie der Universität Potsdam in Kooperation mit dem Institut für Chemie des GKSS Forschungszentrums in Teltow unter der Leitung von Herrn Prof. Dr. B. Micheel und Herrn Prof. Dr. Th. Groth angefertigt. Im Rahmen dieser Arbeit wurden die Wechselwirkungen von Immunzellen mit verschiedenen Kultursubstraten untersucht. Dafür wurden drei verschiedene Hybridomzelllinien eingesetzt. Eine Hybridomzelllinie (K2) ist im Laufe dieser Arbeit hergestellt und etabliert worden. Der Einsatz von synthetischen und proteinbeschichteten Kulturoberflächen führte bei Hybridomzellen zu einer deutlich gesteigerten Antikörpersynthese im Vergleich zu herkömmlichen Zellkulturmaterialien. Obwohl diese Zellen in der Regel als Suspensionszellen kultiviert werden, führten die eingesetzten Polymermembranen (PAN, NVP) zu einer verbesserten Antikörpersynthese (um 30%) gegenüber Polystyrol als Referenz. Es konnte gezeigt werden, dass es einen Zusammenhang zwischen der Produktivität und dem Adh asionsverhalten der Hybridomzellen gibt. Um den Einfluss von Proteinen der extrazellulären Matrix auf Zellwachstum und Antikörpersynthese von Hybridomzellen zu untersuchen, wurden proteinbeschichtete Polystyrol-Oberflächen eingesetzt. Für die Modifikationen wurden Fibronektin, Kollagen I, Laminin und BSA ausgewählt. Die Modifikation der Polystyrol-Oberfläche mit geringen Mengen Fibronektin (0,2-0,4 µg/ml) führte zu einer beträchtlichen Steigerung der Antikörpersynthese um 70-120%. Für Kollagen I- und BSA-Beschichtungen konnten Steigerungen von 40% beobachtet werden. Modifikationen der Polystyrol-Oberfläche mit Laminin zeigten nur marginale Effekte. Durch weitere Versuche wurde bestätigt, dass die Adhäsion der Zellen an Kollagen I- und Laminin-beschichteten Oberflächen verringert ist. Die alpha2-Kette des alpha2beta1-Integrins konnte auf der Zelloberfläche nicht nachgewiesen werden. Durch ihr Fehlen wird wahrscheinlich die Bindungsfähigkeit der Zellen an Kollagen I und Laminin beeinflusst. Durch die Ergebnisse konnte gezeigt werden, dass Hybridomzellen nicht nur Suspensionszellen sind und das Kultursubstrate das Zellwachstum und die Produktivität dieser Zellen stark beeinflussen können. Der Einsatz von synthetischen und proteinbeschichteten Kultursubstraten zur Steigerung der Antikörpersynthese kann damit für die industrielle Anwendung von großer Relevanz sein. Für die Modellierung einer Lymphknotenmatrix wurden Fibronektin, Kollagen I, Heparansulfat und N-Acetylglucosamin-mannose in verschiedenen Kombinationen an Glasoberflächen adsorbiert und für Versuche zur In-vitro-Immunisierung eingesetzt. Es konnte gezeigt werden, dass die Modifikation der Oberflächen die Aktivierung und Interaktion von dendritischen Zellen, T- und B-Lymphozyten begünstigt, was durch den Nachweis spezifischer Interleukine (IL12, IL6) und durch die Synthese spezifischer Antikörper bestätigt wurde. Eine spezifische Immunreaktion gegen das Antigen Ovalbumin konnte mit den eingesetzten Zellpopulationen aus Ovalbumin-T-Zell-Rezeptor-transgenen Mäusen nachgewiesen werden. Die In-vitro-Immunantwort wurde dabei am stärksten durch eine Kombination von Kollagen I, Heparansulfat und N-Acetylglucosamin-mannose auf einer Glasoberfläche gefördert. Die Etablierung einer künstlichen Immunreaktion kann eine gesteuerte Aktivierung bzw. Inaktivierung von körpereigenen dendritischen Zellen gegen bestehende Krankheitsmerkmale in vitro ermöglichen. Durch die Versuche wurden Grundlagen für spezifische Immunantworten erarbeitet, die u.a. für die Herstellung von humanen Antikörpern eingesetzt werden können.
Weltweit versuchen Wissenschaftler, künstliche Viren für den Gentransfer zu konstruieren, die nicht reproduktionsfähig sind. Diese sollen die Vorteile der natürlichen Viren besitzen (effizienter Transport von genetischem Material), jedoch keine Antigene auf ihrer Oberfläche tragen, die Immunreaktionen auslösen. Ziel dieses Projektes ist es, einen künstlichen Viruspartikel herzustellen, dessen Basis eine Polyelektrolytenhohlkugel bildet, die mit einer Lipiddoppelschicht bedeckt ist. Um intakte Doppelschichten zu erzeugen, muss die Wechselwirkung zwischen Lipid und Polyelektrolyt (z.B. DNA) verstanden und optimiert werden. Dazu ist es notwendig, die strukturelle Grundlage der Interaktion aufzuklären. Positiv geladene Lipide gehen zwar starke Wechselwirkungen mit der negativ geladenen DNA ein, sie wirken jedoch toxisch auf biologische Zellen. In der vorliegenden Arbeit wurde daher die durch zweiwertige Kationen vermittelte Kopplung von genomischer oder Plasmid-DNA an zwitterionische oder negativ geladene Phospholipide an zwei Modellsystemen untersucht. 1. Modellsystem: Lipidmonoschicht an der Wasser/Luft-Grenzfläche Methoden: Filmwaagentechnik in Kombination mit IR-Spektroskopie (IRRAS), Röntgenreflexion (XR), Röntgendiffraktion (GIXD), Brewsterwinkel-Mikroskopie (BAM), Röntgenfluoreszenz (XRF) und Oberflächenpotentialmessungen Resultate: A) Die Anwesenheit der zweiwertigen Kationen Ba2+, Mg2+, Ca2+ oder Mn2+ in der Subphase hat keinen nachweisbaren Einfluss auf die Struktur der zwitterionischen DMPE- (1,2-Dimyristoyl-phosphatidyl-ethanolamin) Monoschicht. B) In der Subphase gelöste DNA adsorbiert nur in Gegenwart dieser Kationen an der DMPE-Monoschicht. C) Sowohl die Adsorption genomischer Kalbsthymus-DNA als auch der Plasmid-DNA pGL3 bewirkt eine Reduktion des Neigungswinkels der Alkylketten, die auf einen veränderten Platzbedarf der Kopfgruppe zurückzuführen ist. Durch die Umorientierung der Kopfgruppe wird die elektrostatische Wechselwirkung zwischen den positiv geladenen Stickstoffatomen der Lipidkopfgruppen und den negativ geladenen DNA-Phosphaten erhöht. D) Die adsorbierte DNA weist eine geordnete Struktur auf, wenn sie durch Barium-, Magnesium-, Calcium- oder Manganionen komplexiert ist. Der Abstand zwischen parallelen DNA-Strängen hängt dabei von der Größe der DNA-Fragmente sowie von der Art des Kations ab. Die größten Abstände ergeben sich mit Bariumionen, gefolgt von Magnesium- und Calciumionen. Die kleinsten DNA-Abstände werden durch Komplexierung mit Manganionen erhalten. Diese Ionenreihenfolge stellt sich sowohl für genomische DNA als auch für Plasmid-DNA ein. E) Die DNA-Abstände werden durch die Kompression des Lipidfilms nicht beeinflusst. Zwischen der Lipidmonoschicht und der adsorbierten DNA besteht demnach nur eine schwache Wechselwirkung. Offensichtlich befindet sich die durch zweiwertige Kationen komplexierte DNA als weitgehend eigenständige Schicht unter dem Lipidfilm. 2. Modellsystem: Lipiddoppelschicht an der fest/flüssig-Grenzfläche Methoden: Neutronenreflexion (NR) und Quarzmikrowaage (QCM-D) Resultate: A) Das zwitterionische Phospholipid DMPC (1,2-Dimyristoyl-phosphatidylcholin) bildet keine Lipiddoppelschicht auf planaren Polyelektrolytmultischichten aus, deren letzte Lage das positiv geladene PAH (Polyallylamin) ist. B) Hingegen bildet DMPC auf dem negativ geladenen PSS (Polystyrolsulfonat) eine Doppelschicht aus, die jedoch Defekte aufweist. C) Eine Adsorption von genomischer Kalbsthymus-DNA auf dieser Lipidschicht findet nur in Gegenwart von Calciumionen statt. Andere zweiwertige Kationen wurden nicht untersucht. D) Das negativ geladene Phospholipid DLPA (1,2-Dilauryl-phosphatidsäure) bildet auf dem positiv geladenen PAH eine Lipiddoppelschicht aus, die Defekte aufweist. E) DNA adsorbiert ebenfalls erst in Anwesenheit von Calciumionen in der Lösung an die DLPA-Schicht. F) Durch die Zugabe von EDTA (Ethylendiamintetraessigsäure) werden die Calciumionen dem DLPA/DNA-Komplex entzogen, wodurch dieser dissoziiert. Demnach ist die calciuminduzierte Bildung dieser Komplexe reversibel.
Im Rahmen dieser Arbeit gelang es, katalytische Antikörper zur Hydrolyse von Benzylphenylcarbamaten sowie zahlreiche monoklonale Antikörper gegen Haptene herzustellen. Es wurden verschiedene Hapten-Protein-Konjugate unter Verwendung unterschiedlicher Kopplungsmethoden hergestellt und charakterisiert. Zur Generierung der hydrolytisch aktiven Antikörper wurden Inzuchtmäuse mit KLH-Konjugaten von 4 Übergangszustandsanaloga (ÜZA) immunisiert. Mit Hilfe der Hybridomtechnik wurden verschiedene monoklonale Antikörper gegen diese ÜZA gewonnen. Dabei wurden sowohl verschiedene Immunisierungsschemata als auch verschiedene Inzuchtmausstämme und Fusionstechniken verwendet. Insgesamt wurden 32 monoklonale Antikörper gegen die verwendeten ÜZA selektiert. Diese Antikörper wurden in großen Mengen hergestellt und gereinigt. Zum Nachweis der Antikörper-vermittelten Katalyse wurden verschiedene Methoden entwickelt und eingesetzt, darunter immunologische Nachweismethoden mit Anti-Substrat- und Anti-Produkt-Antikörpern und eine photometrische Methode mit Dimethylaminozimtaldehyd. Der Nachweis der hydrolytischen Aktivität gelang mit Hilfe eines Enzymsensors, basierend auf immobilisierter Tyrosinase. Die Antikörper N1-BC1-D11, N1-FA7-C4, N1-FA7-D12 und R3-LG2-F9 hydrolysierten die Benzylphenylcarbamate POCc18, POCc19 und Substanz 27. Der Nachweis der hydrolytischen Aktivität dieser Antikörper gelang auch mit Hilfe der HPLC. Der katalytische Antikörper N1-BC1-D11 wurde kinetisch und thermodynamisch untersucht. Es wurde eine Michaelis-Menten-Kinetik mit Km von 210 µM, vmax von 3 mM/min und kcat von 222 min-1 beobachtet. Diese Werte korrelieren mit den Werten der wenigen bekannten Diphenylcarbamat-spaltenden Abzyme. Die Beschleunigungsrate des Antikörpers N1-BC1-D11 betrug 10. Das ÜZA Hei3 hemmte die hydrolytische Aktivität. Dies beweist, dass die Hydrolyse in der Antigenbindungsstelle stattfindet. Weiter wurde zwischen der Antikörperkonzentration und der Umsatzgeschwindigkeit eine lineare Abhängigkeit festgestellt. Die thermodynamische Gleichtgewichtsdissoziationskonstante KD des Abzyms von 2,6 nM zeugt von einer sehr guten Affinität zum ÜZA. Hydrolytisch aktiv waren nur Antikörper, die gegen das Übergangszustandsanalogon Hei3 hergestellt worden waren. Es wird vermutet, dass die Hydrolyse der Benzylphenylcarbamate über einen Additions-Eliminierungsmechanismus unter Ausbildung eines tetraedrischen Übergangszustandes verläuft, dessen analoge Verbindung Hei3 ist. Im Rahmen der Generierung von Nachweisantikörpern zur Detektion der Substratabnahme bei der Hydrolyse wurden Anti-Diuron-Antikörper hergestellt. Einer der Antikörper (B91-CG5) ist spezifisch für das Herbizid Diuron und hat einen IC50-Wert von 0,19 µg/l und eine untere Nachweisgrenze von 0,04 µg/l. Ein anderer Antikörper (B91-KF5) reagiert kreuz mit einer Palette ähnlicher Herbizide. Mit diesen Antikörpern wurde ein empfindlicher Labortest, der ein Monitoring von Diuron auf Grundlage des durch die Trinkwasserverordnung festgeschriebenen Wertes für Pflanzenschutzmittel von 0,1 µg/l erlaubt, aufgebaut. Der Effekt der Anti-Diuron-Antikörper auf die Diuron-inhibierte Photosynthese wurde in vitro und in vivo untersucht. Es wurde nachgewiesen, dass sowohl in isolierten Thylakoiden, als auch in intakten Algen eine Vorinkubation der Anti-Diuron-Antikörper mit Diuron zur Inaktivierung seiner Photosynthese-hemmenden Wirkung führt. Wurde der Elektronentransport in den isolierten Thylakoiden oder in Algen durch Diuron unterbrochen, so führte die Zugabe der Anti-Diuron-Antikörper zur Reaktivierung der Elektronenübertragung.
Escherichia (E.) coli ist als kommensales Bakterium ein wichtiger Bestandteil des Mikrobioms von Säugern, jedoch zudem der häufigste Infektionserreger des Menschen. Entsprechend des Infektionsortes werden intestinal (InPEC) und extraintestinal pathogene E. coli (ExPEC) unterschieden. Die Pathogenese von E. coli-Infektionen ist durch Virulenzfaktoren determiniert, welche von jeweils spezifischen virulenzassoziierten Genen (inVAGs und exVAGs) kodiert werden. Häufig werden exVAGs auch in E. coli-Isolaten aus dem Darm gesunder Wirte nachgewiesen. Dies führte zu der Vermutung, dass exVAGs die intestinale Kolonisierung des Wirtes durch E. coli unterstützen. Das Hauptziel dieser Arbeit bestand darin, das Wissen über den Einfluss von exVAGs auf die Besiedlung und damit die Adhäsion von E. coli an Epithelzellen des Darmtraktes zu erweitern. Die Durchführung einer solch umfassenden E. coli-Populationsstudie erforderte die Etablierung neuer Screeningmethoden. Für die genotypische Charakterisierung wurden mikropartikelbasierte Multiplex-PCR-Assays zum Nachweis von 44 VAGs und der Phylogenie etabliert. Für die phänotypische Charakterisierung wurden Adhäsions- und Zytotoxizitätsassays etabliert. Die Screeningmethoden basieren auf der VideoScan-Technologie, einem automatisierten bildbasierten Multifluoreszenzdetektionssystem. Es wurden 398 E. coli-Isolate aus 13 Wildsäugerarten und 5 Wildvogelarten sowie aus gesunden und harnwegserkrankten Menschen und Hausschweinen charakterisiert. Die Adhäsionsassays hatten zum Ziel, sowohl die Adhäsionsraten als auch die Adhäsionsmuster der 317 nicht hämolytischen Isolate auf 5 Epithelzelllinien zu bestimmen. Die Zytotoxizität der 81 hämolytischen Isolate wurde in Abhängigkeit der Inkubationszeit auf 4 Epithelzelllinien geprüft. In den E. coli-Isolaten wurde eine Reihe von VAGs nachgewiesen. Potentielle InPEC, insbesondere shigatoxinproduzierende und enteropathogene E. coli wurden aus Menschen, Hausschweinen und Wildtieren, vor allem aus Rehen und Feldhasen isoliert. exVAGs wurden mit stark variierender Prävalenz in Isolaten aus allen Arten detektiert. Die größte Anzahl und das breiteste Spektrum an exVAGs wurde in Isolaten aus Urin harnwegserkrankter Menschen, gefolgt von Isolaten aus Dachsen und Rehen nachgewiesen. In Isolaten der phylogenetischen Gruppe B2 wurden mehr exVAGs detektiert als in den Isolaten der phylogenetischen Gruppen A, B1 und D. Die Ergebnisse der Adhäsionsassays zeigten, dass die meisten Isolate zelllinien-, gewebe- oder wirtsspezifisch adhärierten. Ein Drittel der Isolate adhärierte an keiner Zelllinie und nur zwei Isolate adhärierten stark an allen Zelllinien. Grundsätzlich adhärierten mehr Isolate an humanen sowie an intestinalen Zelllinien. Besonders Isolate aus Eichhörnchen und Amseln sowie aus Urin harnwegserkrankter Menschen und Hausschweine waren in der Lage, stark zu adhärieren. Hierbei bildeten die Isolate als Adhäsionsmuster diffuse Adhäsion, Mikrokolonien, Ketten und Agglomerationen. Mittels statistischer Analysen wurden Assoziationen zwischen exVAGs und einer hohen Adhäsionsrate ersichtlich. So war beispielsweise das Vorkommen von afa/dra mit einer höheren Adhäsionsrate auf Caco-2- und 5637-Zellen und von sfa/foc auf IPEC-J2-Zellen assoziiert. Die Ergebnisse der Zytotoxizitätsassays zeigten eine sehr starke und zeitabhängige Zerstörung der Monolayer aller Epithelzelllinien durch die α-Hämolysin-positiven Isolate. Auffallend war die hohe Toxizität hämolytischer Isolate aus Wildtieren gegenüber den humanen Zelllinien. Mit den innerhalb dieser Arbeit entwickelten Screeningmethoden war es möglich, große Mengen an Bakterien zu charakterisieren. Es konnte ein Überblick über die Verbreitung von VAGs in E. coli aus unterschiedlichen Wirten gewonnen werden. Besonders Wildtiere wurden sowohl durch den Nachweis von VAGs in den entsprechenden Isolaten, verbunden mit deren Adhäsionsfähigkeit und ausgeprägter Zytotoxizität als Reservoire pathogener E. coli identifiziert. Ebenso wurde eine zelllinienspezifische Adhäsion von Isolaten mit bestimmten exVAGs deutlich. Damit konnte der mögliche Einfluss von exVAGs auf die intestinale Kolonisierung bestätigt werden. In weiterführenden Arbeiten sind jedoch Expressions- und Funktionsanalysen der entsprechenden Proteine unerlässlich. Es wird anhand der Mikrokoloniebildung durch kommensale E. coli vermutet, dass Adhäsionsmuster und demzufolge Kolonisierungsstrategien, die bisher pathogenen E. coli zugeschrieben wurden, eher als generelle Kolonisierungsstrategien zu betrachten sind. Das E. coli-α-Hämolysin wirkt im Allgemeinen zytotoxisch auf Epithelzellen. Ein in der Fachliteratur diskutierter adhäsionsunterstützender Mechanismus dieses Toxins ist demnach fragwürdig. Innerhalb dieser Arbeit konnte gezeigt werden, dass die entwickelten Screeningmethoden umfassende Analysen einer großen Anzahl an E. coli-Isolaten ermöglichen.
Vergleich von rekombinanten Vaccinia- und DNA-Vektoren zur Tumorimmuntherapie im C57BL/6-Mausmodell
(2002)
In der vorliegenden Arbeit wurden Tumorimpfstoffe auf der Basis des Plasmid-Vektors pCI, modified vaccinia virus Ankara (MVA) und MVA-infizierten dendritischen Zellen entwickelt und durch Sequenzierung, Western blotting und durchflußzytometrische Analyse überprüft. Die in vivo Wirksamkeit der Vakzinen wurde in verschiedenen Tumormodellen in C57BL/6 Mäusen verglichen. Die auf dem eukaryotischen Expressionsvektor pCI basierende DNA-Vakzinierung induzierte einen sehr wirksamen, antigenspezifischen und langfristigen Schutz vor Muzin, CEA oder beta-Galactosidase exprimierenden Tumoren. Eine MVA-Vakzinierung bietet in den in dieser Arbeit durchgeführten Tumormodellen keinen signifikanten Schutz vor Muzin oder beta-Galactosidase exprimierenden Tumoren. Sowohl humane, als auch murine in vitro generierte dendritische Zellen lassen sich mit MVA – im Vergleich zu anderen viralen Vektoren – sehr gut infizieren. Die Expressionsrate der eingefügten Gene ist aber gering im Vergleich zur Expression in permissiven Wirtszellen des Virus (embryonale Hühnerfibroblasten). Es konnte gezeigt werden, daß eine MVA-Infektion dendritischer Zellen ähnliche Auswirkungen auf den Reifezustand humaner und muriner dendritischer Zellen hat, wie eine Infektion mit replikationskompetenten Vakzinia-Stämmen, und außerdem die Hochregulation von CD40 während der terminalen Reifung von murinen dendritischen Zellen inhibiert wird. Die während der langfristigen in vitro Kultur auf CEF-Zellen entstandenen Deletionen im MVA Genom führten zu einer starken Attenuierung und dem Verlust einiger Gene, die immunmodulatorische Proteine kodieren, jedoch nicht zu einer Verminderung des zytopathischen Effekts in dendritischen Zellen. Die geringe Expressionsrate und die beobachtete Inhibition der Expression kostimulatorischer Moleküle auf dendritischen Zellen kann für eine wenig effektive Induktion einer Immunantwort in MVA vakzinierten Tieren durch cross priming oder die direkte Infektion antigenpräsentierender Zellen verantwortlich sein. Durch die Modifikation einer Methode zur intrazellulären IFN-gamma Färbung konnten in vakzinierten Mäusen tumorantigenspezifische CTL sensitiv und quantitativ detektiert werden. Die so bestimmte CTL-Frequenz, nicht jedoch die humorale Antwort, korrelierte mit der in vivo Wirksamkeit der verschiedenen Vakzinen: DNA vakzinierte Tiere entwickeln starke tumorantigenspezifische CTL-Antworten, wohingegen in MVA-vakzinierten Tieren überwiegend gegen virale Epitope gerichtete CD4 und CD8-T-Zellen detektiert wurden. Die Wirksamkeit der pCI-DNA-Vakzine spricht für die Weiterentwicklung in weiteren präklinischen Mausmodellen, beispielsweise unter Verwendung von MUC1 oder HLA-A2 transgenen Mäusen. Die Methoden zur Detektion Tumorantigen-spezifischer CTL in 96-Loch-Mikrotiterplatten können dabei zur systematischen Suche nach im Menschen immundominanten T-Zell-Epitopen im Muzin-Molekül genutzt werden. Der durchgeführte Vergleich der auf den Vektoren pCI und MVA basierenden Vakzinen und die Analyse neuerer Publikationen führen zu dem Ergebnis, daß vor allem DNA-Vakzinen in Zukunft eine wichtige Rolle bei der Entwicklung von aktiven Tumorimpfstoffen spielen werden. Rekombinante MVA-Viren, eventuell in Kombination mit DNA- oder anderen Vektoren, haben sich dagegen in zahlreichen Studien als wirksame Impfstoffe zur Kontrolle von durch Pathogene hervorgerufenen Infektionserkrankungen erwiesen.
Der Buchfinkengesang wurde in Potsdam in zwei Hauptpopulationen über drei Jahre aufgenommen. Jedes Individuum wurde eindeutig am individuellen Strophentypenrepertoire identifiziert. Ein weiterer Punkt der die individuelle Wiedererkennung bestätigt ist die hohe Standorttreue der adulten Männchen. Die beschriebene Methode eignet sich für die Untersuchung von gesamten Populationen, um den Wandel des Gesangs von Populationen in Raum und Zeit zu beschreiben. Die Haupterkenntnisse der Arbeit sind: - Die Gesamtanzahl der Grundstrophentypen innerhalb einer Population bleibt über Jahre konstant. - Die relative Häufigkeit jedes einzelnen Strophentyps variiert von Jahr zu Jahr und von Population zu Population. - Gesangslernen erfolgt exakt mit einem Korrektheitsgrad von mindestens 96%. - Das Song-Sharing ist innerhalb der Population hoch. Die diskutierten Mechanismen für das Song-Sharing sind: Die Lebenserwartung, das Zugverhalten, das Lernverhalten, die Etabliertheit von Strophentypen, Weibchenpräferenzen und die Reaktionen der territorialen Männchen. - Weiterhin wurde ein Modell zur kulturellen Evolution des Buchfinkengesangs programmiert, um die Rolle der Einflussfaktoren, wie Fehlerquote, Abwanderungsrate und Laufzeit zu ermitteln. Der Wandel des Dialektes erfolgt graduell in Raum und Zeit. Daher sind keine scharfen Dialektgrenzen anzutreffen. Trotz dieser Tatsache markieren die etablierten Strophentypen die Population. 50 % der Juvenilen siedeln am Geburtsort, auf diese Weise bleibt der Dialekt erhalten und Inzest wird vermieden. -Analysiert man das Repertoire benachbarten Männchen bei isolierten Alleen, so entspricht die Gesangsangleichung in etwa dem Zufall. -Intraindividuelle Vergleiche der quantitativen Parameter des jeweiligen Strophentyps wurden saisonal und annuell durchgeführt. Saisonal konnten für einen Strophentyp ein Trend ermittelt werden. Bei jährlichen Vergleichen konnten intraindividuell ausschließlich nicht signifikante Ergebnisse ermittelt werden, wohingegen die interindividuelle Variation in zwei Fällen signifikant war. In einem Fall bestand ein Trend und in einem weiteren Fall war die Variationsunterschiede nicht signifikant. - Der Verlauf der Brutsaison lässt sich an der jährlichen Gesangsaktivität nachvollziehen.
Using individual-based modeling to understand grassland diversity and resilience in the Anthropocene
(2020)
The world’s grassland systems are increasingly threatened by anthropogenic change. Susceptible to a variety of different stressors, from land-use intensification to climate change, understanding the mechanisms driving the maintenance of these systems’ biodiversity and stability, and how these mechanisms may shift under human-mediated disturbance, is thus critical for successfully navigating the next century. Within this dissertation, I use an individual-based and spatially-explicit model of grassland community assembly (IBC-grass) to examine several processes, thought key to understanding their biodiversity and stability and how it changes under stress. In the first chapter of my thesis, I examine the conditions under which intraspecific trait variation influences the diversity of simulated grassland communities. In the second and third chapters of my thesis, I shift focus towards understanding how belowground herbivores influence the stability of these grassland systems to either a disturbance that results in increased, stochastic, plant mortality, or eutrophication.
Intraspecific trait variation (ITV), or variation in trait values between individuals of the same species, is fundamental to the structure of ecological communities. However, because it has historically been difficult to incorporate into theoretical and statistical models, it has remained largely overlooked in community-level analyses. This reality is quickly shifting, however, as a consensus of research suggests that it may compose a sizeable proportion of the total variation within an ecological community and that it may play a critical role in determining if species coexist. Despite this increasing awareness that ITV matters, there is little consensus of the magnitude and direction of its influence. Therefore, to better understand how ITV changes the assembly of grassland communities, in the first chapter of my thesis, I incorporate it into an established, individual-based grassland community model, simulating both pairwise invasion experiments as well as the assembly of communities with varying initial diversities. By varying the amount of ITV in these species’ functional traits, I examine the magnitude and direction of ITV’s influence on pairwise invasibility and community coexistence. During pairwise invasion, ITV enables the weakest species to more frequently invade the competitively superior species, however, this influence does not generally scale to the community level. Indeed, unless the community has low alpha- and beta- diversity, there will be little effect of ITV in bolstering diversity. In these situations, since the trait axis is sparsely filled, the competitively inferior may suffer less competition and therefore ITV may buffer the persistence and abundance of these species for some time.
In the second and third chapters of my thesis, I model how one of the most ubiquitous trophic interactions within grasslands, herbivory belowground, influences their diversity and stability. Until recently, the fundamental difficulty in studying a process within the soil has left belowground herbivory “out of sight, out of mind.” This dilemma presents an opportunity for simulation models to explore how this understudied process may alter community dynamics. In the second chapter of my thesis, I implement belowground herbivory – represented by the weekly removal of plant biomass – into IBC-grass. Then, by introducing a pulse disturbance, modelled as the stochastic mortality of some percentage of the plant community, I observe how the presence of belowground herbivores influences the resistance and recovery of Shannon diversity in these communities. I find that high resource, low diversity, communities are significantly more destabilized by the presence of belowground herbivores after disturbance. Depending on the timing of the disturbance and whether the grassland’s seed bank persists for more than one season, the impact of the disturbance – and subsequently the influence of the herbivores – can be greatly reduced. However, because human-mediated eutrophication increases the amount of resources in the soil, thus pressuring grassland systems, our results suggest that the influence of these herbivores may become more important over time.
In the third chapter of my thesis, I delve further into understanding the mechanistic underpinnings of belowground herbivores on the diversity of grasslands by replicating an empirical mesocosm experiment that crosses the presence of herbivores above- and below-ground with eutrophication. I show that while aboveground herbivory, as predicted by theory and frequently observed in experiments, mitigates the impact of eutrophication on species diversity, belowground herbivores counterintuitively reduce biodiversity. Indeed, this influence positively interacts with the eutrophication process, amplifying its negative impact on diversity. I discovered the mechanism underlying this surprising pattern to be that, as the herbivores consume roots, they increase the proportion of root resources to root biomass. Because root competition is often symmetric, herbivory fails to mitigate any asymmetries in the plants’ competitive dynamics. However, since the remaining roots have more abundant access to resources, the plants’ competition shifts aboveground, towards asymmetric competition for light. This leads the community towards a low-diversity state, composed of mostly high-performance, large plant species. We further argue that this pattern will emerge unless the plants’ root competition is asymmetric, in which case, like its counterpart aboveground, belowground herbivory may buffer diversity by reducing this asymmetry between the competitively superior and inferior plants.
I conclude my dissertation by discussing the implications of my research on the state of the art in intraspecific trait variation and belowground herbivory, with emphasis on the necessity of more diverse theory development in the study of these fundamental interactions. My results suggest that the influence of these processes on the biodiversity and stability of grassland systems is underappreciated and multidimensional, and must be thoroughly explored if researchers wish to predict how the world’s grasslands will respond to anthropogenic change. Further, should researchers myopically focus on understanding central ecological interactions through only mathematically tractable analyses, they may miss entire suites of potential coexistence mechanisms that can increase the coviability of species, potentially leading to coexistence over ecologically-significant timespans. Individual-based modelling, therefore, with its focus on individual interactions, will prove a critical tool in the coming decades for understanding how local interactions scale to larger contexts, and how these interactions shape ecological communities and further predicting how these systems will change under human-mediated stress.
Water is essential to life and thus, an essential resource. However, freshwater resources are limited and their maintenance is crucial. Pollution with chemicals and pathogens through urbanization and a growing population impair the quality of freshwater. Furthermore, water can serve as vector for the transmission of pathogens resulting in water-borne illness.
The Interdisciplinary Research Group III – "Water" of the Leibniz alliance project INFECTIONS‘21 investigated water as a hub for pathogens focusing on Clostridioides difficile and avian influenza A viruses that may be shed into the water. Another aim of this study was to characterize the bacterial communities in a wastewater treatment plant (WWTP) of the capital Berlin, Germany to further assess potential health risks associated with wastewater management practices.
Bacterial communities of WWTP inflow and effluent differed significantly. The proportion of fecal/enteric bacteria was relatively low and OTUs related to potential enteric pathogens were largely removed from inflow to effluent. However, a health risk might exist as an increased relative abundance of potential pathogenic Legionella spp. such as L. lytica was observed. Three Clostridioides difficile isolates from wastewater inflow and an urban bathing lake in Berlin (‗Weisser See‘) were obtained and sequenced. The two isolates from the wastewater did not carry toxin genes, whereas the isolate from the lake was positive for the toxin genes. All three isolates were closely related to human strains. This indicates a potential, but rather sporadic health risk. Avian influenza A viruses were detected in 38.8% of sediment samples by PCR, but virus isolation failed. An experiment with inoculated freshwater and sediment samples showed that virus isolation from sediment requires relatively high virus concentrations and worked much better in Madin-Darby Canine Kidney (MDCK) cell cultures than in embryonated chicken eggs, but low titre of influenza contamination in freshwater samples was sufficient to recover virus.
In conclusion, this work revealed potential health risks coming from bacterial groups with pathogenic potential such as Legionella spp. whose relative abundance is higher in the released effluent than in the inflow of the investigated WWTP. It further indicates that water bodies such as wastewater and lake sediments can serve as reservoir and vector, even for non-typical water-borne or water-transmitted pathogens such as C. difficile.
Die 11beta-HSD1 reguliert intrazellulär die Cortisolkonzentration durch Regeneration von Cortison z.B. aus dem Blutkreislauf, zu Cortisol. Daher stellt diese ein wichtiges Element in der Glucocorticoid-vermittelten Genregulation dar. Die 11beta-HSD1 wird ubiquitär exprimiert, auf hohem Niveau besonders in Leber, Fettgewebe und glatten Muskelzellen. Insbesondere die Bedeutung der 11beta-HSD1 in Leber und Fettgewebe konnte mehrfach nachgewiesen werden. In der Leber führte eine erhöhte Aktivität aufgrund einer Überexpression in Mäusen zu einer verstärkten Gluconeogeneserate. Des Weiteren konnte gezeigt werden, dass eine erhöhte Expression und erhöhte Enzymaktivität der 11beta-HSD1 im subkutanen und viszeralen Fettgewebe assoziiert ist mit Fettleibigkeit, Insulinresistenz und Dyslipidämie. Über die Regulation ist jedoch noch wenig bekannt. Zur Untersuchung der Promotoraktivität wurde der Promotorbereich von -3034 bis +188, vor und nach dem Translations- und Transkriptionsstart, der 11beta-HSD1 kloniert. 8 Promotorfragmente wurden mittels Dual-Luciferase-Assay in humanen HepG2-Zellen sowie undifferenzierten und differenzierten murinen 3T3-L1-Zellen untersucht. Anschließend wurde mittels nicht-radioaktiven EMSA die Bindung des TATA-Binding Proteins (TBP) sowie von CCAAT/Enhancer-Binding-Proteinen (C/EBP) an ausgewählte Promotorregionen analysiert. Nach der Charakterisierung des Promotors wurden spezifische endogene und exogene Regulatoren untersucht. Fettsäuren modifizieren die Entstehung von Adipositas und Insulinresistenz. Ihre Wirkung wird u.a. PPARgamma-abhängig vermittelt und kann durch das Inkretin (Glucose-dependent insulinotropic Peptide) GIP modifiziert werden. So wurden die Effekte von unterschiedlichen Fettsäuren, vom PPARgamma Agonisten Rosiglitazon sowie dem Inkretin GIP auf die Expression und Enzymaktivität der 11beta-HSD1 untersucht. Dies wurde in-vitro-, tierexperimentell und in humanen in-vivo-Studien realisiert. Zuletzt wurden 2 Single Nucleotide Polymorphismen (SNP) im Promotorbereich der 11beta-HSD1 in der Zellkultur im Hinblick auf potentielle Funktionalität analysiert sowie die Assoziation mit Diabetes mellitus Typ 2 und Körpergewicht in der MeSyBePo-Kohorte bei rund 1.800 Personen untersucht. Die Luciferase-Assays zeigten basal eine zell-spezifische Regulation der 11beta-HSD1, wobei in allen 3 untersuchten Zelltypen die Bindung eines Repressors nachgewiesen werden konnte. Zudem konnte eine mögliche Bindung des TBPs sowie von C/EBP-Proteinen an verschiedene Positionen gezeigt werden. Die Transaktivierungsassays mit den C/EBP-Proteinen -alpha, -beta und -delta zeigten eben-falls eine zellspezifische Regulation des 11beta-HSD1-Promotors. Die Aktivität und Expression der 11beta-HSD1 wurde durch die hier untersuchten endogenen und exogenen Faktoren spezifisch modifiziert, was sowohl in-vitro als auch in-vivo in unterschiedlichen Modellsystemen dargestellt werden konnte. Die Charakterisierung der MeSyBePo-Kohorte ergab keine direkten Assoziationen zwischen Polymorphismus und klinischem Phänotyp, jedoch Tendenzen für eine erhöhtes Körper-gewicht und Typ 2 Diabetes mellitus in Abhängigkeit des Genotyps. Der Promotor der 11beta-HSD1 konnte aufgrund der Daten aus den Luciferaseassays sowie den Daten aus den EMSA-Analysen näher charakterisiert werden. Dieser zeigt eine variable und zell-spezifische Regulation. Ein wichtiger Regulator stellen insbesondere in den HepG2-Zellen die C/EBP-Proteine -alpha, -beta und -delta dar. Aus den in-vivo-Studien ergab sich eine Regulation der 11beta-HSD1 durch endogene, exogene und pharmakologische Substanzen, die durch die Zellkulturversuche bestätigt und näher charakterisiert werden konnten.
Alle Organismen sind für ihr Überleben auf Metalle angewiesen. Hierbei gibt es für jedes Metall einen Konzentrationsbereich, der das Optimum zwischen Metallmangel, -bedarf und -toxizität darstellt. Es gilt mittlerweile als erwiesen, dass alle Organismen zur Aufrechterhaltung des Metallgleichgewichts ein komplexes Netzwerk von Proteinen und niedermolekularen Verbindungen entwickelt haben. Die molekularen Komponenten dieses Netzwerks sind nur zu einem Teil bekannt und charakterisiert: In den letzten Jahren wurden einige Proteinfamilien identifiziert, deren Mitglieder Metalle durch Lipidmembranen transportieren. Eine dieser Metalltransporterfamilien ist die Cation Diffusion Facilitator (CDF)-Familie: Alle charakterisierten Mitglieder exportieren Metalle aus dem Zytoplasma – entweder in zelluläre Kompartimente oder aus der Zelle heraus. Von den zwölf Mitgliedern dieser Familie in Arabidopsis thaliana (A. thaliana) – Metall Toleranz Protein (MTP)-1 bis -12 – wurden bisher AtMTP1 und AtMTP3 charakterisiert. In dieser Arbeit wird die Charakterisierung von AtMTP2 beschrieben. Wie die homologen Proteine AtMTP1 und AtMTP3 führt AtMTP2 zu Zn-Toleranz, wenn es heterolog in Zn-sensitiven Hefemutanten exprimiert wird. Mit AtMTP2 transformierte Hefemutanten zeigten darüber hinaus erhöhte Co-Toleranz. Expression von chimären AtMTP2/GFP Fusionsproteinen in Hefe, A.thaliana protoplasten und in stabil transformierten A.thalinana Planzenlinien deutet auf Lokalisation of AtMTP2 in Membranen des Endoplasmatischen Retikulums (ER) hin, wenn GFP an den C-Terminus von MTP2 fusioniert wird. Fusion of GFP an den N-Terminus von AtMTP2 führte zu Lokalisation in der vakuolären Membran, was wahrscheinlichsten auf Fehllokalisierung durch Maskierung eines ER-Retentionsmotivs (XXRR) am N-Terminus von AtMTP2 zurückgeht. Dies legt nahe, dass AtMTP2 die erwähnten Metalle in das Endomembransystem der Zelle transportieren kann. Eine gewebespezifische Lokalisierung wurde mit Pflanzen durchgeführt, die das β-Glucuronidase (GUS)-Reporterprotein bzw. chimäre Fusionsproteine aus EGFP und AtMTP2 unter Kontrolle des nativen pMTP2-Promotors exprimierten. Diese Experimente bestätigten zum einen, dass der pMTP2-Promotor nur unter Zn-Defizienz aktiv ist. GUS-Aktivität wurde unter diesen Bedingungen in zwei Zonen der Wurzelspitze beobachtet: in den isodiametrischen Zellen der meristematischen Zone und in der beginnenden Wurzelhaarzone. Darüber hinaus konnte gezeigt werden, dass die EGFP-Fusionsproteine unter Kontrolle des nativen pMTP2-Promotors nur in epidermalen Zellen exprimiert werden. Für eine homozygote Knockout- Linie, mtp2-S3, konnte bisher kein eindeutiger Phänotyp identifiziert werden. Auf Grundlage der bisher durchgeführten Charakterisierung von AtMTP2 erscheinen zwei Modelle der Funktion von AtMTP2 in der Pflanze möglich: AtMTP2 könnte essentiell für die Versorgung des ER mit Zn unter Zn-Mangelbedingungen sein. Hierfür spricht, dass AtMTP2 in jungen, teilungsaktiven und damit Zn-benötigenden Wurzelzonen exprimiert wird. Die auf die Epidermis beschränkte Lokalisation könnte bei diesem Modell auf die Möglichkeit der zwischenzellulären Zn-Verteilung innerhalb des ER über Desmotubules hindeuten. Alternativ könnte AtMTP2 eine Funktion bei der Detoxifizierung von Zn unter Zn-Schock Bedingungen haben: Es ist bekannt, dass unter Zn- Mangelbedingungen die Expression der zellulären Zn-Aufnahmesysteme hochreguliert wird. Wenn nun die Zn-Verfügbarkeit im Boden z. B durch eine pH-Änderung innerhalb kurzer Zeit stark ansteigt, besteht die Notwendigkeit der Entgiftung von Zn innerhalb der Zelle, bis der starke Einstrom von Zn ins Zytoplasma durch die Deaktivierung der Zn-Aufnahmesysteme und einer geringeren Expression in der Pflanze gedrosselt ist. Ein ähnlicher Mechanismus wurde in der Bäckerhefe S. cerevisae beschrieben, in der darüber hinaus ein Zn-Transporter verstärkt exprimiert wird, der Zn durch Transport in die Vakuole entgiften kann. Es ist durchaus möglich, dass in Arabidopsis AtMTP2 die Zn-Detoxifizierung unter diesen speziellen Bedingungen durch Zn-Transport in das ER oder die Vakuole vermittelt. Zur Identifikation weiterer Komponenten des Metallhomöostasenetzwerks sind verschiedene Ansätze denkbar. In dieser Arbeit wurde in Hefe ein heterologer Screen durchgeführt, um Interaktoren für vier Mitglieder der Arabidopsis-CDF-Familie zu identifizieren. Unter den 11 im Hefesystem bestätigten Kandidaten befindet sich mit AtSPL1 ein AtMTP1-Interaktionskandidat, der möglicherweise eine Rolle bei der Cu-,Zn-Homöostase spielt. Als wahrscheinliche AtMTP3-Interaktionskandidaten wurde die c”-Untereinheit der vakuolären H+-ATPase AtVHA identifiziert sowie mit AtNPSN13 ein Protein, das vermutlich eine Rolle bei Fusionen von Vesikeln mit Zielmembranen spielt. Ein anderer Ansatz zur Identifikation neuer Metallhomöostasegene ist die vergleichende Elementanalyse von natürlichen oder mutagenisierten Pflanzenpopulationen. Voraussetzung für diesen Ansatz ist die schnelle und genaue Analyse des Elementgehalts von Pflanzen. Eine etablierte Methode zur simultanen Bestimmung von bis zu 65 Elementen in einer Probe ist die Inductively Coupled Plasma Optical Emission Spectrometry (ICP OES). Der limitierende Faktor für einen hohen Probendurchsatz ist die Notwendigkeit, Proben für die Analyse zu verflüssigen. Eine alternative Methode der Probenzuführung zum Analysegerät ist die elektrothermale Verdampfung (ETV) der Probe. Zur weitgehend automatisierten Analyse von Pflanzenmaterial mit minimiertem Arbeitsaufwand wurde eine Methode entwickelt, die auf der Kopplung der ETV mit der ICP OES basiert.
Arachidonsäurelipoxygenasen (ALOX-Isoformen) sind Lipid-peroxidierenden Enzyme, die bei der Zelldifferenzierung und bei der Pathogenese verschiedener Erkrankungen bedeutsam sind. Im menschlichen Genom gibt es sechs funktionelle ALOX-Gene, die als Einzelkopiegene vorliegen. Für jedes humane ALOX-Gen gibt es ein orthologes Mausgen. Obwohl sich die sechs humanen ALOX-Isoformen strukturell sehr ähnlich sind, unterscheiden sich ihre funktionellen Eigenschaften deutlich voneinander. In der vorliegenden Arbeit wurden vier unterschiedliche Fragestellungen zum Vorkommen, zur biologischen Rolle und zur Evolutionsabhängigkeit der enzymatischen Eigenschaften von Säugetier-ALOX-Isoformen untersucht:
1) Spitzhörnchen (Tupaiidae) sind evolutionär näher mit dem Menschen verwandt als Nagetiere und wurden deshalb als Alternativmodelle für die Untersuchung menschlicher Erkrankungen vorgeschlagen. In dieser Arbeit wurde erstmals der Arachidonsäurestoffwechsel von Spitzhörnchen untersucht. Dabei wurde festgestellt, dass im Genom von Tupaia belangeri vier unterschiedliche ALOX15-Gene vorkommen und die Enzyme sich hinsichtlich ihrer katalytischen Eigenschaften ähneln. Diese genomische Vielfalt, die weder beim Menschen noch bei Mäusen vorhanden ist, erschwert die funktionellen Untersuchungen zur biologischen Rolle des ALOX15-Weges. Damit scheint Tupaia belangeri kein geeigneteres Tiermodel für die Untersuchung des ALOX15-Weges des Menschen zu sein.
2) Entsprechend der Evolutionshypothese können Säugetier-ALOX15-Orthologe in Arachidonsäure-12-lipoxygenierende- und Arachidonsäure-15-lipoxygenierende Enzyme eingeteilt werden. Dabei exprimieren Säugetierspezies, die einen höheren Evolutionsgrad als Gibbons aufweisen, Arachidonsäure-15-lipoxygenierende ALOX15-Orthologe, während evolutionär weniger weit entwickelte Säugetiere Arachidonsäure-12 lipoxygenierende Enzyme besitzen. In dieser Arbeit wurden elf neue ALOX15-Orthologe als rekombinante Proteine exprimiert und funktionell charakterisiert. Die erhaltenen Ergebnisse fügen sich widerspruchsfrei in die Evolutionshypothese ein und verbreitern deren experimentelle Basis. Die experimentellen Daten bestätigen auch das Triadenkonzept.
3) Da humane und murine ALOX15B-Orthologe unterschiedliche funktionelle Eigenschaften aufweisen, können Ergebnisse aus murinen Krankheitsmodellen zur biologischen Rolle der ALOX15B nicht direkt auf den Menschen übertragen werden. Um die ALOX15B-Orthologen von Maus und Mensch funktionell einander anzugleichen, wurden im Rahmen der vorliegenden Arbeit Knock-in Mäuse durch die In vivo Mutagenese mittels CRISPR/Cas9-Technik hergestellt. Diese exprimieren eine humanisierte Mutante (Doppelmutation von Tyrosin603Asparaginsäure+Histidin604Valin) der murinen Alox15b. Diese Mäuse waren lebens- und fortpflanzungsfähig, zeigten aber geschlechtsspezifische Unterschiede zu ausgekreuzten Wildtyp-Kontrolltieren im Rahmen ihre Individualentwicklung.
4) In vorhergehenden Untersuchungen zur Rolle der ALOX15B in Rahmen der Entzündungsreaktion wurde eine antiinflammatorische Wirkung des Enzyms postuliert. In der vorliegenden Arbeit wurde untersucht, ob eine Humanisierung der murinen Alox15b die Entzündungsreaktion in zwei verschiedenen murinen Entzündungsmodellen beeinflusst. Eine Humanisierung der murinen Alox15b führte zu einer verstärkten Ausbildung von Entzündungssymptomen im induzierten Dextran-Natrium-Sulfat-Kolitismodell. Im Gegensatz dazu bewirkte die Humanisierung der Alox15b eine Abschwächung der Entzündungssymptome im Freund‘schen Adjuvans Pfotenödemmodell. Diese Daten deuten darauf hin, dass sich die Rolle der ALOX15B in verschiedenen Entzündungsmodellen unterscheidet.
Even though the structure of the plant cell wall is by and large quite well characterized, its synthesis and regulation remains largely obscure. However, it is accepted that the building blocks of the polysaccharidic part of the plant cell wall are nucleotide sugars. Thus to gain more insight into the cell wall biosynthesis, in the first part of this thesis, plant genes possibly involved in the nucleotide sugar interconversion pathway were identified using a bioinformatics approach and characterized in plants, mainly in Arabidopsis. For the computational identification profile hidden markov models were extracted from the Pfam and TIGR databases. Mainly with these, plant genes were identified facilitating the “hmmer” program. Several gene families were identified and three were further characterized, the UDP-rhamnose synthase (RHM), UDP-glucuronic acid epimerase (GAE) and the myo-inositol oxygenase (MIOX) families. For the three-membered RHM family relative ubiquitous expression was shown using variuos methods. For one of these genes, RHM2, T-DNA lines could be obtained. Moreover, the transcription of the whole family was downregulated facilitating an RNAi approach. In both cases a alteration of cell wall typic polysaccharides and developmental changes could be shown. In the case of the rhm2 mutant these were restricted to the seed or the seed mucilage, whereas the RNAi plants showed profound changes in the whole plant. In the case of the six-membered GAE family, the gene expressed to the highest level (GAE6) was cloned, expressed heterologously and its function was characterized. Thus, it could be shown that GAE6 encodes for an enzyme responsible for the conversion of UDP-glucuronic acid to UDP-galacturonic acid. However, a change in transcript level of variuos GAE family members achieved by T-DNA insertions (gae2, gae5, gae6), overexpression (GAE6) or an RNAi approach, targeting the whole family, did not reveal any robust changes in the cell wall. Contrary to the other two families the MIOX gene family had to be identified using a BLAST based approach due to the lack of enough suitable candidate genes for building a hidden markov model. An initial bioinformatic characterization was performed which will lead to further insights into this pathway. In total it was possible to identify the two gene families which are involved in the synthesis of the two pectin backbone sugars galacturonic acid and rhamnose. Moreover with the identification of the MIOX genes a genefamily, important for the supply of nucleotide sugar precursors was identified. In a second part of this thesis publicly available microarray datasets were analyzed with respect to co-responsive behavior of transcripts on a global basis using nearly 10,000 genes. The data has been made available to the community in form of a database providing additional statistical and visualization tools (http://csbdb.mpimp-golm.mpg.de). Using the framework of the database to identify nucleotide sugar converting genes indicated that co-response might be used for identification of novel genes involved in cell wall synthesis based on already known genes.
Mit der vorliegenden Arbeit sollten mit Hilfe elektronenmikroskopischer Methoden verschiedene Liposomen-DNA-Komplexe zum Gentransfer charakterisiert sowie die Aufnahme und Verteilung in der Zellkultur untersucht werden. Dabei waren vor allem solche Präparationen von besonderem Interesse, die in unserer Arbeitsgruppe 'Drug Targeting' getestet oder entwickelt und verwendet wurden, wie Sendai-Virus Liposomen (HVJ-Liposomen), Virosomen sowie DAC-Chol und DOCSPER-Liposomen als Vertreter der kationischen Lipide. Im ersten Teil der Arbeit wurden fusogene Liposomen und Virosomen charakterisiert. Bei diesen Untersuchungen wurden folgende Ergebnisse erzielt: ·Sendai-Viren fusionieren mit Liposomen unterschiedlicher Lipidzusammensetzung. ·Die daraus resultierenden HVJ-Liposomen sind mit elektronenmikroskopischen Methoden identifizierbar. ·Die Spikes auf den HVJ-Liposomen besitzen fusogene Eigenschaften. ·HVJ-Liposomen eignen sich auf Grund der geringen Ausbeute sowie der geringen Transfektionseffizienz nicht zum in vitro Gentransfer. ·Virosomen stellen einen weiteren Typ fusogener Gentransfervesikel dar. ·Ihre Größe und fusogenen Eigenschaften sind abhängig von der externen Zugabe einer optimierten Lipidmischung. ·Im Innenraum der Virosomen kann mit Poly-L-Lysin vorkomplexierte DNA verkapselt werden. ·Die fusogenen Eigenschaften der Virosomen wurden mit Hilfe immunelektronenmikroskopischer Techniken und monoklonaler Antikörper gegen Hämagglutinin/Neuraminidase und das Fusionsprotein sowie mit polyklonalen Antiseren gezeigt. ·An Hand goldmarkierter DNA sind Virosomen nach der Transfektion in der Zelle nachweisbar. Da in unserer Arbeitsgruppe bevorzugt kationische Liposomen zum Gentransfer verwendet werden, wurde auch die Struktur der Liposomen untersucht und folgende Ergebnisse dokumentiert: ·Die Struktur und die Größe kationischer Liposomen werden hauptsächlich durch die Lipidzusammensetzung bestimmt. ·Die Bildung von Liposomen-DNA-Komplexen ist mit einer Größenzunahme der Komplexe gekoppelt. ·Die Anzahl gebundener Plasmide steigt mit der Größe der Lipoplexe. ·Gentransferaktive Lipopolyplexe (mit Protaminsulfat komplexierte DNA und DAC-Chol- Liposomen) sind kleiner als Lipoplexe. Ihre Struktur wird von der Zusammensetzung bestimmt. Eine weitere wichtige Frage betrifft den Weg der Gencarrier in der Zelle. Kenntnisse über diese Vorgänge sind vorteilhaft, um die einzelnen Schritte zu verstehen und möglichst gezielt zu verbessern. Bei der Untersuchung der Partikel im Hinblick auf zelluläre Barrieren beim Gentransfer konnten folgende Ergebnisse erzielt werden: ·Die Bindung der Partikel an die Zellmembran und Aufnahme sind abhängig von den eingesetzten Zellen und Komplexen sowie derInkubationszeit. ·Die Aufnahme erfolgt über endozytotische Mechanismen, wobei Lipopolyplexe schneller als Lipoplexe in die Zellen gelangen. Nicht alle gebundenen Komplexe werden aufgenommen. ·Die aufgenommenen Partikel befinden sich in Endosomen und werden ins Innere der Zelle transportiert. ·Freisetzung der DNA und Eintritt in den Zellkern über Kernporen konnte nicht beobachtet werden. ·DNA-haltige Vesikel in Kernnähe deuten auf einen weiteren Mechanismus hin (Vesikeltransfer zum Zellkern).
Auf dem Weg der genetischen Information stellt die Translation der RNA in eine Aminosäuresequenz den letzten Schritt dar. In Chloroplasten, den grünen Organellen der Pflanzenzellen, findet ein Großteil der Regulation der Genexpression auf Ebene der Initiation dieses Schrittes statt. Eine Vielzahl von Eigenschaften der RNA und von Faktoren, die an die RNA binden, entfalten einen Einfluss auf diesen Schritt. Bisher unvollständig aufgeklärt ist die Rolle einer konservierten Nukleotidsequenz in der untranslatierten Region der RNA -- der Shine-Dalgarno-Sequenz. Diese stellt in Bakterien, wie z.B. E. coli als Ribosomenbindestelle sicher, dass Ribosomen den Anfang der zu translatierenden Sequenz zuverlässig erkennen. Im Rahmen dieser Arbeit wurden diverse DNA-Konstrukte in Plastiden von Tabak eingebracht. Hierzu zählten Konstrukte, die sowohl eine erhöhte Anzahl von Ribosomenbindestellen enthielten als auch vermehrte Startpunkte der Translation. Zusätzlich wurden Konstrukte hergestellt, die die Situation von mehreren zu translatierenden Regionen in der RNA nachstellten. Es konnte festgestellt werden, dass plastidäre Ribosomen die strangaufwärts gelegenen Translationsstartpunkte bevorzugen -- im Gegensatz zu E. coli, wo alle Startpunkte gleichmäßig genutzt wurden. Hierdurch zeigten die prokaryotischen Ribosomen aus Chloroplasten, die sich aus bakteriellen Systemen ableiten, Eigenschaften von eukaryotischen Ribosomen. Ein zweites Teilprojekt dieser Arbeit beschäftigte sich mit der Inkompatibilität von Chloroplasten mit dem Kerngenom. In Kreuzungen von Arten der Gattung Pelargonium fielen Kombinationen auf, bei denen die Tochterpflanzen bleiche Blattbereiche bis hin zu vollständig weißen Pflanzen zeigten. Dieses Phänomen wird als Bastardbleichheit bezeichnet. In der Gattung Pelargonium werden Chloroplasten von beiden Elternteilen an die Tochterpflanzen vererbt. Da das Phänomen der Bastardbleichheit nur in einem der Plastiden vorkommt, nicht jedoch im anderen in der gleichen Pflanze, muss von einem Effekt ausgegangen werden, der von Plastiden ausgeht. Die Interaktionen zwischen Zellkern und Chloroplasten sind offensichtlich stark gestört. Zur detaillierten Untersuchung dieses Effekts wurde die Nukleotidsequenz von drei Chloroplastengenomen aufgeklärt. Es konnte eine Reihe von Sequenzunterschieden der Genome ermittelt werden. Aus diesen wurde eine Reihe von Unterschieden beobachtet, die einen solchen Effekt zur Folge haben können. Aus diesen Unterschieden wurde eine Reihe von potentiellen Kandidatengenen zusammengestellt, die in weiteren Arbeiten auf ihre Rolle in der Entstehung der Bastardbleichheit untersucht werden.
Untersuchungen PEG-basierter thermo-responsiver Polymeroberflächen zur Steuerung der Zelladhäsion
(2010)
Moderne Methoden für die Einzelzellanalyse werden dank der fortschreitenden Weiterentwicklung immer sensitiver. Dabei steigen jedoch auch die Anforderungen an das Probenmaterial. Viele Aufbereitungsprotokolle adhärenter Zellen beinhalten eine enzymatische Spaltung der Oberflächenproteine, um die Ablösung vom Zellkultursubstrat zu ermöglichen. Verschiedene Methoden, wie die Patch-Clamp-Technik oder eine auf der Markierung extrazellulärer Domänen von Membranproteinen basierende Durchflusszytometrie können dann nur noch eingeschränkt eingesetzt werden. Daher ist die Etablierung neuer Zellablösemethoden dringend notwendig. In der vorliegenden Arbeit werden erstmals PEG-basierte thermo-responsive Oberflächen erfolgreich für die Zellkultur eingesetzt. Dabei wird das zerstörungsfreie Ablösen verschiedener Zelllinien von den Oberflächen durch Temperatursenkung realisiert. Die Funktionalität der Oberflächen wird durch Variation der Polymerstruktur, sowie der Konzentration der Beschichtungslösung, durch Beschichtung der Oberflächen mit einem zelladhäsionsfördernden Protein (Fibronektin) und durch Adsorption zelladhäsionsvermittelnder Peptide (RGD) optimiert. Um den Zellablösungsprozess detaillierter zu untersuchen, wird hier zum ersten Mal der direkte Zellkontakt mit thermo-responsiven Oberflächen mittels oberflächensensitiver Mikroskopie (TIRAF) sichtbar gemacht. Mit dieser Technik sind die exakte Quantifizierung und die Analyse der Reduktion der Zelladhäsionsfläche während des Abkühlens möglich. Hierbei werden in Abhängigkeit von der Zelllinie Unterschiede im Zellverhalten während des Ablösens festgestellt: Zellen, wie eine Brustkrebszelllinie und eine Ovarzelllinie, die bekanntermaßen stärker mit ihrer Umgebung in Kontakt treten, vergrößern im Verlauf des Beobachtungszeitraumes den Abstand zwischen Zellmembran und Oberfläche, reduzieren jedoch ihre Zell-Substratkontaktfläche kaum. Mausfibroblasten hingegen verkleinern drastisch die Zelladhäsionsfläche. Der Ablösungsprozess wird vermutlich aktiv von den Zellen gesteuert. Diese Annahme wird durch zwei Beobachtungen gestützt: Erstens verläuft die Reduktion der Zelladhäsionsfläche bei Einschränkung des Zellmetabolismus durch eine Temperatursenkung auf 4 °C verzögert. Zweitens hinterlassen die Zellen Spuren, die nach dem Ablösen der Zellen auf den Oberflächen zurückbleiben. Mittels Kombination von TIRAF- und TIRF-Mikroskopie werden die Zelladhäsionsfläche und die Aktinstruktur gleichzeitig beobachtet. Die Verknüpfung beider Methoden stellt eine neue Möglichkeit dar, intrazelluläre Prozesse mit der Zellablösung von thermo-responsiven Oberflächen zu korrelieren.
Leaf senescence is an active process required for plant survival, and it is flexibly controlled, allowing plant adaptation to environmental conditions. Although senescence is largely an age-dependent process, it can be triggered by environmental signals and stresses. Leaf senescence coordinates the breakdown and turnover of many cellular components, allowing a massive remobilization and recycling of nutrients from senescing tissues to other organs (e.g., young leaves, roots, and seeds), thus enhancing the fitness of the plant. Such metabolic coordination requires a tight regulation of gene expression. One important mechanism for the regulation of gene expression is at the transcriptional level via transcription factors (TFs). The NAC TF family (NAM, ATAF, CUC) includes various members that show elevated expression during senescence, including ORE1 (ANAC092/AtNAC2) among others. ORE1 was first reported in a screen for mutants with delayed senescence (oresara1, 2, 3, and 11). It was named after the Korean word “oresara,” meaning “long-living,” and abbreviated to ORE1, 2, 3, and 11, respectively. Although the pivotal role of ORE1 in controlling leaf senescence has recently been demonstrated, the underlying molecular mechanisms and the pathways it regulates are still poorly understood. To unravel the signaling cascade through which ORE1 exerts its function, we analyzed particular features of regulatory pathways up-stream and down-stream of ORE1. We identified characteristic spatial and temporal expression patterns of ORE1 that are conserved in Arabidopsis thaliana and Nicotiana tabacum and that link ORE1 expression to senescence as well as to salt stress. We proved that ORE1 positively regulates natural and dark-induced senescence. Molecular characterization of the ORE1 promoter in silico and experimentally suggested a role of the 5’UTR in mediating ORE1 expression. ORE1 is a putative substrate of a calcium-dependent protein kinase named CKOR (unpublished data). Promising data revealed a positive regulation of putative ORE1 targets by CKOR, suggesting the phosphorylation of ORE1 as a requirement for its regulation. Additionally, as part of the ORE1 up-stream regulatory pathway, we identified the NAC TF ATAF1 which was able to transactivate the ORE1 promoter in vivo. Expression studies using chemically inducible ORE1 overexpression lines and transactivation assays employing leaf mesophyll cell protoplasts provided information on target genes whose expression was rapidly induced upon ORE1 induction. First, a set of target genes was established and referred to as early responding in the ORE1 regulatory network. The consensus binding site (BS) of ORE1 was characterized. Analysis of some putative targets revealed the presence of ORE1 BSs in their promoters and the in vitro and in vivo binding of ORE1 to their promoters. Among these putative target genes, BIFUNCTIONAL NUCLEASE I (BFN1) and VND-Interacting2 (VNI2) were further characterized. The expression of BFN1 was found to be dependent on the presence of ORE1. Our results provide convincing data which support a role for BFN1 as a direct target of ORE1. Characterization of VNI2 in age-dependent and stress-induced senescence revealed ORE1 as a key up-stream regulator since it can bind and activate VNI2 expression in vivo and in vitro. Furthermore, VNI2 was able to promote or delay senescence depending on the presence of an activation domain located in its C-terminal region. The plasticity of this gene might include alternative splicing (AS) to regulate its function in different organs and at different developmental stages, particularly during senescence. A model is proposed on the molecular mechanism governing the dual role of VNI2 during senescence.
The sequencing of the human genome in the early 2000s led to an increased interest in cheap and fast sequencing technologies. This interest culminated in the advent of next generation sequencing (NGS). A number of different NGS platforms have arisen since then all promising to do the same thing, i.e. produce large amounts of genetic information for relatively low costs compared to more traditional methods such as Sanger sequencing. The capabilities of NGS meant that researchers were no longer bound to species for which a lot of previous work had already been done (e.g. model organisms and humans) enabling a shift in research towards more novel and diverse species of interest. This capability has greatly benefitted many fields within the biological sciences, one of which being the field of evolutionary biology. Researchers have begun to move away from the study of laboratory model organisms to wild, natural populations and species which has greatly expanded our knowledge of evolution. NGS boasts a number of benefits over more traditional sequencing approaches. The main benefit comes from the capability to generate information for drastically more loci for a fraction of the cost. This is hugely beneficial to the study of wild animals as, even when large numbers of individuals are unobtainable, the amount of data produced still allows for accurate, reliable population and species level results from a small selection of individuals.
The use of NGS to study species for which little to no previous research has been carried out on and the production of novel evolutionary information and reference datasets for the greater scientific community were the focuses of this thesis. Two studies in this thesis focused on producing novel mitochondrial genomes from shotgun sequencing data through iterative mapping, bypassing the need for a close relative to serve as a reference sequence. These mitochondrial genomes were then used to infer species level relationships through phylogenetic analyses. The first of these studies involved reconstructing a complete mitochondrial genome of the bat eared fox (Otocyon megalotis). Phylogenetic analyses of the mitochondrial genome confidently placed the bat eared fox as sister to the clade consisting of the raccoon dog and true foxes within the canidae family. The next study also involved reconstructing a mitochondrial genome but in this case from the extinct Macrauchenia of South America. As this study utilised ancient DNA, it involved a lot of parameter testing, quality controls and strict thresholds to obtain a near complete mitochondrial genome devoid of contamination known to plague ancient DNA studies. Phylogenetic analyses confidently placed Macrauchenia as sister to all living representatives of Perissodactyla with a divergence time of ~66 million years ago. The third and final study of this thesis involved de novo assemblies of both nuclear and mitochondrial genomes from brown and striped hyena and focussed on demographic, genetic diversity and population genomic analyses within the brown hyena. Previous studies of the brown hyena hinted at very low levels of genomic diversity and, perhaps due to this, were unable to find any notable population structure across its range. By incorporating a large number of genetic loci, in the form of complete nuclear genomes, population structure within the brown hyena was uncovered. On top of this, genomic diversity levels were compared to a number of other species. Results showed the brown hyena to have the lowest genomic diversity out of all species included in the study which was perhaps caused by a continuous and ongoing decline in effective population size that started about one million years ago and dramatically accelerated towards the end of the Pleistocene.
The studies within this thesis show the power NGS sequencing has and its utility within evolutionary biology. The most notable capabilities outlined in this thesis involve the study of species for which no reference data is available and in the production of large amounts of data, providing evolutionary answers at the species and population level that data produced using more traditional techniques simply could not.
Plants are unable to move away from unwanted environments and therefore have to locally adapt to changing conditions. Arabidopsis thaliana (Arabidopsis), a model organism in plant biology, has been able to rapidly colonize a wide spectrum of environments with different biotic and abiotic challenges. In recent years, natural variation in Arabidopsis has shown to be an excellent resource to study genes underlying adaptive traits and hybridization’s impact on natural diversity. Studies on Arabidopsis hybrids have provided information on the genetic basis of hybrid incompatibilities and heterosis, as well as inheritance patterns in hybrids. However, previous studies have focused mainly on global accessions and yet much remains to be known about variation happening within a local growth habitat. In my PhD, I investigated the impact of heterozygosity at a local collection site of Arabidopsis and its role in local adaptation. I focused on two different projects, both including hybrids among Arabidopsis individuals collected around Tübingen in Southern Germany. The first project sought to understand the impact of hybridization on metabolism and growth within a local Arabidopsis collection site. For this, the inheritance patterns in primary and secondary metabolism, together with rosette size of full diallel crosses among seven parents originating from Southern Germany were analyzed. In comparison to primary metabolites, compounds from secondary metabolism were more variable and showed pronounced non-additive inheritance patterns. In addition, defense metabolites, mainly glucosinolates, displayed the highest degree of variation from the midparent values and were positively correlated with a proxy for plant size.
In the second project, the role of ACCELERATED CELL DEATH 6 (ACD6) in the defense response pathway of Arabidopsis necrotic hybrids was further characterized. Allelic interactions of ACD6 have been previously linked to hybrid necrosis, both among global and local Arabidopsis accessions. Hence, I characterized the early metabolic and ionic changes induced by ACD6, together with marker gene expression assays of physiological responses linked to its activation. An upregulation of simple sugars and metabolites linked to non-enzymatic antioxidants and the TCA cycle were detected, together with putrescine and acids linked to abiotic stress responses. Senescence was found to be induced earlier in necrotic hybrids and cytoplasmic calcium signaling was unaffected in response to temperature. In parallel, GFP-tagged constructs of ACD6 were developed.
This work therefore gave novel insights on the role of heterozygosity in natural variation and adaptation and expanded our current knowledge on the physiological and molecular responses associated with ACD6 activation.
Predators can have numerical and behavioral effects on prey animals. While numerical effects are well explored, the impact of behavioral effects is unclear. Furthermore, behavioral effects are generally either analyzed with a focus on single individuals or with a focus on consequences for other trophic levels. Thereby, the impact of fear on the level of prey communities is overlooked, despite potential consequences for conservation and nature management. In order to improve our understanding of predator-prey interactions, an assessment of the consequences of fear in shaping prey community structures is crucial.
In this thesis, I evaluated how fear alters prey space use, community structure and composition, focusing on terrestrial mammals. By integrating landscapes of fear in an existing individual-based and spatially-explicit model, I simulated community assembly of prey animals via individual home range formation. The model comprises multiple hierarchical levels from individual home range behavior to patterns of prey community structure and composition. The mechanistic approach of the model allowed for the identification of underlying mechanism driving prey community responses under fear.
My results show that fear modified prey space use and community patterns. Under fear, prey animals shifted their home ranges towards safer areas of the landscape. Furthermore, fear decreased the total biomass and the diversity of the prey community and reinforced shifts in community composition towards smaller animals. These effects could be mediated by an increasing availability of refuges in the landscape. Under landscape changes, such as habitat loss and fragmentation, fear intensified negative effects on prey communities. Prey communities in risky environments were subject to a non-proportional diversity loss of up to 30% if fear was taken into account. Regarding habitat properties, I found that well-connected, large safe patches can reduce the negative consequences of habitat loss and fragmentation on prey communities. Including variation in risk perception between prey animals had consequences on prey space use. Animals with a high risk perception predominantly used safe areas of the landscape, while animals with a low risk perception preferred areas with a high food availability. On the community level, prey diversity was higher in heterogeneous landscapes of fear if individuals varied in their risk perception compared to scenarios in which all individuals had the same risk perception.
Overall, my findings give a first, comprehensive assessment of the role of fear in shaping prey communities. The linkage between individual home range behavior and patterns at the community level allows for a mechanistic understanding of the underlying processes. My results underline the importance of the structure of the landscape of fear as a key driver of prey community responses, especially if the habitat is threatened by landscape changes. Furthermore, I show that individual landscapes of fear can improve our understanding of the consequences of trait variation on community structures. Regarding conservation and nature management, my results support calls for modern conservation approaches that go beyond single species and address the protection of biotic interactions.
The movement of organisms has formed our planet like few other processes. Movements shape populations, communities, entire ecosystems, and guarantee fundamental ecosystem functions and services, like seed dispersal and pollination. Global, regional and local anthropogenic impacts influence animal movements across ecosystems all around the world. In particular, land-use modification, like habitat loss and fragmentation disrupt movements between habitats with profound consequences, from increased disease transmissions to reduced species richness and abundance. However, neither the influence of anthropogenic change on animal movement processes nor the resulting effects on ecosystems are well understood. Therefore, we need a coherent understanding of organismal movement processes and their underlying mechanisms to predict and prevent altered animal movements and their consequences for ecosystem functions.
In this thesis I aim at understanding the influence of anthropogenically caused land-use change on animal movement processes and their underlying mechanisms. In particular, I am interested in the synergistic influence of large-scale landscape structure and fine-scale habitat features on basic-level movement behaviours (e.g. the daily amount of time spend running, foraging, and resting) and their emerging higher-level movements (home range formation). Based on my findings, I identify the likely consequences of altered animal movements that lead to the loss of species richness and abundances.
The study system of my thesis are hares in agricultural landscapes. European brown hares (Lepus europaeus) are perfectly suited to study animal movements in agricultural landscapes, as hares are hermerophiles and prefer open habitats. They have historically thrived in agricultural landscapes, but their numbers are in decline. Agricultural areas are undergoing strong land-use changes due to increasing food demand and fast developing agricultural technologies. They are already the largest land-use class, covering 38% of the world’s terrestrial surface. To consider the relevance of a given landscape structure for animal movement behaviour I selected two differently structured agricultural landscapes – a simple landscape in Northern Germany with large fields and few landscape elements (e.g. hedges and tree stands), and a complex landscape in Southern Germany with small fields and many landscape elements.
I applied GPS devices (hourly fixes) with internal high-resolution accelerometers (4 min samples) to track hares, receiving an almost continuous observation of the animals’ behaviours via acceleration analyses. I used the spatial and behavioural information in combination with remote sensing data (normalized difference vegetation index, or NDVI, a proxy for resource availability), generating an almost complete idea of what the animal was doing when, why and where. Apart from landscape structure (represented by the two differently structured study areas), I specifically tested whether the following fine-scale habitat features influence animal movements: resource, agricultural management events, habitat diversity, and habitat structure.
My results show that, irrespective of the movement process or mechanism and the type of fine-scale habitat features, landscape structure was the overarching variable influencing hare movement behaviour. High resource variability forces hares to enlarge their home ranges, but only in the simple and not in the complex landscape. Agricultural management events result in home range shifts in both landscapes, but force hares to increase their home ranges only in the simple landscape. Also the preference of habitat patches with low vegetation and the avoidance of high vegetation, was stronger in the simple landscape. High and dense crop fields restricted hare movements temporarily to very local and small habitat patch remnants. Such insuperable barriers can separate habitat patches that were previously connected by mobile links. Hence, the transport of nutrients and genetic material is temporarily disrupted. This mechanism is also working on a global scale, as human induced changes from habitat loss and fragmentation to expanding monocultures cause a reduction in animal movements worldwide.
The mechanisms behind those findings show that higher-level movements, like increasing home ranges, emerge from underlying basic-level movements, like the behavioural modes. An increasing landscape simplicity first acts on the behavioural modes, i.e. hares run and forage more, but have less time to rest. Hence, the emergence of increased home range sizes in simple landscapes is based on an increased proportion of time running and foraging, largely due to longer travelling times between distant habitats and scarce resource items in the landscape. This relationship was especially strong during the reproductive phase, demonstrating the importance of high-quality habitat for reproduction and the need to keep up self-maintenance first, in low quality areas. These changes in movement behaviour may release a cascade of processes that start with more time being allocated to running and foraging, resulting into an increased energy expenditure and may lead to a decline in individual fitness. A decrease in individual fitness and reproductive output will ultimately affect population viability leading to local extinctions.
In conclusion, I show that landscape structure has one of the most important effects on hare movement behaviour. Synergistic effects of landscape structure, and fine-scale habitat features, first affect and modify basic-level movement behaviours, that can scales up to altered higher-level movements and may even lead to the decline of species richness and abundances, and the disruption of ecosystem functions. Understanding the connection between movement mechanisms and processes can help to predict and prevent anthropogenically induced changes in movement behaviour. With regard to the paramount importance of landscape structure, I strongly recommend to decrease the size of agricultural fields and increase crop diversity. On the small-scale, conservation policies should assure the year round provision of areas with low vegetation height and high quality forage. This could be done by generating wildflower strips and additional (semi-) natural habitat patches. This will not only help to increase the populations of European brown hares and other farmland species, but also ensure and protects the continuity of mobile links and their intrinsic value for sustaining important ecosystem functions and services.
This is a publication-based dissertation comprising three original research stud-ies (one published, one submitted and one ready for submission; status March 2019). The dissertation introduces a generic computer model as a tool to investigate the behaviour and population dynamics of animals in cyclic environments. The model is further employed for analysing how migratory birds respond to various scenarios of altered food supply under global change. Here, ecological and evolutionary time-scales are considered, as well as the biological constraints and trade-offs the individual faces, which ultimately shape response dynamics at the population level. Further, the effect of fine-scale temporal patterns in re-source supply are studied, which is challenging to achieve experimentally. My findings predict population declines, altered behavioural timing and negative carry-over effects arising in migratory birds under global change. They thus stress the need for intensified research on how ecological mechanisms are affected by global change and for effective conservation measures for migratory birds. The open-source modelling software created for this dissertation can now be used for other taxa and related research questions. Overall, this thesis improves our mechanistic understanding of the impacts of global change on migratory birds as one prerequisite to comprehend ongoing global biodiversity loss. The research results are discussed in a broader ecological and scientific context in a concluding synthesis chapter.
The nutrient exchange between plant and fungus is the key element of the arbuscular mycorrhizal (AM) symbiosis. The fungus improves the plant’s uptake of mineral nutrients, mainly phosphate, and water, while the plant provides the fungus with photosynthetically assimilated carbohydrates. Still, the knowledge about the mechanisms of the nutrient exchange between the symbiotic partners is very limited. Therefore, transport processes of both, the plant and the fungal partner, are investigated in this study. In order to enhance the understanding of the molecular basis underlying this tight interaction between the roots of Medicago truncatula and the AM fungus Rhizophagus irregularis, genes involved in transport processes of both symbiotic partners are analysed here. The AM-specific regulation and cell-specific expression of potential transporter genes of M. truncatula that were found to be specifically regulated in arbuscule-containing cells and in non-arbusculated cells of mycorrhizal roots was confirmed. A model for the carbon allocation in mycorrhizal roots is suggested, in which carbohydrates are mobilized in non-arbusculated cells and symplastically provided to the arbuscule-containing cells. New insights into the mechanisms of the carbohydrate allocation were gained by the analysis of hexose/H+ symporter MtHxt1 which is regulated in distinct cells of mycorrhizal roots. Metabolite profiling of leaves and roots of a knock-out mutant, hxt1, showed that it indeed does have an impact on the carbohydrate balance in the course of the symbiosis throughout the whole plant, and on the interaction with the fungal partner. The primary metabolite profile of M. truncatula was shown to be altered significantly in response to mycorrhizal colonization. Additionally, molecular mechanisms determining the progress of the interaction in the fungal partner of the AM symbiosis were investigated. The R. irregularis transcriptome in planta and in extraradical tissues gave new insight into genes that are differentially expressed in these two fungal tissues. Over 3200 fungal transcripts with a significantly altered expression level in laser capture microdissection-collected arbuscules compared to extraradical tissues were identified. Among them, six previously unknown specifically regulated potential transporter genes were found. These are likely to play a role in the nutrient exchange between plant and fungus. While the substrates of three potential MFS transporters are as yet unknown, two potential sugar transporters are might play a role in the carbohydrate flow towards the fungal partner. In summary, this study provides new insights into transport processes between plant and fungus in the course of the AM symbiosis, analysing M. truncatula on the transcript and metabolite level, and provides a dataset of the R. irregularis transcriptome in planta, providing a high amount of new information for future works.
Die Strahlentherapie ist neben der Chemotherapie und einer operativen Entfernung die stärkste Waffe für die Bekämpfung bösartiger Tumore in der Krebsmedizin. Nach Herz-Kreislauf-Erkrankungen ist Krebs die zweithäufigste Todesursache in der westlichen Welt, wobei Prostatakrebs heutzutage die häufigste, männliche Krebserkrankung darstellt. Trotz technologischer Fortschritte der radiologischen Verfahren kann es noch viele Jahre nach einer Radiotherapie zu einem Rezidiv kommen, was zum Teil auf die hohe Resistenzfähigkeit einzelner, entarteter Zellen des lokal vorkommenden Tumors zurückgeführt werden kann. Obwohl die moderne Strahlenbiologie viele Aspekte der Resistenzmechanismen näher beleuchtet hat, bleiben Fragestellungen, speziell über das zeitliche Ansprechen eines Tumors auf ionisierende Strahlung, größtenteils unbeantwortet, da systemweite Untersuchungen nur begrenzt vorliegen. Als Zellmodelle wurden vier Prostata-Krebszelllinien (PC3, DuCaP, DU-145, RWPE-1) mit unterschiedlichen Strahlungsempfindlichkeiten kultiviert und auf ihre Überlebensfähigkeit nach ionisierender Bestrahlung durch einen Trypanblau- und MTT-Vitalitätstest geprüft. Die proliferative Kapazität wurde mit einem Koloniebildungstest bestimmt. Die PC3 Zelllinie, als Strahlungsresistente, und die DuCaP Zelllinie, als Strahlungssensitive, zeigten dabei die größten Differenzen bezüglich der Strahlungsempfindlichkeit. Auf Grundlage dieser Ergebnisse wurden die beiden Zelllinien ausgewählt, um anhand ihrer transkriptomweiten Genexpressionen, eine Identifizierung potentieller Marker für die Prognose der Effizienz einer Strahlentherapie zu ermöglichen. Weiterhin wurde mit der PC3 Zelllinie ein Zeitreihenexperiment durchgeführt, wobei zu 8 verschiedenen Zeitpunkten nach Bestrahlung mit 1 Gy die mRNA mittels einer Hochdurchsatz-Sequenzierung quantifiziert wurde, um das dynamisch zeitversetzte Genexpressionsverhalten auf Resistenzmechanismen untersuchen zu können. Durch das Setzen eines Fold Change Grenzwertes in Verbindung mit einem P-Wert < 0,01 konnten aus 10.966 aktiven Genen 730 signifikant differentiell exprimierte Gene bestimmt werden, von denen 305 stärker in der PC3 und 425 stärker in der DuCaP Zelllinie exprimiert werden. Innerhalb dieser 730 Gene sind viele stressassoziierte Gene wiederzufinden, wie bspw. die beiden Transmembranproteingene CA9 und CA12. Durch Berechnung eines Netzwerk-Scores konnten aus den GO- und KEGG-Datenbanken interessante Kategorien und Netzwerke abgeleitet werden, wobei insbesondere die GO-Kategorien Aldehyd-Dehydrogenase [NAD(P)+] Aktivität (GO:0004030) und der KEGG-Stoffwechselweg der O-Glykan Biosynthese (hsa00512) als relevante Netzwerke auffällig wurden. Durch eine weitere Interaktionsanalyse konnten zwei vielversprechende Netzwerke mit den Transkriptionsfaktoren JUN und FOS als zentrale Elemente identifiziert werden. Zum besseren Verständnis des dynamisch zeitversetzten Ansprechens der strahlungsresistenten PC3 Zelllinie auf ionisierende Strahlung, konnten anhand der 10.840 exprimierten Gene und ihrer Expressionsprofile über 8 Zeitpunkte interessante Einblicke erzielt werden. Während es innerhalb von 30 min (00:00 - 00:30) nach Bestrahlung zu einer schnellen Runterregulierung der globalen Genexpression kommt, folgen in den drei darauffolgenden Zeitabschnitten (00:30 - 01:03; 01:03 - 02:12; 02:12 - 04:38) spezifische Expressionserhöhungen, die eine Aktivierung schützender Netzwerke, wie die Hochregulierung der DNA-Reparatursysteme oder die Arretierung des Zellzyklus, auslösen. In den abschließenden drei Zeitbereichen (04:38 - 09:43; 09:43 - 20:25; 20:25 - 42:35) liegt wiederum eine Ausgewogenheit zwischen Induzierung und Supprimierung vor, wobei die absoluten Genexpressionsveränderungen ansteigen. Beim Vergleich der Genexpressionen kurz vor der Bestrahlung mit dem letzten Zeitpunkt (00:00 - 42:53) liegen mit 2.670 die meisten verändert exprimierten Gene vor, was einer massiven, systemweiten Genexpressionsänderung entspricht. Signalwege wie die ATM-Regulierung des Zellzyklus und der Apoptose, des NRF2-Signalwegs nach oxidativer Stresseinwirkung und die DNA-Reparaturmechanismen der homologen Rekombination, des nicht-homologen End Joinings, der MisMatch-, der Basen-Exzision- und der Strang-Exzision-Reparatur spielen bei der zellulären Antwort eine tragende Rolle. Äußerst interessant sind weiterhin die hohen Aktivitäten RNA-gesteuerter Ereignisse, insbesondere von small nucleolar RNAs und Pseudouridin-Prozessen. Demnach scheinen diese RNA-modifizierenden Netzwerke einen bisher unbekannten funktionalen und schützenden Einfluss auf das Zellüberleben nach ionisierender Bestrahlung zu haben. All diese schützenden Netzwerke mit ihren zeitspezifischen Interaktionen sind essentiell für das Zellüberleben nach Einwirkung von oxidativem Stress und zeigen ein komplexes aber im Einklang befindliches Zusammenspiel vieler Einzelkomponenten zu einem systemweit ablaufenden Programm.
Die Etablierung der Transkription von kompletten Genen auf planaren Oberflächen soll eine Verbindung zwischen der Mikroarraytechnologie und der Transkriptomforschung herstellen. Darüber hinaus kann mit diesem Verfahren ein Brückenschlag zwischen der Synthese der Gene und ihrer kodierenden Proteine auf einer Oberfläche erfolgen. Alle transkribierten RNAs wurden mittels RT-PCR in cDNA umgeschrieben und in einer genspezifischen PCR amplifiziert. Die PCR-Produkte wurden hierfür entweder per Hand oder maschinell auf die Oberfläche transferiert. Über eine Oberflächen-PCR war es möglich, die Gensequenz des Reportergens EGFP direkt auf der Oberfläche zu synthetisieren und anschließend zu transkribieren. Somit war eine Transkription mit weniger als 1 ng an Matrize möglich. Der Vorteil einer Oberflächen-Transkription gegenüber der in Lösung liegt in der mehrfachen Verwendung der immobilisierten Matrize, wie sie in dieser Arbeit dreimal erfolgreich absolviert wurde. Die Oberflächen-Translation des EGFP-Gens konnte ebenfalls zweimal an einer immobilisierten Matrize gezeigt werden, wobei Zweifel über eine echte Festphasen-Translation nicht ausgeräumt werden konnten. Zusammenfassend kann festgestellt werden, dass die Transkription und Translation von immobilisierten Gensequenzen auf planaren Oberflächen möglich ist, wofür die linearen Matrizen direkt auf der Oberfläche synthetisiert werden können.
For more than two centuries, plant ecologists have aimed to understand how environmental gradients and biotic interactions shape the distribution and co-occurrence of plant species. In recent years, functional trait–based approaches have been increasingly used to predict patterns of species co-occurrence and species distributions along environmental gradients (trait–environment relationships). Functional traits are measurable properties at the individual level that correlate well with important processes. Thus, they allow us to identify general patterns by synthesizing studies across specific taxonomic compositions, thereby fostering our understanding of the underlying processes of species assembly. However, the importance of specific processes have been shown to be highly dependent on the spatial scale under consideration. In particular, it remains uncertain which mechanisms drive species assembly and allow for plant species coexistence at smaller, more local spatial scales. Furthermore, there is still no consensus on how particular environmental gradients affect the trait composition of plant communities. For example, increasing drought because of climate change is predicted to be a main threat to plant diversity, although it remains unclear which traits of species respond to increasing aridity. Similarly, there is conflicting evidence of how soil fertilization affects the traits related to establishment ability (e.g., seed mass). In this cumulative dissertation, I present three empirical trait-based studies that investigate specific research questions in order to improve our understanding of species distributions along environmental gradients.
In the first case study, I analyze how annual species assemble at the local scale and how environmental heterogeneity affects different facets of biodiversity—i.e. taxonomic, functional, and phylogenetic diversity—at different spatial scales. The study was conducted in a semi-arid environment at the transition zone between desert and Mediterranean ecosystems that features a sharp precipitation gradient (Israel). Different null model analyses revealed strong support for environmentally driven species assembly at the local scale, since species with similar traits tended to co-occur and shared high abundances within microsites (trait convergence). A phylogenetic approach, which assumes that closely related species are functionally more similar to each other than distantly related ones, partly supported these results. However, I observed that species abundances within microsites were, surprisingly, more evenly distributed across the phylogenetic tree than expected (phylogenetic overdispersion). Furthermore, I showed that environmental heterogeneity has a positive effect on diversity, which was higher on functional than on taxonomic diversity and increased with spatial scale. The results of this case study indicate that environmental heterogeneity may act as a stabilizing factor to maintain species diversity at local scales, since it influenced species distribution according to their traits and positively influenced diversity. All results were constant along the precipitation gradient.
In the second case study (same study system as case study one), I explore the trait responses of two Mediterranean annuals (Geropogon hybridus and Crupina crupinastrum) along a precipitation gradient that is comparable to the maximum changes in precipitation predicted to occur by the end of this century (i.e., −30%). The heterocarpic G. hybridus showed strong trends in seed traits, suggesting that dispersal ability increased with aridity. By contrast, the homocarpic C. crupinastrum showed only a decrease in plant height as aridity increased, while leaf traits of both species showed no consistent pattern along the precipitation gradient. Furthermore, variance decomposition of traits revealed that most of the trait variation observed in the study system was actually found within populations. I conclude that trait responses towards aridity are highly species-specific and that the amount of precipitation is not the most striking environmental factor at this particular scale.
In the third case study, I assess how soil fertilization mediates—directly by increased nutrient addition and indirectly by increased competition—the effect of seed mass on establishment ability. For this experiment, I used 22 species differing in seed mass from dry grasslands in northeastern Germany and analyzed the interacting effects of seed mass with nutrient availability and competition on four key components of seedling establishment: seedling emergence, time of seedling emergence, seedling survival, and seedling growth. (Time of) seedling emergence was not affected by seed mass. However, I observed that the positive effect of seed mass on seedling survival is lowered under conditions of high nutrient availability, whereas the positive effect of seed mass on seedling growth was only reduced by competition. Based on these findings, I developed a conceptual model of how seed mass should change along a soil fertility gradient in order to reconcile conflicting findings from the literature. In this model, seed mass shows a U-shaped pattern along the soil fertility gradient as a result of changing nutrient availability and competition.
Overall, the three case studies highlight the role of environmental factors on species distribution and co-occurrence. Moreover, the findings of this thesis indicate that spatial heterogeneity at local scales may act as a stabilizing factor that allows species with different traits to coexist. In the concluding discussion, I critically debate intraspecific trait variability in plant community ecology, the use of phylogenetic relationships and easily measured key functional traits as a proxy for species’ niches. Finally, I offer my outlook for the future of functional plant community research.
The increasing introduction of non-native plant species may pose a threat to local biodiversity. However, the basis of successful plant invasion is not conclusively understood, especially since these plant species can adapt to the new range within a short period of time despite impoverished genetic diversity of the starting populations. In this context, DNA methylation is considered promising to explain successful adaptation mechanisms in the new habitat. DNA methylation is a heritable variation in gene expression without changing the underlying genetic information. Thus, DNA methylation is considered a so-called epigenetic mechanism, but has been studied in mainly clonally reproducing plant species or genetic model plants. An understanding of this epigenetic mechanism in the context of non-native, predominantly sexually reproducing plant species might help to expand knowledge in biodiversity research on the interaction between plants and their habitats and, based on this, may enable more precise measures in conservation biology.
For my studies, I combined chemical DNA demethylation of field-collected seed material from predominantly sexually reproducing species and rearing offsping under common climatic conditions to examine DNA methylation in an ecological-evolutionary context. The contrast of chemically treated (demethylated) plants, whose variation in DNA methylation was artificially reduced, and untreated control plants of the same species allowed me to study the impact of this mechanism on adaptive trait differentiation and local adaptation. With this experimental background, I conducted three studies examining the effect of DNA methylation in non-native species along a climatic gradient and also between climatically divergent regions.
The first study focused on adaptive trait differentiation in two invasive perennial goldenrod species, Solidago canadensis sensu latu and S. gigantea AITON, along a climate gradient of more than 1000 km in length in Central Europe. I found population differences in flowering timing, plant height, and biomass in the temporally longer-established S. canadensis, but only in the number of regrowing shoots for S. gigantea. While S. canadensis did not show any population structure, I was able to identify three genetic groups along this climatic gradient in S. gigantea. Surprisingly, demethylated plants of both species showed no change in the majority of traits studied. In the subsequent second study, I focused on the longer-established goldenrod species S. canadensis and used molecular analyses to infer spatial epigenetic and genetic population differences in the same specimens from the previous study. I found weak genetic but no epigenetic spatial variation between populations. Additionally, I was able to identify one genetic marker and one epigenetic marker putatively susceptible to selection. However, the results of this study reconfirmed that the epigenetic mechanism of DNA methylation appears to be hardly involved in adaptive processes within the new range in S. canadensis.
Finally, I conducted a third study in which I reciprocally transplanted short-lived plant species between two climatically divergent regions in Germany to investigate local adaptation at the plant family level. For this purpose, I used four plant families (Amaranthaceae, Asteraceae, Plantaginaceae, Solanaceae) and here I additionally compared between non-native and native plant species. Seeds were transplanted to regions with a distance of more than 600 kilometers and had either a temperate-oceanic or a temperate-continental climate. In this study, some species were found to be maladapted to their own local conditions, both in non-native and native plant species alike. In demethylated individuals of the plant species studied, DNA methylation had inconsistent but species-specific effects on survival and biomass production. The results of this study highlight that DNA methylation did not make a substantial contribution to local adaptation in the non-native as well as native species studied.
In summary, my work showed that DNA methylation plays a negligible role in both adaptive trait variation along climatic gradients and local adaptation in non-native plant species that either exhibit a high degree of genetic variation or rely mainly on sexual reproduction with low clonal propagation. I was able to show that the adaptive success of these non-native plant species can hardly be explained by DNA methylation, but could be a possible consequence of multiple introductions, dispersal corridors and meta-population dynamics. Similarly, my results illustrate that the use of plant species that do not predominantly reproduce clonally and are not model plants is essential to characterize the effect size of epigenetic mechanisms in an ecological-evolutionary context.
This work presents mathematical and computational approaches to cover various aspects of metabolic network modelling, especially regarding the limited availability of detailed kinetic knowledge on reaction rates. It is shown that precise mathematical formulations of problems are needed i) to find appropriate and, if possible, efficient algorithms to solve them, and ii) to determine the quality of the found approximate solutions. Furthermore, some means are introduced to gain insights on dynamic properties of metabolic networks either directly from the network structure or by additionally incorporating steady-state information. Finally, an approach to identify key reactions in a metabolic networks is introduced, which helps to develop simple yet useful kinetic models. The rise of novel techniques renders genome sequencing increasingly fast and cheap. In the near future, this will allow to analyze biological networks not only for species but also for individuals. Hence, automatic reconstruction of metabolic networks provides itself as a means for evaluating this huge amount of experimental data. A mathematical formulation as an optimization problem is presented, taking into account existing knowledge and experimental data as well as the probabilistic predictions of various bioinformatical methods. The reconstructed networks are optimized for having large connected components of high accuracy, hence avoiding fragmentation into small isolated subnetworks. The usefulness of this formalism is exemplified on the reconstruction of the sucrose biosynthesis pathway in Chlamydomonas reinhardtii. The problem is shown to be computationally demanding and therefore necessitates efficient approximation algorithms. The problem of minimal nutrient requirements for genome-scale metabolic networks is analyzed. Given a metabolic network and a set of target metabolites, the inverse scope problem has as it objective determining a minimal set of metabolites that have to be provided in order to produce the target metabolites. These target metabolites might stem from experimental measurements and therefore are known to be produced by the metabolic network under study, or are given as the desired end-products of a biotechological application. The inverse scope problem is shown to be computationally hard to solve. However, I assume that the complexity strongly depends on the number of directed cycles within the metabolic network. This might guide the development of efficient approximation algorithms. Assuming mass-action kinetics, chemical reaction network theory (CRNT) allows for eliciting conclusions about multistability directly from the structure of metabolic networks. Although CRNT is based on mass-action kinetics originally, it is shown how to incorporate further reaction schemes by emulating molecular enzyme mechanisms. CRNT is used to compare several models of the Calvin cycle, which differ in size and level of abstraction. Definite results are obtained for small models, but the available set of theorems and algorithms provided by CRNT can not be applied to larger models due to the computational limitations of the currently available implementations of the provided algorithms. Given the stoichiometry of a metabolic network together with steady-state fluxes and concentrations, structural kinetic modelling allows to analyze the dynamic behavior of the metabolic network, even if the explicit rate equations are not known. In particular, this sampling approach is used to study the stabilizing effects of allosteric regulation in a model of human erythrocytes. Furthermore, the reactions of that model can be ranked according to their impact on stability of the steady state. The most important reactions in that respect are identified as hexokinase, phosphofructokinase and pyruvate kinase, which are known to be highly regulated and almost irreversible. Kinetic modelling approaches using standard rate equations are compared and evaluated against reference models for erythrocytes and hepatocytes. The results from this simplified kinetic models can simulate acceptably the temporal behavior for small changes around a given steady state, but fail to capture important characteristics for larger changes. The aforementioned approach to rank reactions according to their influence on stability is used to identify a small number of key reactions. These reactions are modelled in detail, including knowledge about allosteric regulation, while all other reactions were still described by simplified reaction rates. These so-called hybrid models can capture the characteristics of the reference models significantly better than the simplified models alone. The resulting hybrid models might serve as a good starting point for kinetic modelling of genome-scale metabolic networks, as they provide reasonable results in the absence of experimental data, regarding, for instance, allosteric regulations, for a vast majority of enzymatic reactions.
Thermoresponsive Zellkultursubstrate für zeitlich-räumlich gesteuertes Auswachsen neuronaler Zellen
(2019)
Ein wichtiges Ziel der Neurowissenschaften ist das Verständnis der komplexen und zugleich faszinierenden, hochgeordneten Vernetzung der Neurone im Gehirn, welche neuronalen Prozessen, wie zum Beispiel dem Wahrnehmen oder Lernen wie auch Neuropathologien zu Grunde liegt. Für verbesserte neuronale Zellkulturmodelle zur detaillierten Untersuchung dieser Prozesse ist daher die Rekonstruktion von geordneten neuronalen Verbindungen dringend erforderlich. Mit Oberflächenstrukturen aus zellattraktiven und zellabweisenden Beschichtungen können neuronale Zellen und ihre Neuriten in vitro strukturiert werden. Zur Kontrolle der neuronalen Verbindungsrichtung muss das Auswachsen der Axone zu benachbarten Zellen dynamisch gesteuert werden, zum Beispiel über eine veränderliche Zugänglichkeit der Oberfläche.
In dieser Arbeit wurde untersucht, ob mit thermoresponsiven Polymeren (TRP) beschichtete Zellkultursubstrate für eine dynamische Kontrolle des Auswachsens neuronaler Zellen geeignet sind. TRP können über die Temperatur von einem zellabweisenden in einen zellattraktiven Zustand geschaltet werden, womit die Zugänglichkeit der Oberfläche für Zellen dynamisch gesteuert werden kann. Die TRP-Beschichtung wurde mikrostrukturiert, um einzelne oder wenige neuronale Zellen zunächst auf der Oberfläche anzuordnen und das Auswachsen der Zellen und Neuriten über definierte TRP-Bereiche in Abhängigkeit der Temperatur zeitlich und räumlich zu kontrollieren. Das Protokoll wurde mit der neuronalen Zelllinie SH-SY5Y etabliert und auf humane induzierte Neurone übertragen. Die Anordnung der Zellen konnte bei Kultivierung im zellabweisenden Zustand des TRPs für bis zu 7 Tage aufrecht erhalten werden. Durch Schalten des TRPs in den zellattraktiven Zustand konnte das Auswachsen der Neuriten und Zellen zeitlich und räumlich induziert werden. Immunozytochemische Färbungen und Patch-Clamp-Ableitungen der Neurone demonstrierten die einfache Anwendbarkeit und Zellkompatibilität der TRP-Substrate.
Eine präzisere räumliche Kontrolle des Auswachsens der Zellen sollte durch lokales Schalten der TRP-Beschichtung erreicht werden. Dafür wurden Mikroheizchips mit Mikroelektroden zur lokalen Jouleschen Erwärmung der Substratoberfläche entwickelt. Zur Evaluierung der generierten Temperaturprofile wurde eine Temperaturmessmethode entwickelt und die erhobenen Messwerte mit numerisch simulierten Werten abgeglichen. Die Temperaturmessmethode basiert auf einfach zu applizierenden Sol-Gel-Schichten, die den temperatursensitiven Fluoreszenzfarbstoff Rhodamin B enthalten. Sie ermöglicht oberflächennahe Temperaturmessungen in trockener und wässriger Umgebung mit hoher Orts- und Temperaturauflösung. Numerische Simulationen der Temperaturprofile korrelierten gut mit den experimentellen Daten. Auf dieser Basis konnten Geometrie und Material der Mikroelektroden hinsichtlich einer lokal stark begrenzten Temperierung optimiert werden. Ferner wurden für die Kultvierung der Zellen auf den Mikroheizchips eine Zellkulturkammer und Kontaktboard für die elektrische Kontaktierung der Mikroelektroden geschaffen.
Die vorgestellten Ergebnisse demonstrieren erstmalig das enorme Potential thermoresponsiver Zellkultursubstrate für die zeitlich und räumlich gesteuerte Formation geordneter neuronaler Verbindungen in vitro. Zukünftig könnte dies detaillierte Studien zur neuronalen Informationsverarbeitung oder zu Neuropathologien an relevanten, humanen Zellmodellen ermöglichen.
Among the bloom-forming and potentially harmful cyanobacteria, the genus Microcystis represents a most diverse taxon, on the genomic as well as on morphological and secondary metabolite levels. Microcystis communities are composed of a variety of diversified strains. The focus of this study lies on potential interactions between Microcystis representatives and the roles of secondary metabolites in these interaction processes.
The role of secondary metabolites functioning as signaling molecules in the investigated interactions is demonstrated exemplary for the prevalent hepatotoxin microcystin. The extracellular and intracellular roles of microcystin are tested in microarray-based transcriptomic approaches. While an extracellular effect of microcystin on Microcystis transcription is confirmed and connected to a specific gene cluster of another secondary metabolite in this study, the intracellularly occurring microcystin is related with several pathways of the primary metabolism. A clear correlation of a microcystin knockout and the SigE-mediated regulation of carbon metabolism is found. According to the acquired transcriptional data, a model is proposed that postulates the regulating effect of microcystin on transcriptional regulators such as the alternative sigma factor SigE, which in return captures an essential role in sugar catabolism and redox-state regulation.
For the purpose of simulating community conditions as found in the field, Microcystis colonies are isolated from the eutrophic lakes near Potsdam, Germany and established as stably growing under laboratory conditions. In co-habitation simulations, the recently isolated field strain FS2 is shown to specifically induce nearly immediate aggregation reactions in the axenic lab strain Microcystis aeruginosa PCC 7806. In transcriptional studies via microarrays, the induced expression program in PCC 7806 after aggregation induction is shown to involve the reorganization of cell envelope structures, a highly altered nutrient uptake balance and the reorientation of the aggregating cells to a heterotrophic carbon utilization, e.g. via glycolysis. These transcriptional changes are discussed as mechanisms of niche adaptation and acclimation in order to prevent competition for resources.
Protein-metal coordination complexes are well known as active centers in enzymatic catalysis, and to contribute to signal transduction, gas transport, and to hormone function. Additionally, they are now known to contribute as load-bearing cross-links to the mechanical properties of several biological materials, including the jaws of Nereis worms and the byssal threads of marine mussels. The primary aim of this thesis work is to better understand the role of protein-metal cross-links in the mechanical properties of biological materials, using the mussel byssus as a model system. Specifically, the focus is on histidine-metal cross-links as sacrificial bonds in the fibrous core of the byssal thread (Chapter 4) and L-3,4-dihydroxyphenylalanine (DOPA)-metal bonds in the protective thread cuticle (Chapter 5).
Byssal threads are protein fibers, which mussels use to attach to various substrates at the seashore. These relatively stiff fibers have the ability to extend up to about 100 % strain, dissipating large amounts of mechanical energy from crashing waves, for example. Remarkably, following damage from cyclic loading, initial mechanical properties are subsequently recovered by a material-intrinsic self-healing capability. Histidine residues coordinated to transition metal ions in the proteins comprising the fibrous thread core have been suggested as reversible sacrificial bonds that contribute to self-healing; however, this remains to be substantiated in situ. In the first part of this thesis, the role of metal coordination bonds in the thread core was investigated using several spectroscopic methods. In particular, X-ray absorption spectroscopy (XAS) was applied to probe the coordination environment of zinc in Mytilus californianus threads at various stages during stretching and subsequent healing. Analysis of the extended X-ray absorption fine structure (EXAFS) suggests that tensile deformation of threads is correlated with the rupture of Zn-coordination bonds and that self-healing is connected with the reorganization of Zn-coordination bond topologies rather than the mere reformation of Zn-coordination bonds. These findings have interesting implications for the design of self-healing metallopolymers.
The byssus cuticle is a protective coating surrounding the fibrous thread core that is both as hard as an epoxy and extensible up to 100 % strain before cracking. It was shown previously that cuticle stiffness and hardness largely depend on the presence of Fe-DOPA coordination bonds. However, the byssus is known to concentrate a large variety of metals from seawater, some of which are also capable of binding DOPA (e.g. V). Therefore, the question arises whether natural variation of metal composition can affect the mechanical performance of the byssal thread cuticle. To investigate this hypothesis, nanoindentation and confocal Raman spectroscopy were applied to the cuticle of native threads, threads with metals removed (EDTA treated), and threads in which the metal ions in the native tissue were replaced by either Fe or V. Interestingly, replacement of metal ions with either Fe or V leads to the full recovery of native mechanical properties with no statistical difference between each other or the native properties. This likely indicates that a fixed number of metal coordination sites are maintained within the byssal thread cuticle – possibly achieved during thread formation – which may provide an evolutionarily relevant mechanism for maintaining reliable mechanics in an unpredictable environment.
While the dynamic exchange of bonds plays a vital role in the mechanical behavior and self-healing in the thread core by allowing them to act as reversible sacrificial bonds, the compatibility of DOPA with other metals allows an inherent adaptability of the thread cuticle to changing circumstances. The requirements to both of these materials can be met by the dynamic nature of the protein-metal cross-links, whereas covalent cross-linking would fail to provide the adaptability of the cuticle and the self-healing of the core. In summary, these studies of the thread core and the thread cuticle serve to underline the important and dynamic roles of protein-metal coordination in the mechanical function of load-bearing protein fibers, such as the mussel byssus.
Plants and some unicellular algae store carbon in the form of transitory starch on a diurnal basis. The turnover of this glucose polymer is tightly regulated and timely synthesis as well as mobilization is essential to provide energy for heterotrophic growth. Especially for starch degradation, novel enzymes and mechanisms have been proposed recently. However, the catalytic properties of these enzymes and their coordination with metabolic regulation are still to be discovered. This thesis develops theoretical methods in order to interpret and analyze enzymes and their role in starch degradation. In the first part, a novel description of interfacial enzyme catalysis is proposed. Since the initial steps of starch degradation involve reactions at the starch-stroma interface it is necessary to have a framework which allows the derivation of interfacial enzyme rate laws. A cornerstone of the method is the introduction of the available area function - a concept from surface physics - to describe the adsorption step in the catalytic cycle. The method is applied to derive rate laws for two hydrolases, the Beta-amylase (BAM3) and the Isoamylase (DBE/ISA3), as well as to the Glucan, water dikinase (GWD) and a Phosphoglucan phosphatase (DSP/SEX4). The second part uses the interfacial rate laws to formulate a kinetic model of starch degradation. It aims at reproducing the stimulatory effect of reversible phosphorylation by GWD and DSP on the breakdown of the granule. The model can describe the dynamics of interfacial properties during degradation and suggests that interfacial amylopectin side-chains undergo spontaneous helix-coil transitions. Reversible phosphorylation has a synergistic effect on glucan release especially in the early phase dropping off during degradation. Based on the model, the hypothesis is formulated that interfacial phosphorylation is important for the rapid switch from starch synthesis to starch degradation. The third part takes a broader perspective on carbohydrate-active enzymes (CAZymes) but is motivated by the organization of the downstream pathway of starch breakdown. This comprises Alpha-1,4-glucanotransferases (DPE1 and DPE2) and Alpha-glucan-phosphorylases (Pho or PHS) both in the stroma and in the cytosol. CAZymes accept many different substrates and catalyze numerous reactions and therefore cannot be characterized in classical enzymological terms. A concise characterization is provided by conceptually linking statistical thermodynamics and polymer biochemistry. Each reactant is interpreted as an energy level, transitions between which are constrained by the enzymatic mechanisms. Combinations of in vitro assays of polymer-active CAZymes essential for carbon metabolism in plants confirmed the dominance of entropic gradients. The principle of entropy maximization provides a generalization of the equilibrium constant. Stochastic simulations confirm the results and suggest that randomization of metabolites in the cytosolic pool of soluble heteroglycans (SHG) may contribute to a robust integration of fluctuating carbon fluxes coming from chloroplasts.
Adenylates are metabolites with essential function in metabolism and signaling in all living organisms. As Cofactors, they enable thermodynamically unfavorable reactions to be catalyzed enzymatically within cells. Outside the cell, adenylates are involved in signalling processes in animals and emerging evidence suggests similar signaling mechanisms in the plants’ apoplast. Presumably, apoplastic apyrases are involved in this signaling by hydrolyzing the signal mediating molecules ATP and ADP to AMP. This PhD thesis focused on the role of adenylates on metabolism and development of potato (Solanum tuberosum) by using reverse genetics and biochemical approaches. To study the short and long term effect of cellular ATP and the adenylate energy charge on potato tuber metabolism, an apyrase from Escherichia coli targeted into the amyloplast was expressed inducibly and constitutively. Both approaches led to the identification of adaptations to reduced ATP/energy charge levels on the molecular and developmental level. These comprised a reduction of metabolites and pathway fluxes that require significant amounts of ATP, like amino acid or starch synthesis, and an activation of processes that produce ATP, like respiration and an immense increase in the surface-to-volume ratio. To identify extracellular enzymes involved in adenylate conversion, green fluorescent protein and activity localization studies in potato tissue were carried out. It was found that extracellular ATP is imported into the cell by an apoplastic enzyme complement consisting of apyrase, unspecific phosphatase, adenosine nucleosidase and an adenine transport system. By changing the expression of a potato specific apyrase via transgenic approaches, it was found that this enzyme has strong impact on plant and particular tuber development in potato. Whereas metabolite levels were hardly altered, transcript profiling of tubers with reduced apyrase activity revealed a significant upregulation of genes coding for extensins, which are associated with polar growth. The results are discussed in context of adaptive responses of plants to changes in the adenylate levels and the proposed role of apyrase in apoplastic purinergic signaling and ATP salvaging. In summary, this thesis provides insight into adenylate regulated processes within and outside non-photosynthetic plant cells.
The cytoskeleton is an essential component of living cells. It is composed of different types of protein filaments that form complex, dynamically rearranging, and interconnected networks. The cytoskeleton serves a multitude of cellular functions which further depend on the cell context. In animal cells, the cytoskeleton prominently shapes the cell's mechanical properties and movement. In plant cells, in contrast, the presence of a rigid cell wall as well as their larger sizes highlight the role of the cytoskeleton in long-distance intracellular transport. As it provides the basis for cell growth and biomass production, cytoskeletal transport in plant cells is of direct environmental and economical relevance. However, while knowledge about the molecular details of the cytoskeletal transport is growing rapidly, the organizational principles that shape these processes on a whole-cell level remain elusive.
This thesis is devoted to the following question: How does the complex architecture of the plant cytoskeleton relate to its transport functionality? The answer requires a systems level perspective of plant cytoskeletal structure and transport. To this end, I combined state-of-the-art confocal microscopy, quantitative digital image analysis, and mathematically powerful, intuitively accessible graph-theoretical approaches.
This thesis summarizes five of my publications that shed light on the plant cytoskeleton as a transportation network: (1) I developed network-based frameworks for accurate, automated quantification of cytoskeletal structures, applicable in, e.g., genetic or chemical screens; (2) I showed that the actin cytoskeleton displays properties of efficient transport networks, hinting at its biological design principles; (3) Using multi-objective optimization, I demonstrated that different plant cell types sustain cytoskeletal networks with cell-type specific and near-optimal organization; (4) By investigating actual transport of organelles through the cell, I showed that properties of the actin cytoskeleton are predictive of organelle flow and provided quantitative evidence for a coordination of transport at a cellular level; (5) I devised a robust, optimization-based method to identify individual cytoskeletal filaments from a given network representation, allowing the investigation of single filament properties in the network context. The developed methods were made publicly available as open-source software tools.
Altogether, my findings and proposed frameworks provide quantitative, system-level insights into intracellular transport in living cells. Despite my focus on the plant cytoskeleton, the established combination of experimental and theoretical approaches is readily applicable to different organisms. Despite the necessity of detailed molecular studies, only a complementary, systemic perspective, as presented here, enables both understanding of cytoskeletal function in its evolutionary context as well as its future technological control and utilization.
Over the last years there is an increasing awareness that historical land cover changes and associated land use legacies may be important drivers for present-day species richness and biodiversity due to time-delayed extinctions or colonizations in response to historical environmental changes. Historically altered habitat patches may therefore exhibit an extinction debt or colonization credit and can be expected to lose or gain species in the future. However, extinction debts and colonization credits are difficult to detect and their actual magnitudes or payments have rarely been quantified because species richness patterns and dynamics are also shaped by recent environmental conditions and recent environmental changes.
In this thesis we aimed to determine patterns of herb-layer species richness and recent species richness dynamics of forest herb layer plants and link those patterns and dynamics to historical land cover changes and associated land use legacies. The study was conducted in the Prignitz, NE-Germany, where the forest distribution remained stable for the last ca. 100 years but where a) the deciduous forest area had declined by more than 90 per cent (leaving only remnants of "ancient forests"), b) small new forests had been established on former agricultural land ("post-agricultural forests"). Here, we analyzed the relative importance of land use history and associated historical land cover changes for herb layer species richness compared to recent environmental factors and determined magnitudes of extinction debt and colonization credit and their payment in ancient and post-agricultural forests, respectively.
We showed that present-day species richness patterns were still shaped by historical land cover changes that ranged back to more than a century. Although recent environmental conditions were largely comparable we found significantly more forest specialists, species with short-distance dispersal capabilities and clonals in ancient forests than in post-agricultural forests. Those species richness differences were largely contingent to a colonization credit in post-agricultural forests that ranged up to 9 species (average 4.7), while the extinction debt in ancient forests had almost completely been paid. Environmental legacies from historical agricultural land use played a minor role for species richness differences. Instead, patch connectivity was most important. Species richness in ancient forests was still dependent on historical connectivity, indicating a last glimpse of an extinction debt, and the colonization credit was highest in isolated post-agricultural forests. In post-agricultural forests that were better connected or directly adjacent to ancient forest patches the colonization credit was way smaller and we were able to verify a gradual payment of the colonization credit from 2.7 species to 1.5 species over the last six decades.
In semi-arid savannah ecosystems, the vegetation structure and composition, i.e. the architecture of trees, shrubs, grass tussocks and herbaceous plants, offer a great variety of habitats and niches to sustain animal diversity. In the last decades intensive human land use practises like livestock farming have altered the vegetation in savannah ecosystems worldwide. Extensive grazing leads to a reduction of the perennial and herbaceous vegetation cover, which results in an increased availability of bare soil. Both, the missing competition with perennial grasses and the increase of bare soils favour shrub on open ground and lead to area-wide shrub encroachment. As a consequence of the altered vegetation structure and composition, the structural diversity declines. It has been shown that with decreasing structural diversity animal diversity decline across a variety of taxa. Knowledge on the effects of overgrazing on reptiles, which are an important part of the ecosystem, are missing. Furthermore, the impact of habitat degradation on factors of a species population dynamic and life history, e.g., birth rate, survival rate, predation risk, space requirements or behavioural adaptations are poorly known. Therefore, I investigated the impact of overgrazing on the reptile community in the southern Kalahari. Secondly I analysed population dynamics and the behaviour of the Spotted Sand Lizard, Pedioplanis l. lineoocellata. All four chapters clearly demonstrate that habitat degradation caused by overgrazing had a severe negative impact upon (i) the reptile community as a whole and (ii) on population parameters of Pedioplanis l. lineoocellata. Chapter one showed a significant decline of regional reptile diversity and abundance in degraded habitats. In chapter two I demonstrated that P. lineoocellata moves more frequently, spends more time moving and covers larger distances in degraded than in non-degraded habitats. In addition, home range size of the lizard species increases in degraded habitats as shown by chapter three. Finally, chapter four showed the negative impacts of overgrazing on several population parameters of P. lineoocellata. Absolute population size of adult and juvenile lizards, survival rate and birth rate are significantly lower in degraded habitats. Furthermore, the predation risk was greatly increased in degraded habitats. A combination of a variety of aspects can explain the negative impact of habitat degradation on reptiles. First, reduced prey availability negatively affects survival rate, the birth rate and overall abundance. Second, the loss of perennial plant cover leads to a loss of niches and to a reduction of opportunities to thermoregulate. Furthermore, a loss of cover and is associated with increased predation risk. A major finding of my thesis is that the lizard P. lineoocellata can alter its foraging strategy. Species that are able to adapt and change behaviour, such as P. lineoocellata can effectively buffer against changes in their environment. Furthermore, perennial grass cover can be seen as a crucial ecological component of the vegetation in the semi-arid savannah system of the southern Kalahari. If perennial grass cover is reduced to a certain degree reptile diversity will decline and most other aspects of reptile life history will be negatively influenced. Savannah systems are characterised by a mixture of trees, shrubs and perennial grasses. These three vegetation components determine the composition and structure of the vegetation and accordingly influence the faunal diversity. Trees are viewed as keystone structures and focal points of animal activity for a variety of species. Trees supply animals with shelter, shade and food and act as safe sites, nesting sites, observation posts and foraging sites. Recent research demonstrates a positive influence of shrub patches on animal diversity. Moreover, it would seem that intermediate shrub cover can also sustain viable populations in savannah landscapes as has been demonstrated for small carnivores and rodent species. The influence of perennial grasses on faunal diversity did not receive the same attention as the influence of trees and shrubs. In my thesis I didn’t explicitly measure the direct effects of perennial grasses but my results strongly imply that it has an important role. If the perennial grass cover is significantly depleted my results suggest it will negatively influence reptile diversity and abundance and on several populations parameters of P. lineoocellata. Perennial grass cover is associated with the highest prey abundance, reptile diversity and reptile abundance. It provides reptiles both a refuge from predators and opportunities to optimise thermoregulation. The relevance of each of the three vegetation structural elements is different for each taxa and species. In conclusion, I can all three major vegetation structures in the savannah system are important for faunal diversity.
In littoral zones of lakes, multiple processes determine lake ecology and water quality. Lacustrine groundwater discharge (LGD), most frequently taking place in littoral zones, can transport or mobilize nutrients from the sediments and thus contribute significantly to lake eutrophication. Furthermore, lake littoral zones are the habitat of benthic primary producers, namely submerged macrophytes and periphyton, which play a key role in lake food webs and influence lake water quality. Groundwater-mediated nutrient-influx can potentially affect the asymmetric competition between submerged macrophytes and periphyton for light and nutrients. While rooted macrophytes have superior access to sediment nutrients, periphyton can negatively affect macrophytes by shading. LGD may thus facilitate periphyton production at the expense of macrophyte production, although studies on this hypothesized effect are missing.
The research presented in this thesis is aimed at determining how LGD influences periphyton, macrophytes, and the interactions between these benthic producers. Laboratory experiments were combined with field experiments and measurements in an oligo-mesotrophic hard water lake.
In the first study, a general concept was developed based on a literature review of the existing knowledge regarding the potential effects of LGD on nutrients and inorganic and organic carbon loads to lakes, and the effect of these loads on periphyton and macrophytes. The second study includes a field survey and experiment examining the effects of LGD on periphyton in an oligotrophic, stratified hard water lake (Lake Stechlin). This study shows that LGD, by mobilizing phosphorus from the sediments, significantly promotes epiphyton growth, especially at the end of the summer season when epilimnetic phosphorus concentrations are low. The third study focuses on the potential effects of LGD on submerged macrophytes in Lake Stechlin. This study revealed that LGD may have contributed to an observed change in macrophyte community composition and abundance in the shallow littoral areas of the lake. Finally, a laboratory experiment was conducted which mimicked the conditions of a seepage lake. Groundwater circulation was shown to mobilize nutrients from the sediments, which significantly promoted periphyton growth. Macrophyte growth was negatively affected at high periphyton biomasses, confirming the initial hypothesis.
More generally, this thesis shows that groundwater flowing into nutrient-limited lakes may import or mobilize nutrients. These nutrients first promote periphyton, and subsequently provoke radical changes in macrophyte populations before finally having a possible influence on the lake’s trophic state. Hence, the eutrophying effect of groundwater is delayed and, at moderate nutrient loading rates, partly dampened by benthic primary producers. The present research emphasizes the importance and complexity of littoral processes, and the need to further investigate and monitor the benthic environment. As present and future global changes can significantly affect LGD, the understanding of these complex interactions is required for the sustainable management of lake water quality.
This work presents the development of entropy-elastic gelatin based networks in the form of films or scaffolds. The materials have good prospects for biomedical applications, especially in the context of bone regeneration. Entropy-elastic gelatin based hydrogel films with varying crosslinking densities were prepared with tailored mechanical properties. Gelatin was covalently crosslinked above its sol gel transition, which suppressed the gelatin chain helicity. Hexamethylene diisocyanate (HDI) or ethyl ester lysine diisocyanate (LDI) were applied as chemical crosslinkers, and the reaction was conducted either in dimethyl sulfoxide (DMSO) or water. Amorphous films were prepared as measured by Wide Angle X-ray Scattering (WAXS), with tailorable degrees of swelling (Q: 300-800 vol. %) and wet state Young’s modulus (E: 70 740 kPa). Model reactions showed that the crosslinking reaction resulted in a combination of direct crosslinks (3-13 mol.-%), grafting (5-40 mol.-%), and blending of oligoureas (16-67 mol.-%). The knowledge gained with this bulk material was transferred to the integrated process of foaming and crosslinking to obtain porous 3-D gelatin-based scaffolds. For this purpose, a gelatin solution was foamed in the presence of a surfactant, Saponin, and the resulting foam was fixed by chemical crosslinking with a diisocyanate. The amorphous crosslinked scaffolds were synthesized with varied gelatin and HDI concentrations, and analyzed in the dry state by micro computed tomography (µCT, porosity: 65±11–73±14 vol.-%), and scanning electron microscopy (SEM, pore size: 117±28–166±32 µm). Subsequently, the work focused on the characterization of the gelatin scaffolds in conditions relevant to biomedical applications. Scaffolds showed high water uptake (H: 630-1680 wt.-%) with minimal changes in outer dimension. Since a decreased scaffold pore size (115±47–130±49 µm) was revealed using confocal laser scanning microscopy (CLSM) upon wetting, the form stability could be explained. Shape recoverability was observed after removal of stress when compressing wet scaffolds, while dry scaffolds maintained the compressed shape. This was explained by a reduction of the glass transition temperature upon equilibration with water (dynamic mechanical analysis at varied temperature (DMTA)). The composition dependent compression moduli (Ec: 10 50 kPa) were comparable to the bulk micromechanical Young’s moduli, which were measured by atomic force microscopy (AFM). The hydrolytic degradation profile could be adjusted, and a controlled decrease of mechanical properties was observed. Partially-degraded scaffolds displayed an increase of pore size. This was likely due to the pore wall disintegration during degradation, which caused the pores to merge. The scaffold cytotoxicity and immunologic responses were analyzed. The porous scaffolds enabled proliferation of human dermal fibroblasts within the implants (up to 90 µm depth). Furthermore, indirect eluate tests were carried out with L929 cells to quantify the material cytotoxic response. Here, the effect of the sterilization method (Ethylene oxide sterilization), crosslinker, and surfactant were analyzed. Fully cytocompatible scaffolds were obtained by using LDI as crosslinker and PEO40 PPO20-PEO40 as surfactant. These investigations were accompanied by a study of the endotoxin material contamination. The formation of medical-grade materials was successfully obtained (<0.5 EU/mL) by using low-endotoxin gelatin and performing all synthetic steps in a laminar flow hood.
Sustainable management of semi-arid African savannas under environmental and political change
(2012)
Drylands cover about 40% of the earth’s land surface and provide the basis for the livelihoods of 38% of the global human population. Worldwide, these ecosystems are prone to heavy degradation. Increasing levels of dryland degradation result a strong decline of ecosystem services. In addition, in highly variable semi-arid environments changing future environmental conditions will potentially have severe consequences for productivity and ecosystem dynamics. Hence, global efforts have to be made to understand the particular causes and consequences of dryland degradation and to promote sustainable management options for semi-arid and arid ecosystems in a changing world. Here I particularly address the problem of semi-arid savanna degradation, which mostly occurs in form of woody plant encroachment. At this, I aim at finding viable sustainable management strategies and improving the general understanding of semi-arid savanna vegetation dynamics under conditions of extensive livestock production. Moreover, the influence of external forces, i.e. environmental change and land reform, on the use of savanna vegetation and on the ecosystem response to this land use is assessed. Based on this I identify conditions and strategies that facilitate a sustainable use of semi-arid savanna rangelands in a changing world. I extended an eco-hydrological model to simulate rangeland vegetation dynamics for a typical semi-arid savanna in eastern Namibia. In particular, I identified the response of semi-arid savanna vegetation to different land use strategies (including fire management) also with regard to different predicted precipitation, temperature and CO2 regimes. Not only environmental but also economic and political constraints like e.g. land reform programmes are shaping rangeland management strategies. Hence, I aimed at understanding the effects of the ongoing process of land reform in southern Africa on land use and the semi-arid savanna vegetation. Therefore, I developed and implemented an agent-based ecological-economic modelling tool for interactive role plays with land users. This tool was applied in an interdisciplinary empirical study to identify general patterns of management decisions and the between-farm cooperation of land reform beneficiaries in eastern Namibia. The eco-hydrological simulations revealed that the future dynamics of semi-arid savanna vegetation strongly depend on the respective climate change scenario. In particular, I found that the capacity of the system to sustain domestic livestock production will strongly depend on changes in the amount and temporal distribution of precipitation. In addition, my simulations revealed that shrub encroachment will become less likely under future climatic conditions although positive effects of CO2 on woody plant growth and transpiration have been considered. While earlier studies predicted a further increase in shrub encroachment due to increased levels of atmospheric CO2, my contrary finding is based on the negative impacts of temperature increase on the drought sensitive seedling germination and establishment of woody plant species. Further simulation experiments revealed that prescribed fires are an efficient tool for semi-arid rangeland management, since they suppress woody plant seedling establishment. The strategies tested have increased the long term productivity of the savanna in terms of livestock production and decreased the risk for shrub encroachment (i.e. savanna degradation). This finding refutes the views promoted by existing studies, which state that fires are of minor importance for the vegetation dynamics of semi-arid and arid savannas. Again, the difference in predictions is related to the bottleneck at the seedling establishment stage of woody plants, which has not been sufficiently considered in earlier studies. The ecological-economic role plays with Namibian land reform beneficiaries showed that the farmers made their decisions with regard to herd size adjustments according to economic but not according to environmental variables. Hence, they do not manage opportunistically by tracking grass biomass availability but rather apply conservative management strategies with low stocking rates. This implies that under the given circumstances the management of these farmers will not per se cause (or further worsen) the problem of savanna degradation and shrub encroachment due to overgrazing. However, as my results indicate that this management strategy is rather based on high financial pressure, it is not an indicator for successful rangeland management. Rather, farmers struggle hard to make any positive revenue from their farming business and the success of the Namibian land reform is currently disputable. The role-plays also revealed that cooperation between farmers is difficult even though obligatory due to the often small farm sizes. I thus propose that cooperation needs to be facilitated to improve the success of land reform beneficiaries.
In this work different approaches are undertaken to improve the understanding of the sucrose-to-starch pathway in developing potato tubers. At first an inducible gene expression system from fungal origin is optimised for the use of studying metabolism in the potato tuber. It is found that the alc system from Aspergillus nidulans responds more rapidly to acetaldehyde than ethanol, and that acetaldehyde has less side-effects on metabolism. The optimal induction conditions then are used to study the effects of temporally controlled cytosolic expression of a yeast invertase on metabolism of potato tubers. The observed differences between induced and constitutive expression of the invertase lead to the conclusion that glycolysis is induced after an ATP demand has been created by an increase in sucrose cycling. Furthermore, the data suggest that in the potato tuber maltose is a product of glucose condensation rather than starch degradation. In the second part of the work it is shown that the expression of a yeast invertase in the vacuole of potato tubers has similar effects on metabolism than the expression of the same enzyme in the apoplast. These observations give further evidence to the presence of a mechanism by which sucrose is taken up via endocytosis to the vacuole rather than via transporters directly to the cytosol. Finally, a kinetic in silico model of sucrose breakdown is presented that is able to simulate this part of potato tuber metabolism on a quantitative level. Furthermore, it can predict the metabolic effects of the introduction of a yeast invertase in the cytosol of potato tubers with an astonishing precision. In summary, these data prove that inducible gene expression and kinetic computer models of metabolic pathways are useful tools to greatly improve the understanding of plant metabolism.
Subcellular compartmentation of primary carbon metabolism in mesophyll cells of Arabidopsis thaliana
(2011)
Metabolism in plant cells is highly compartmented, with many pathways involving reactions in more than one compartment. For example, during photosynthesis in leaf mesophyll cells, primary carbon fixation and starch synthesis take place in the chloroplast, whereas sucrose is synthesized in the cytosol and stored in the vacuole. These reactions are tightly regulated to keep a fine balance between the carbon pools of the different compartments and to fulfil the energy needs of the organelles. I applied a technique which fractionates the cells under non-aqueous conditions, whereby the metabolic state is frozen at the time of harvest and held in stasis throughout the fractionation procedure. With the combination of non-aqueous fractionation and mass spectrometry based metabolite measurements (LC-MS/MS, GC-MS) it was possible to investigate the intracellular distributions of the intermediates of photosynthetic carbon metabolism and its products in subsequent metabolic reactions. With the knowledge about the in vivo concentrations of these metabolites under steady state photosynthesis conditions it was possible to calculate the mass action ratio and change in Gibbs free energy in vivo for each reaction in the pathway, to determine which reactions are near equilibrium and which are far removed from equilibrium. The Km value and concentration of each enzyme were compared with the concentrations of its substrates in vivo to assess which reactions are substrate limited and so sensitive to changes in substrate concentration. Several intermediates of the Calvin-Benson cycle are substrates for other pathways, including dihydroxyacetone-phosphate (DHAP,sucrose synthesis), fructose 6-phosphate (Fru6P, starch synthesis), erythrose 4-phosphate (E4P,shikimate pathway) and ribose 5-phosphate (R5P, nucleotide synthesis). Several of the enzymes that metabolise these intermediates, and so lie at branch points in the pathway, are triose-phosphate isomerase (DHAP), transketolase (E4P, Fru6P), sedoheptulose-1,7-bisphosphate aldolase (E4P) and ribose-5-phosphate isomerase (R5P) are not saturated with their respective substrate as the metabolite concentration is lower than the respective Km value. In terms of metabolic control these are the steps that are most sensitive to changes in substrate availability, while the regulated irreversible reactions of fructose-1,6-bisphosphatase and sedoheptulose-1,7-bisphosphatase are relatively insensitive to changes in the concentrations of their substrates. In the pathway of sucrose synthesis it was shown that the concentration of the catalytic binding site of the cytosolic aldolase is lower than the substrate concentration of DHAP, and that the concentration of Suc6P is lower than the Km of sucrose-phosphatase for this substrate. Both the sucrose-phosphate synthase and sucrose-phosphatase reactions are far removed from equilibrium in vivo. In wild type A. thaliana Columbia-0 leaves, all of the ADPGlc was found to be localised in the chloroplasts. ADPglucose pyrophosphorylase is localised to the chloroplast and synthesises ADPGlc from ATP and Glc1P. This distribution argues strongly against the hypothesis proposed by Pozueta-Romero and colleagues that ADPGlc for starch synthesis is produced in the cytosol via ADP-mediated cleavage of sucrose by sucrose synthase. Based on this observation and other published data it was concluded that the generally accepted pathway of starch synthesis from ADPGlc produced by ADPglucose pyrophosphorylase in the chloroplasts is correct, and that the alternative pathway is untenable. Within the pathway of starch synthesis the concentration of ADPGlc was found to be well below the Km value of starch synthase for ADPGlc, indicating that the enzyme is substrate limited. A general finding in the comparison of the Calvin-Benson cycle with the synthesis pathways of sucrose and starch is that many enzymes in the Calvin Benson cycle have active binding site concentrations that are close to the metabolite concentrations, while for nearly all enzymes in the synthesis pathways the active binding site concentrations are much lower than the metabolite concentrations.
Im Mittelpunkt dieser Arbeit standen Signaltransduktionsprozesse in den Strukturen der Kraftübertragung quergestreifter Muskelzellen, d. h. in den Costameren (Zell-Matrix-Kontakten) und den Glanzstreifen (Zell-Zell-Kontakten der Kardiomyozyten).Es ließ sich zeigen, dass sich die Morphologie der Zell-Matrix-Kontakte während der Differenzierung von Skelettmuskelzellen dramatisch ändert, was mit einer veränderten Proteinzusammensetzung einhergeht. Immunfluoreszenz-Analysen von Skelettmuskelzellen verschiedener Differenzierungsstadien implizieren, dass die Signalwege, welche die Dynamik der Fokalkontakte in Nichtmuskelzellen bestimmen, nur für frühe Stadien der Muskeldifferenzierung Relevanz haben können. Ausgehend von diesem Befund wurde begonnen, noch unbekannte Signalwege zu identifizieren, welche die Ausbildung von Costameren kontrollieren: In den Vorläuferstrukturen der Costamere gelang es, eine transiente Interaktion der Proteine Paxillin und Ponsin zu identifizieren. Biochemische Untersuchungen legen nahe, dass Ponsin über eine Skelettmuskel-spezifische Insertion im Carboxyterminus das Adapterprotein Nck2 in diesen Komplex rekrutiert. Es wird vorgeschlagen, dass die drei Proteine einen ternären Signalkomplex bilden, der die Umbauvorgänge der Zell-Matrix-Kontakte kontrolliert und dessen Aktivität von mitogen activated protein kinases (MAPK) reguliert wird.Die Anpassungsvorgänge der Strukturen der Kraftübertragung an pathologische Situtation (Kardiomyopathien) in der adulten quergestreiften Muskulatur wurden ausgehend von einem zweiten Protein, dem muscle LIM protein (MLP), untersucht. Es konnte gezeigt werden, dass ein mutiertes MLP-Protein, das im Menschen eine hypertrophe Kardiomyopathie (HCM) auslöst, strukturelle Defekte aufweist und weniger stabil ist. Weiterhin zeigte dieses mutierte Protein eine verringerte Bindungsfähigkeit an die beiden Liganden N-RAP und alpha-Actinin. Die molekulare Grundlage der HCM-verursachenden Mutationen im MLP-Gen könnte folglich eine Veränderung der Homöostase im ternären Komplex MLP – N-RAP – alpha-Actinin sein. Die Expressionsdaten eines neu generierten monoklonalen MLP-Antikörpers deuten darauf hin, dass die Funktionen des MLP nicht nur für die Integrität des Myokards, sondern auch für die der Skelettmuskulatur notwendig sind.
Predator-prey interactions provide central links in food webs. These interaction are directly or indirectly impacted by a number of factors. These factors range from physiological characteristics of individual organisms, over specifics of their interaction to impacts of the environment. They may generate the potential for the application of different strategies by predators and prey. Within this thesis, I modelled predator-prey interactions and investigated a broad range of different factors driving the application of certain strategies, that affect the individuals or their populations. In doing so, I focused on phytoplankton-zooplankton systems as established model systems of predator-prey interactions.
At the level of predator physiology I proposed, and partly confirmed, adaptations to fluctuating availability of co-limiting nutrients as beneficial strategies. These may allow to store ingested nutrients or to regulate the effort put into nutrient assimilation. We found that these two strategies are beneficial at different fluctuation frequencies of the nutrients, but may positively interact at intermediate frequencies. The corresponding experiments supported our model results. We found that the temporal structure of nutrient fluctuations indeed has strong effects on the juvenile somatic growth rate of {\itshape Daphnia}.
Predator colimitation by energy and essential biochemical nutrients gave rise to another physiological strategy. High-quality prey species may render themselves indispensable in a scenario of predator-mediated coexistence by being the only source of essential biochemical nutrients, such as cholesterol. Thereby, the high-quality prey may even compensate for a lacking defense and ensure its persistence in competition with other more defended prey species.
We found a similar effect in a model where algae and bacteria compete for nutrients. Now, being the only source of a compound that is required by the competitor (bacteria) prevented the competitive exclusion of the algae. In this case, the essential compounds were the organic carbon provided by the algae. Here again, being indispensable served as a prey strategy that ensured its coexistence.
The latter scenario also gave rise to the application of the two metabolic strategies of autotrophy and heterotrophy by algae and bacteria, respectively. We found that their coexistence allowed the recycling of resources in a microbial loop that would otherwise be lost. Instead, these resources were made available to higher trophic levels, increasing the trophic transfer efficiency in food webs.
The predation process comprises the next higher level of factors shaping the predator-prey interaction, besides these factors that originated from the functioning or composition of individuals. Here, I focused on defensive mechanisms and investigated multiple scenarios of static or adaptive combinations of prey defense and predator offense. I confirmed and extended earlier reports on the coexistence-promoting effects of partially lower palatability of the prey community. When bacteria and algae are coexisting, a higher palatability of bacteria may increase the average predator biomass, with the side effect of making the population dynamics more regular. This may facilitate experimental investigations and interpretations. If defense and offense are adaptive, this allows organisms to maximize their growth rate. Besides this fitness-enhancing effect, I found that co-adaptation may provide the predator-prey system with the flexibility to buffer external perturbations.
On top of these rather internal factors, environmental drivers also affect predator-prey interactions. I showed that environmental nutrient fluctuations may create a spatio-temporal resource heterogeneity that selects for different predator strategies. I hypothesized that this might favour either storage or acclimation specialists, depending on the frequency of the environmental fluctuations.
We found that many of these factors promote the coexistence of different strategies and may therefore support and sustain biodiversity. Thus, they might be relevant for the maintenance of crucial ecosystem functions that also affect us humans. Besides this, the richness of factors that impact predator-prey interactions might explain why so many species, especially in the planktonic regime, are able to coexist.
Stimuli-promoted in situ formation of hydrogels with thiol/thioester containing peptide precursors
(2022)
Hydrogels are potential synthetic ECM-like substitutes since they provide functional and structural similarities compared to soft tissues. They can be prepared by crosslinking of macromolecules or by polymerizing suitable precursors. The crosslinks are not necessarily covalent bonds, but could also be formed by physical interactions such as π-π interactions, hydrophobic interactions, or H-bonding. On demand in situ forming hydrogels have garnered increased interest especially for biomedical applications over preformed gels due to the relative ease of in vivo delivery and filling of cavities. The thiol-Michael addition reaction provides a straightforward and robust strategy for in situ gel formation with its fast reaction kinetics and ability to proceed under physiological conditions. The incorporation of a trigger function into a crosslinking system becomes even more interesting since gelling can be controlled with stimulus of choice. The use of small molar mass crosslinker precursors with active groups orthogonal to thiol-Michael reaction type electrophile provides the opportunity to implement an on-demand in situ crosslinking without compromising the fast reaction kinetics.
It was postulated that short peptide sequences due to the broad range structural-function relations available with the different constituent amino acids, can be exploited for the realisation of stimuli-promoted in situ covalent crosslinking and gelation applications. The advantages of this system over conventional polymer-polymer hydrogel systems are the ability tune and predict material property at the molecular level.
The main aim of this work was to develop a simplified and biologically-friendly stimuli-promoted in situ crosslinking and hydrogelation system using peptide mimetics as latent crosslinkers. The approach aims at using a single thiodepsipeptide sequence to achieve separate pH- and enzyme-promoted gelation systems with little modification to the thiodepsipeptide sequence. The realization of this aim required the completion of three milestones.
In the first place, after deciding on the thiol-Michael reaction as an effective in situ crosslinking strategy, a thiodepsipeptide, Ac-Pro-Leu-Gly-SLeu-Leu-Gly-NEtSH (TDP) with expected propensity towards pH-dependent thiol-thioester exchange (TTE) activation, was proposed as a suitable crosslinker precursor for pH-promoted gelation system. Prior to the synthesis of the proposed peptide-mimetic, knowledge of the thiol-Michael reactivity of the would-be activated thiol moiety SH-Leu, which is internally embedded in the thiodepsipeptide was required. In line with pKa requirements for a successful TTE, the reactivity of a more acidic thiol, SH-Phe was also investigated to aid the selection of the best thiol to be incorporated in the thioester bearing peptide based crosslinker precursor. Using ‘pseudo’ 2D-NMR investigations, it was found that only reactions involving SH-Leu yielded the expected thiol-Michael product, an observation that was attributed to the steric hindrance of the bulkier nature of SH-Phe. The fast reaction rates and complete acrylate/maleimide conversion obtained with SH-Leu at pH 7.2 and higher aided the direct elimination of SH-Phe as a potential thiol for the synthesis of the peptide mimetic.
Based on the initial studies, for the pH-promoted gelation system, the proposed Ac-Pro-Leu-Gly-SLeu-Leu-Gly-NEtSH was kept unmodified. The subtle difference in pKa values between SH-Leu (thioester thiol) and the terminal cysteamine thiol from theoretical conditions should be enough to effect a ‘pseudo’ intramolecular TTE. In polar protic solvents and under basic aqueous conditions, TDP successfully undergoes a ‘pseudo’ intramolecular TTE reaction to yield an α,ω-dithiol tripeptide, HSLeu-Leu-Gly-NEtSH. The pH dependence of thiolate ion generation by the cysteamine thiol aided the incorporation of the needed stimulus (pH) for the overall success of TTE (activation step) – thiol-Michael addition (crosslinking) strategy.
Secondly, with potential biomedical applications in focus, the susceptibility of TDP, like other thioesters, to intermolecular TTE reaction was probed with a group of thiols of varying thiol pKa values, since biological milieu characteristically contain peptide/protein thiols. L-cysteine, which is a biologically relevant thiol, and a small molecular weight thiol, methylthioglycolate both with relatively similar thiol pKa, values, led to an increase concentration of the dithiol crosslinker when reacted with TDP. In the presence of acidic thiols (p-NTP and 4MBA), a decrease in the dithiol concentration was observed, an observation that can be attributed to the inability of the TTE tetrahedral intermediate to dissociate into exchange products and is in line with pKa requirements for successful TTE reaction. These results additionally makes TDP more attractive and the potentially the first crosslinker precursor for applications in biologically relevant media.
Finally, the ability of TDP to promote pH-sensitive in situ gel formation was probed with maleimide functionalized 4-arm polyethylene glycol polymers in tris-buffered media of varying pHs. When a 1:1 thiol: maleimide molar ratio was used, TDP-PEG4MAL hydrogels formed within 3, 12 and 24 hours at pH values of 8.5, 8.0 and 7.5 respectively. However, gelation times of 3, 5 and 30 mins were observed for the same pH trend when the thiol: maleimide molar was increased to 2:1.
A direct correlation of thiol content with G’ of the gels at each pH could also be drawn by comparing gels with thiol: maleimide ratios of 1:1 to those with 2:1 thiol: maleimide mole ratios. This is supported by the fact that the storage modulus (G') is linearly dependent on the crosslinking density of the polymer. The values of initial G′ for all gels ranged between (200 – 5000 Pa), which falls in the range of elasticities of certain tissue microenvironments for example brain tissue 200 – 1000 Pa and adipose tissue (2500 – 3500 Pa).
Knowledge so far gained from the study on the ability to design and tune the exchange reaction of thioester containing peptide mimetic will give those working in the field further insight into the development of new sequences tailored towards specific applications.
TTE substrate design using peptide mimetic as presented in this work has revealed interesting new insights considering the state-of-the-art. Using the results obtained as reference, the strategy provides a possibility to extend the concept to the controlled delivery of active molecules needed for other robust and high yielding crosslinking reactions for biomedical applications. Application for this sequentially coupled functional system could be seen e.g. in the treatment of inflamed tissues associated with urinary tract like bladder infections for which pH levels above 7 were reported. By the inclusion of cell adhesion peptide motifs, the hydrogel network formed at this pH could act as a new support layer for the healing of damage epithelium as shown in interfacial gel formation experiments using TDP and PEG4MAL droplets.
The versatility of the thiodepsipeptide sequence, Ac-Pro-Leu-Gly-SLeu-Leu-Gly-(TDPo) was extended for the design and synthesis of a MMP-sensitive 4-arm PEG-TDPo conjugate. The purported cleavage of TDPo at the Gly-SLeu bond yields active thiol units for subsequent reaction of orthogonal Michael acceptor moieties. One of the advantages of stimuli-promoted in situ crosslinking systems using short peptides should be the ease of design of required peptide molecules due to the predictability of peptide functions their sequence structure. Consequently the functionalisation of a 4-arm PEG core with the collagenase active TDPo sequence yielded an MMP-sensitive 4-arm thiodepsipeptide-PEG conjugate (PEG4TDPo) substrate.
Cleavage studies using thiol flourometric assay in the presence of MMPs -2 and -9 confirmed the susceptibility of PEG4TDPo towards these enzymes. The resulting time-dependent increase in fluorescence intensity in the presence of thiol assay signifies the successful cleavage of TDPo at the Gly-SLeu bond as expected. It was observed that the cleavage studies with thiol flourometric assay introduces a sigmoid non-Michaelis-Menten type kinetic profile, hence making it difficult to accurately determine the enzyme cycling parameters, kcat and KM .
Gelation studies with PEG4MAL at 10 % wt. concentrations revealed faster gelation with MMP-2 than MMP-9 with 28 and 40 min gelation times respectively. Possible contributions by hydrolytic cleavage of PEG4TDPo has resulted in the gelation of PEG4MAL blank samples but only after 60 minutes of reaction. From theoretical considerations, the simultaneous gelation reaction would be expected to more negatively impact the enzymatic than hydrolytic cleavage. The exact contributions from hydrolytic cleavage of PEG4TDPo would however require additional studies.
In summary this new and simplified in situ crosslinking system using peptide-based crosslinker precursors with tuneable properties exhibited in situ crosslinking gelation kinetics on similar levels with already active dithiols reported. The advantageous on-demand functionality associated with its pH-sensitivity and physiological compatibility makes it a strong candidate worth further research as biomedical applications in general and on-demand material synthesis is concerned.
Results from MMP-promoted gelation system unveils a simple but unexplored approach for in situ synthesis of covalently crosslinked soft materials, that could lead to the development of an alternative pathway in addressing cancer metastasis by making use of MMP overexpression as a trigger. This goal has so far not being reach with MMP inhibitors despite the extensive work this regard.
In the light of climate change, rising demands for agricultural products and the intensification and specialization of agricultural systems, ensuring an adequate and reliable supply of food is fundamental for food security. Maintaining diversity and redundancy has been postulated as one generic principle to increase the resilience of agricultural production and other ecosystem services. For example, if one crop fails due to climate instability and extreme events, others can compensate the losses. Crop diversity might be particularly important if different crops show asynchronous production trends. Furthermore, spatial heterogeneity has been suggested to increase stability at larger scales as production losses in some areas can be buffered by surpluses in undisturbed ones. Besides systematically investigating the mechanisms underlying stability, identifying transformative pathways that foster them is important.
In my thesis, I aim at answering the following questions: (i) How does yield stability differ between nations, regions and farms, and what is the effect of crop diversity on yield stability in relation to agricultural inputs, climate heterogeneity, climate instability and time at the national, regional or farm level? (ii) Is asynchrony between crops a better predictor of production stability than crop diversity? (iii) What is the effect of asynchrony between and within crops on stability and how is it related to crop diversity and space, respectively? (iv) What is the state of the art and what are knowledge gaps in exploring resilience and its multidimensionality in ecological and social-ecological systems with agent-based models and what are potential ways forward?
In the first chapter, I provide the theoretical background for the subsequent analyses. I stress the need to better understand the resilience of social-ecological systems and particularly the stability of agricultural production. Moreover, I introduce diversity and spatial heterogeneity as two prominently discussed resilience mechanisms and describe approaches to assess resilience.
In the second chapter, I combined agriculture and climate data at three levels of organization and spatial extents to investigate yield stability patterns and their relation to crop diversity, fertilizer, irrigation, climate heterogeneity and instability and time of nations globally, regions in Europe and farms in Germany using statistical analyses. Yield stability decreased from the national to the farm level. Several nations and regions substantially contributed to larger-scale stability. Crop diversity was positively associated with yield stability across all three levels of organization. This effect was typically more profound at smaller scales and in variable climates. In addition to crop diversity, climate heterogeneity was an important stabilizing mechanism especially at larger scales. These results confirm the stabilizing effect of crop diversity and spatial heterogeneity, yet their importance depends on the scale and agricultural management.
Building on the findings of the second chapter, I deepened in the third chapter my research on the effect of crop diversity at the national level. In particular, I tested if asynchrony between crops, i.e. between the temporal production patterns of different crops, better predicts agricultural production stability than crop diversity. The stabilizing effect of asynchrony was multiple times higher than the effect of crop diversity, i.e. asynchrony is one important property that can explain why a higher diversity supports the stability of national food production. Therefore, strategies to stabilize agricultural production through crop diversification also need to account for the asynchrony of the crops considered.
The previous chapters suggest that both asynchrony between crops and spatial heterogeneity are important stabilizing mechanisms. In the fourth chapter, I therefore aimed at better understanding the relative importance of asynchrony between and within crops, i.e. between the temporal production patterns of different crops and between the temporal production patterns of different cultivation areas of the same crop. Better understanding their relative importance is important to inform agricultural management decisions, but so far this has been hardly assessed. To address this, I used crop production data to study the effect of asynchrony between and within crops on the stability of agricultural production in regions in Germany and nations in Europe. Both asynchrony between and within crops consistently stabilized agricultural production. Adding crops increased asynchrony between crops, yet this effect levelled off after eight crops in regions in Germany and after four crops in nations in Europe. Combining already ten farms within a region led to high asynchrony within crops, indicating distinct production patters, while this effect was weaker when combining multiple regions within a nation. The results suggest, that both mechanisms need to be considered in agricultural management strategies that strive for more resilient farming systems.
The analyses in the foregoing chapters focused at different levels of organization, scales and factors potentially influencing agricultural stability. However, these statistical analyses are restricted by data availability and investigate correlative relationships, thus they cannot provide a mechanistic understanding of the actual processes underlying resilience. In this regard, agent-based models (ABM) are a promising tool. Besides their ability to measure different properties and to integrate multiple situations through extensive manipulation in a fully controlled system, they can capture the emergence of system resilience from individual interactions and feedbacks across different levels of organization. In the fifth chapter, I therefore reviewed the state of the art and potential knowledge gaps in exploring resilience and its multidimensionality in ecological and social-ecological systems with ABMs. Next, I derived recommendations for a more effective use of ABMs in resilience research. The review suggests that the potential of ABMs is not utilized in most models as they typically focus on a single dimension of resilience and are mostly limited to one reference state, disturbance type and scale. Moreover, only few studies explicitly test the ability of different mechanisms to support resilience. To solve real-world problems related to the resilience of complex systems, ABMs need to assess multiple stability properties for different situations and under consideration of the mechanisms that are hypothesized to render a system resilient.
In the sixth chapter, I discuss the major conclusions that can be drawn from the previous chapters. Moreover, I showcase the use of simulation models to identify management strategies to enhance asynchrony and thus stability, and the potential of ABMs to identify pathways to implement such strategies.
The results of my thesis confirm the stabilizing effect of crop diversity, yet its importance depends on the scale, agricultural management and climate. Moreover, strategies to stabilize agricultural production through crop diversification also need to account for the asynchrony of the crops considered. As spatial heterogeneity and particularly asynchrony within crops strongly enhances stability, integrated management approaches are needed that simultaneously address multiple resilience mechanisms at different levels of organization, scales and time horizons. For example, the simulation suggests that only increasing the number of crops at both the pixel and landscape level avoids trade-offs between asynchrony between and within crops. If their potential is better exploited, agent-based models have the capacity to systematically assess resilience and to identify comprehensive pathways towards resilient farming systems.
Daylength is one of several parameters controlling flowering time in many plant species. The day length is perceived in leaves, but how the floral signal is transduced to the shoot apex via the phloem to induce flowering remains to be elucidated. This study aimed at the identification of new candidates involved in the induction of flowering by employing three plant species, Arabidopsis thaliana, Sinapis alba and Brassica napus in combination with transcript profiling by Affymetrix chip hybridization, metabolite profiling by gas chromatography – mass spectrometry and targeted protein analysis using antibodies. All analyses were performed on tissue-specific samples and focused on phloem sap or phloem exudates. To find common transcript and metabolite candidates potentially associated with the floral transition, two independent induction systems in Arabidopsis were used: a photoextension system, whereby plants received fourteen additional hours of light, and a parallel dexamethasone-inducible system, which was centered on the induction of the known flowering gene CONSTANS (CO). Identification of signals preceding the CO cascade was possible using the light extension regime, while downstream events dependent on CO activation were compared in both systems. Altogether, a number of interesting transcript and metabolite candidates were identified in both systems with some degree of overlap. Sinapis alba was used to investigate the universality of the floral signals between species. Comparisons of metabolite data revealed a few common candidates that may prove interesting for further studies. In addition, a targeted approach was carried out to investigate the presence of the Flowering Locus T (FT) protein during different stages of flower development using an antibody. Interesting changes in the sizes of antigens from rape phloem were seen and appeared consistent in Arabidopsis and to a lesser extent in Sinapis. Overall, the broad surveying approaches for transcripts and metabolites used in this study revealed several new potential candidates involved in the induction and/or regulation of flowering. As far as the protein work, additional experiments will reveal the link between FT and floral induction as well as its role in maintaining the floral state using the abovementioned plant species.
The fragmentation of natural habitat caused by anthropogenic land use changes is one of the main drivers of the current rapid loss of biodiversity. In face of this threat, ecological research needs to provide predictions of communities' responses to fragmentation as a prerequisite for the effective mitigation of further biodiversity loss. However, predictions of communities' responses to fragmentation require a thorough understanding of ecological processes, such as species dispersal and persistence. Therefore, this thesis seeks an improved understanding of community dynamics in fragmented landscapes. In order to approach this overall aim, I identified key questions on the response of plant diversity and plant functional traits to variations in species' dispersal capability, habitat fragmentation and local environmental conditions. All questions were addressed using spatially explicit simulations or statistical models. In chapter 2, I addressed scale-dependent relationships between dispersal capability and species diversity using a grid-based neutral model. I found that the ratio of survey area to landscape size is an important determinant of scale-dependent dispersal-diversity relationships. With small ratios, the model predicted increasing dispersal-diversity relationships, while decreasing dispersal-diversity relationships emerged, when the ratio approached one, i.e. when the survey area approached the landscape size. For intermediate ratios, I found a U-shaped pattern that has not been reported before. With this study, I unified and extended previous work on dispersal-diversity relationships. In chapter 3, I assessed the type of regional plant community dynamics for the study area in the Southern Judean Lowlands (SJL). For this purpose, I parameterised a multi-species incidence-function model (IFM) with vegetation data using approximate Bayesian computation (ABC). I found that the type of regional plant community dynamics in the SJL is best characterized as a set of isolated “island communities” with very low connectivity between local communities. Model predictions indicated a significant extinction debt with 33% - 60% of all species going extinct within 1000 years. In general, this study introduces a novel approach for combining a spatially explicit simulation model with field data from species-rich communities. In chapter 4, I first analysed, if plant functional traits in the SJL indicate trait convergence by habitat filtering and trait divergence by interspecific competition, as predicted by community assembly theory. Second, I assessed the interactive effects of fragmentation and the south-north precipitation gradient in the SJL on community-mean plant traits. I found clear evidence for trait convergence, but the evidence for trait divergence fundamentally depended on the chosen null-model. All community-mean traits were significantly associated with the precipitation gradient in the SJL. The trait associations with fragmentation indices (patch size and connectivity) were generally weaker, but statistically significant for all traits. Specific leaf area (SLA) and plant height were consistently associated with fragmentation indices along the precipitation gradient. In contrast, seed mass and seed number were interactively influenced by fragmentation and precipitation. In general, this study provides the first analysis of the interactive effects of climate and fragmentation on plant functional traits. Overall, I conclude that the spatially explicit perspective adopted in this thesis is crucial for a thorough understanding of plant community dynamics in fragmented landscapes. The finding of contrasting responses of local diversity to variations in dispersal capability stresses the importance of considering the diversity and composition of the metacommunity, prior to implementing conservation measures that aim at increased habitat connectivity. The model predictions derived with the IFM highlight the importance of additional natural habitat for the mitigation of future species extinctions. In general, the approach of combining a spatially explicit IFM with extensive species occupancy data provides a novel and promising tool to assess the consequences of different management scenarios. The analysis of plant functional traits in the SJL points to important knowledge gaps in community assembly theory with respect to the simultaneous consequences of habitat filtering and competition. In particular, it demonstrates the importance of investigating the synergistic consequences of fragmentation, climate change and land use change on plant communities. I suggest that the integration of plant functional traits and of species interactions into spatially explicit, dynamic simulation models offers a promising approach, which will further improve our understanding of plant communities and our ability to predict their dynamics in fragmented and changing landscapes.
Variation in traits permeates and affects all levels of biological organisation, from within individuals to between species. Yet, intraspecific trait variation (ITV) is not sufficiently represented in many ecological theories. Instead, species averages are often assumed. Especially ITV in behaviour has only recently attracted more attention as its pervasiveness and magnitude became evident. The surge in interest in ITV in behaviour was accompanied by a methodological and technological leap in the field of movement ecology. Many aspects of behaviour become visible via movement, allowing us to observe inter-individual differences in fundamental processes such as foraging, mate searching, predation or migration. ITV in movement behaviour may result from within-individual variability and consistent, repeatable among-individual differences. Yet, questions on why such among-individual differences occur in the first place and how they are integrated with life-history have remained open. Furthermore, consequences of ITV, especially of among-individual differences in movement behaviour, on populations and species communities are not sufficiently understood. In my thesis, I approach timely questions on the sources and consequences of ITV, particularly, in movement behaviour. After outlining fundamental concepts and the current state of knowledge, I approach these questions by using agent-based models to integrate concepts from behavioural and movement ecology and to develop novel perspectives.
Modern coexistence theory is a central pillar of community ecology, yet, insufficiently considers ITV in behaviour. In chapter 2, I model a competitive two-species system of ground-dwelling, central-place foragers to investigate the consequences of among-individual differences in movement behaviour on species coexistence. I show that the simulated among-individual differences, which matched with empirical data, reduce fitness differences betweem species, i.e. provide an equalising coexistence mechanism. Furthermore, I explain this result mechanistically and, thus, resolve an apparent ambiguity of the consequences of ITV on species coexistence described in previous studies.
In chapter 3, I turn the focus to sources of among-individual differences in movement behaviour and their potential integration with life-history. The pace-of-life syndrome (POLS) theory predicts that the covariation between among-individual differences in behaviour and life-history is mediated by a trade-off between early and late reproduction. This theory has generated attention but is also currently scrutinised. In chapter 3, I present a model which supports a recent conceptual development that suggests fluctuating density-dependent selection as a cause of the POLS. Yet, I also identified processes that may alter the association between movement behaviour and life-history across levels of biological organization.
ITV can buffer populations, i.e. reduce their extinction risk. For instance, among-individual differences can mediate portfolio effects or increase evolvability and, thereby, facilitate rapid evolution which can alleviate extinction risk. In chapter 4, I review ITV, environmental heterogeneity, and density-dependent processes which constitute local buffer mechanisms. In the light of habitat isolation, which reduces connectivity between populations, local buffer mechanisms may become more relevant compared to dispersal-related regional buffer mechanisms. In this chapter, I argue that capacities, latencies, and interactions of local buffer mechanisms should motivate more process-based and holistic integration of local buffer mechanisms in theoretical and empirical studies.
Recent perspectives propose to apply principles from movement and community ecology to study filamentous fungi. It is an open question whether and how the arrangement and geometry of microstructures select for certain movement traits, and, thus, facilitate coexistence-stabilising niche partitioning. As a coauthor of chapter 5, I developed an agent-based model of hyphal tips navigating in soil-like microstructures along a gradient of soil porosity. By measuring network properties, we identified changes in the optimal movement behaviours along the gradient. Our findings suggest that the soil architecture facilitates niche partitioning.
The core chapters are framed by a general introduction and discussion. In the general introduction, I outline fundamental concepts of movement ecology and describe theory and open questions on sources and consequences of ITV in movement behaviour. In the general discussion, I consolidate the findings of the core chapters and critically discuss their respective value and, if applicable, their impact. Furthermore, I emphasise promising avenues for further research.
Simulating the impact of herbicide drift exposure on non-target terrestrial plant communities
(2019)
In Europe, almost half of the terrestrial landscape is used for agriculture. Thus, semi-natural habitats such as field margins are substantial for maintaining diversity in intensively managed farmlands. However, plants located at field margins are threatened by agricultural practices such as the application of pesticides within the fields. Pesticides are chemicals developed to control for undesired species within agricultural fields to enhance yields. The use of pesticides implies, however, effects on non-target organisms within and outside of the agricultural fields. Non-target organisms are organisms not intended to be sprayed or controlled for. For example, plants occurring in field margins are not intended to be sprayed, however, can be impaired due to herbicide drift exposure. The authorization of plant protection products such as herbicides requires risk assessments to ensure that the application of the product has no unacceptable effects on the environment. For non-target terrestrial plants (NTTPs), the risk assessment is based on standardized greenhouse studies on plant individual level. To account for the protection of plant populations and communities under realistic field conditions, i.e. extrapolating from greenhouse studies to field conditions and from individual-level to community-level, assessment factors are applied. However, recent studies question the current risk assessment scheme to meet the specific protection goals for non-target terrestrial plants as suggested by the European Food Safety Authority (EFSA). There is a need to clarify the gaps of the current risk assessment and to include suitable higher tier options in the upcoming guidance document for non-target terrestrial plants.
In my thesis, I studied the impact of herbicide drift exposure on NTTP communities using a mechanistic modelling approach. I addressed main gaps and uncertainties of the current risk assessment and finally suggested this modelling approach as a novel higher tier option in future risk assessments. Specifically, I extended the plant community model IBC-grass (Individual-based community model for grasslands) to reflect herbicide impacts on plant individuals. In the first study, I compared model predictions of short-term herbicide impacts on artificial plant communities with empirical data. I demonstrated the capability of the model to realistically reflect herbicide impacts. In the second study, I addressed the research question whether or not reproductive endpoints need to be included in future risk assessments to protect plant populations and communities. I compared the consequences of theoretical herbicide impacts on different plant attributes for long-term plant population dynamics in the community context. I concluded that reproductive endpoints only need to be considered if the herbicide effect is assumed to be very high. The endpoints measured in the current vegetative vigour and seedling emergence studies had high impacts for the dynamic of plant populations and communities already at lower effect intensities. Finally, the third study analysed long-term impacts of herbicide application for three different plant communities. This study highlighted the suitability of the modelling approach to simulate different communities and thus detecting sensitive environmental conditions.
Overall, my thesis demonstrates the suitability of mechanistic modelling approaches to be used as higher tier options for risk assessments. Specifically, IBC-grass can incorporate available individual-level effect data of standardized greenhouse experiments to extrapolate to community-level under various environmental conditions. Thus, future risk assessments can be improved by detecting sensitive scenarios and including worst-case impacts on non-target plant communities.
Flüssigkeitssekretion und Proteinsekretion werden in Speicheldrüsen von Insekten über Hormone und Neurotransmitter gesteuert. Diese entfalten ihre physiologische Wirkung in den sekretorischen Drüsenzellen hauptsächlich über den zyklischen Adenosinmonophosphat (cAMP)-Signalweg und den Inositoltrisphosphat (IP<SUB>3</SUB>) / Ca<sup>2+-Signalweg. Die Mechanismen möglicher Wechselwirkungen zwischen diesen Signalwegen und ihre physiologischen Auswirkungen sind unzureichend bekannt. Im Mittelpunkt dieser Arbeit stand die Frage, ob und wie sich der Ca<sup>2+-Signalweg und der cAMP-Signalweg in der Speicheldrüse der Diptere Calliphora vicina beeinflussen. Substanzen wie 5-Fluoro-α-Methyltryptamin und Histamin wurden in früheren Arbei-ten als Agonisten genutzt, um in den Speicheldrüsen von C. vicina selektiv den cAMP-Signalweg (getrennt vom IP<SUB>3</SUB>/Ca<sup>2+-Signalweg) zu aktivieren. Es zeigte sich in transepithelialen Potentialmessungen und mikrofluorometrischen Ca<sup>2+-Untersuchungen, dass beide Substanzen sowohl den cAMP-Weg als auch den Ca<sup>2+-Signalweg aktivierten. Die physiologischen Ursachen der Histamin-induzierten Ca<sup>2+-Erhöhung wurden genauer untersucht. Zusammengefasst zeigten diese Untersuchungen, dass Histamin wie 5-HT den cAMP-Weg und die Phosphoinositidkaskade aktivierte. Im Gegensatz zu den 5-HT-induzierten Ca<sup>2+-Oszillationen, welche durch interzelluläre Ca<sup>2+-Wellen synchronisiert werden, verursachte Histamin bei niedrigen Konzentrationen lokale Ca<sup>2+-Oszillationen in einzelnen Zellen (keine Wellen). Bei höheren Histamin-Konzentrationen war eine anhaltende Ca<sup>2+-Erhöhung oder ein synchrones <quote>Ca<sup>2+-beating</quote> in der gesamten Drüse zu beobachten. Des Weiteren wurde die Frage untersucht, ob eine Erhöhung der intrazellulären cAMP-Konzentration den IP<SUB>3</SUB> Ca<sup>2+-Signalweg in den Epithelzellen der Speicheldrüse beeinflussen kann. Es zeigte sich, dass cAMP den durch schwellennahe 5-HT-Konzentrationen induzierten Ca<sup>2+-Anstieg verstärkte. Diese Verstärkung wurde durch eine PKA-vermittelte Sensitivierung des IP<SUB>3</SUB>-Rezeptor/Ca<sup>2+-Kanals für IP<SUB>3</SUB> verursacht. Immunzytochemische Untersuchungen deuten dar-auf hin, dass die Proteinkinase A eng mit dem IP<SUB>3</SUB>-Rezeptor/Ca<sup>2+-Kanal assoziiert ist. Diese Messungen zeigen erstmals, dass auch bei Invertebraten der Botenstoff cAMP, PKA-vermittelt, den IP<SUB>3</SUB>-Rezeptor/Ca<sup>2+-Kanal des ER für IP<SUB>3</SUB> sensitiviert.
From its first use in the field of biochemistry, instrumental analysis offered a variety of invaluable tools for the comprehensive description of biological systems. Multi-selective methods that aim to cover as many endogenous compounds as possible in biological samples use different analytical platforms and include methods like gene expression profile and metabolite profile analysis. The enormous amount of data generated in application of profiling methods needs to be evaluated in a manner appropriate to the question under investigation. The new field of system biology rises to the challenge to develop strategies for collecting, processing, interpreting, and archiving this vast amount of data; to make those data available in form of databases, tools, models, and networks to the scientific community. On the background of this development a multi-selective method for the determination of phytohormones was developed and optimised, complementing the profile analyses which are already in use (Chapter I). The general feasibility of a simultaneous analysis of plant metabolites and phytohormones in one sample set-up was tested by studies on the analytical robustness of the metabolite profiling protocol. The recovery of plant metabolites proved to be satisfactory robust against variations in the extraction protocol by using common extraction procedures for phytohormones; a joint extraction of metabolites and hormones from plant tissue seems practicable (Chapter II). Quantification of compounds within the context of profiling methods requires particular scrutiny (Chapter II). In Chapter III, the potential of stable-isotope in vivo labelling as normalisation strategy for profiling data acquired with mass spectrometry is discussed. First promising results were obtained for a reproducible quantification by stable-isotope in vivo labelling, which was applied in metabolomic studies. In-parallel application of metabolite and phytohormone analysis to seedlings of the model plant Arabidopsis thaliana exposed to sulfate limitation was used to investigate the relationship between the endogenous concentration of signal elements and the ‘metabolic phenotype’ of a plant. An automated evaluation strategy was developed to process data of compounds with diverse physiological nature, such as signal elements, genes and metabolites – all which act in vivo in a conditional, time-resolved manner (Chapter IV). Final data analysis focussed on conditionality of signal-metabolome interactions.
Climate change and human-driven eutrophication promote the spread of harmful cyanobacteria blooms in lakes worldwide, which affects water quality and impairs the aquatic food chain. In recent times, sedimentary ancient DNA-based (sedaDNA) studies were used to probe how centuries of climate and environmental changes have affected cyanobacterial assemblages in temperate lakes. However, there is a lack of information on the consistency between sediment-deposited cyanobacteria communities versus those of the water column, and on the individual role of natural climatic changes versus human pressure on cyanobacteria community dynamics over multi-millennia time scales.
Therefore, this thesis uses sedimentary ancient DNA of Lake Tiefer See in northeastern Germany to trace the deposition of cyanobacteria along the water column into the sediment, and to reconstruct cyanobacteria communities spanning the last 11,000 years using a set of molecular techniques including quantitative PCR, biomarkers, metabarcoding, and metagenome sequence analyses.
The results of this thesis proved that cyanobacterial composition and species richness did not significantly differ among different water depths, sediment traps, and surface sediments. This means that the cyanobacterial community composition from the sediments reflects the water column communities. However, there is a skewed sediment deposition of different cyanobacteria groups because of DNA alteration and/or deterioration during transport along the water column to the sediment. Specifically, single filament taxa, such as Planktothrix, are poorly represented in sediments despite being abundant in the water column as shown by an additional study of the thesis on cyanobacteria seasonality. In contrast, aggregate-forming taxa, like Aphanizomenon, are relatively overrepresented in sediment although they are not abundant in the water column. These different deposition patterns of cyanobacteria taxa should be considered in future DNA-based paleolimnological investigations. The thesis also reveals a substantial increase in total cyanobacteria abundance during the Bronze Age which is not apparent in prior phases of the early to middle Holocene and is suggested to be caused by human farming, deforestation, and excessive nutrient addition to the lake. Not only cyanobacterial abundance was influenced by human activity but also cyanobacteria community composition differed significantly between phases of no, moderate, and intense human impact.
The data presented in this thesis are the first on sedimentary cyanobacteria DNA since the early Holocene in a temperate lake. The results bring together archaeological, historical climatic, and limnological data with deep DNA-sequencing and paleoecology to reveal a legacy impact of human pressure on lake cyanobacteria populations dating back to approximately 4000 years.
Savannas cover a broad geographical range across continents and are a biome best described by a mix of herbaceous and woody plants. The former create a more or less continuous layer while the latter should be sparse enough to leave an open canopy. What has long intrigued ecologists is how these two competing plant life forms of vegetation coexist.
Initially attributed to resource competition, coexistence was considered the stable outcome of a root niche differentiation between trees and grasses. The importance of environmental factors became evident later, when data from moister environments demonstrated that tree cover was often lower than what the rainfall conditions would allow for. Our current understanding relies on the interaction of competition and disturbances in space and time. Hence, the influence of grazing and fire and the corresponding feedbacks they generate have been keenly investigated. Grazing removes grass cover, initiating a self-reinforcing process propagating tree cover expansion. This is known as the encroachment phenomenon. Fire, on the other hand, imposes a bottleneck on the tree population by halting the recruitment of young trees into adulthood. Since grasses fuel fires, a feedback linking grazing, grass cover, fire, and tree cover is created. In African savannas, which are the focus of this dissertation, these feedbacks play a major role in the dynamics.
The importance of these feedbacks came into sharp focus when the notion of alternative states began to be applied to savannas. Alternative states in ecology arise when different states of an ecosystem can occur under the same conditions. According to this an open savanna and a tree-dominated savanna can be classified as alternative states, since they can both occur under the same climatic conditions. The aforementioned feedbacks are critical in the creation of alternative states. The grass-fire feedback can preserve an open canopy as long as fire intensity and frequency remain above a certain threshold. Conversely, crossing a grazing threshold can force an open savanna to shift to a tree-dominated state. Critically, transitions between such alternative states can produce hysteresis, where a return to pre-transition conditions will not suffice to restore the ecosystem to its original state.
In the chapters that follow, I will cover aspects relating to the coexistence mechanisms and the role of feedbacks in tree-grass interactions. Coming back to the coexistence question, due to the overwhelming focus on competition and disturbance another important ecological process was neglected: facilitation. Therefore, in the first study within this dissertation I examine how facilitation can expand the tree-grass coexistence range into drier conditions. For the second study I focus on another aspect of savanna dynamics which remains underrepresented in the literature: the impacts of inter-annual rainfall variability upon savanna trees and the resilience of the savanna state. In the third and final study within this dissertation I approach the well-researched encroachment phenomenon from a new perspective: I search for an early warning indicator of the process to be used as a prevention tool for savanna conservation. In order to perform all this work I developed a mathematical ecohydrological model of Ordinary Differential Equations (ODEs) with three variables: soil moisture content, grass cover and tree cover.
Facilitation: Results showed that the removal of grass cover through grazing was detrimental to trees under arid conditions, contrary to expectation based on resource competition. The reason was that grasses preserved moisture in the soil through infiltration and shading, thus ameliorating the harsh conditions for trees in accordance with the Stress Gradient Hypothesis. The exclusion of grasses from the model further demonstrated this: tree cover was lower in the absence of grasses, indicating that the benefits of grass facilitation outweighed the costs of grass competition for trees. Thus, facilitation expanded the climatic range where savannas persisted into drier conditions.
Rainfall variability: By adjusting the model to current rainfall patterns in East Africa, I simulated conditions of increasing inter-annual rainfall variability for two distinct mean rainfall scenarios: semi-arid and mesic. Alternative states of tree-less grassland and tree-dominated savanna emerged in both cases. Increasing variability reduced semi-arid savanna tree cover to the point that at high variability the savanna state was eliminated, because variability intensified resource competition and strengthened the fire disturbance during high rainfall years. Mesic savannas, on the other hand, became more resilient along the variability gradient: increasing rainfall variability created more opportunities for the rapid growth of trees to overcome the fire disturbance, boosting the chances of savannas persisting and thus increasing mesic savanna resilience.
Preventing encroachment: The breakdown in the grass-fire feedback caused by heavy grazing promoted the expansion of woody cover. This could be irreversible due to the presence of alternative states of encroached and open savanna, which I found along a simulated grazing gradient. When I simulated different short term heavy grazing treatments followed by a reduction to the original grazing conditions, certain cases converged to the encroached state. Utilising woody cover changes only during the heavy grazing treatment, I developed an early warning indicator which identified these cases with a high risk of such hysteresis and successfully distinguished them from those with a low risk. Furthermore, after validating the indicator on encroachment data, I demonstrated that it appeared early enough for encroachment to be prevented through realistic grazing-reduction treatments.
Though this dissertation is rooted in the theory of savanna dynamics, its results can have significant applications in savanna conservation. Facilitation has only recently become a topic of interest within savanna literature. Given the threat of increasing droughts and a general anticipation of drier conditions in parts of Africa, insights stemming from this research may provide clues for preserving arid savannas. The impacts of rainfall variability on savannas have not yet been thoroughly studied, either. Conflicting results appear as a result of the lack of a robust theoretical understanding of plant interactions under variable conditions. . My work and other recent studies argue that such conditions may increase the importance of fast resource acquisition creating a ‘temporal niche’. Woody encroachment has been extensively studied as phenomenon, though not from the perspective of its early identification and prevention. The development of an encroachment forecasting tool, as the one presented in this work, could protect both the savanna biome and societies dependent upon it for (economic) survival. All studies which follow are bound by the attempt to broaden the horizons of savanna-related research in order to deal with extreme conditions and phenomena; be it through the enhancement of the coexistence debate or the study of an imminent external threat or the development of a management-oriented tool for the conservation of savannas.
Although the basic structure of biological membranes is provided by the lipid bilayer, most of the specific functions are carried out by membrane proteins (MPs) such as channels, ion-pumps and receptors. Additionally, it is known, that mutations in MPs are directly or indirectly involved in many diseases. Thus, structure determination of MPs is of major interest not only in structural biology but also in pharmacology, especially for drug development. Advances in structural biology of membrane proteins (MPs) have been strongly supported by the success of three leading techniques: X-ray crystallography, electron microscopy and solution NMR spectroscopy. However, X-ray crystallography and electron microscopy, require highly diffracting 3D or 2D crystals, respectively. Today, structure determination of non-crystalline solid protein preparations has been made possible through rapid progress of solid-state MAS NMR methodology for biological systems. Castellani et. al. solved and refined the first structure of a microcrystalline protein using only solid-state MAS NMR spectroscopy. These successful application open up perspectives to access systems that are difficult to crystallise or that form large heterogeneous complexes and insoluble aggregates, for example ligands bound to a MP-receptor, protein fibrils and heterogeneous proteins aggregates. Solid-state MAS NMR spectroscopy is in principle well suited to study MP at atomic resolution. In this thesis, different types of MP preparations were tested for their suitability to be studied by solid-state MAS NMR. Proteoliposomes, poorly diffracting 2D crystals and a PEG precipitate of the outer membrane protein G (OmpG) were prepared as a model system for large MPs. Results from this work, combined with data found in the literature, show that highly diffracting crystalline material is not a prerequirement for structural analysis of MPs by solid-state MAS NMR. Instead, it is possible to use non-diffracting 3D crystals, MP precipitates, poorly diffracting 2D crystals and proteoliposomes. For the latter two types of preparations, the MP is reconstituted into a lipid bilayer, which thus allows the structural investigation in a quasi-native environment. In addition, to prepare a MP sample for solid-state MAS NMR it is possible to use screening methods, that are well established for 3D and 2D crystallisation of MPs. Hopefully, these findings will open a fourth method for structural investigation of MP. The prerequisite for structural studies by NMR in general, and the most time consuming step, is always the assignment of resonances to specific nuclei within the protein. Since the last few years an ever-increasing number of assignments from solid-state MAS NMR of uniformly carbon and nitrogen labelled samples is being reported, mostly for small proteins of up to around 150 amino acids in length. However, the complexity of the spectra increases with increasing molecular weight of the protein. Thus the conventional assignment strategies developed for small proteins do not yield a sufficiently high degree of assignment for the large MP OmpG (281 amino acids). Therefore, a new assignment strategy to find starting points for large MPs was devised. The assignment procedure is based on a sample with [2,3-13C, 15N]-labelled Tyr and Phe and uniformly labelled alanine and glycine. This labelling pattern reduces the spectral overlap as well as the number of assignment possibilities. In order to extend the assignment, four other specifically labelled OmpG samples were used. The assignment procedure starts with the identification of the spin systems of each labelled amino acid using 2D 13C-13C and 3D NCACX correlation experiments. In a second step, 2D and 3D NCOCX type experiments are used for the sequential assignment of the observed resonances to specific nuclei in the OmpG amino acid sequence. Additionally, it was shown in this work, that biosynthetically site directed labelled samples, which are normally used to observe long-range correlations, were helpful to confirm the assignment. Another approach to find assignment starting points in large protein systems, is the use of spectroscopic filtering techniques. A filtering block that selects methyl resonances was used to find further assignment starting points for OmpG. Combining all these techniques, it was possible to assign nearly 50 % of the observed signals to the OmpG sequence. Using this information, a prediction of the secondary structure elements of OmpG was possible. Most of the calculated motifs were in good aggreement with the crystal structures of OmpG. The approaches presented here should be applicable to a wide variety of MPs and MP-complexes and should thus open a new avenue for the structural biology of MPs.
Das biogene Amin Serotonin (5-Hydroxytryptamin, 5-HT) agiert als wichtiger chemischer Botenstoff bei einer Vielzahl von Organismen. Das durch 5 HT vermittelte Signal wird dabei durch spezifische Rezeptoren wahrgenommen und in eine zelluläre Reaktion umgesetzt. Diese 5 HT Rezeptoren gehören überwiegend zur Familie der G Protein gekoppelten Rezeptoren (GPCRs). Die Honigbiene Apis mellifera bietet unter anderem aufgrund ihrer eusozialen Lebensweise vielfältige Ansatzpunkte zur Erforschung der Funktionen des serotonergen Systems in Insekten. Bei A. mellifera wurden bereits vier 5-HT-Rezeptor-Subtypen beschrieben und molekular sowie pharmakologisch charakterisiert: Am5 HT1A, Am5 HT2α, Am5 HT2β und Am5 HT7. Ziel dieser Arbeit war es, gewebespezifische sowie alters- und tageszeitabhängige Expressionsmuster der 5 HT Rezeptor-Subtypen zu untersuchen, um zu einem umfassenden Verständnis des serotonergen Systems der Honigbiene beizutragen und eine Basis zur Hypothesenentwicklung für mögliche physiologische Funktionen zu schaffen.
Es wurde die Expression der 5 HT Rezeptorgene sowohl im zentralen Nervensystem, als auch in Teilen des Verdauungs-, Exkretions- und Speicheldrüsensystems gemessen. Dabei konnte gezeigt werden, dass die untersuchten 5-HT-Rezeptor-Subtypen generell weit im Organismus der Honigbiene verbreitet sind. Interessanterweise unterschieden sich die untersuchten Gewebe hinsichtlich der mRNA-Expressionsmuster der untersuchten Rezeptoren. Während beispielsweise im Gehirn Am5 ht1A und Am5 ht7 stärker als Am5 ht2α und Am5 ht2β exprimiert wurden, zeigte sich in Darmgewebe ein umgekehrtes Muster.
Es war bereits bekannt, dass es bei der Expression der Am5-ht2-Gene zu alternativem Spleißen kommt. Dies führt zur Entstehung der verkürzten mRNA-Varianten Am5 ht2αΔIII und Am5 ht2βΔII. Die daraus resultierenden Proteine können nicht als funktionelle GPCRs agieren. Es konnte gezeigt werden, dass diese verkürzten Spleißvarianten dennoch ubiquitär in der Honigbiene exprimiert werden. Bemerkenswerterweise wurden gewebeübergreifende Ähnlichkeiten der Expressionsmuster der Spleißvarianten gegenüber deren zugehörigen Volllängenvarianten festgestellt, welche auf Funktionen der verkürzten Varianten in vivo hindeuten.
Im Hinblick auf die bei A. mellifera hauptsächlich altersbedingte Arbeitsteilung wurde die Expression der 5 HT Rezeptor-Subtypen in Gehirnen von unterschiedlich alten Arbeiterinnen mit unterschiedlichen sozialen Rollen verglichen. Während auf mRNA-Ebene keines der vier 5 HT Rezeptor-Subtypen eine altersabhängig unterschiedliche Expression zeigte, konnte für das Am5-HT1A-Protein eine höhere Konzentration in den Gehirnen älterer Tiere gefunden werden. Dies deutet auf eine posttranskriptionale Regulation der 5 HT1A Rezeptorexpression hin, welche im Zusammenhang mit der Arbeitsteilung stehen könnte.
Es erfolgte die Untersuchung tageszeitlicher Änderungen sowohl der Expression der 5 HT Rezeptor-Subtypen, als auch des biogenen Amins 5 HT selbst. Während es in den Gehirnen von Arbeiterinnen, welche unter natürlichen Bedingungen gehalten wurden, zu keiner tageszeitabhängigen Veränderung des 5 HT-Titers kam, zeigte die mRNA-Expression von Am5-ht2α und Am5-ht2β eine periodische Oszillation mit Zunahme während des Tages und Abnahme während der Nacht. Diese Regulation wird durch externe Faktoren hervorgerufen und ist nicht auf einen endogenen circadianen Rhythmus zurückzuführen. Dies ging aus der Wiederholung der Expressionsmessungen an Gehirnen von Bienen, welche unter konstanten Laborbedingungen gehalten wurden, hervor.
Weiterhin wurde die Beteiligung des serotonergen Systems an der Steuerung von Aspekten des circadianen lokomotorischen Aktivitätsrhythmus anhand von Verhaltensexperimenten untersucht. Mit 5 HT gefütterte Arbeiterinnen zeigten dabei unter konstanten Bedingungen eine längere Periode des Aktivitätsrhythmus als Kontrolltiere. Dies deutet auf einen Einfluss von 5 HT auf die Modulation der Synchronisation der inneren Uhr hin.
Die vorliegenden Ergebnisse tragen wesentlich zum tieferen Verständnis des serotonergen Systems der Honigbiene bei und bieten Ansatzpunkte für weitergehende Studien zur Funktion von 5 HT im Zusammenhang mit der Modulation von physiologischen Prozessen, Arbeitsteilung und circadianen Rhythmen.
Die Speicheldrüsen der Schmeißfliege Calliphora vicina produzieren bei Stimulierung mit dem Neurohormon Serotonin (5-Hydroxytryptamine, 5-HT) einen KCl-reichen Primärspeichel. Der transepitheliale K+-Transport wird durch eine apikal lokalisierte vakuoläre H+-ATPase (V-ATPase) energetisiert. Stimulierung der Speicheldrüsen mit 5-HT aktiviert die apikale V-ATPase, die Protonen aus der Zelle in das Drüsenlumen transportiert. Trotz des auswärts gerichteten Protonentransportes führt die 5-HT-Stimulierung kurioserweise zu einer intrazellulären Ansäuerung. Die Ursachen dieser 5-HT-induzierten Ansäuerung waren unzureichend untersucht. Deshalb war das Ziel dieser Arbeit die Identifikation aller Transporter, die an der intrazellulären pH-(pHi)-Regulation in unstimulierten Speicheldrüsen von Calliphora vicina beteiligt sind und an der Entstehung und Regulation der 5-HT-induzierten pHi-Änderungen mitwirken. Von besonderem Interesse war hierbei die funktionelle Mitwirkung der V-ATPase, deren Beteiligung an der pHi-Regulation in tierischen Zellen bisher wenig untersucht war. Wesentliche Ergebnisse dieser Arbeit waren: • Messungen des pHi-Wertes in der unstimulierten Drüse zeigten, dass vor allem die V-ATPase und mindestens ein Na+-abhängiger HCO3--Transporter an der Aufrechterhaltung des Ruhe-pHi beteiligt sind. • Zur Wiederherstellung des Ruhe-pHi nach einer intrazellulären Ansäuerung (NH4Cl-Vorpuls) tragen ebenfalls im Wesentlichen die V-ATPase und mindestens ein Na+-abhängiger HCO3--Transporter bei. Der Na+/H+-Antiporter hat in der unstimulierten Drüse keinen messbaren Einfluss auf den Ruhe-pHi. • Die Wiederherstellung des Ruhe-pHi nach einer intrazellulären Alkalisierung (Na-acetat-Vorpuls) ist Cl--abhängig, aber auch unter extremen Bedingungen waren die Zellen noch in der Lage sich vollständig von einer intrazellullären Alkalisierung zu erholen. Einen entscheidenden Anteil daran hat offenbar die hohe intrazelluläre Pufferkapazität. • Ein Na+-abhängiger Glutamat-Transporter ist per se kein pHi-regulierender Transporter, seine Aktivität hat jedoch Einfluss auf den Ruhe-pHi in der unstimulierten Speicheldrüse von Calliphora vicina. • 10 nM 5-HT induzieren in den Calliphora Speicheldrüsen eine intrazelluläre Ansäuerung. An dieser Ansäuerung ist der Na+/H+-Antiporter entscheidend beteiligt. Auch eine klare Cl--Abhängigkeit der 5-HT-induzierten Ansäuerung konnte beobachtet werden. Wahrscheinlich ist eine gekoppelte Aktivität von Na+/H+-Antiporter und Cl-/HCO3--Antiporter. • Messungen mit einem O2-empfindlichen Fluoreszenzfarbstoff zeigten, dass Stimulierung der Speicheldrüsen mit 5-HT die Zellatmung aktivierte. Der cAMP- und der IP3/Ca2+-Weg tragen auf komplexe Weise zu der 5-HT-induzierten Aktivierung der Zellatmung und damit auch zu den 5-HT-induzierten pHi-Änderungen bei. • Mit molekularbiologischen Untersuchungen ist es gelungen den Na+-abhängigen Glutamat-Transporter, den Na+/H+-Antiporter, die Carboanhydrase und die Untereinheit C der V-ATPase in den Calliphora Speicheldrüsen direkt nachzuweisen. Zudem konnte erstmals der direkte Nachweis für die Expression eines nH+/K+-Antiporters in den Speicheldrüsen von Calliphora vicina erbracht werden. Diese Arbeit trug ganz wesentlich zum Verständnis der pHi-Regulation in der unstimulierten und stimulierten Speicheldrüse von Calliphora vicina bei. Mechanismen die zur Aufrechterhaltung und Wiederherstellung des Ruhe-pHi nach einer intrazellulären Ansäuerung bzw. Alkalisierung beitragen, konnten mit pHi-Messungen und auch molekularbiologisch nachgewiesen werden. Die Mechanismen, welche die 5-HT-induzierte intrazelluläre Ansäuerung verursachen, konnten ebenfalls aufgeklärt werden. Zudem wurde an den Calliphora Speicheldrüsen eine neue optische Methode zur Messung des O2-Verbrauchs in tierischen Geweben etabliert.
Aldehyde oxidases (AOXs) (E.C. 1.2.3.1) are molybdoflavo-enzymes belonging to the xanthine oxidase (XO) family. AOXs in mammals contain one molybdenum cofactor (Moco), one flavin adenine dinucleotide (FAD) and two [2Fe-2S] clusters, the presence of which is essential for the activity of the enzyme. Human aldehyde oxidase (hAOX1) is a cytosolic enzyme mainly expressed in the liver. hAOX1is involved in the metabolism of xenobiotics. It oxidizes aldehydes to their corresponding carboxylic acids and hydroxylates N-heterocyclic compounds. Since these functional groups are widely present in therapeutics, understanding the behaviour of hAOX1 has important implications in medicine. During the catalytic cycle of hAOX1, the substrate is oxidized at Moco and electrons are internally transferred to FAD via the FeS clusters. An electron acceptor juxtaposed to the FAD receives the electrons and re-oxidizes the enzyme for the next catalytic cycle. Molecular oxygen is the endogenous electron acceptor of hAOX1 and in doing so it is reduced and produces reactive oxygen species (ROS) including hydrogen peroxide (H2O2) and superoxide (O2.-). The production of ROS has patho-physiological importance, as ROS can have a wide range of effects on cell components including the enzyme itself.
In this thesis, we have shown that hAOX1 loses its activity over multiple cycles of catalysis due to endogenous ROS production and have identified a cysteine rich motif that protects hAOX1 from the ROS damaging effects. We have also shown that a sulfido ligand, which is bound at Moco and is essential for the catalytic activity of the enzyme, is vulnerable during turnover. The ROS produced during the course of the reaction are also able to remove this sulfido ligand from Moco. ROS, in addition, oxidize particular cysteine residues. The combined effects of ROS on the sulfido ligand and on specific cysteine residues in the enzyme result in its inactivation. Furthermore, we report that small reducing agents containing reactive sulfhydryl groups, in a selective manner, inactivate some of the mammalian AOXs by modifying the sulfido ligand at Moco. The mechanism of ROS production by hAOX1 is another scope that has been investigated as part of the work in this thesis. We have shown that the ratio of type of ROS, i.e. hydrogen peroxide (H2O2) and superoxide (O2.-), produced by hAOX1 is determined by a particular position on a flexible loop that locates in close proximity of FAD. The size of the cavity at the ROS producing site, i.e. the N5 position of the FAD isoalloxazine ring, kinetically affects the amount of each type of ROS generated by hAOX1. Taken together, hAOX1 is an enzyme with emerging importance in pharmacological and medical studies, not only due to its involvement in drug metabolism, but also due to ROS production which has physiological and pathological implications.
Sulfur is essential for the functionality of some important biomolecules in humans. Biomolecules like the Iron-sulfur clusters, tRNAs, Molybdenum cofactor, and some vitamins. The trafficking of sulfur involves proteins collectively called sulfurtransferase. Among these are TUM1, MOCS3, and NFS1.
This research investigated the role of TUM1 for molybdenum cofactor biosynthesis and cytosolic tRNA thiolation in humans. The rhodanese-like protein MOCS3 and the L-cysteine desulfurase (NFS1) have been previously demonstrated to interact with TUM1. These interactions suggested a dual function of TUM1 in sulfur transfer for Moco biosynthesis and cytosolic tRNA thiolation. TUM1 deficiency has been implicated to be responsible for a rare inheritable disorder known as mercaptolactate cysteine disulfiduria (MCDU), which is associated with a mental disorder. This mental disorder is similar to the symptoms of sulfite oxidase deficiency which is characterised by neurological disorders. Therefore, the role of TUM1 as a sulfurtransferase in humans was investigated, in CRISPR/Cas9 generated TUM1 knockout HEK 293T cell lines.
For the first time, TUM1 was implicated in Moco biosynthesis in humans by quantifying the intermediate product cPMP and Moco using HPLC. Comparing the TUM1 knockout cell lines to the wild-type, accumulation and reduction of cPMP and Moco were observed respectively. The effect of TUM1 knockout on the activity of a Moco-dependent enzyme, Sulfite oxidase, was also investigated. Sulfite oxidase is essential for the detoxification of sulfite to sulfate. Sulfite oxidase activity and protein abundance were reduced due to less availability of Moco. This shows that TUM1 is essential for efficient sulfur transfer for Moco biosynthesis. Reduction in cystathionin -lyase in TUM1 knockout cells was quantified, a possible coping mechanism of the cell against sulfite production through cysteine catabolism.
Secondly, the involvement of TUM1 in tRNA thio-modification at the wobble Uridine-34 was reported by quantifying the amount of mcm5s2U and mcm5U via HPLC. The reduction and accumulation of mcm5s2U and mcm5U in TUM1 knockout cells were observed in the nucleoside analysis. Herein, exogenous treatment with NaHS, a hydrogen sulfide donor, rescued the Moco biosynthesis, cytosolic tRNA thiolation, and cell proliferation deficits in TUM1 knockout cells.
Further, TUM1 was shown to impact mitochondria bioenergetics through the measurement of the oxygen consumption rate and extracellular acidification rate (ECAR) via the seahorse cell Mito stress analyzer. Reduction in total ATP production was also measured. This reveals how important TUM1 is for H2S biosynthesis in the mitochondria of HEK 293T.
Finally, the inhibition of NFS1 in HEK 293T and purified NFS1 protein by 2-methylene 3-quinuclidinone was demonstrated via spectrophotometric and radioactivity quantification. Inhibition of NFS1 by MQ further affected the iron-sulfur cluster-dependent enzyme aconitase activity.
Scope: Several studies show that excessive lipid intake can cause hepatic steatosis. To investigate lipotoxicity on cellular level, palmitate (PA) is often used to highly increase lipid droplets (LDs). One way to remove LDs is autophagy, while it is controversially discussed if autophagy is also affected by PA. It is aimed to investigate whether PA-induced LD accumulation can impair autophagy and punicalagin, a natural autophagy inducer from pomegranate, can improve it.
Methods and results: To verify the role of autophagy in LD degradation, HepG2 cells are treated with PA and analyzed for LD and perilipin 2 content in presence of autophagy inducer Torin 1 and inhibitor 3-Methyladenine. PA alone seems to initially induce autophagy-related proteins but impairs autophagic-flux in a time-dependent manner, considering 6 and 24 h PA. To examine whether punicalagin can prevent autophagy impairment, cells are cotreated for 24 h with PA and punicalagin. Results show that punicalagin preserves expression of autophagy-related proteins and autophagic flux, while simultaneously decreasing LDs and perilipin 2.
Conclusion: Data provide new insights into the role of PA-induced excessive LD content on autophagy and suggest autophagy-inducing properties of punicalagin, indicating that punicalagin can be a health-beneficial compound for future research on lipotoxicity in liver.
Ribosomes decode mRNA to synthesize proteins. Ribosomes, once considered static, executing machines, are now viewed as dynamic modulators of translation. Increasingly detailed analyses of structural ribosome heterogeneity led to a paradigm shift toward ribosome specialization for selective translation. As sessile organisms, plants cannot escape harmful environments and evolved strategies to withstand. Plant cytosolic ribosomes are in some respects more diverse than those of other metazoans. This diversity may contribute to plant stress acclimation. The goal of this thesis was to determine whether plants use ribosome heterogeneity to regulate protein synthesis through specialized translation. I focused on temperature acclimation, specifically on shifts to low temperatures. During cold acclimation, Arabidopsis ceases growth for seven days while establishing the responses required to resume growth. Earlier results indicate that ribosome biogenesis is essential for cold acclimation. REIL mutants (reil-dkos) lacking a 60S maturation factor do not acclimate successfully and do not resume growth. Using these genotypes, I ascribed cold-induced defects of ribosome biogenesis to the assembly of the polypeptide exit tunnel (PET) by performing spatial statistics of rProtein changes mapped onto the plant 80S structure. I discovered that growth cessation and PET remodeling also occurs in barley, suggesting a general cold response in plants. Cold triggered PET remodeling is consistent with the function of Rei-1, a REIL homolog of yeast, which performs PET quality control. Using seminal data of ribosome specialization, I show that yeast remodels the tRNA entry site of ribosomes upon change of carbon sources and demonstrate that spatially constrained remodeling of ribosomes in metazoans may modulate protein synthesis. I argue that regional remodeling may be a form of ribosome specialization and show that heterogeneous cytosolic polysomes accumulate after cold acclimation, leading to shifts in the translational output that differs between wild-type and reil-dkos. I found that heterogeneous complexes consist of newly synthesized and reused proteins. I propose that tailored ribosome complexes enable free 60S subunits to select specific 48S initiation complexes for translation. Cold acclimated ribosomes through ribosome remodeling synthesize a novel proteome consistent with known mechanisms of cold acclimation. The main hypothesis arising from my thesis is that heterogeneous/ specialized ribosomes alter translation preferences, adjust the proteome and thereby activate plant programs for successful cold acclimation.
Sehzellen von Insekten sind epitheliale Zellen mit einer charakteristischen, hochpolaren Morphologie und Organisation. Die molekularen Komponenten der Sehkaskade befinden sich im Rhabdomer, einem Saum dicht gepackter Mikrovilli entlang der Sehzelle. Bereits in den 70er Jahren des letzten Jahrhunderts wurde beschrieben, dass die Mikrovilli entlang einer Sehzelle eine unterschiedliche Ausrichtung besitzen, oder in anderen Worten, die Rhabdomere entlang der Sehzell-Längsachse verdreht sind. So sind in den Sehzellen R1-R6 bei dipteren Fliegen (Calliphora, Drosophila) die Mikrovilli im distalen und proximalen Bereich eines Rhabdomers etwa rechtwinkelig zueinander angeordnet. Dieses Phänomen wird in der Fachliteratur als rhabdomere twisting bezeichnet und reduziert die Empfindlichkeit für polarisiertes Licht. Es wurde für das Drosophila-Auge gezeigt, dass diese strukturelle Asymmetrie der Sehzellen mit einer molekularen Asymmetrie in der Verteilung phosphotyrosinierter Proteine an die Stielmembran (einem nicht-mikrovillären Bereich der apikalen Plasmamembran) einhergeht. Zudem wurde gezeigt, dass die immuncytochemische Markierung mit anti-Phosphotyrosin (anti-PY) als lichtmikroskopischer Marker für das rhabdomere twisting verwendet werden kann. Bisher wurde hauptsächlich die physiologische Bedeutung der Rhabdomerverdrehung untersucht. Es ist wenig über die entwicklungs- und zellbiologischen Grundlagen bekannt. Ziel der vorliegenden Arbeit war es, die Identität der phosphotyrosinierten Proteine an der Stielmembran zu klären und ihre funktionelle Bedeutung für die Entwicklung des rhabdomere twisting zu analysieren. Zudem sollte untersucht werden, welchen Einfluss die inneren Sehzellen R7 und R8 auf die Verdrehung der Rhabdomere von R1-R6 haben. Für die zwei Proteinkinasen Rolled (ERK) und Basket (JNK) vom Typ der Mitogen-aktivierten Proteinkinasen (MAPK) konnte ich zeigen, dass sie in ihrer aktivierten (= phosphorylierten) Form (pERK bzw. pJNK) eine asymmetrische Verteilung an der Stielmembran aufweisen vergleichbar der Markierung mit anti-PY. Weiterhin wurde diese asymmetrische Verteilung von pERK und pJNK ebenso wie die von PY erst kurz vor Schlupf der Fliegen (bei ca. 90% pupaler Entwicklung) etabliert. Durch Präinkubationsexperimente mit anti-PY wurde die Markierung mit anti-pERK bzw. anti-pJNK unterbunden. Diese Ergebnisse sprechen dafür, dass pERK und pJNK zu den Proteinen gehören, die von anti-PY an der Stielmembran erkannt werden. Da es sich bei ERK und JNK um Kinasen handelt, ist es naheliegend, dass diese an der Entwicklung des rhabdomere twisting beteiligt sein könnten. Diese Hypothese wurde durch die Analyse von hypermorphen (rl SEM)und hypomorphen (rl 1/rl 10a) Rolled-Mutanten überprüft. In der rl SEM-Mutante mit erhöhter Aktivität der Proteinkinase erfolgte die asymmetrische Positionierung von pERK an der Stielmembran sowie die Mikrovillikippung schon zu einem früheren Zeitpunkt in der pupalen Entwicklung. Im adulten Auge war die anti-PY-Markierung im distalen Bereich der Sehzellen intensiver sowie der Kippwinkel vergrößert. In der rl 1/rl 10a-Mutanten mit reduzierter Kinaseaktivität waren die anti-PY-Markierung und der Kippwinkel im proximalen Bereich der Sehzellen verringert. Die Proteinkinase ERK hat somit einen Einfluss auf die zeitliche Etablierung des rhabdomere twisting wie auch auf dessen Ausprägung im Adulttier. Die Rhabdomerverdrehung sowie die Änderung im anti-PY-Markierungsmuster erfolgen an den Sehzellen R1-R6 relativ abrupt auf halber Ommatidienlänge, dort wo das Rhabdomer von R7 endet und das von R8 beginnt. Es stellte sich deshalb die Frage, ob die Rhabdomerverdrehung an R1-R6 durch die Sehzelle R7 und/oder R8 beeinflusst wird. Um dieser Frage nachzugehen wurden Mutanten analysiert, denen die R7- oder die R8-Photorezeptoren bzw. R7 und R8 fehlten. Das wichtigste Ergebnis dieser Untersuchungen war, dass bei Fehlen von R8 die Rhabdomerverdrehung bei R1-R6 nach keinen erkennbaren Regeln erfolgt. R8 ist somit Voraussetzung für die Etablierung der Rhabdomerverdrehung in R1-R6. Folgendes Modell wurde auf Grundlage dieses und weiterer Ergebnisse erarbeitet: Im dritten Larvenstadium rekrutiert R8 die Sehzellpaare R2/R5, R3/R4 und R1/R6. Dabei werden R1-R6 durch den Kontakt zu R8 „polarisiert“. Abschließend wird R7 durch R8 rekrutiert. Dies führt zu einer Fixierung der Polarität von R1-R6 durch R7. Die Ausführung der Mikrovillikippung anhand der festgelegten Polarität erfolgt in der späten Puppenphase. Die Proteinkinase ERK ist an diesem letzten Morphogeneseprozess beteiligt.
Die vakuoläre Protonen-ATPase, kurz V-ATPase, ist ein multimerer Enzymkomplex, der in fast jeder eukaryotischen Zelle zu finden ist und den aktiven elektrogenen Transport von Protonen über Membranen katalysiert. Die Aktivität der V-ATPase ist essentiell für eine Vielzahl physiologischer Prozesse. Ein grundlegender Mechanismus zur Regulation der V-ATPase-Aktivität ist die reversible Dissoziation des Holoenzyms in den integralen VO-Komplex, der als Protonenkanal dient, und den cytosolischen V1-Komplex, der ATP hydrolysiert und somit den Protonentransport energetisiert. Die Untereinheit C, die im dissoziierten Zustand der V-ATPase als einzige Untereinheit isoliert im Cytoplasma vorliegt, scheint bei der Bildung des aktiven Holoenzyms eine Schlüsselrolle zu übernehmen. In den Speicheldrüsen der Schmeißfliege Calliphora vicina ist die V-ATPase an der Speichelsekretion beteiligt. In den sekretorischen Zellen wird die Bildung des V-ATPase-Holoenzyms in der apikalen Plasmamembran durch das Neurohormon Serotonin (5-HT) stimuliert. Der Effekt von 5-HT auf die V-ATPase wird intrazellulär durch die Proteinkinase A (PKA) vermittelt und hält nur für die Dauer der Stimulierung an. In der vorliegenden Arbeit wurde mittels Phosphoproteinfärbungen und 2D-Elektrophorese nachgewiesen, dass infolge einer Stimulierung der Drüsenzellen mit 5-HT die Untereinheit C der V-ATPase durch die PKA reversibel phosphoryliert wird. Die Phosphorylierung geht einher mit einer Umverteilung der Untereinheit C aus dem Cytoplasma zur apikalen Plasmamembran und der Bildung des aktiven Holoenzyms. Immuncytochemische Untersuchungen zeigten, dass die katalytische Untereinheit der PKA ebenfalls umverteilt wird und in stimulierten Zellen im Bereich der apikalen Plasmamembran konzentriert vorliegt. Um herauszufinden welche Proteinphosphatase der PKA entgegenwirkt, wurden luminale pH-Messungen durchgeführt und der Effekt von spezifischen Proteinphosphatase-Inhibitoren und veresterten Komplexbildnern zweiwertiger Kationen auf die V-ATPase-Aktivität untersucht. Diese Messungen führten zu der Schlussfolgerung, dass eine Proteinphosphatase des Typs 2C an der Inaktivierung der V-ATPase beteiligt ist. Mit weiteren Phosphoproteinfärbungen konnte gezeigt werden, dass die Dephosphorylierung der Untereinheit C ebenfalls durch eine Proteinphosphatase 2C katalysiert wird und dies vermutlich die Dissoziation des VO- und V1-Komplexes begünstigt. Darüber hinaus konnte durch luminale pH-Messungen und ergänzende biochemische Untersuchungen eine Calcineurin-vermittelte Modulation des cAMP/PKA-Signalweges durch den parallel aktivierten IP3/Ca2+-Signalweg und damit einhergehend eine Beeinflussung der V-ATPase-Aktivität durch den [Ca2+]-Spiegel nachgewiesen werden.
Post-translational redox-regulation is a well-known mechanism to regulate enzymes of the Calvin cycle, oxidative pentose phosphate cycle, NADPH export and ATP synthesis in response to light. The aim of the present thesis was to investigate whether a similar mechanism is also regulating carbon storage in leaves. Previous studies have shown that the key-regulatory enzyme of starch synthesis, ADPglucose pyrophosphorylase (AGPase) is inactivated by formation of an intermolecular disulfide bridge between the two catalytic subunits (AGPB) of the heterotetrameric holoenzyme in potato tubers, but the relevance of this mechanism to regulate starch synthesis in leaves was not investigated. The work presented in this thesis shows that AGPase is subject to post-translational redox-regulation in leaves of pea, potato and Arabidopsis in response to day night changes. Light was shown to trigger posttranslational redox-regulation of AGPase. AGPB was rapidly converted from a dimer to a monomer when isolated pea chloroplasts were illuminated and from a monomer to a dimer when preilluminated leaves were darkened. Conversion of AGPB from dimer to monomer was accompanied by an increase in activity due to changes in the kinetik properties of the enzyme. Studies with pea chloroplast extracts showed that AGPase redox-activation is mediated by thioredoxins f and m from spinach in-vitro. In a further set of experiments it was shown that sugars provide a second input leading to AGPase redox activation and increased starch synthesis and that they can act as a signal which is independent from light. External feeding of sugars such as sucrose or trehalose to Arabidopsis leaves in the dark led to conversion of AGPB from dimer to monomer and to an increase in the rate of starch synthesis, while there were no significant changes in the level of 3PGA, an allosteric activator of the enyzme, and in the NADPH/NADP+ ratio. Experiments with transgenic Arabidopsis plants with altered levels of trehalose 6-phosphate (T6P), the precursor of trehalose synthesis, provided genetic evidence that T6P rather than trehalose is leading to AGPase redox-activation. Compared to Wt, leaves expressing E.coli trehalose-phosphate synthase (TPS) in the cytosol showed increased activation of AGPase and higher starch level during the day, while trehalose-phosphate phosphatase (TPP) overexpressing leaves showed the opposite. These changes occurred independently of changes in sugar and sugar-phosphate levels and NADPH/NADP+ ratio. External supply of sucrose to Wt and TPS-overexpressing leaves led to monomerisation of AGPB, while this response was attenuated in TPP expressing leaves, indicating that T6P is involved in the sucrose-dependent redox-activation of AGPase. To provide biochemical evidence that T6P promotes redox-activation of AGPase independently of cytosolic elements, T6P was fed to intact isolated chloroplasts for 15 min. incubation with concentrations down to 100 µM of T6P, but not with sucrose 6-phosphate, sucrose, trehalose or Pi as controls, significantly and specifically increased AGPB monomerisation and AGPase activity within 15 minutes, implying T6P as a signal reporting the cytosolic sugar status to the chloroplast. The response to T6P did not involve changes in the NADPH/NADP+ ratio consistent with T6P modulating redox-transfer to AGPase independently of changes in plastidial redox-state. Acetyl-CoA carboxylase (ACCase) is known as key-regulatory enzyme of fatty acid and lipid synthesis in plants. At the start of the present thesis there was mainly in vitro evidence in the literature showing redox-regulation of ACCase by DTT, and thioredoxins f and m. In the present thesis the in-vivo relevance of this mechanism to regulate lipid synthesis in leaves was investigated. ACCase activity measurement in leaf tissue collected at the end of the day and night in Arabidopsis leaves revealed a 3-fold higher activation state of the enzyme in the light than in the dark. Redox-activation was accompanied by change in kinetic properties of ACCase, leading to an increase affinity to its substrate acetyl-CoA . In further experiments, DTT as well as sucrose were fed to leaves, and both treatments led to a stimulation in the rate of lipid synthesis accompanied by redox-activation of ACCase and decrease in acetyl-CoA content. In a final approach, comparison of metabolic and transcript profiling after DTT feeding and after sucrose feeding to leaves provided evidence that redox-modification is an important regulatory mechanism in central metabolic pathways such as TCA cycle and amino acid synthesis, which acts independently of transcript levels.
Redox signalling in plants
(2020)
Once proteins are synthesized, they can additionally be modified by post-translational modifications (PTMs). Proteins containing reactive cysteine thiols, stabilized in their deprotonated form due to their local environment as thiolates (RS-), serve as redox sensors by undergoing a multitude of oxidative PTMs (Ox-PTMs). Ox-PTMs such as S-nitrosylation or formation of inter- or intra-disulfide bridges induce functional changes in these proteins. Proteins containing cysteines, whose thiol oxidation state regulates their functions, belong to the so-called redoxome. Such Ox-PTMs are controlled by site-specific cellular events that play a crucial role in protein regulation, affecting enzyme catalytic sites, ligand binding affinity, protein-protein interactions or protein stability. Reversible protein thiol oxidation is an essential regulatory mechanism of photosynthesis, metabolism, and gene expression in all photosynthetic organisms. Therefore, studying PTMs will remain crucial for understanding plant adaptation to external stimuli like fluctuating light conditions. Optimizing methods suitable for studying plants Ox-PTMs is of high importance for elucidation of the redoxome in plants. This study focusses on thiol modifications occurring in plant and provides novel insight into in vivo redoxome of Arabidopsis thaliana in response to light vs. dark. This was achieved by utilizing a resin-assisted thiol enrichment approach. Furthermore, confirmation of candidates on the single protein level was carried out by a differential labelling approach. The thiols and disulfides were differentially labelled, and the protein levels were detected using immunoblot analysis. Further analysis was focused on light-reduced proteins. By the enrichment approach many well studied redox-regulated proteins were identified. Amongst those were fructose 1,6-bisphosphatase (FBPase) and sedoheptulose-1,7-bisphosphatase (SBPase) which have previously been described as thioredoxin system targeted enzymes. The redox regulated proteins identified in the current study were compared to several published, independent results showing redox regulated proteins in Arabidopsis leaves, root, mitochondria and specifically S-nitrosylated proteins. These proteins were excluded as potential new candidates but remain as a proof-of-concept to the enrichment experiments to be effective. Additionally, CSP41A and CSP41B proteins, which emerged from this study as potential targets of redox-regulation, were analyzed by Ribo-Seq. The active translatome study of csp41a mutant vs. wild-type showed most of the significant changes at end of the night, similarly as csp41b. Yet, in both mutants only several chloroplast-encoded genes were altered. Further studies of CSP41A and CSP41B proteins are needed to reveal their functions and elucidate the role of redox regulation of these proteins.
Bottom-up synthetic biology is used for the understanding of how a cell works. It is achieved through developing techniques to produce lipid-based vesicular structures as cellular mimics. The most common techniques used to produce cellular mimics or synthetic cells is through electroformation and swelling method. However, the abovementioned techniques cannot efficiently encapsulate macromolecules such as proteins, enzymes, DNA and even liposomes as synthetic organelles. This urges the need to develop new techniques that can circumvent this issue and make the artificial cell a reality where it is possible to imitate a eukaryotic cell through encapsulating macromolecules. In this thesis, the aim to construct a cell system using giant unilamellar vesicles (GUVs) to reconstitute the mitochondrial molybdenum cofactor biosynthetic pathway. This pathway is highly conserved among all life forms, and therefore is known for its biological significance in disorders induced through its malfunctioning. Furthermore, the pathway itself is a multi-step enzymatic reaction that takes place in different compartments. Initially, GTP in the mitochondrial matrix is converted to cPMP in the presence of cPMP synthase. Further, produced cPMP is transported across the membrane to the cytosol, to be converted by MPT synthase into MPT. This pathway provides a possibility to address the general challenges faced in the development of a synthetic cell, to encapsulate large biomolecules with good efficiency and greater control and to evaluate the enzymatic reactions involved in the process.
For this purpose, the emulsion-based technique was developed and optimised to allow rapid production of GUVs (~18 min) with high encapsulation efficiency (80%). This was made possible by optimizing various parameters such as density, type of oil, the impact of centrifugation speed/time, lipid concentration, pH, temperature, and emulsion droplet volume. Furthermore, the method was optimised in microtiter plates for direct experimentation and visualization after the GUV formation. Using this technique, the two steps - formation of cPMP from GTP and the formation of MPT from cPMP were encapsulated in different sets of GUVs to mimic the two compartments. Two independent fluorescence-based detection systems were established to confirm the successful encapsulation and conversion of the reactants. Alternatively, the enzymes produced using bacterial expression and measured. Following the successful encapsulation and evaluation of enzymatic reactions, cPMP transport across mitochondrial membrane has been mimicked using GUVs using a complex mitochondrial lipid composition. It was found that the cPMP interaction with the lipid bilayer results in transient pore-formation and leakage of internal contents.
Overall, it can be concluded that in this thesis a novel technique has been optimised for fast production of functional synthetic cells. The individual enzymatic steps of the Moco biosynthetic pathway have successfully implemented and quantified within these cellular mimics.
Vegetation change at high latitudes is one of the central issues nowadays with respect to ongoing climate changes and triggered potential feedback. At high latitude ecosystems, the expected changes include boreal treeline advance, compositional, phenological, physiological (plants), biomass (phytomass) and productivity changes. However, the rate and the extent of the changes under climate change are yet poorly understood and projections are necessary for effective adaptive strategies and forehanded minimisation of the possible negative feedbacks.
The vegetation itself and environmental conditions, which are playing a great role in its development and distribution are diverse throughout the Subarctic to the Arctic. Among the least investigated areas is central Chukotka in North-Eastern Siberia, Russia. Chukotka has mountainous terrain and a wide variety of vegetation types on the gradient from treeless tundra to northern taiga forests. The treeline there in contrast to subarctic North America and north-western and central Siberia is represented by a deciduous conifer, Larix cajanderi Mayr. The vegetation varies from prostrate lichen Dryas octopetala L. tundra to open graminoid (hummock and non-hummock) tundra to tall Pinus pumila (Pall.) Regel shrublands to sparse and dense larch forests.
Hence, this thesis presents investigations on recent compositional and above-ground biomass (AGB) changes, as well as potential future changes in AGB in central Chukotka. The aim is to assess how tundra-taiga vegetation develops under changing climate conditions particularly in Fareast Russia, central Chukotka. Therefore, three main research questions were considered:
1) What changes in vegetation composition have recently occurred in central Chukotka?
2) How have the above-ground biomass AGB rates and distribution changed in central Chukotka?
3) What are the spatial dynamics and rates of tree AGB change in the upcoming millennia in the northern tundra-taiga of central Chukotka?
Remote sensing provides information on the spatial and temporal variability of vegetation. I used Landsat satellite data together with field data (foliage projective cover and AGB) from two expeditions in 2016 and 2018 to Chukotka to upscale vegetation types and AGB for the study area. More specifically, I used Landsat spectral indices (Normalised Difference Vegetation Index (NDVI), Normalised Difference Water Index (NDWI) and Normalised Difference Snow Index (NDSI)) and constrained ordination (Redundancy analysis, RDA) for further k-means-based land-cover classification and general additive model (GAM)-based AGB maps for 2000/2001/2002 and 2016/2017. I also used Tandem-X DEM data for a topographical correction of the Landsat satellite data and to derive slope, aspect, and Topographical Wetness Index (TWI) data for forecasting AGB.
Firstly, in 2016, taxa-specific projective cover data were collected during a Russian-German expedition. I processed the field data and coupled them with Landsat spectral Indices in the RDA model that was used for k-means classification. I could establish four meaningful land-cover classes: (1) larch closed-canopy forest, (2) forest tundra and shrub tundra, (3) graminoid tundra and (4) prostrate herb tundra and barren areas, and accordingly, I produced the land cover maps for 2000/2001/2002 and 2016/20017. Changes in land-cover classes between the beginning of the century (2000/2001/2002) and the present time (2016/2017) were estimated and interpreted as recent compositional changes in central Chukotka. The transition from graminoid tundra to forest tundra and shrub tundra was interpreted as shrubification and amounts to a 20% area increase in the tundra-taiga zone and 40% area increase in the northern taiga. Major contributors of shrubification are alder, dwarf birch and some species of the heather family. Land-cover change from the forest tundra and shrub tundra class to the larch closed-canopy forest class is interpreted as tree infilling and is notable in the northern taiga. We find almost no land-cover changes in the present treeless tundra.
Secondly, total AGB state and change were investigated for the same areas. In addition to the total vegetation AGB, I provided estimations for the different taxa present at the field sites. As an outcome, AGB in the study region of central Chukotka ranged from 0 kg m-2 at barren areas to 16 kg m-2 in closed-canopy forests with the larch trees contributing the highest. A comparison of changes in AGB within the investigated period from 2000 to 2016 shows that the greatest changes (up to 1.25 kg m 2 yr 1) occurred in the northern taiga and in areas where land cover changed to larch closed-canopy forest. Our estimations indicate a general increase in total AGB throughout the investigated tundra-taiga and northern taiga, whereas the tundra showed no evidence of change in AGB within the 15 years from 2002 to 2017.
In the third manuscript, potential future AGB changes were estimated based on the results of simulations of the individual-based spatially explicit vegetation model LAVESI using different climate scenarios, depending on Representative Concentration Pathways (RCPs) RCP 2.6, RCP 4.5 and RCP 8.5 with or without cooling after 2300 CE. LAVESI-based AGB was simulated for the current state until 3000 CE for the northern tundra-taiga study area for larch species because we expect the most notable changes to occur will be associated with forest expansion in the treeline ecotone. The spatial distribution and current state of tree AGB was validated against AGB field data, AGB extracted from Landsat satellite data and a high spatial resolution image with distinctive trees visible. The simulation results are indicating differences in tree AGB dynamics plot wise, depending on the distance to the current treeline. The simulated tree AGB dynamics are in concordance with fundamental ecological (emigrational and successional) processes: tree stand formation in simulated results starts with seed dispersion, tree stand establishment, tree stand densification and episodic thinning. Our results suggest mostly densification of existing tree stands in the study region within the current century in the study region and a lagged forest expansion (up to 39% of total area in the RCP 8.5) under all considered climate scenarios without cooling in different local areas depending on the closeness to the current treeline. In scenarios with cooling air temperature after 2300 CE, forests stopped expanding at 2300 CE (up to 10%, RCP 8.5) and then gradually retreated to their pre-21st century position. The average tree AGB rates of increase are the strongest in the first 300 years of the 21st century. The rates depend on the RCP scenario, where the highest are as expected under RCP 8.5.
Overall, this interdisciplinary thesis shows a successful integration of field data, satellite data and modelling for tracking recent and predicting future vegetation changes in mountainous subarctic regions. The obtained results are unique for the focus area in central Chukotka and overall, for mountainous high latitude ecosystems.
The advent of large-scale and high-throughput technologies has recently caused a shift in focus in contemporary biology from decades of reductionism towards a more systemic view. Alongside the availability of genome sequences the exploration of organisms utilizing such approach should give rise to a more comprehensive understanding of complex systems. Domestication and intensive breeding of crop plants has led to a parallel narrowing of their genetic basis. The potential to improve crops by conventional breeding using elite cultivars is therefore rather limited and molecular technologies, such as marker assisted selection (MAS) are currently being exploited to re-introduce allelic variance from wild species. Molecular breeding strategies have mostly focused on the introduction of yield or resistance related traits to date. However given that medical research has highlighted the importance of crop compositional quality in the human diet this research field is rapidly becoming more important. Chemical composition of biological tissues can be efficiently assessed by metabolite profiling techniques, which allow the multivariate detection of metabolites of a given biological sample. Here, a GC/MS metabolite profiling approach has been applied to investigate natural variation of tomatoes with respect to the chemical composition of their fruits. The establishment of a mass spectral and retention index (MSRI) library was a prerequisite for this work in order to establish a framework for the identification of metabolites from a complex mixture. As mass spectral and retention index information is highly important for the metabolomics community this library was made publicly available. Metabolite profiling of tomato wild species revealed large differences in the chemical composition, especially of amino and organic acids, as well as on the sugar composition and secondary metabolites. Intriguingly, the analysis of a set of S. pennellii introgression lines (IL) identified 889 quantitative trait loci of compositional quality and 326 yield-associated traits. These traits are characterized by increases/decreases not only of single metabolites but also of entire metabolic pathways, thus highlighting the potential of this approach in uncovering novel aspects of metabolic regulation. Finally the biosynthetic pathway of the phenylalanine-derived fruit volatiles phenylethanol and phenylacetaldehyde was elucidated via a combination of metabolic profiling of natural variation, stable isotope tracer experiments and reverse genetic experimentation.
Hantaviruses (HVs) are a group of zoonotic viruses that infect human beings primarily through aerosol transmission of rodent excreta and urine samplings. HVs are classified geographically into: Old World HVs (OWHVs) that are found in Europe and Asia, and New World HVs (NWHVs) that are observed in the Americas. These different strains can cause severe hantavirus diseases with pronounced renal syndrome or severe cardiopulmonary system distress. HVs can be extremely lethal, with NWHV infections reaching up to 40 % mortality rate. HVs are known to generate epidemic outbreaks in many parts of the world including Germany, which has seen periodic HV infections over the past decade. HV has a trisegmented genome. The small segment (S) encodes the nucleocapsid protein (NP), the middle segment (M) encodes the glycoproteins (GPs) Gn and Gc which forms up to tetramers and primarily monomers \& dimers upon independent expression respectively and large segment (L) encodes RNA dependent RNA polymerase (RdRp). Interactions between these viral proteins are crucial in providing mechanistic insights into HV virion development. Despite best efforts, there continues to be lack of quantification of these associations in living cells. This is required in developing the mechanistic models for HV viral assembly. This dissertation focuses on three key questions pertaining to the initial steps of virion formation that primarily involves the GPs and NP.
The research investigations in this work were completed using Fluorescence Correlation Spectroscopy (FCS) approaches. FCS is frequently used in assessing the biophysical features of bio-molecules including protein concentration and diffusion dynamics and circumvents the requirement of protein overexpression. FCS was primarily applied in this thesis to evaluate protein multimerization, at single cell resolution.
The first question addressed which GP spike formation model proposed by Hepojoki et al.(2010) appropriately describes the evidence in living cells. A novel in cellulo assay was developed to evaluate the amount of fluorescently labelled and unlabeled GPs upon co-expression. The results clearly showed that Gn and Gc initially formed a heterodimeric Gn:Gc subunit. This sub-unit then multimerizes with congruent Gn:Gc subunits to generate the final GP spike. Based on these interactions, models describing the formation of GP complex (with multiple GP spike subunits) were additionally developed.
HV GP assembly primarily takes place in the Golgi apparatus (GA) of infected cells. Interestingly, NWHV GPs are hypothesized to assemble at the plasma membrane (PM). This led to the second research question in this thesis, in which a systematic comparison between OWHV and NWHV GPs was conducted to validate this hypothesis. Surprisingly, GP localization at the PM was congruently observed with OWHV and NWHV GPs. Similar results were also discerned with OWHV and NWHV GP localization in the absence of cytoskeletal factors that regulate HV trafficking in cells.
The final question focused on quantifying the NP-GP interactions and understanding their influence of NP and GP multimerization. Gc mutlimers were detected in the presence of NP and complimented by the presence of localized regions of high NP-Gc interactions in the perinuclear region of living cells. Gc-CT domain was shown to influence NP-Gc associations. Gn, on the other hand, formed up to tetrameric complexes, independent from the presence of NP.
The results in this dissertation sheds light on the initial steps of HV virion formation by quantifying homo and heterotypic interactions involving NP and GPs, which otherwise are very difficult to perform. Finally, the in cellulo methodologies implemented in this work can be potentially extended to understand other key interactions involved in HV virus assembly.
Biomolecules such as proteins and lipids have vital roles in numerous cellular functions, including biomolecule transport, protein functions, cellular homeostasis and biomembrane integrity. Traditional biochemistry methods do not provide precise information about cellular biomolecule distribution and behavior under native environmental conditions since they are not transferable to live cell samples. Consequently, this can lead to inaccuracies in quantifying biomolecule interactions due to potential complexities arising from the heterogeneity of native biomembranes. To overcome these limitations, minimal invasive microscopic techniques, such as fluorescence fluctuation spectroscopy (FFS) in combination with fluorescence proteins (FPs) and fluorescence lipid analogs, have been developed. FFS techniques and membrane property sensors enable the quantification of various parameters, including concentration, dynamics, oligomerization, and interaction of biomolecules in live cell samples.
In this work, several FFS approaches and membrane property sensors were implemented and employed to examine biological processes of diverse context. Multi-color scanning fluorescence fluctuation spectroscopy (sFCS) was used the examine protein oligomerization, protein-protein interactions (PPIs) and protein dynamics at the cellular plasma membrane (PM). Additionally, two-color number and brightness (N&B) analysis was extended with the cross-correlation analysis in order to quantify hetero-interactions of proteins in the PM with very slow motion, which would not accessible with sFCS due strong initial photobleaching. Furthermore, two semi-automatic analysis pipelines were designed: spectral Förster resonance energy transfer (FRET) analysis to study changes in membrane charge at the inner leaflet of the PM, and spectral generalized polarization (GP) imaging and spectral phasor analysis to monitor changes in membrane fluidity and order.
An important parameter for studying PPIs is molecular brightness, which directly determines oligomerization and can be extracted from FFS data. However, FPs often display complex photophysical transitions, including dark states. Therefore, it is crucial to characterize FPs for their dark-states to ensure reliable oligomerization measurements. In this study, N&B and sFCS analysis were applied to determine photophysical properties of novel green FPs under different conditions (i.e., excitation power and pH) in living cells. The results showed that the new FPs, mGreenLantern (mGL) and Gamillus, exhibited the highest molecular brightness at the cost of lower photostability. The well-established monomeric enhanced green fluorescent protein (mEGFP) remained the best option to investigate PPIs at lower pH, while mGL was best suited for neutral pH, and Gamillus for high pH. These findings provide guidance for selecting an appropriate FP to quantify PPIs via FFS under different environmental conditions.
Next, several biophysical fluorescence microscopy approaches (i.e., sFCS, GP imaging, membrane charge FRET) were employed to monitor changes in lipid-lipid-packing in biomembranes in different biological context. Lipid metabolism in cancer cells is known to support rapid proliferation and metastasis. Therefore, targeting lipid synthesis or membrane integrity holds immense promise as an anticancer strategy. However, the mechanism of action of the novel agent erufosine (EPC3) on membrane stability is not fully under
stood. The present work revealed that EPC3 reduces lipid packing and composition as well as increased membrane fluidity and dynamic, hence, modifies lipid-lipid-interaction. These effects on membrane integrity were likely triggered by modulations in lipid metabolism and membrane organization. In the case of influenza A virus (IAV) infection, regulation of lipid metabolism is crucial for multiple steps in IAV replication and is related to the pathogenicity of IAV. Here, it is shown for the first time that IAV infection triggers a local enrichment of negatively charged lipids at the inner leaflet of the PM, which decreases membrane fluidity and dynamic, as well as increases lipid packing at the assembly site in living cells. This suggests that IAV alters lipid-lipid interactions and organization at the PM. Overall, this work highlights the potential of biophysical techniques as a screening platform for studying membrane properties in living cells at the single-cell level.
Finally, this study addressed remaining questions about the early stage of IAV assembly. The recruitment of matrix protein 1 (M1) and its interaction with other viral surface proteins, hemagglutinin (HA), neuraminidase (NA), and matrix protein 2 (M2), has been a subject of debate due to conflicting results. In this study, different FFS approaches were performed in transfected cells to investigate interactions between IAV proteins themselves and host factors at the PM. FFS measurements revealed that M2 interacts strongly with M1, leading to the translocation of M1 to the PM. This interaction likely took place along the non-canonical pathway, as evidenced by the detection of an interaction between M2 and the host factor LC3-II, leading to the recruitment of LC3-II to the PM. Moreover, weaker interaction was observed between HA and membrane-bound M1, and no interaction between NA and M1. Interestingly, higher oligomeric states of M1 were only detectable in infected cells. These results indicate that M2 initiates virion assembly by recruiting M1 to the PM, which may serve as a platform for further interactions with viral proteins and host factors.
Das Superoxidradikal kann mit fast allen Bestandteilen von Zellen reagieren und diese schädigen. Die medizinische Forschung stellte eine Beteiligung des Radikals an Krebs, Herzinfarkten und neuraler Degeneration fest. Ein empfindlicher Superoxidnachweis ist daher zum besseren Verständnis von Krankheitsverläufen wichtig. Dabei stellen die geringen typischen Konzentrationen und seine kurze Lebensdauer große Anforderungen. Ziel dieser Arbeit war es zum einen, zwei neuartige Proteinarchitekturen auf Metallelektroden zu entwickeln und deren elektrochemisches Ansprechverhalten zu charakterisieren. Zum anderen waren diese Elektroden zur empfindlichen quantitativen Superoxiddetektion einzusetzen. Im ersten Teil der Arbeit wurde eine Protein-Multischichtelektrode aus Cytochrom c und dem Polyelektrolyten Poly(anilinsulfonsäure) nach dem Layer-by-layer-Verfahren aufgebaut. Für zwei bis 15 Schichten an Protein wurde eine deutliche Zunahme an elektrodenaktivem Cytochrom c mit jedem zusätzlichen Aufbringungsschritt nachgewiesen. Die Zunahme verlief linear und ergab bei 15 Schichten eine Zunahme der redoxaktiven Proteinmenge um deutlich mehr als eine Größenordnung. Während das formale Potential im Multischichtsystem sich im Vergleich zur Monoschichtelektrode nicht veränderte, wurde für die Kinetik eine Abhängigkeit der Geschwindigkeit des Elektronentransfers von der Zahl der Proteinschichten beobachtet. Mit zunehmender Scangeschwindigkeit trat ein reversibler Kontaktverlust zu den äußeren Schichten auf. Die lineare Zunahme an elektroaktivem Protein mit steigender Zahl an Depositionsschritten unterscheidet sich deutlich von in der Literatur beschriebenen Protein/Polyelektrolyt-Multischichtelektroden, bei denen ab etwa 6-8 Schichten keine Zunahme an elektroaktivem Protein mehr festgestelltwurde. Auch ist bei diesen die Zunahme an kontaktierbaren Proteinmolekülen auf das Zwei- bis Fünffache limitiert. Diese Unterschiede des neu vorgestellten Systems zu bisherigen Multischichtassemblaten erklärt sich aus einem in dieser Arbeit für derartige Systeme erstmals beschriebenen Elektronentransfermechanismus. Der Transport von Elektronen zwischen der Elektrodenoberfläche und den Proteinmolekülen in den Schichten verläuft über einen Protein-Protein-Elektronenaustausch. Dieser Mechanismus beruht auf dem schnellen Selbstaustausch von Cytochrom c-Molekülen und einer verbleibenden Rotationsflexibilität des Proteins im Multischichtsystem. Die Reduzierung des Proteins durch das Superoxidradikal und eine anschließende Reoxidation durch die Elektrode konnten nachgewiesen werden. In einem amperometrischen Messansatz wurde das durch Superoxidradikale hervorgerufene elektrochemische Signal in Abhängigkeit von der Zahl an Proteinschichten gemessen. Ein maximales Ansprechverhalten auf das Radikal wurde mit 6-Schichtelektroden erzielt. Die Empfindlichkeit der 6-Schichtelektroden wurde im Vergleich zum Literaturwert der Monoschichtelektrode um Faktor 14, also mehr als eine Größenordnung, verbessert. Somit konnte eine Elektrode mit 6 Schichten aus Cytochrom c und Poly(anilinsulfonsäure) als neuartiger Superoxidsensor mit einer 14-fachen Verbesserung der Empfindlichkeit im Vergleich zum bislang benutzten System entwickelt werden. Der zweite Teil dieser Arbeit beschreibt die Auswahl, Gewinnung und Charakterisierung von Mutanten des Proteins Cu,Zn-Superoxiddismutase zur elektrochemischen Quantifizierung von Superoxidradikalen. Monomere Mutanten des humanen dimeren Enzyms wurden entworfen, die durch Austausch von Aminosäuren ein oder zwei zusätzliche Cysteinreste besaßen, mit welchem sie direkt auf der Goldelektrodenoberfläche chemisorbieren sollten. 6 derartige Mutanten konnten in ausreichender Menge und Reinheit in aktiver Form gewonnen werden. Die Bindung der Superoxiddismutase-Mutanten an Goldoberflächen konnte durch Oberflächen-plasmonresonanz und Impedanzspektroskopie nachgewiesen werden. Alle Mutanten wiesen einen quasi-reversiblen Elektronentransfer zwischen SOD und Elektrode auf. Durch Untersuchung von kupferfreien SOD-Mutanten sowie des Wildtyps konnte nachgewiesen werden, das die Mutanten über die eingefügten Cysteinreste auf der Elektrode chemisorptiv gebunden wurden und der Elektronentransfer zwischen der Elektrode und dem Kupfer im aktiven Zentrum der SOD erfolgte. Die Superoxiddismutase katalysiert die Zersetzung von Superoxidmolekülen durch Oxidation und durch Reduktion der Radikale. Somit sind beide Teilreaktionen von analytischem Interesse. Zyklovoltammetrisch konnte sowohl die Oxidation als auch die Reduktion des Radikals durch die immobilisierten Superoxiddismutase-Mutanten nachgewiesen werden. In amperometrischen Messanordnungen konnten beide Teilreaktionen zur analytischen Quantifizierung von Superoxidradikalen genutzt werden. Im positiven Potentialfenster wurde die Empfindlichkeit um einen Faktor von etwa 10 gegenüber der Cytochrom c–Monoschichtelektrode verbessert.
Life on Earth is diverse and ranges from unicellular organisms to multicellular creatures like humans. Although there are theories about how these organisms might have evolved, we understand little about how ‘life’ started from molecules. Bottom-up synthetic biology aims to create minimal cells by combining different modules, such as compartmentalization, growth, division, and cellular communication.
All living cells have a membrane that separates them from the surrounding aqueous medium and helps to protect them. In addition, all eukaryotic cells have organelles that are enclosed by intracellular membranes. Each cellular membrane is primarily made of a lipid bilayer with membrane proteins. Lipids are amphiphilic molecules that assemble into molecular bilayers consisting of two leaflets. The hydrophobic chains of the lipids in the two leaflets face each other, and their hydrophilic headgroups face the aqueous surroundings. Giant unilamellar vesicles (GUVs) are model membrane systems that form large compartments with a size of many micrometers and enclosed by a single lipid bilayer. The size of GUVs is comparable to the size of cells, making them good membrane models which can be studied using an optical microscope. However, after the initial preparation, GUV membranes lack membrane proteins which have to be reconstituted into these membranes by subsequent preparation steps. Depending on the protein, it can be either attached via anchor lipids to one of the membrane leaflets or inserted into the lipid bilayer via its transmembrane domains.
The first step is to prepare the GUVs and then expose them to an exterior solution with proteins. Various protocols have been developed for the initial preparation of GUVs. For the second step, the GUVs can be exposed to a bulk solution of protein or can be trapped in a microfluidic device and then supplied with the protein solution. To minimize the amount of solution and for more precise measurements, I have designed a microfluidic device that has a main channel, and several dead-end side channels that are perpendicular to the main channel. The GUVs are trapped in the dead-end channels. This design exchanges the solution around the GUVs via diffusion from the main channel, thus shielding the GUVs from the flow within the main channel. This device has a small volume of just 2.5 μL, can be used without a pump and can be combined with a confocal microscope, enabling uninterrupted imaging of the GUVs during the experiments. I used this device for most of the experiments on GUVs that are discussed in this thesis.
In the first project of the thesis, a lipid mixture doped with an anchor lipid was used that can bind to a histidine chain (referred to as His-tag(ged) or 6H) via the metal cation Ni2+. This method is widely used for the biofunctionalization of GUVs by attaching proteins without a transmembrane domain. Fluorescently labeled His-tags which are bound to a membrane can be observed in a confocal microscope. Using the same lipid mixture, I prepared the GUVs with different protocols and investigated the membrane composition of the resulting GUVs by evaluating the amount of fluorescently labeled His-tagged molecules bound to their membranes. I used the microfluidic device described above to expose the outer leaflet of the vesicle to a constant concentration of the His-tagged molecules. Two fluorescent molecules with a His-tag were studied and compared: green fluorescent protein (6H-GFP) and fluorescein isothiocyanate (6H-FITC). Although the quantum yield in solution is similar for both molecules, the brightness of the membrane-bound 6H-GFP is higher than the brightness of the membrane-bound 6H-FITC. The observed difference in the brightness reveals that the fluorescence of the 6H-FITC is quenched by the anchor lipid via the Ni2+ ion. Furthermore, my measurements also showed that the fluorescence intensity of the membranebound His-tagged molecules depends on microenvironmental factors such as pH. For both 6H-GFP and 6H-FITC, the interaction with the membrane is quantified by evaluating the equilibrium dissociation constant. The membrane fluorescence is measured as a function of the fluorophores’ molar concentration. Theoretical analysis of these data leads to the equilibrium dissociation constants of (37.5 ± 7.5) nM for 6H-GFP and (18.5 ± 3.7) nM for 6H-FITC.
The anchor lipid mentioned previously used the metal cation Ni2+ to mediate the bond between the anchor lipid and the His-tag. The Ni2+ ion can be replaced by other transition metal ions. Studies have shown that Co3+ forms the strongest bonds with the His-tags attached to proteins. In these studies, strong oxidizing agents were used to oxidize the Co2+ mediated complex with the His-tagged protein to a Co3+ mediated complex. This procedure puts the proteins at risk of being oxidized as well. In this thesis, the vesicles were first prepared with anchor lipids without any metal cation. The Co3+ was added to these anchor lipids and finally the His-tagged protein was added to the GUVs to form the Co3+ mediated bond. This system was also established using the microfluidic device.
The different preparation procedures of GUVs usually lead to vesicles with a spherical morphology. On the other hand, many cell organelles have a more complex architecture with a non spherical topology. One fascinating example is provided by the endoplasmic reticulum (ER) which is made of a continuous membrane and extends throughout the cell in the form of tubes and sheets. The tubes are connected by three-way junctions and form a tubular network of irregular polygons. The formation and maintenance of these reticular networks requires membrane proteins that hydrolyize guanosine triphosphate (GTP). One of these membrane proteins is atlastin. In this thesis, I reconstituted the atlastin protein in GUV membranes using detergent-assisted reconstitution protocols to insert the proteins directly into lipid bilayers.
This thesis focuses on protein reconstitution by binding His-tagged proteins to anchor lipids and by detergent-assisted insertion of proteins with transmembrane domains. It also provides the design of a microfluidic device that can be used in various experiments, one example is the evaluation of the equilibrium dissociation constant for membrane-protein interactions. The results of this thesis will help other researchers to understand the protocols for preparing GUVs, to reconstitute proteins in GUVs, and to perform experiments using the microfluidic device. This knowledge should be beneficial for the long-term goal of combining the different modules of synthetic biology to make a minimal cell.
The ubiquitin-proteasome-system (UPS) is a cellular cascade involving three enzymatic steps for protein ubiquitination to target them to the 26S proteasome for proteolytic degradation. Several components of the UPS have been shown to be central for regulation of defense responses during infections with phytopathogenic bacteria. Upon recognition of the pathogen, local defense is induced which also primes the plant to acquire systemic resistance (SAR) for enhanced immune responses upon challenging infections. Here, ubiquitinated proteins were shown to accumulate locally and systemically during infections with Psm and after treatment with the SAR-inducing metabolites salicylic acid (SA) and pipecolic acid (Pip). The role of the 26S proteasome in local defense has been described in several studies, but the potential role during SAR remains elusive and was therefore investigated in this project by characterizing the Arabidopsis proteasome mutants rpt2a-2 and rpn12a-1 during priming and infections with Pseudomonas. Bacterial replication assays reveal decreased basal and systemic immunity in both mutants which was verified on molecular level showing impaired activation of defense- and SAR-genes. rpt2a-2 and rpn12a-1 accumulate wild type like levels of camalexin but less SA. Endogenous SA treatment restores local PR gene expression but does not rescue the SAR-phenotype. An RNAseq experiment of Col-0 and rpt2a-2 reveal weak or absent induction of defense genes in the proteasome mutant during priming. Thus, a functional 26S proteasome was found to be required for induction of SAR while compensatory mechanisms can still be initiated.
E3-ubiquitin ligases conduct the last step of substrate ubiquitination and thereby convey specificity to proteasomal protein turnover. Using RNAseq, 11 E3-ligases were found to be differentially expressed during priming in Col-0 of which plant U-box 54 (PUB54) and ariadne 12 (ARI12) were further investigated to gain deeper understanding of their potential role during priming.
PUB54 was shown to be expressed during priming and /or triggering with virulent Pseudomonas. pub54 I and pub54-II mutants display local and systemic defense comparable to Col-0. The heavy-metal associated protein 35 (HMP35) was identified as potential substrate of PUB54 in yeast which was verified in vitro and in vivo. PUB54 was shown to be an active E3-ligase exhibiting auto-ubiquitination activity and performing ubiquitination of HMP35. Proteasomal turnover of HMP35 was observed indicating that PUB54 targets HMP35 for ubiquitination and subsequent proteasomal degradation. Furthermore, hmp35-I benefits from increased resistance in bacterial replication assays. Thus, HMP35 is potentially a negative regulator of defense which is targeted and ubiquitinated by PUB54 to regulate downstream defense signaling. ARI12 is transcriptionally activated during priming or triggering and hyperinduced during priming and triggering. Gene expression is not inducible by the defense related hormone salicylic acid (SA) and is dampened in npr1 and fmo1 mutants consequently depending on functional SA- and Pip-pathways, respectively. ARI12 accumulates systemically after priming with SA, Pip or Pseudomonas. ari12 mutants are not altered in resistance but stable overexpression leads to increased resistance in local and systemic tissue. During priming and triggering, unbalanced ARI12 levels (i.e. knock out or overexpression) leads to enhanced FMO1 activation indicating a role of ARI12 in Pip-mediated SAR. ARI12 was shown to be an active E3-ligase with auto-ubiquitination activity likely required for activation with an identified ubiquitination site at K474. Mass spectrometrically identified potential substrates were not verified by additional experiments yet but suggest involvement of ARI12 in regulation of ROS in turn regulating Pip-dependent SAR pathways.
Thus, data from this project provide strong indications about the involvement of the 26S proteasome in SAR and identified a central role of the two so far barely described E3-ubiquitin ligases PUB54 and ARI12 as novel components of plant defense.
Understanding the interactions of predators and their prey and their responses to environmental changes is one of the striking features of ecological research. In this thesis, spring dynamics of phytoplankton and its consumers, zooplankton, were considered in dependence on the environmental conditions in a deep lake (Lake Constance) and a shallow marine water (mesocosms from Kiel Bight), using descriptive statistics, multiple regression models, and process-oriented dynamic simulation models. The development of the spring phytoplankton bloom, representing a dominant feature in the plankton dynamics in temperate and cold oceans and lakes, may depend on temperature, light, and mixing intensity, and the success of over-wintering phyto- and zooplankton. These factors are often correlated in the field. Unexpectedly, irradiance often dominated algal net growth rather than vertical mixing even in deep Lake Constance. Algal net losses from the euphotic layer to larger depth were induced by vertical mixing, but were compensated by the input from larger depth when algae were uniformly distributed over the water column. Dynamics of small, fast-growing algae were well predicted by abiotic variables, such as surface irradiance, vertical mixing intensity, and temperature. A simulation model additionally revealed that even in late winter, grazing may represent an important loss factor of phytoplankton during calm periods when losses due to mixing are small. The importance of losses by mixing and grazing changed rapidly as it depended on the variable mixing intensity. Higher temperature, lower global irradiance and enhanced mixing generated lower algal biomass and primary production in the dynamic simulation model. This suggests that potential consequences of climate change may partly counteract each other. The negative effect of higher temperatures on phytoplankton biomass was due to enhanced temperature-sensitive grazing losses. Comparing the results from deep Lake Constance to those of the shallow mesocosm experiments and simulations, confirmed the strong direct effect of light in contrast to temperature, and the importance of grazing already in early spring as soon as moderate algal biomasses developed. In Lake Constance, ciliates dominated the herbivorous zooplankton in spring. The start of ciliate net growth in spring was closely linked to that of edible algae, chlorophyll a and the vertical mixing intensity but independent of water temperature. The duration of ciliate dominance in spring was largely controlled by the highly variable onset of the phytoplankton bloom, and little by the less variable termination of the ciliate bloom by grazing of meta-zooplankton. During years with an extended spring bloom of algae and ciliates, they coexisted at relatively high biomasses over 15-30 generations, and internally forced species shifts were observed in both communities. Interception feeders alternated with filter feeders, and cryptomonads with non-cryptomonads in their relative importance. These dynamics were not captured by classical 1-predator-1-prey models which consistently predict pronounced predator-prey cycles or equilibria with either the predator or the prey dominating or suppressed. A multi-species predator-prey model with predator species differing in their food selectivity, and prey species in their edibility reproduced the observed patterns. Food-selectivity and edibility were related to the feeding and growth characteristics of the species, which represented ecological trade-offs. For example, the prey species with the highest edibility also had the highest maximum growth rate. Data and model revealed endogenous driven ongoing species alternations, which yielded a higher variability in species-specific biomasses than in total predator and prey biomass. This holds for a broad parameter space as long as the species differ functionally. A more sophisticated model approach enabled the simulation of a continuum of different functional types and adaptability of predator and prey communities to altered environmental conditions, and the maintenance of a rather low model complexity, i.e., low number of equations and free parameters. The community compositions were described by mean functional traits --- prey edibility and predator food-selectivity --- and their variances. The latter represent the functional diversity of the communities and thus, the potential for adaptation. Oscillations in the mean community trait values indicated species shifts. The community traits were related to growth and grazing characteristics representing similar trade-offs as in the multi-species model. The model reproduced the observed patterns, when nonlinear relationships between edibility and capacity, and edibility and food availability for the predator were chosen. A constant minimum amount of variance represented ongoing species invasions and thus, preserved a diversity which allows adaptation on a realistic time-span.
Starch is a biopolymer for which, despite its simple composition, understanding the precise mechanism behind its formation and regulation has been challenging. Several approaches and bioanalytical tools can be used to expand the knowledge on the different parts involved in the starch metabolism. In this sense, a comprehensive analysis targeting two of the main groups of molecules involved in this process: proteins, as effectors/regulators of the starch metabolism, and maltodextrins as starch components and degradation products, was conducted in this research work using potato plants (Solanum tuberosum L. cv. Desiree) as model of study. On one side, proteins physically interacting to potato starch were isolated and analyzed through mass spectrometry and western blot for their identification. Alternatively, starch interacting proteins were explored in potato tubers from transgenic plants having antisense inhibition of starch-related enzymes and on tubers stored under variable environmental conditions. Most of the proteins recovered from the starch granules corresponded to previously described proteins having a specific role in the starch metabolic pathway. Another set of proteins could be grouped as protease inhibitors, which were found weakly interacting to starch. Variations in the protein profile obtained after electrophoresis separation became clear when tubers were stored under different temperatures, indicating a differential expression of proteins in response to changing environmental conditions.
On the other side, since maltodextrin metabolism is thought to be involved in both starch initiation and degradation, soluble maltooligosaccharide content in potato tubers was analyzed in this work under diverse experimental variables. For this, tuber disc samples from wild type and transgenic lines strongly repressing either the plastidial or cytosolic form of the -glucan phosphorylase and phosphoglucomutase were incubated with glucose, glucose-6-phosphate, and glucose-1-phosphate solutions to evaluate the influence of such enzymes on the conversion of the carbon sources into soluble maltodextrins, in comparison to wild-type samples. Relative maltodextrin amounts analyzed through capillary electrophoresis equipped with laser-induced fluorescence (CE-LIF) revealed that tuber discs could immediately uptake glucose-1-phosphate and use it to produce maltooligosaccharides with a degree of polymerization of up to 30 (DP30), in contrast to transgenic tubers with strong repression of the plastidial glucan phosphorylase. The results obtained from the maltodextrin analysis support previous indications that a specific transporter for glucose-1-phosphate may exist in both the plant cells and the plastidial membranes, thereby allowing a glucose-6-phosphate independent transport. Furthermore, it confirms that the plastidial glucan phosphorylase is responsible for producing longer maltooligosaccharides in the plastids by catalyzing a glucan polymerization reaction when glucose-1-phosphate is available. All these findings contribute to a better understanding of the role of the plastidial glucan phosphorylase as a key enzyme directly involved in the synthesis and degradation of glucans and their implication on starch metabolism.
Gene expression describes the process of making functional gene products (e.g. proteins or special RNAs) from instructions encoded in the genetic information (e.g. DNA). This process is heavily regulated, allowing cells to produce the appropriate gene products necessary for cell survival, adapting production as necessary for different cell environments. Gene expression is subject to regulation at several levels, including transcription, mRNA degradation, translation and protein degradation. When intact, this system maintains cell homeostasis, keeping the cell alive and adaptable to different environments. Malfunction in the system can result in disease states and cell death. In this dissertation, we explore several aspects of gene expression control by analyzing data from biological experiments. Most of the work following uses a common mathematical model framework based on Markov chain models to test hypotheses, predict system dynamics or elucidate network topology. Our work lies in the intersection between mathematics and biology and showcases the power of statistical data analysis and math modeling for validation and discovery of biological phenomena.
Nob1 (New Zealand obese 1) bezeichnet einen Adipositas-QTL auf Chr. 5 der Maus (LODBMI >3,3), der in einem Rückkreuzungsexperiment der Mausstämme NZO (adipös) und SJL (schlank) identifiziert wurde. Um Kandidatengene für Adipositas zu finden, wurden mehr als 300 Nob1-Transkripte mit Hilfe von Genexpressionsanalysen auf Unterschiede in stoffwechselrelevanten Geweben zwischen beiden Mausstämmen untersucht. Sieben Gene zeigten eine differentielle Expression: 2310045A20Rik, Tbc1d1, Ppp1cb, Mll5, Insig1, Abhd1 und Alox5ap. Die codierenden Bereiche dieser Gene wurden anschließend auf Sequenzunterschiede zwischen NZO und SJL untersucht. Nur im Gen Tbc1d1, das im Peak-Bereich des Nob1 lokalisiert ist, wurde eine SJL-spezifische Deletion von sieben Basen detektiert, die zu einer Leserasterverschiebung und einem vorzeitigen Abbruch des Proteins in der funktionellen Rab-GAP-Domäne führt (Loss-of-Function-Mutation). Interessanterweise wurde eine Variante von TBC1D1 (R125W) in Kopplungsanalysen mit Adipositas beim Menschen assoziiert (Stone et al., 2006). TBC1D1 zeigt eine hohe Homologie zu TBC1D4 (AS160), das im Insulinsignalweg eine wichtige Rolle spielt. In 17 weiteren Genen im Peak-Bereich des Nob1 wurde keine weitere SJL-spezifischen Mutation detektiert. Bei NZO-Tieren erfolgte die Tbc1d1-mRNA-Expression vorwiegend in glycolytischen Fasern des Skelettmuskels. Zudem wurden zwei gewebsspezifisch exprimierte Tbc1d1-Isoformen identifiziert, die sich durch alternatives Splicen der Exone 12 und 13 unterscheiden. Die im Rahmen dieser Arbeit gefundenen Ergebnisse machen Tbc1d1 zu einem plausiblen Kandidatengen für den Nob1-QTL. Welche Funktion Tbc1d1 im Glucose- und Fettstoffwechsel des Skelettmuskels hat, muss in weiteren Analysen untersucht werden.
Poly(A) Polymerase 1 (PAPS1) influences organ size and pathogen response in Arabidopsis thaliana
(2014)
Polyadenylation of pre-mRNAs is critical for efficient nuclear export, stability, and translation of the mature mRNAs, and thus for gene expression. The bulk of pre-mRNAs are processed by canonical nuclear poly(A) polymerase (PAPS). Both vertebrate and higher-plant genomes encode more than one isoform of this enzyme, and these are coexpressed in different tissues. However, in neither case is it known whether the isoforms fulfill different functions or polyadenylate distinct subsets of pre-mRNAs. This thesis shows that the three canonical nuclear PAPS isoforms in Arabidopsis are functionally specialized owing to their evolutionarily divergent C-terminal domains. A moderate loss-of-function mutant in PAPS1 leads to increase in floral organ size, whereas leaf size is reduced. A strong loss-of-function mutation causes a male gametophytic defect, whereas a weak allele leads to reduced leaf growth. By contrast, plants lacking both PAPS2 and PAPS4 function are viable with wild-type leaf growth. Polyadenylation of SMALL AUXIN UP RNA (SAUR) mRNAs depends specifically on PAPS1 function. The resulting reduction in SAUR activity in paps1 mutants contributes to their reduced leaf growth, providing a causal link between polyadenylation of specific pre-mRNAs by a particular PAPS isoform and plant growth. Additionally, opposite effects of PAPS1 on leaf and flower growth reflect the different identities of these organs. The overgrowth of paps1 mutant petals is due to increased recruitment of founder cells into early organ primordia whereas the reduced leaf size is due to an ectopic pathogen response. This constitutive immune response leads to increased resistance to the biotrophic oomycete Hyaloperonospora arabidopsidis and reflects activation of the salicylic acid-independent signalling pathway downstream of ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1)/PHYTOALEXIN DEFICIENT4 (PAD4). Immune responses are accompanied by intracellular redox changes. Consistent with this, the redox-status of the chloroplast is altered in paps1-1 mutants. The molecular effects of the paps1-1 mutation were analysed using an RNA sequencing approach that distinguishes between long- and short tailed mRNA. The results shown here suggest the existence of an additional layer of regulation in plants and possibly vertebrate gene expression, whereby the relative activities of canonical nuclear PAPS isoforms control de novo synthesized poly(A) tail length and hence expression of specific subsets of mRNAs.
Plant-derived Transcription Factors for Orthologous Regulation of Gene Expression in the Yeast Saccharomyces cerevisiae
Control of gene expression by transcription factors (TFs) is central in many synthetic biology projects where tailored expression of one or multiple genes is often needed. As TFs from evolutionary distant organisms are unlikely to affect gene expression in a host of choice, they represent excellent candidates for establishing orthogonal control systems. To establish orthogonal regulators for use in yeast (Saccharomyces cerevisiae), we chose TFs from the plant Arabidopsis thaliana. We established a library of 106 different combinations of chromosomally integrated TFs, activation domains (yeast GAL4 AD, herpes simplex virus VP64, and plant EDLL) and synthetic promoters harbouring cognate cis-regulatory motifs driving a yEGFP reporter. Transcriptional output of the different driver / reporter combinations varied over a wide spectrum, with EDLL being a considerably stronger transcription activation domain in yeast, than the GAL4 activation domain, in particular when fused to Arabidopsis NAC TFs. Notably, the strength of several NAC - EDLL fusions exceeded that of the strong yeast TDH3 promoter by 6- to 10-fold. We furthermore show that plant TFs can be used to build regulatory systems encoded by centromeric or episomal plasmids. Our library of TF – DNA-binding site combinations offers an excellent tool for diverse synthetic biology applications in yeast.
COMPASS: Rapid combinatorial optimization of biochemical pathways based on artificial transcription factors
We established a high-throughput cloning method, called COMPASS for COMbinatorial Pathway ASSembly, for the balanced expression of multiple genes in Saccharomyces cerevisiae. COMPASS employs orthogonal, plant-derived artificial transcription factors (ATFs) for controlling the expression of pathway genes, and homologous recombination-based cloning for the generation of thousands of individual DNA constructs in parallel. The method relies on a positive selection of correctly assembled pathway variants from both, in vivo and in vitro cloning procedures. To decrease the turnaround time in genomic engineering, we equipped COMPASS with multi-locus CRISPR/Cas9-mediated modification capacity. In its current realization, COMPASS allows combinatorial optimization of up to ten pathway genes, each transcriptionally controlled by nine different ATFs spanning a 10-fold difference in expression strength. The application of COMPASS was demonstrated by generating cell libraries producing beta-carotene and co-producing beta-ionone and biosensor-responsive naringenin. COMPASS will have many applications in other synthetic biology projects that require gene expression balancing.
CaPRedit: Genome editing using CRISPR-Cas9 and plant-derived transcriptional regulators for the redirection of flux through the FPP branch-point in yeast. Technologies developed over the past decade have made Saccharomyces cerevisiae a promising platform for production of different natural products. We developed CRISPR/Ca9- and plant derived regulator-mediated genome editing approach (CaPRedit) to greatly accelerate strain modification and to facilitate very low to very high expression of key enzymes using inducible regulators. CaPRedit can be implemented to enhance the production of yeast endogenous or heterologous metabolites in the yeast S. cerevisiae. The CaPRedit system aims to faciltiate modification of multiple targets within a complex metabolic pathway through providing new tools for increased expression of genes encoding rate-limiting enzymes, decreased expression of essential genes, and removed expression of competing pathways. This approach is based on CRISPR/Cas9-mediated one-step double-strand breaks to integrate modules containing IPTG-inducible plant-derived artificial transcription factor and promoter pair(s) in a desired locus or loci. Here, we used CaPRedit to redirect the yeast endogenous metabolic flux toward production of farnesyl diphosphate (FPP), a central precursor of nearly all yeast isoprenoid products, by overexpression of the enzymes lead to produce FPP from glutamate. We found significantly higher beta-carotene accumulation in the CaPRedit-mediated modified strain than in the wild type (WT) strain. More specifically, CaPRedit_FPP 1.0 strain was generated, in which three genes involved in FPP synthesis, tHMG1, ERG20, and GDH2, were inducibly overexpressed under the control of strong plant-derived ATFPs. The beta–carotene accumulated in CaPRedit_FPP 1.0 strain to a level 1.3-fold higher than the previously reported optimized strain that carries the same overexpressed genes (as well as additional genetic modifications to redirect yeast endogenous metabolism toward FPP production). Furthermore, the genetic modifications implemented in CaPRedit_FPP 1.0 strain resulted in only a very small growth defect (growth rate relative to the WT is ~ -0.03).
Phytol aus dem Chlorophyllabbau ist limitierend für die Tocopherol (Vitamin E)-Synthese Als Bestandteil von Chlorophyll ist Phytol das am häufigsten vorkommende Isoprenoid in der Biosphäre. Große Mengen an Chlorophyll werden jährlich degradiert und dabei wird Phytol freigesetzt, über dessen Verbleib jedoch wenig bekannt ist. Es sollte der Nachweis erbracht werden, dass im Zuge des Chlorophyllabbaus hydrolysiertes Phytol Eingang in die Synthese anderer Phytylderivate findet. Während der Gehalt an Tocopherol, Chlorophyll und Fettsäurephytylester entwicklungs- bzw. seneszenzabhängig ist, bleibt der Gehalt an Phyllochinon etwa gleich. Auch in Samen ist der Gehalt von Tocopherol, Chlorophyll und Fettsäurephytylester entwicklungsabhängig. Es wurde gefolgert, dass nur die Synthesen von Tocopherol und Fettsäurephytylester während des Chlorophyllabbaus stimuliert werden. Daher sollten Mutanten analysiert werden, welche im Chlorophyllabbau inhibiert sind. Da Chlorophyllase den ersten Schritt des Chlorophyllabbaus katalysiert, wurden zwei unabhängige T-DNA-Insertionsmutanten für Chlorophyllase1 (CHL1) und eine T-DNA-Insertionsmutante für Chlorophyllase2 (CHL2) identifiziert und eine chl1-1chl2-Doppelmutante erzeugt. Die Analyse der Chlorophyllidanteile ergab eine im Vergleich zum Wildtyp starke Reduktion in den chl1-Mutanten, während der Chlorophyllidanteil von chl2 ähnlich hoch dem Wildtyp ist. Der Chlorophyllidanteil sich entwickelnder chl1-1chl2-Pflanzen nahm in der Seneszenz zu. Die Chlorophyllasemutanten zeigten kein verändertes Seneszenzverhalten im Vergleich zu den Wildtypen. Ferner konnte in den chl1-Linien nur geringfügig weniger Tocopherol und Fettsäurephytylester als in den Wildtypen nachgewiesen werden. Auch der Tocopherolgehalt der Samen war in den Chlorophyllasemutanten unverändert zu den Wildtypen. Aufgrund dessen wurde gefolgert, dass neben den Chorophyllasen CHL1 und CHL2 weitere Chlorophyllhydrolasen in Samen und Blättern von Arabidopsis existieren. Daher wurde auf andere Mutanten zurückgegriffen, in denen der Chlorophyllabbau stark inhibiert ist und die Seneszenz nach Dunkelinkubation im Vergleich zum Wildtyp deutlich verzögert ist. Eine deutliche Korrelation zwischen vermindertem Chlorophyllabbau und Gehalt an Tocopherol und Fettsäurephytylester konnte in den staygreen-Mutanten pao1 und zwei unabhängigen SGR (staygreen)-RNAi-Linien nachgewiesen werden. Damit konnte eindeutig gezeigt werden, dass die Synthese von Tocopherol und der Fettsäurephytylester durch die Chlorophyllhydrolyse induziert wird. Es wurde gefolgert, dass vor allem unter Seneszenz- bzw. Stressbedingungen dieser alternative Syntheseweg von Phytol eine Rolle spielt. Dennoch kommt der Phytylsynthese durch die de novo-Isoprenoidsynthese auch eine Bedeutung zu. Nach Behandlung von stickstoffmangelgestressten Wildtyppflanzen mit dem Inhibitor Fosmidomycin, welcher die plastidäre de novo-Isoprenoidsynthese hemmt, war der Tocopherolgehalt gegenüber stickstoffmangelgestressten Kontrollpflanzen stark reduziert. Ferner konnte eine T-DNA-Insertionsmutante der Geranylgeranylreduktase (GGR) identifiziert werden. Diese Mutante kann nur auf Nährmedium überleben, hat nur wenige grüne Blätter und bildet keine Samen. Es konnte kein Phyllochinon, Chlorophyll und keine Fettsäurephytylester, jedoch geringe Mengen Tocopherol nachgewiesen werden. Der Resttocopherolgehalt wird auf die Nebenaktivität einer anderen Reduktase zurückgeführt. Weiterhin wurde nur das Geranylgeranylderivat des Chlorophylls identifiziert. Diese Ergebnisse erlauben den Schluss, dass die phytylgruppenübertragenen Enzyme der Tocopherol-, Phyllochinon- und Fettsäurephytylestersynthese eine hohe Substratspezifität für die Phytylgruppe aufweisen. Nach Fütterung von Phytol konnte in ggr Tocopherol und Chlorophyll bestimmt werden. Aufgrund dessen kann gefolgert werden, dass Chlorophyllsynthetase aus Arabidopsis sowohl Geranylgeranyl-, als auch Phytylpyrophosphat als Substrat nutzen kann und damit ein breiteres Substratspektrum aufweist.
Monoclonal antibodies (mAbs) are an innovative group of drugs with increasing clinical importance in oncology, combining high specificity with generally low toxicity. There are, however, numerous challenges associated with the development of mAbs as therapeutics. Mechanistic understanding of factors that govern the pharmacokinetics (PK) of mAbs is critical for drug development and the optimisation of effective therapies; in particular, adequate dosing strategies can improve patient quality life and lower drug cost. Physiologically-based PK (PBPK) models offer a physiological and mechanistic framework, which is of advantage in the context of animal to human extrapolation. Unlike for small molecule drugs, however, there is no consensus on how to model mAb disposition in a PBPK context. Current PBPK models for mAb PK hugely vary in their representation of physiology and parameterisation. Their complexity poses a challenge for their applications, e.g., translating knowledge from animal species to humans.
In this thesis, we developed and validated a consensus PBPK model for mAb disposition taking into account recent insights into mAb distribution (antibody biodistribution coefficients and interstitial immunoglobulin G (IgG) pharmacokinetics) to predict tissue PK across several pre-clinical species and humans based on plasma data only. The model allows to a priori predict target-independent (unspecific) mAb disposition processes as well as mAb disposition in concentration ranges, for which the unspecific clearance (CL) dominates target-mediated CL processes. This is often the case for mAb therapies at steady state dosing.
The consensus PBPK model was then used and refined to address two important problems:
1) Immunodeficient mice are crucial models to evaluate mAb efficacy in cancer therapy. Protection from elimination by binding to the neonatal Fc receptor is known to be a major pathway influencing the unspecific CL of both, endogenous and therapeutic IgG. The concentration of endogenous IgG, however, is reduced in immunodeficient mouse models, and this effect on unspecific mAb CL is unknown, yet of great importance for the extrapolation to human in the context of mAb cancer therapy.
2) The distribution of mAbs into solid tumours is of great interest. To comprehensively investigate mAb distribution within tumour tissue and its implications for therapeutic efficacy, we extended the consensus PBPK model by a detailed tumour distribution model incorporating a cell-level model for mAb-target interaction. We studied the impact of variations in tumour microenvironment on therapeutic efficacy and explored the plausibility of different mechanisms of action in mAb cancer therapy.
The mathematical findings and observed phenomena shed new light on therapeutic utility and dosing regimens in mAb cancer treatment.
This work describes the realization of physically crosslinked networks based on gelatin by the introduction of functional groups enabling specific supramolecular interactions. Molecular models were developed in order to predict the material properties and permit to establish a knowledge-based approach to material design. The effect of additional supramolecular interactions with hydroxyapaptite was then studied in composite materials. The calculated properties are compared to experimental results to validate the models. The models are then further used for the study of physically crosslinked networks. Gelatin was functionalized with desaminotyrosine (DAT) and desaminotyrosyl-tyrosine (DATT) side groups, derived from the natural amino acid tyrosine. These group can potentially undergo to π-π and hydrogen bonding interactions also under physiological conditions. Molecular dynamics (MD) simulations were performed on models with 0.8 wt.-% or 25 wt.-% water content, using the second generation forcefield CFF91. The validation of the models was obtained by the comparison with specific experimental data such as, density, peptide conformational angles and X-ray scattering spectra. The models were then used to predict the supramolecular organization of the polymer chain, analyze the formation of physical netpoints and calculate the mechanical properties. An important finding of simulation was that with the increase of aromatic groups also the number of observed physical netpoints increased. The number of relatively stable physical netpoints, on average zero 0 for natural gelatin, increased to 1 and 6 for DAT and DATT functionalized gelatins respectively. A comparison with the Flory-Rehner model suggested reduced equilibrium swelling by factor 6 of the DATT-functionalized materials in water. The functionalized gelatins could be synthesized by chemoselective coupling of the free carboxylic acid groups of DAT and DATT to the free amino groups of gelatin. At 25 wt.-% water content, the simulated and experimentally determined elastic mechanical properties (e.g. Young Modulus) were both in the order of GPa and were not influenced by the degree of aromatic modification. The experimental equilibrium degree of swelling in water decreased with increasing the number of inserted aromatic functions (from 2800 vol.-% for pure gelatin to 300 vol.-% for the DATT modified gelatin), at the same time, Young’s modulus, elongation at break, and maximum tensile strength increased. It could be show that the functionalization with DAT and DATT influences the chain organization of gelatin based materials together with a controlled drying condition. Functionalization with DAT and DATT lead to a drastic reduction of helical renaturation, that could be more finely controlled by the applied drying conditions. The properties of the materials could then be influenced by application of two independent methods. Composite materials of DAT and DATT functionalized gelatins with hydroxyapatite (HAp) show a drastic reduction of swelling degree. In tensile tests and rheological measurements, the composites equilibrated in water had increased Young’s moduli (from 200 kPa up to 2 MPa) and tensile strength (from 57 kPa up to 1.1 MPa) compared to the natural polymer matrix without affecting the elongation at break. Furthermore, an increased thermal stability from 40 °C to 85 °C of the networks could be demonstrated. The differences of the behaviour of the functionalized gelatins to pure gelatin as matrix suggested an additional stabilizing bond between the incorporated aromatic groups to the hydroxyapatite.
The existence of diverse and active microbial ecosystems in the deep subsurface – a biosphere that was originally considered devoid of life – was discovered in multiple microbiological studies. However, most of the studies are restricted to marine ecosystems, while our knowledge about the microbial communities in the deep subsurface of lake systems and their potentials to adapt to changing environmental conditions is still fragmentary. This doctoral thesis aims to build up a unique data basis for providing the first detailed high-throughput characterization of the deep biosphere of lacustrine sediments and to emphasize how important it is to differentiate between the living and the dead microbial community in deep biosphere studies.
In this thesis, up to 3.6 Ma old sediments (up to 317 m deep) of the El’gygytgyn Crater Lake were examined, which represents the oldest terrestrial climate record of the Arctic. Combining next generation sequencing with detailed geochemical characteristics and other environmental parameters, the microbial community composition was analyzed in regard to changing climatic conditions within the last 3.6 Ma to 1.0 Ma (Pliocene and Pleistocene). DNA from all investigated sediments was successfully extracted and a surprisingly diverse (6,910 OTUs) and abundant microbial community in the El’gygytgyn deep sediments were revealed. The bacterial abundance (10³-10⁶ 16S rRNA copies g⁻¹ sediment) was up to two orders of magnitudes higher than the archaeal abundance (10¹-10⁵) and fluctuates with the Pleistocene glacial/interglacial cyclicality. Interestingly, a strong increase in the microbial diversity with depth was observed (approximately 2.5 times higher diversity in Pliocene sediments compared to Pleistocene sediments). The increase in diversity with depth in the Lake El’gygytgyn is most probably caused by higher sedimentary temperatures towards the deep sediment layers as well as an enhanced temperature-induced intra-lake bioproductivity and higher input of allochthonous organic-rich material during Pliocene climatic conditions. Moreover, the microbial richness parameters follow the general trends of the paleoclimatic parameters, such as the paleo-temperature and paleo-precipitation. The most abundant bacterial representatives in the El’gygytgyn deep biosphere are affiliated with the phyla Proteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria, which are also commonly distributed in the surrounding permafrost habitats. The predominated taxon was the halotolerant genus Halomonas (in average 60% of the total reads per sample).
Additionally, this doctoral thesis focuses on the live/dead differentiation of microbes in cultures and environmental samples. While established methods (e.g., fluorescence in situ hybridization, RNA analyses) are not applicable to the challenging El’gygytgyn sediments, two newer methods were adapted to distinguish between DNA from live cells and free (extracellular, dead) DNA: the propidium monoazide (PMA) treatment and the cell separation adapted for low amounts of DNA. The applicability of the DNA-intercalating dye PMA was successfully evaluated to mask free DNA of different cultures of methanogenic archaea, which play a major role in the global carbon cycle. Moreover, an optimal procedure to simultaneously treat bacteria and archaea was developed using 130 µM PMA and 5 min of photo-activation with blue LED light, which is also applicable on sandy environmental samples with a particle load of ≤ 200 mg mL⁻¹. It was demonstrated that the soil texture has a strong influence on the PMA treatment in particle-rich samples and that in particular silt and clay-rich samples (e.g., El’gygytgyn sediments) lead to an insufficient shielding of free DNA by PMA. Therefore, a cell separation protocol was used to distinguish between DNA from live cells (intracellular DNA) and extracellular DNA in the El’gygytgyn sediments. While comparing these two DNA pools with a total DNA pool extracted with a commercial kit, significant differences in the microbial composition of all three pools (mean distance of relative abundance: 24.1%, mean distance of OTUs: 84.0%) was discovered. In particular, the total DNA pool covers significantly fewer taxa than the cell-separated DNA pools and only inadequately represents the living community. Moreover, individual redundancy analyses revealed that the microbial community of the intra- and extracellular DNA pool are driven by different environmental factors. The living community is mainly influenced by life-dependent parameters (e.g., sedimentary matrix, water availability), while the extracellular DNA is dependent on the biogenic silica content. The different community-shaping parameters and the fact, that a redundancy analysis of the total DNA pool explains significantly less variance of the microbial community, indicate that the total DNA represents a mixture of signals of the live and dead microbial community.
This work provides the first fundamental data basis of the diversity and distribution of microbial deep biosphere communities of a lake system over several million years. Moreover, it demonstrates the substantial importance of extracellular DNA in old sediments. These findings may strongly influence future environmental community analyses, where applications of live/dead differentiation avoid incorrect interpretations due to a failed extraction of the living microbial community or an overestimation of the past community diversity in the course of total DNA extraction approaches.
In this work, different strategies for the construction of biohybrid photoelectrodes are investigated and have been evaluated according to their intrinsic catalytic activity for the oxidation of the cofactor NADH or for the connection with the enzymes PQQ glucose dehydrogenase (PQQ-GDH), FAD-dependent glucose dehydrogenase (FAD-GDH) and fructose dehydrogenase (FDH). The light-controlled oxidation of NADH has been analyzed with InGaN/GaN nanowire-modified electrodes. Upon illumination with visible light the InGaN/GaN nanowires generate an anodic photocurrent, which increases in a concentration-dependent manner in the presence of NADH, thus allowing determination of the cofactor. Furthermore, different approaches for the connection of enzymes to quantum dot (QD)-modified electrodes via small redox molecules or redox polymers have been analyzed and discussed. First, interaction studies with diffusible redox mediators such as hexacyanoferrate(II) and ferrocenecarboxylic acid have been performed with CdSe/ZnS QD-modified gold electrodes to build up photoelectrochemical signal chains between QDs and the enzymes FDH and PQQ-GDH. In the presence of substrate and under illumination of the electrode, electrons are transferred from the enzyme via the redox mediators to the QDs. The resulting photocurrent is dependent on the substrate concentration and allows a quantification of the fructose and glucose content in solution. A first attempt with immobilized redox mediator, i.e. ferrocenecarboxylic acid chemically coupled to PQQ-GDH and attached to QD-modified gold electrodes, reveal the potential to build up photoelectrochemical signal chains even without diffusible redox mediators in solution. However, this approach results in a significant deteriorated photocurrent response compared to the situation with diffusing mediators. In order to improve the photoelectrochemical performance of such redox mediator-based, light-switchable signal chains, an osmium complex-containing redox polymer has been evaluated as electron relay for the electronic linkage between QDs and enzymes. The redox polymer allows the stable immobilization of the enzyme and the efficient wiring with the QD-modified electrode. In addition, a 3D inverse opal TiO2 (IO-TiO2) electrode has been used for the integration of PbS QDs, redox polymer and FAD-GDH in order to increase the electrode surface. This results in a significantly improved photocurrent response, a quite low onset potential for the substrate oxidation and a broader glucose detection range as compared to the approach with ferrocenecarboxylic acid and PQQ-GDH immobilized on CdSe/ZnS QD-modified gold electrodes. Furthermore, IO-TiO2 electrodes are used to integrate sulfonated polyanilines (PMSA1) and PQQ-GDH, and to investigate the direct interaction between the polymer and the enzyme for the light-switchable detection of glucose. While PMSA1 provides visible light excitation and ensures the efficient connection between the IO-TiO2 electrode and the biocatalytic entity, PQQ-GDH enables the oxidation of glucose. Here, the IO-TiO2 electrodes with pores of approximately 650 nm provide a suitable interface and morphology, which is required for a stable and functional assembly of the polymer and enzyme. The successful integration of the polymer and the enzyme can be confirmed by the formation of a glucose-dependent anodic photocurrent. In conclusion, this work provides insights into the design of photoelectrodes and presents different strategies for the efficient coupling of redox enzymes to photoactive entities, which allows for light-directed sensing and provides the basis for the generation of power from sun light and energy-rich compounds.
Functional metabolism of storage carbohydrates is vital to plants and animals. The water-soluble glycogen in animal cells and the amylopectin which is the major component of water-insoluble starch granules residing in plant plastids are chemically similar as they consist of α-1,6 branched α-1,4 glucan chains. Synthesis and degradation of transitory starch and of glycogen are accomplished by a set of enzymatic activities that to some extend are also similar in plants and animals. Chain elongation, branching, and debranching are achieved by synthases, branching enzymes, and debranching enzymes, respectively. Similarly, both types of polyglucans contain low amounts of phosphate esters whose abundance varies depending on species and organs. Starch is selectively phosphorylated by at least two dikinases (GWD and PWD) at the glucosyl carbons C6 and C3 and dephosphorylated by the phosphatase SEX4 and SEX4-like enzymes. In Arabidopsis insufficiency in starch phosphorylation or dephosphorylation results in largely impaired starch turnover, starch accumulation, and often in retardation of growth. In humans the progressive neurodegenerative epilepsy, Lafora disease, is the result of a defective enzyme (laforin) that is functional equivalent to the starch phosphatase SEX4 and capable of glycogen dephosphorylation. Patients lacking laforin progressively accumulate unphysiologically structured insoluble glycogen-derived particles (Lafora bodies) in many tissues including brain. Previous results concerning the carbon position of glycogen phosphate are contradictory. Currently it is believed that glycogen is esterified exclusively at the carbon positions C2 and C3 and that the monophosphate esters, being incorporated via a side reaction of glycogen synthase (GS), lack any specific function but are rather an enzymatic error that needs to be corrected. In this study a versatile and highly sensitive enzymatic cycling assay was established that enables quantification of very small G6P amounts in the presence of high concentrations of non-target compounds as present in hydrolysates of polysaccharides, such as starch, glycogen, or cytosolic heteroglycans in plants. Following validation of the G6P determination by analyzing previously characterized starches G6P was quantified in hydrolysates of various glycogen samples and in plant heteroglycans. Interestingly, glucosyl C6 phosphate is present in all glycogen preparations examined, the abundance varying between glycogens of different sources. Additionally, it was shown that carbon C6 is severely hyperphosphorylated in glycogen of Lafora disease mouse model and that laforin is capable of removing C6 phosphate from glycogen. After enrichment of phosphoglucans from amylolytically degraded glycogen, several techniques of two-dimensional NMR were applied that independently proved the existence of 6-phosphoglucosyl residues in glycogen and confirmed the recently described phosphorylation sites C2 and C3. C6 phosphate is neither Lafora disease- nor species-, or organ-specific as it was demonstrated in liver glycogen from laforin-deficient mice and in that of wild type rabbit skeletal muscle. The distribution of 6-phosphoglucosyl residues was analyzed in glycogen molecules and has been found to be uneven. Gradual degradation experiments revealed that C6 phosphate is more abundant in central parts of the glycogen molecules and in molecules possessing longer glucan chains. Glycogen of Lafora disease mice consistently contains a higher proportion of longer chains while most short chains were reduced as compared to wild type. Together with results recently published (Nitschke et al., 2013) the findings of this work completely unhinge the hypothesis of GS-mediated phosphate incorporation as the respective reaction mechanism excludes phosphorylation of this glucosyl carbon, and as it is difficult to explain an uneven distribution of C6 phosphate by a stochastic event. Indeed the results rather point to a specific function of 6-phosphoglucosyl residues in the metabolism of polysaccharides as they are present in starch, glycogen, and, as described in this study, in heteroglycans of Arabidopsis. In the latter the function of phosphate remains unclear but this study provides evidence that in starch and glycogen it is related to branching. Moreover a role of C6 phosphate in the early stages of glycogen synthesis is suggested. By rejecting the current view on glycogen phosphate to be a stochastic biochemical error the results permit a wider view on putative roles of glycogen phosphate and on alternative biochemical ways of glycogen phosphorylation which for many reasons are likely to be mediated by distinct phosphorylating enzymes as it is realized in starch metabolism of plants. Better understanding of the enzymology underlying glycogen phosphorylation implies new possibilities of Lafora disease treatment.
Since available phosphate (Pi) resources in soil are limited, symbiotic interactions between plant roots and arbuscular mycorrhizal (AM) fungi are a widespread strategy to improve plant phosphate nutrition. The repression of AM symbiosis by a high plant Pi-status indicates a link between Pi homeostasis signalling and AM symbiosis development. This assumption is supported by the systemic induction of several microRNA399 (miR399) primary transcripts in shoots and a simultaneous accumulation of mature miR399 in roots of mycorrhizal plants. However, the physiological role of this miR399 expression pattern is still elusive and offers the question whether other miRNAs are also involved in AM symbiosis. Therefore, a deep sequencing approach was applied to investigate miRNA-mediated posttranscriptional gene regulation in M. truncatula mycorrhizal roots. Degradome analysis revealed that 185 transcripts were cleaved by miRNAs, of which the majority encoded transcription factors and disease resistance genes, suggesting a tight control of transcriptional reprogramming and a downregulation of defence responses by several miRNAs in mycorrhizal roots. Interestingly, 45 of the miRNA-cleaved transcripts showed a significant differentially regulated between mycorrhizal and non-mycorrhizal roots. In addition, key components of the Pi homeostasis signalling pathway were analyzed concerning their expression during AM symbiosis development. MtPhr1 overexpression and time course expression data suggested a strong interrelation between the components of the PHR1-miR399-PHO2 signalling pathway and AM symbiosis, predominantly during later stages of symbiosis. In situ hybridizations confirmed accumulation of mature miR399 in the phloem and in arbuscule-containing cortex cells of mycorrhizal roots. Moreover, a novel target of the miR399 family, named as MtPt8, was identified by the above mentioned degradome analysis. MtPt8 encodes a Pi-transporter exclusively transcribed in mycorrhizal roots and its promoter activity was restricted to arbuscule-containing cells. At a low Pi-status, MtPt8 transcript abundance inversely correlated with a mature miR399 expression pattern. Increased MtPt8 transcript levels were accompanied by elevated symbiotic Pi-uptake efficiency, indicating its impact on balancing plant and fungal Pi-acquisition. In conclusion, this study provides evidence for a direct link of the regulatory mechanisms of plant Pi-homeostasis and AM symbiosis at a cell-specific level. The results of this study, especially the interaction of miR399 and MtPt8 provide a fundamental step for future studies of plant-microbe-interactions with regard to agricultural and ecological aspects.
AM symbiosis has a positive influence on plant P-nutrition and growth, but little is known about the molecular mechanism of the symbiosis adaptation to different phosphate conditions. The recently described induction of several pri-miR399 transcripts in mycorrhizal shoots and subsequent accumulation of mature miR399 in mycorrhizal roots indicates that local PHO2 expression must be controlled during symbiosis, presumably in order to sustain AM symbiosis development, in spite of locally increased Pi-concentration. A reverse genetic approach used in this study demonstrated that PHO2 and thus the PHR1-miR399-PHO2 signaling pathway, is involved in certain stages of progressive root colonization. In addition, a transcriptomic approach using a split-root system provided a comprehensive insight into the systemic transcriptional changes in mycorrhizal roots and shoots of M. truncatula in response to high phosphate conditions. With regard to the transcriptional responses of the root system, the results indicate that, although the colonization is drastically reduced, AM symbiosis is still functional at high Pi concentrations and might still be beneficial to the plant. Additionally, the data suggest that a specific root-borne mycorrhizal signal systemically induces protein synthesis, amino acid metabolism and photosynthesis at low Pi conditions, which is abolished at high Pi conditions. MiRNAs, such as miR399, are involved in long-distance signaling and are therefore potential systemic signals involved in AM symbiosis. A deep-sequencing approach identified 243 novel miRNAs in the root tissue of M. truncatula. Read-count analysis, qRT-PCR measurements and in situ hybridizations clearly indicated a regulation of miR5229a/b, miR5204, miR160f*, miR160c, miR169 and miR169d*/l*/m*/e.2* during arbuscular mycorrhizal symbiosis. Moreover, miR5204* represses a GRAS TF, which is specifically transcribed in mycorrhizal roots. Since miR5204* is induced by high Pi it might represent a further Pi status-mediating signal beside miR399. This study provides additional evidence that MtNsp2, a key regulator of symbiosis-signaling, is regulated and presumably spatially restricted by miR171h cleavage. In summary, a repression of mycorrhizal root colonization at high phosphate status is most likely due to a repression of the phosphate starvation responses and the loss of beneficial responses in mycorrhizal shoots. These findings provide a new basis for investigating the regulatory network leading to cellular reprogramming during interaction between plants, arbuscular mycorrhizal fungi and different phosphate conditions.
Pectic polysaccharides, a class of plant cell wall polymers, form one of the most complex networks known in nature. Despite their complex structure and their importance in plant biology, little is known about the molecular mechanism of their biosynthesis, modification, and turnover, particularly their structure-function relationship. One way to gain insight into pectin metabolism is the identification of mutants with an altered pectin structure. Those were obtained by a recently developed pectinase-based genetic screen. Arabidopsis thaliana seedlings grown in liquid medium containing pectinase solutions exhibited particular phenotypes: they were dwarfed and slightly chlorotic. However, when genetically different A. thaliana seed populations (random T-DNA insertional populations as well as EMS-mutagenized populations and natural variations) were subjected to this treatment, individuals were identified that exhibit a different visible phenotype compared to wild type or other ecotypes and may thus contain a different pectin structure (pec-mutants). After confirming that the altered phenotype occurs only when the pectinase is present, the EMS mutants were subjected to a detailed cell wall analysis with particular emphasis on pectins. This suite of mutants identified in this study is a valuable resource for further analysis on how the pectin network is regulated, synthesized and modified. Flanking sequences of some of the T-DNA lines have pointed toward several interesting genes, one of which is PEC100. This gene encodes a putative sugar transporter gene, which, based on our data, is implicated in rhamnogalacturonan-I synthesis. The subcellular localization of PEC100 was studied by GFP fusion and this protein was found to be localized to the Golgi apparatus, the organelle where pectin biosynthesis occurs. Arabidopsis ecotype C24 was identified as a susceptible one when grown with pectinases in liquid culture and had a different oligogalacturonide mass profile when compared to ecotype Col-0. Pectic oligosaccharides have been postulated to be signal molecules involved in plant pathogen defense mechanisms. Indeed, C24 showed elevated accumulation of reactive oxygen species upon pectinase elicitation and had altered response to the pathogen Alternaria brassicicola in comparison to Col-0. Using a recombinant inbred line population three major QTLs were identified to be responsible for the susceptibility of C24 to pectinases. In a reverse genetic approach members of the qua2 (putative pectin methyltransferase) family were tested for potential target genes that affect pectin methyl-esterification. The list of these genes was determined by in silico study of the pattern of expression and co-expression of all 34 members of this family resulting in 6 candidate genes. For only for one of the 6 analyzed genes a difference in the oligogalacturonide mass profile was observed in the corresponding knock-out lines, confirming the hypothesis that the methyl-esterification pattern of pectin is fine tuned by members of this gene family. This study of pectic polysaccharides through forward and reverse genetic screens gave new insight into how pectin structure is regulated and modified, and how these modifications could influence pectin mediated signalling and pathogenicity.
Im Fokus dieser Arbeit stand der Aufbau einer auf DNA basierenden Nanostruktur. Der universelle Vier-Buchstaben-Code der DNA ermöglicht es, Bindungen auf molekularer Ebene zu adressieren. Die chemischen und physikalischen Eigenschaften der DNA prädestinieren dieses Makromolekül für den Einsatz und die Verwendung als Konstruktionselement zum Aufbau von Nanostrukturen. Das Ziel dieser Arbeit war das Aufspannen eines DNA-Stranges zwischen zwei Fixpunkten. Hierfür war es notwendig, eine Methode zu entwickeln, welche es ermöglicht, Funktionsmoleküle als Ankerelemente ortsaufgelöst auf eine Oberfläche zu deponieren. Das Deponieren dieser Moleküle sollte dabei im unteren Mikrometermaßstab erfolgen, um den Abmaßen der DNA und der angestrebten Nanostruktur gerecht zu werden. Das eigens für diese Aufgabe entwickelte Verfahren zum ortsaufgelösten Deponieren von Funktionsmolekülen nutzt das Bindungspaar Biotin-Neutravidin. Mit Hilfe eines Rasterkraftmikroskops (AFM) wurde eine zu einem „Stift“ umfunktionierte Rasterkraftmikroskopspitze so mit der zu deponierenden „Tinte“ beladen, dass das Absetzen von Neutravidin im unteren Mikrometermaßstab möglich war. Dieses Neutravidinmolekül übernahm die Funktion als Bindeglied zwischen der biotinylierten Glasoberfläche und dem eigentlichen Adressmolekül. Das somit generierte Neutravidin-Feld konnte dann mit einem biotinylierten Adressmolekül durch Inkubation funktionalisiert werden. Namensgebend für dieses Verfahren war die Möglichkeit, Neutravidin mehrmals zu deponieren und zu adressieren. Somit ließ sich sequenziell ein Mehrkomponenten-Feld aufbauen. Die Einschränkung, mit einem AFM nur eine Substanz deponieren zu können, wurde so umgangen. Ferner mußten Ankerelemente geschaffen werden, um die DNA an definierten Punkten immobilisieren zu können. Die Bearbeitung der DNA erfolgte mit molekularbiologischen Methoden und zielte darauf ab, einen DNA-Strang zu generieren, welcher an seinen beiden Enden komplementäre Adressequenzen enthält, um gezielt mit den oberflächenständigen Ankerelementen binden zu können. Entsprechend der Geometrie der mit dem AFM erzeugten Fixpunkte und den oligonukleotidvermittelten Adressen kommt es zur Ausbildung einer definierten DNA-Struktur. Mit Hilfe von fluoreszenzmikroskopischen Methoden wurde die aufgebaute DNA-Nanostruktur nachgewiesen. Der Nachweis der nanoskaligen Interaktion von DNA-bindenden Molekülen mit der generierten DNA-Struktur wurde durch die Bindung von PNA (peptide nucleic acid) an den DNA-Doppelstrang erbracht. Diese PNA-Bindung stellt ihrerseits ein funktionales Strukturelement im Nanometermaßstab dar und wird als Nanostrukturbaustein verstanden.
Die Enzymsuperfamilie der löslichen Sulfotransferasen (SULT) spielt eine wichtige Rolle in der Phase II des Fremdstoffmetabolismus. Sie katalysieren den Transfer einer Sulfonylgruppe auf nucleophile Gruppen endogener und exogener Substrate. Die Sulfokonjugation von Fremdstoffen erhöht deren Wasserlöslichkeit und behindert die passive Permeation von Zellmembranen. Dadurch wird die Ausscheidung dieser konjugierten Substanzen erleichtert. In Abhängigkeit von der Struktur des Zielmoleküls kann die Sulfokonjugation aber auch zur metabolischen Aktivierung von Fremdstoffen durch die Bildung instabiler Metabolite führen. Die SULT-vermittelte Aktivierung promutagener Substanzen ist somit von toxikologischem Interesse. Für die Detektion SULT-vermittelter Mutagenität mittels bakterieller in-vitro Testsysteme ist die heterologe Expression der fremdstoffmetabolisierenden Enzyme direkt in den Indikatorzellen notwendig. S. typhimurium exprimieren selbst keine SULT, und externe Metabolisierungssysteme sind problematisch, weil die negativ geladenen, kurzlebigen Metabolite nur schlecht die Zellmembran penetrieren können. Die Expression humaner Enyme in Bakterien ist jedoch zum Teil sehr kritisch. So zeigen z.B. sehr ähnliche Enzyme (SULT1A2*1 und *2) deutliche Unterschiede im Expressionsniveau bei exakt gleichen äußeren Bedingungen. Dies erschwert den Vergleich der enzymatischen Aktivitäten dieser Enzyme im in-vitro Testsystem. Andere Enzyme (z.B. SULT2B1b) werden unter Verwendung ihrer Wildtyp-cDNA zum Teil nicht detektierbar exprimiert. Deshalb sollte in dieser Arbeit eine Methode zur Optimierung der heterologen Expression fremdstoffmetabolisierender Enzyme für Genotoxizitätsuntersuchungen etabliert werden. Es wurde bereits gezeigt dass synonyme Codonaustausche am 5’-Ende der humanen SULT1A2-cDNA zu einer Erhöhung der Expression des entsprechenden Enzyms in S. typhimurium führten. Dementsprechend wurden in dieser Arbeit Codonaustausche am 5’-Ende der cDNA verschiedener SULT (1A1*1, 1A2*1, 2B1b) sowie der Ratten Glutathion-S-Transferase Theta 2 (rGSTT2) und dem Reportergen Luciferase durchgeführt. Die Expression der so generierten Konstrukte wurde in verschiedenen S. typhimurium und E. coli Stämmen quantifiziert und die Aktivität der überexprimierten Enzyme im Ames-Test bzw. im Enzym-Aktivitätsassay überprüft. Durch das Einführen seltener Codons in die cDNA konnte die Proteinexpression von SULT1A1*1, SULT1A2*1 und SULT2B1b maximal 7-fach, 18-fach und 100-fach im Vergleich zur Wildtyp-cDNA gesteigert werden. Die Expression der rGSTT2 wurde ebenfalls durch das Einführen seltener Codons erhöht (maximal 5-fach). Bei dem Reportergen Luciferase jedoch führte das Austauschen häufiger Codons gegen seltene Codons zu einer Reduktion der Proteinexpression um 80 %. Die Expression von Fusionsproteinen aus 2B1b (5’-Ende) und Luciferase (3’-Ende) wurde durch das Einführen seltener Codons ebenfalls um 50 % reduziert. Die S. typhimurium Stämme mit optimierter SULT 1A1*1- bzw. 1A2*1-Expression wurden im Ames-Test eingesetzt und zeigten im Vergleich zu den geringer exprimierenden Stämmen eine höhere Sensitivität. Für SULT2B1b konnte keine Mutagenaktivierung im Ames-Test nachgewiesen werden. Allerdings zeigte ein Enzym-Aktivitätsassay mit Dehydroepiandosteron, dass das bakteriell exprimierte Enzym funktionell war. Da in der Literatur der Effekt seltener Codons auf die Expression in Bakterien bisher fast ausschließlich als inhibitorisch beschrieben wurde, sollte die Wirkungsweise der hier beobachteten Expressionserhöhung durch seltene Codons genauer untersucht werden. Dazu wurden verschiedene Konstrukte der SULT1A2*1 und der SULT2B1b, die unterschiedlich viele seltene Codons in verschiedenen Kombinationen besaßen, hergestellt. Es konnten jedoch keine einzelnen Codons, die für die Expressionssteigerung allein verantwortlich waren, identifiziert werden. Die Plasmidkopienzahl in den verschiedenen SULT2B1b-Klonen war konstant und die SULT2B1b-mRNA-Konzentration zeigte nur moderate Schwankungen, die nicht als Ursache für die dramatische Erhöhung der SULT2B1b-Expression in Frage kommen. Die berechnete Stabilität der potentiellen mRNA-Sekundärstrukturen wurde durch die seltenen Codons häufig stark gesenkt und ist als eine mögliche Ursache für die Expressionssteigerung anzusehen. Zusätzlich erhöhten die seltenen Codons den Consensus der Downstream Box zur 16S rRNA, was ebenfalls eine Ursache für die Expressionssteigerung sein kann. In dieser Arbeit konnte somit die Expression der humanen SULT1A1*1, 1A2*1 und der 2B1b sowie der rGSTT2 erfolgreich mittels synonymer Codonaustausche erhöht werden. Die so optimierten S. typhimurium Stämme zeigten im Ames-Test eine erhöhte Sensitivität gegenüber SULT aktivierten Promutagenen bzw. erhöhte Aktivität in spezifischen Enymaktivitätsassays.
Predation drives coexistence, evolution and population dynamics of species in food webs, and has strong impacts on related ecosystem functions (e.g. primary production). The effect of predation on these processes largely depends on the trade-offs between functional traits in the predator and prey community. Trade-offs between defence against predation and competitive ability, for example, allow for prey speciation and predator-mediated coexistence of prey species with different strategies (defended or competitive), which may stabilize the overall food web dynamics. While the importance of such trade-offs for coexistence is widely known, we lack an understanding and the empirical evidence of how the variety of differently shaped trade-offs at multiple trophic levels affect biodiversity, trait adaptation and biomass dynamics in food webs. Such mechanistic understanding is crucial for predictions and management decisions that aim to maintain biodiversity and the capability of communities to adapt to environmental change ensuring their persistence.
In this dissertation, after a general introduction to predator-prey interactions and tradeoffs, I first focus on trade-offs in the prey between qualitatively different types of defence (e.g. camouflage or escape behaviour) and their costs. I show that these different types lead to different patterns of predator-mediated coexistence and population dynamics, by using a simple predator-prey model. In a second step, I elaborate quantitative aspects of trade-offs and demonstrates that the shape of the trade-off curve in combination with trait-fitness relationships strongly affects competition among different prey types: Either specialized species with extreme trait combinations (undefended or completely defended) coexist, or a species with an intermediate defence level dominates. The developed theory on trade-off shapes and coexistence is kept general, allowing for applications apart from defence-competitiveness trade-offs. Thirdly, I tested the theory on trade-off shapes on a long-term field data set of phytoplankton from Lake Constance. The measured concave trade-off between defence and growth governs seasonal trait changes of phytoplankton in response to an altering grazing pressure by zooplankton, and affects the maintenance of trait variation in the community. In a fourth step, I analyse the interplay of different tradeoffs at multiple trophic levels with plankton data of Lake Constance and a corresponding tritrophic food web model. The results show that the trait and biomass dynamics of the different three trophic levels are interrelated in a trophic biomass-trait cascade, leading to unintuitive patterns of trait changes that are reversed in comparison to predictions from bitrophic systems. Finally, in the general discussion, I extract main ideas on trade-offs in multitrophic systems, develop a graphical theory on trade-off-based coexistence, discuss the interplay of intra- and interspecific trade-offs, and end with a management-oriented view on the results of the dissertation, describing how food webs may respond to future global changes, given their trade-offs.
The transcriptional regulation of the cellular mechanisms involves many different components and different levels of control which together contribute to fine tune the response of cells to different environmental stimuli. In some responses, diverse signaling pathways can be controlled simultaneously. One of the most important cellular processes that seem to possess multiple levels of regulation is photosynthesis. A model organism for studying photosynthesis-related processes is the unicellular green algae Chlamydomonas reinhardtii, due to advantages related to culturing, genetic manipulation and availability of genome sequence. In the present study, we were interested in understanding the regulatory mechanisms underlying photosynthesis-related processes. To achieve this goal different molecular approaches were followed. In order to indentify protein transcriptional regulators we optimized a method for isolation of nuclei and performed nuclear proteome analysis using shotgun proteomics. This analysis permitted us to improve the genome annotation previously published and to discover conserved and enriched protein motifs among the nuclear proteins. In another approach, a quantitative RT-PCR platform was established for the analysis of gene expression of predicted transcription factor (TF) and other transcriptional regulator (TR) coding genes by transcript profiling. The gene expression profiles for more than one hundred genes were monitored in time series experiments under conditions of changes in light intensity (200 µE m-2 s-1 to 700 µE m-2 s-1), and changes in concentration of carbon dioxide (5% CO2 to 0.04% CO2). The results indicate that many TF and TR genes are regulated in both environmental conditions and groups of co-regulated genes were found. Our findings also suggest that some genes can be common intermediates of light and carbon responsive regulatory pathways. These approaches together gave us new insights about the regulation of photosynthesis and revealed new candidate regulatory genes, helping to decipher the gene regulatory networks in Chlamydomonas. Further experimental studies are necessary to clarify the function of the candidate regulatory genes and to elucidate how cells coordinately regulate the assimilation of carbon and light responses.
Nitrogen is an essential macronutrient for plants and nitrogen fertilizers are indispensable for modern agriculture. Unfortunately, we know too little about how plants regulate their use of soil nitrogen, to maximize fertilizers-N use by crops and pastures. This project took a dual approach, involving forward and reverse genetics, to identify N-regulators in plants, which may prove useful in the future to improve nitrogen-use efficiency in agriculture. To identify nitrogen-regulated transcription factor genes in Arabidopsis that may control N-use efficiency we developed a unique resource for qRT-PCR measurements on all Arabidpsis transcription factor genes. Using closely spaced, gene-specific primer pairs and SYBR® Green to monitor amplification of double-stranded DNA, transcript levels of 83% of all target genes could be measured in roots or shoots of young Arabidopsis wild-type plants. Only 4% of reactions produced non-specific PCR products, and 13% of TF transcripts were undetectable in these organs. Measurements of transcript abundance were quantitative over six orders of magnitude, with a detection limit equivalent to one transcript molecule in 1000 cells. Transcript levels for different TF genes ranged between 0.001-100 copies per cell. Real-time RT-PCR revealed 26 root-specific and 39 shoot-specific TF genes, most of which have not been identified as organ-specific previously. An enlarged and improved version of the TF qRT-PCR platform contains now primer pairs for 2256 Arabidopsis TF genes, representing 53 gene families and sub-families arrayed on six 384-well plates. Set-up of real-time PCR reactions is now fully robotized. One researcher is able to measure expression of all 2256 TF genes in a single biological sample in a just one working day. The Arabidopsis qRT-PCT platform was successfully used to identify 37 TF genes which transcriptionaly responded at the transcriptional level to N-deprivation or to nitrate per se. Most of these genes have not been characterized previously. Further selection of TF genes based on the responses of selected candidates to other macronutrients and abiotic stresses allowed to distinguish between TFs regulated (i) specifically by nitrogen (29 genes) (ii) regulated by general macronutrient or by salt and osmotic stress (6 genes), and (iii) responding to all major macronutrients and to abiotic stresses. Most of the N-regulated TF genes were also regulated by carbon. Further characterization of sixteen selected TF genes, revealed: (i) lack of transcriptional response to organic nitrogen, (ii) two major types of kinetics of induction by nitrate, (iii) specific responses for the majority of the genes to nitrate but not downstream products of nitrate assimilation. All sixteen TF genes were cloned into binary vectors for constitutive and ethanol inducible over expression, and the first generation of transgenic plants were obtained for almost all of them. Some of the plants constitutively over expressing TF genes under control of the 35S promoter revealed visible phenotypes in T1 generation. Homozygous T-DNA knock out lines were also obtained for many of the candidate TF genes. So far, one knock out line revealed a visible phenotype: retardation of flowering time. A forward genetic approach using an Arabidopsis ATNRT2.1 promoter : Luciferase reporter line, resulted in identification of eleven EMS mutant reporter lines affected in induction of ATNRT2.1 expression by nitrate. These lines could by divided in the following classes according to expression of other genes involved in primary nitrogen and carbon metabolism: (i) lines affected exclusively in nitrate transport, (ii) those affected in nitrate transport, acquisition, but also in glycolysis and oxidative pentose pathway, (iii) mutants affected moderately in nitrate transport, oxidative pentose pathway and glycolysis but not in primary nitrate assimilation. Thus, several different N-regulatory genes may have been mutated in this set of mutants. Map-based cloning has begun to identify the genes affected in these mutants.
The major aim of this thesis was to study the effect of nitrate on primary metabolism and in development of the model plant Arabidopsis thaliana. The present work has two separate topics. First, to investigate the GDH family, a small gene family at the interface between nitrogen and carbon metabolisms. Second, to investigate the mechanisms whereby nitrogen is regulating the transition to flowering time in Arabidopsis thaliana. To gain more insights into the regulation of primary metabolism by the functional characterization of the glutamate dehydrogenase (GDH) family, an enzyme putatively involved in the metabolism of amino acids and thus suggested to play different and essential roles in carbon and nitrogen metabolism in plants, knock out mutants and transgenic plants carrying RNA interference construct were generated and characterized. The effect of silencing GDH on carbon and nitrogen metabolisms was investigated, especially the level of carbohydrates and the amino acid pool were further analysed. It has been shown that GDH expression is regulated by light and/or sugar status therefore, phenotypic and metabolic analysis were developed in plants grown at different points of the diurnal rhythm and in response to an extended night period. In addition, we are interested in the effect of nutrient availability in the transition from vegetative growth to flowering and especially in nitrate as a metabolite that triggers widespread and coordinated changes in metabolism and development. Nutrient availability has a dramatic effect on flowering time, with a marked delay of flowering when nitrate is supplied (Stitt, 1999). The use of different mutants and transgenic plants impaired in flowering signalling pathways was crucial to evaluate the impact of different nitrate concentrations on flowering time and to better understand the interaction of nitrate-dependent signals with other main flowering signalling pathways. Plants were grown on glutamine as a constitutive source of nitrogen, and the nitrate supply varied. Low nitrate led to earlier flowering. The response to nitrate is accentuated in short days and in the CONSTANS deficient co2 mutant, whereas long days or overexpression of CONSTANS overrides the nitrate response. These results indicate that nitrates acts downstream of the known flowering signalling pathways for photoperiod, autonomy, vernalization and gibberellic acid. Global analyses of gene expression of two independent flowering systems, a light impaired mutant (co2tt4) and a constitutive over-expresser of the potent repressor of flowering (35S::FLC), were to be investigated under two different concentrations of nitrate in order to identify candidate genes that may be involved in the regulation of flowering time by nitrate.
Viele klinische Schnelltestsysteme benötigen vorpräparierte oder aufgereinigte Analyte mit frisch hergestellten Lösungen. Fernab standardisierter Laborbedingungen wie z.B. in Entwicklungsländern oder Krisengebieten sind solche Voraussetzungen oft nur unter einem hohen Aufwand herstellbar.
Zusätzlich stellt die erforderliche Sensitivität die Entwicklung einfach zu handhabender Testsysteme vor große Herausforderungen.
Autokatalytische Reaktionen, die sich mit Hilfe sehr geringer Initiatorkonzentrationen auslösen lassen, können hier eine Perspektive für Signalverstärkungsprozesse bieten.
Aus diesem Grund wird im ersten Teil der vorliegenden Arbeit das Verhalten der autokatalytischen Arsenit-Jodat-Reaktion in einem mikrofluidischen Kanal untersucht. Dabei werden insbesondere die diffusiven und konvektiven Einflüsse auf die Reaktionskinetik im Vergleich zu makroskopischen Volumenmengen betrachtet.
Im zweiten Teil werden thermoresponsive Hydrogele mit einem kanalstrukturierten Papiernetzwerk zu einem neuartigen, kapillargetriebenen, extern steuerbaren Mikrofluidik-System kombiniert. Das hier vorgestellte Konzept durch Hydrogele ein papierbasiertes LOC-System zu steuern, ermöglicht zukünftig die Herstellung von komplexeren, steuerbaren Point-Of-Care Testsystemen (POCT). Durch z.B. einen thermischen Stimulus, wird das Lösungsverhalten eines Hydrogels so verändert, dass die gespeicherte Flüssigkeit freigesetzt und durch die Kapillarkraft des Papierkanals ins System transportiert wird. Die Eigenschaften dieses Gelnetzwerks können dabei so eingestellt werden, dass eine Freisetzung von Flüssigkeiten sogar bei Körpertemperatur möglich wäre und damit eine Anwendung gänzlich ohne weitere Hilfsmittel denkbar ist. Für die Anwendung notwendige Chemikalien oder Enzyme lassen sich hierbei bequem in getrocknetem Zustand im Papiersubstrat vorlagern und bei Bedarf in Lösung bringen.
Im abschließenden dritten Teil der Arbeit wird ein durch Hydrogele betriebener, Antikörper-basierter Mikroorganismenschnelltest für Escherichia coli präsentiert. Darüber hinaus wird weiterführend eine einfache Methode zur Funktionalisierung eines Hydrogels mit Biomolekülen über EDC/NHS-Kopplung vorgestellt.