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Adhesion to host cells is the first and most crucial step in infections with pathogenic Gram negative bacteria and is often mediated by trimeric autotransporter adhesins (TAAs). TAA-producing bacteria are the causative agent of many human diseases and TAA targeted anti-adhesive compounds might counteract such bacterial infections. The modularly structured Bartonella adhesin A (BadA) is one of the best characterised TAAs and serves as an attractive adhesin to study the domain-function relationship of TAAs during infection. BadA is a major virulence factor of B. henselae and is essential for the initial attachment to host cells via adhesion to extracellular matrix proteins. B. henselae is the causative agent of cat scratch disease and adheres to fibronectin using its long BadA fibres. The life cycle of this pathogen, with alternating host conditions, drives evolutionary and host-specific adaptations.
Human, feline, and laboratory adapted B. henselae isolates display genomic and phenotypic differences. By analysing the genomes of eight B. henselae strains using long-read sequencing, a variable genomic badA island with a diversified and highly repetitive badA gene flanked by badA pseudogenes was identified. Moreover, numerous conserved flanking genes were characterised, however, their influence on the regulation of badA expression and modification remains to be explored. It seems that B. henselae G 5436 is the evolutionary ancestor of the other B. henselae strains analysed in this work. The diversity of the badA island among the B. henselae strains indicates that the downstream badA-like domain region might be used as a ‘toolbox’ for rearrangements in the badA gene. Overall, it is suggested that badA-domain duplications, insertions, and/or deletions are the result of active phase variation via site-specific recombination and contribute to rapid host adaptation in the scope of pathogenicity, immune evasion, and/or enhanced long-term colonisation.
The model strain B. henselae Marseille expresses a badA gene that includes 30 repetitive neck/stalk domains, each consisting of several predicted structural motifs. To further elucidate the motif sequences that mediate fibronectin binding, various modified badA constructs were generated. Their ability to bind fibronectin was assessed via whole-cell ELISA and fluorescence microscopy. In conclusion, it is suggested that BadA adheres to fibronectin in a cumulative fashion with quick saturation via unpaired β-strands appearing in structural motifs present in BadA neck/stalk domains 19, 27, and other homologous domains. Furthermore, antibodies targeting a 15-mer amino acid sequence in the DALL motif of BadA neck/stalk domain 27 were able to reduce fibronectin binding of the B. henselae mutant strain S27. Moreover, this DALL motif sequence is conserved in the genome of all analysed B. henselae strains. The identification of common binding motifs between BadA and fibronectin supports the development of new anti-adhesive compounds that might inhibit the initial adherence of B. henselae and other TAA-producing pathogens during infection.
Lipopolysaccharide (LPS) is a major glycolipid component in the outer leaflet of the outer membrane of Gram-negative bacteria and known as endotoxin exhibited by the lipid A moiety, which serves as a membrane anchor. The effective permeability barrier properties of the outer membrane contributed by the presence of LPS in the extracellular layer of the outer membrane confer Gram-negative bacteria a high resistance against hydrophobic compounds such as antibiotics, bile salts and detergents to survive in harsh environments. The biogenesis of LPS is well studied in Escherichia coli (herewith E. coli) and the LPS transport (Lpt) is carried out by a transenvelope complex composed of seven essential proteins (LptABCDEFG), which are located in the three compartments of the cell such as the outer membrane, the inner membrane and the periplasm. The Lpt system also exists in Anabaena sp. PCC 7120 (herewith Anabaena sp.), however, homologues of LptC and LptE are still missing. BLAST search failed to identify a homologue of LptC, in contrast, the secondary structure analysis using the Pfam database based on the existing ecLptC secondary structure identified one open reading frame All0231 as the putative Anabaena sp. homologue of LptC, which is designated anaLptC. Despite the low sequence similarity, the secondary structure alignment between anaLptC and ecLptC using the HHpred server showed that both proteins share high secondary structural similarities. The genotypic analysis of the insertion mutant anaLptC did not identify a fully segregated genome and its phenotypic analysis revealed that it was sensitive against chemicals, suggesting that the analptC gene is essential for the growth of Anabaena sp. and involved in the outer membrane biogenesis. This is further supported by the observation of the small cell phenotype in the anaLptC mutant via transmission electron microscopy. Moreover, physical interactions between the anaLptC periplasmic domain with anaLptA as well as with anaLptF were established, indicating that the anaLptC periplasmic domain is correctly folded and alone functional and that the transmembrane helix is not required for the interaction with anaLptA and anaLptF. Furthermore, the reduction of the O-antigen containing LPS was observed in the insertion mutant anaLptC and the dissociation constant Kd of the anaLptC periplasmic domain for ecLPS was determined.The three-dimensional structure of the periplasmic domain of anaLptC was solved by X-ray crystallography with a resolution of 2.8 Å. The structural superposition between the ecLptC crystal structure (PDB number 3my2) and the crystal structure of anaLptC periplasmic domain obtained by this study showed the similarity in the folding of the two proteins with a Cα r.m.s.d value of about 1 Å and confirmed that the length of anaLptC is more than two times longer than that of ecLptC. The structural comparison also revealed that both structures share the typical β-jellyroll fold and conserved amino acids, which were shown in ecLptC to bind to LPS in vivo and found in anaLptC. Overall, these data strongly suggest that anaLptC is involved in the transport of LPS and support the model whereby the bridge spanning the inner membrane and the outer membrane would be assembled via interactions of the structurally conserved β-jellyroll domains shared by five (LptACDFG) out of seven Lpt proteins.
Die Spinozerebelläre Ataxie Typ 2 (SCA2) ist eine autosomal dominant vererbte neurodegenerative Krankheit, welche durch die Expansion des Trinukleotids Cytosin-Adenin-Guanin von ~22/23 auf >32 im Ataxin-2 Gen (ATXN2) verursacht wird. Dieses Trinukleotid codiert für die Aminosäure Glutamin weshalb SCA2 auch zu den Polyglutaminerkrankungen zählt. Zu dieser Gruppe zählen außerdem fünf weitere SCA-Subtypen sowie drei weitere neurodegenerative Erkrankungen, darunter die Huntington-Krankheit.
SCA2 wurde 1971 zum ersten Mal von Wadia und Swami beschrieben und unterscheidet sich von den anderen SCAs aufgrund der typischen Störung der sakkadischen Augenbewegungen. Weitere klinische Symptome von SCA2 sind Ataxie, Tremor, Dysmetrie, Dysarthrie, Hyporeflexie und Dysdiadochokinese. Die Symptome gehen auf einen neuronalen Verlust insbesondere im Cerebellum, aber auch in anderen Hirnregionen wie zum Beispiel dem Hirnstamm zurück.
Atxn2 wird in weiten Teilen des Zentralnervensystems aber auch in vielen nicht-neuronalen Geweben exprimiert. Es handelt sich um ein überwiegend cytoplasmatisch lokalisiertes Protein, welches im Gegensatz zu vielen anderen SCA-Proteinen cytoplasmatische und nur selten nukleäre Aggregate bildet. Die exakte Funktion von Atxn2 ist bisher unklar, es wurde allerdings mehrfach gezeigt, dass es in die mRNA Translation involviert ist aufgrund seiner Interaktion mit dem PolyA-bindenden Protein PABPC1.
Eine Expansion des Trinukleotids in Ataxin-2 kann nicht nur zu SCA2 führen, sondern stellt bei Wiederholungen zwischen 27 und 32 CAGs auch ein erhöhtes Risiko für eine Erkrankung an Amyotropher Lateralsklerose (ALS) und anderen neurodegenerativen Krankheiten dar. Eine Interaktion zwischen ATXN2 und dem ALS-verursachenden TDP43 (Tardbp) wurde bereits zahlreich beforscht, da Aggregate von ATXN2 in Motoneuronen des Rückenmarks von ALS-Patienten und aggregiertes TDP43 in SCA2-Neuronen beobachtet wurden.
Generell sind die Mechanismen, die zur Pathologie von SCA2 und ALS führen, noch weitgehend unklar. Ziel dieser Arbeit war es daher auf der einen Seite einen Einblick in den Pathomechanismus von SCA2 zu erhalten, indem mögliche oder bereits bekannte Interaktoren in etablierten Atxn2-Mausmodellen untersucht wurden. Auf der anderen Seite wurden zwei neue Mausmodelle charakterisiert, um ihre Eignung für die Erforschung von ALS und SCA2 zu prüfen.
Für den ersten Teil der Arbeit dienten Daten aus mehreren Transkriptomstudien von Atxn2-Knock-Out (KO) und Atxn2-CAG42-Knock-In (KIN) Mäusen als Grundlage. Konnten die Daten mit einer unabhängigen Methode bestätigt werden, folgten weitere Untersuchungen auf mRNA und Proteinebene sowie unter zusätzlicher Verwendung von Zellkultur und Patientenmaterial. Dadurch konnten neue Interaktionspartner von ATXN2 identifiziert und bereits bekannte in diesen Mausmodellen bestätigt werden.
So wurde zum Beispiel eine Interaktion von ATXN2 mit der E3-Ubiquitin-Protein-Ligasekomponente FBXW8 gezeigt und deren Beteiligung am Abbau von expandiertem ATXN2. Außerdem wurde eine Interaktion von FBXW8 mit dem bereits bekannten ATXN2-degradierenden Protein PARK2 gezeigt. Eine Hochregulierung des Fbxw8 Transkripts wurde sowohl im Atxn2-CAG42-KIN-Mausmodell als auch in SCA2-Patientenfibroblasten gefunden, während Park2 in keinem der Modelle signifikant veränderte Transkriptspiegel aufwies. Diese Daten belegen die Relevanz von Fbxw8 für den Abbau von moderat-expandiertem Atxn2 und begründen weitere Studien zur genauen Funktion dieses Proteins im Pathomechanismus von Atxn2.
Des Weiteren wurden diverse Kalziumhomöostasefaktoren untersucht, welche eine konsistente Herunterregulierung der Transkripte in beiden Mausmodellen aufwiesen. Auf Proteinebene zeigten sich jedoch Unterschiede zwischen den Modellen. Diese Daten belegen, dass zwar ähnliche Transkriptveränderungen im KIN- und KO-Modell auftreten, diesen aber vermutlich verschiedene Mechanismen zugrunde liegen. Welche Mechanismen dies genau sind bleibt zu klären, es ist jedoch wahrscheinlich, dass im KIN-Modell die Aggregatbildung sowie in beiden Modellen die Beteiligung von ATXN2 an der Translationregulation eine Rolle spielen. Die Ergebnisse dieser Studie unterstreichen die Relevanz des Ca2+ Signalwegs für die Entwicklung von SCA2.
Der zweite Teil der Arbeit beinhaltet die Charakterisierung einer ATXN2/TDP43 Doppelmutante auf Verhaltensebene sowie die gründliche Evaluierung des Phänotyps einer vollkommen neuen SCA2 Mausmutante. Während in der Doppelmutante trotz doppelter Genmutation nur ein sehr schwacher Phänotyp auf Verhaltensebene festgestellt werden konnte und bis zu einem Alter von 12 Monaten keine Potenzierung der Mutationen zu beobachten war, zeigte die Atxn2-CAG100-KIN Maus signifikante und früh auftretende Pathologie. Neben einer verminderten Überlebensrate, einem Gewichtsverlust und diversen motorischen Störungen, konnten auch Aggregate des mutierten Proteins in diversen Hirnregionen identifiziert werden. Der Atxn2-CAG100-KIN Phänotyp spiegelt die humanen Symptome daher recht gut wider, weshalb diese Mausmutante ein wertvolles Modell für die weitere SCA2-Forschung darstellt.
Zusammengefasst zeigt diese Arbeit die Bedeutung des ATXN2-Interaktors FBXW8 im SCA2-Mausmodell als auch im Patientenmaterial. Sie betont die Relevanz des Atxn2-KO-Modells in Bezug auf Störungen der Kalziumhomöostase und dokumentiert die Alters- und Gewebespezifität dieser Veränderungen. Außerdem beinhaltet sie die vorläufige Beschreibung eines kombinierten Atxn2/TDP43-Mausmodells und schließlich die ausführliche Charakterisierung eines vollkommen neuen und äußerst wertvollen SCA2-Mausmodells.
This work deals with the characterization of three different type II polyketide synthase systems (PKS II) from the Gram-negative bacteria Xenorhabdus and Photorhabdus.
Particular attention was paid to a biochemically underexplored class of aryl polyene (APE) pigments. Bioinformatic analysis of enzymes involved in the biosynthesis and the in vitro reconstruction proved that the synthesis of APEs involves an unusual fatty acid-like elongation mechanism. Furthermore, the discovery of unexpected protein-protein interactions provided new insights into the multienzyme complex formation of this unusual PKS II system. Through collaboration with the groups from Prof. Michael Groll and junior Prof. Nina Morgner, two protein complexes were structurally solved and several native protein multimerization events were identified and allowed us to suggest a possible protein-interaction network. The results are summarized in publication ‘An Uncommon Type II PKS Catalyzes Biosynthesis of Aryl Polyene Pigments’ (first author; J. Am. Chem. Soc.).
In addition to in vitro-analysis, in vivo-studies were used to investigate the APE compound produced by X. doucetiae in more detail. The activation of the silent biosynthetic gene cluster (BGC) led to the detection of the APE compound in the homologous host. Further combination of homologous expression and targeted deletions of the APE BGC revealed an APE-lipid-like structure. MS-based analyses and purification of intermediates allowed us to deduce structural building blocks of the APE-lipid, which is composed of an APE structural core, a glucosamine residue and an unusual long-chain fatty acid with unusual conjugated double bonds and a phosphoethanolamine head group. In combination with the above stated in vitro-data, we assumed a plausible biosynthetic mechanism of the APE-lipid. The results are summarized in the section ‘Additional Results: Tracing the Full-length APE’.
The biosynthesis of isopropylstilbene (IPS) has already been well-studied by the Bode laboratory and the group of Prof. Ikuro Abe. Studies with Photorhabdus laumondii TT01 by the Bode group revealed the distributed locations and functions of the genes involved in biosynthesis, which originate from two pathways. Particularly, the Bode group first demonstrated that an unusual ketosynthase/cyclase (StlD) catalyzes the condensation of 5-phenyl-2,4-pentadienoyl-ACP and isovaleryl-beta-ketoacyl-ACP via a Michael addition. Such a pathway for stilbene formation is distinct from those widespread in plants. The Abe group solved the structure and biochemical mechanism of StlD and further investigated the aromatization reaction of the aromatase StlC. However, the generation of the required cinnamoyl-precursor 5-phenyl-2,4-pentadienoyl-ACP as a Michael acceptor for this cyclization reaction remained elusive. In this work, we were able to reconstitute the synthesis of the Michael acceptor in vitro, by the action of enzymes from the fatty acid biosynthesis. With the knowledge about the crucial cross-talk from primary and specialized metabolism, we further determined the minimal endowment for stilbene production in a heterologous host. Here, the discovered AasS enzyme StlB is responsible for the generation of cinnamoyl-ACP and among others, plFabH plays a key role as gatekeeper enzyme for further processing. With this information in hand, we were able to obtain IPS production in E. coli. These results are presented in the manuscript ‘Biosynthesis of the Multifunctional Isopropylstilbene in Photorhabdus laumondii Involves Cross-talk Between Specialized and Primary Metabolism’ (co-first author, manuscript).
The biosynthesis of the orange-to-red-pigmented anthraquinones (AQs) is the best-studied type II PKS system according to preliminary results. While several investigations by Brachmann et al. discovered the BGC and the overall product spectrum of the main AQ-256 and its methylated derivatives, data of Quiqin Zhou (Bode group) performed biochemical in vitro analysis paired with in vivo heterologous expression of the ant-genes antA-I. This led to the identification of shunt products that indicated an AQ-scaffold derived from an octaketide intermediate that gets shortened to a heptaketide by the hydrolase AntI, resulting in the main anthraquinone AQ-256. This PKS-shortening mechanism was further confirmed by the protein crystal structure of AntI by the Groll group (publication, minor contributions, co-author, Chem Sci. ‘Molecular Mechanism of Polyketide Shortening in Anthraquinone Biosynthesis of Photorhabdus luminescens’). Further substrate analysis of the P. luminescens AQ-producer and mutants revealed an inhibitory effect of cinnamic acid against the hydrolase AntI. Cinnamic acid might therefore be involved in regulation of AQ biosynthesis (‘Anthraquinone Production is Influenced by Cinnamic Acid’, first author, manuscript).
Biochemical analysis from Quiqin Zhou with the minimal PKS of the AQ-synthase further revealed the exclusive activation of the AQ-ACP by the PPTase AntB. The PPTase is insoluble alone but gets stabilized by the CoA-ligase, most likely inactive, working as a chaperone. Thus, the minimal PKS endowment to produce the octaketide scaffold compromises, besides the ACP, the KS:CLF heterodimer and the MCAT, the co-occurrence of the PPTase AntB and the CoA-ligase AntG. For the first time, X-ray crystallography depicted a minimal PKS in action, by obtaining the structural data of native complexes from an ACP:KS:CLF, the KS:CLF alone and an ACP:MCAT in their non-active and active forms. It was possible to confirm a KS-bound hexaketide, which was built upon heterologous expression of the KS:CLF. Mutagenesis with amino-acids proposed to be involved in protein-protein interactions in the ACP:KS:CLF complex revealed some interesting protein-interaction sites. Additionally, an induced-fit mechanism of the MCAT with the ACP during the malonylation reaction confirmed a monodirectional transfer reaction (‘Structural Snapshots of the Minimal PKS System Responsible for Octaketide Biosynthesis’ co-author, manuscript under review).
Heat stress transcription factors (Hsfs) have an essential role in heat stress response (HSR) and thermotolerance by controlling the expression of hundreds of genes including heat shock proteins (Hsps) with molecular chaperone functions. Hsf family in plants shows a striking multiplicity, with more than 20 members in many species. In Solanum lycopersicum HsfA1a was reported to act as the master regulator of the onset of HSR and therefore is essential for basal thermotolerance. Evidence for this was provided by the analysis of HsfA1a co-suppression (A1CS) transgenic plants, which exhibited hypersensitivity upon exposure to heat stress (HS) due to the inability of the plants to induce the expression of many HS-genes including HsfA2, HsfB1 and several Hsps. Completion of tomato genome sequencing allowed the completion of the Hsf inventory, which is consisted of 27 members, including another three HsfA1 genes, namely HsfA1b, HsfA1c and HsfA1e.
Consequently, the suppression effect of the short interference RNA in A1CS lin e was re-evaluated for all HsfA1 genes. We found that expression of all HsfA1 proteins was suppressed in A1CS protoplasts. This result suggested that the model of single master regulator needs to be re-examined.
Expression analysis revealed that HsfA1a is constitutively expressed in different tissues and in response to HS, while HsfA1c and HsfA1e are minimally expressed in general, and show an induction during fruit ripening and a weak upregulation in late HSR. Instead HsfA1b shows preferential expression in specific tissues and is strongly and rapidly induced in response to HS. At the protein level HsfA1b and HsfA1e are rapidly degraded while HsfA1a and HsfA1c show a higher stability. In addition, HsfA1a and HsfA1c show a nucleocytosolic distribution, while HsfA1b and HsfA1e a strong nuclear retention.
A major property of a master regulator in HSR is thought to be its ability to cause a strong transactivation of a wide range of genes required for the initial activation of protective mechanisms. GUS reporter assays as well as analysis of transcript levels of several endogenous transcripts in protoplasts transiently expressing HsfA1 proteins revealed that HsfA1a can stimulate the transcription of many genes, while the other Hsfs have weaker activity and only on limited set of target genes. The low activity of HsfA1c and HsfA1e can be attributed to the lower DNA capacity of the two factors as judged by a GUS reporter repressor assay.
HsfA1a has been shown to have synergistic activity with the stress induced HsfA2 and HsfB1. The formation of such complexes is considered as important for stimulation of transcription and long term stress adaptation. All HsfA1 members show synergistic activity with HsfA2, while only HsfA1a act as co-activator of HsfB1 and HsfA7. Interestingly, HsfA1b shows an exceptional synergistic activity with HsfA3, suggesting that different Hsf complexes might regulate different HS-related gene networks. Altogether these results suggest that HsfA1a has unique characteristics within HsfA1 subfamily. This result is interesting considering the very high sequencing similarity among HsfA1s, and particularly among HsfA1a and HsfA1c.
To understand the molecular basis of this discrepancy, a series of domain swapping mutants between HsfA1a and HsfA1c were generated. Oligomerization domain and C-terminal swaps did not affect the basal activity or co-activity of the proteins. Remarkably, an HsfA1a mutant harbouring the N-terminus of HsfA1c shows reduced activity and co-activity, while the reciprocal HsfA1c with the N-terminus of HsfA1a cause a gain of activity and enhanced DNA binding capacity.
Sequence analysis of the DBD of HsfA1 proteins revealed a divergence in the highly conserved C-terminus of the turn of β3-β4 sheet. As the vast majority of HsfA1 proteins, HsfA1a at this position comprises an Arg residue (R107), while HsfA1c a Leu and HsfA1e a Cys. An HsfA1a-R107L mutant has reduced DNA binding capacity and consequently activity. Therefore, the results presented here point to the essential function of this amino acid residue for DNA binding function. Interestingly, the mutation did not affect the activity of the protein on Hsp70-1, suggesting that the functionality of the DBD and consequently the transcription factor on different promoters with variable heat stress element number and architecture is dependent on structural peculiarities of the DBD.
In conclusion, the unique properties including expression pattern, transcriptional activities, stability, DBD-peculiarities are likely responsible for the dominant function of HsfA1a as a master regulator of HSR in tomato. Instead, other HsfA1-members are only participating in HSR or developmental regulations by regulating a specific set of genes. Furthermore, HsfA1b and HsfA1e are likely function as stress primers in specific tissues while HsfA1c as a co-regulator in mild HSR. Thereby, tomato subclass A1 presents another example of function diversity not only within the Hsf family but also within the Hsf-subfamily of closely related members. The diversification based on DBD peculiarities is likely to occur in potato as well. Therefore this might have eliminated the functional redundancy observed in other species such as Arabidopsis thaliana but has probably allowed the more refined regulation of Hsf networks possibly under different stress regimes, tissues and cell types.
Characterizing the hologenome of Lasallia pustulata and tracing genomic footprints of lichenization
(2017)
The lichen symbiosis – consisting of fungal mycobionts and photoautotroph photobionts (green algae or cyanobacteria) – is globally successful. It covers an estimated 6% of the global surface with habitats ranging from deserts to the arctic. This success is reflected in the diversity of the mycobionts, with around 21% of all fungal species participating in lichen symbioses that can be facultative or obligate. Lichenization is furthermore evolutionary old, with fossil evidence for lichens reaching back 415 million years. For an individual fungal lineage, the Lecanoromycetes, the lichenization happened around 300 million years ago. This longstanding symbiotic relationship and the diversity of observed symbiotic dependency make them promising models to study the genomic consequences that follow the establishment of symbioses. Despite this, only little is known about the genomic effects of lichenization and extreme symbiotic dependency. To fill this gap we sequenced the hologenome of the lichen Lasallia pustulata, where the mycobiont could so far not been cultivated, suggesting that it might be more dependent on its symbionts.
As the poor culturability of lichen symbionts renders their genomes inaccessible to standard sequencing practices, we evaluated the extent to which different metagenome sequencing- and de novo assembly-strategies can be used to sequence and reconstruct the genomes of the individual symbionts. We find that the abundances of individual genomes present in the L. pustulata hologenome vary substantially, with the mycobiont being most abundant. Using in silico generated data sets and real Illumina sequencing data for L. pustulata we observe that the skewed abundances prevent a contiguous assembly of the underrepresented genomes when using only short-read sequencing. We conclude that short-read sequencing can offer first insights into lichen hologenomes. The fragmentation of the reconstructions hinders downstream analyses into the genomic consequences of lichenization though, as these are focused on identifying the gain and loss of genes.
We thus demonstrate a hybrid genome assembly strategy that is based on both short- and long-read sequencing. We show that this strategy is capable of creating highly contiguous genome reconstructions, not only for the L. pustulata mycobiont but also its photobiont Trebouxia sp., along with substantial amounts of the bacterial microbiome. A subsequent analysis of the microbiome of L. pustulata – performed over nine different samples collected in Germany and Italy – showed a stable taxonomic composition across the geographic range. We find that Acidobacteriaceae, which are known to thrive in nutrient poor habitats, are the dominant taxa. These would make them well adapted for the co-habitation with L. pustulata, which largely grows on rocks. Whether the Acidobacteriaceae are functionally involved in the lichen symbiosis is unclear so far.
As further comparative genomic studies rely on comprehensive genome annotations, we evaluate the completeness and fidelity of the gene annotations for the mycobiont L. pustulata as well as four further Lecanoromycetes. This reveals that un- and mis-annotated genes impact all evaluated genomes, with artificially joined genes and unannotated genes having the largest impact. In addition to these factors we find that the sequence composition – especially G/C-rich inverted repeats – lead to sequencing errors that interfere with the gene prediction. We minimize the effects of these artifacts through a rigorous curation.
Given the extremely sparse taxon sampling of available green alga genomes, we focus our search for the genomic footprints of lichenization on the mycobionts. We compare the genomes of the Lecanoromycetes to their closest relatives, the Eurotiomycetes and Dothideomycetes. This reveals that the last common ancestor of the Lecanoromycetes has lost around 10% of its genes after they split from the non-lichenized ancestor they share with the Eurotiomycetes. These losses are furthermore enriched, showing an excessive loss of genes involved with the degradation of polysaccharides. The loss of these genes fits a change from an ancestral saprotrophic lifestyle that depends on degrading complex plant matter, to the symbiotic lifestyle that relies on simpler nutrients provided by the photobionts. While the last common ancestor of the Lecanoromycetes additionally gained around 400 genes these could so far not be further characterized due to a lack of functionally annotated reference data.
As the mycobiont L. pustulata could so far not been grown in axenic culture, we initially expected to find an extensive genomic remodeling compared to the other mycobionts that easily grow in culture. We do not find evidence for this. Analyzing both the contraction of gene families and the loss of genes, we observe that L. pustulata and Umbilicaria muehlenbergii – its close relative that is easily grown in culture – share most of these. Furthermore, L. pustulata does not show an excessive loss of evolutionary old and well-conserved genes. These effects are mirrored on the functional level, as neither gene family contractions nor gene losses show a functional enrichment. This is partially due to the lack of functional reference data, analogous to the genes gained in the Lecanoromycetes, rendering their characterization hard. Thus, further studies on the genomic consequences of lichenization and differences in symbiotic dependence will have to be conducted, including larger taxon sets. This will be even more important for the photobionts, as the Chlorophyta are even more sparsely sampled today, hindering an effective functional and evolutionary study.
Die oxygene Photosynthese bildet den Grundpfeiler des heutigen Ökosystems unseres Planeten. Neben den gut untersuchten Landpflanzen bilden Mikroalgen eine äußerst bedeutende Organismengruppe der phototrophen Lebewesen. Zu den Mikroalgen zählen die Diatomeen, welche sich beispielsweise durch eine Silikatschale und spezielle Lichtsammelkomplexe auszeichnen und für einen Großteil der marinen Primärproduktion verantwortlich sind. Die stoffwechselphysiologischen Grundlagen des ökologischen Erfolgs der Kieselalgen sind bislang noch unzureichend erforscht. Ein Vertreter der zentrischen Diatomeen, Cyclotella, wurde bereits zur Jahrtausendwende zur biochemischen Charakterisierung der Diatomeen Photosynthese verwendet (Eppard und Rhiel, 1998; Eppard und Rhiel, 2000), das Genom des Organismus aber erst vor kurzem sequenziert (Traller et al., 2016). Die Sequenzierung des Genoms konnte einige Gene für Lichtsammelproteine identifizieren, die Homologie zu den LhcSR-Proteinen aus C. reinhardtii aufweisen, welche nachweislich eine photoprotektive Funktion besitzen (Peers et al., 2009). Diese sogenannten Lhcx-Proteine der Diatomeen sind in den zwei Gruppen der Kieselalgen, den zentrischen und pennaten Diatomeen zu finden, unterscheiden sich aber in ihren jeweiligen Lhcx-Kandidaten. So können in der pennaten Diatomee P. tricornutum vier lhcx-Gene ausgemacht werden, während die zentrische Kieselalge T. pseudonana sechs lhcx-Gene besitzt und C. cryptica vier verschiedene lhcx-Kandidaten genomisch aufweist (Armbrust et al., 2004; Bowler et al., 2008; Traller et al., 2016). Die beschriebenen Diatomeen weisen alle eine Homologie im Lhcx1 auf, während sich die übrigen Lhcx-Kandidaten zwischen pennaten und zentrischen Diatomeen unterscheiden. Ein zwischen T. pseudonana und C. cryptica konserviertes Lhcx ist das Lhcx6_1, welches 2011 das erste Mal massenspektrometrisch an Photosystemen von T. pseudonana nachgewiesen wurde (Grouneva et al., 2011) und in weiteren Massenspektrometrie-gestützten Untersuchungen in beiden zentrischen Diatomeen an Photosynthese-Komplexen gefunden werden konnte (Gundermann et al., 2019; Calvaruso et al., 2020). Die Funktion des Lhcx6_1 ist bislang unklar.
Diese Arbeit konnte das Lhcx6_1 aus C. meneghiniana charakterisieren und Antikörper-gestützt genauer lokalisieren, eine nicht dynamische Phosphorylierung der Thylakoidmembran-Proteine der zentrischen Diatomee nachweisen und die molekularbiologische Zugänglichkeit des Organismus optimieren. qRT-PCR gestützte Expressions-Analysen konnten eine unerwartete Expression des lhcx6_1-Gens aufdecken. Dieses weist, im Vergleich zum Lhcx1, keine Starklicht induzierte Expression auf. Die Expression des Gens konnte nach wenigen Stunden Schwachlicht als maximal bestimmt werden, während sie im Starklicht abnimmt. Das Muster der Genexpression glich im Schwachlicht eher der des lhcf1-Gens. Die Sequenzierung des lhcx6_1 aus C. meneghiniana identifizierte eine verlängerte N-terminale Sequenz des Proteins, welche Homologie zu den minoren Antennen aus A. thaliana besitzt und Teil des reifen Proteins ist. Mittels eines C-terminalen Epitops wurde ein Antikörper gegen das Lhcx6_1 entworfen, welcher das Protein in C. meneghiniana spezifisch nachweisen kann. Die Isolation von Thylakoidmembranen der zentrischen Diatomee und weitergehende Aufreinigung mittels Saccharosedichtegradienten und lpBN-PAGE konnten die Lokalisation des Lhcx6_1 eingrenzen. Das Protein zeigt dabei keine Unterschiede in seiner Lokalisation nach Inkubation in Schwach-, Stark- und Fernrot-Licht und ist vorrangig mit Photosystem I assoziiert. In geringerer Menge konnte es zudem an Photosystem II nachgewiesen werden, während der immunologische Nachweis in Lichtsammelkomplexen (FCPs) minimale Mengen erbrachte. Ferner konnte eine Phosphorylierung des Lhcx6_1 an Threonin-Resten nachgewiesen werden, während die meisten anderen Thylakoidmembran-Proteine mittels Phospho-Serin Antikörper detektiert werden konnten. Weder die Phosphorylierung des Lhcx6_1, noch der anderen Thylakoidmembran-Proteine, zeigt eine dynamische Regulation, im Stile einer state-transition ähnlichen Kinase auf. Die Qualität des Umgebungslichts führte zu keinerlei Unterschieden in Phosphorylierungsmustern. Weiterführende Untersuchungen der Lhcx6_1-Phosphorylierung mittels Phos-tag PAGE identifizieren eine unphosphorylierte und eine einfach phosphorylierte Form des Proteins. Dabei kann an PSI ausschließlich die phosphorylierte Version des Lhcx6_1 gefunden werden. Im Zuge der Arbeit konnte zudem erstmalig die Elektroporation und Konjugation für C. meneghiniana als Transformations-Methoden etabliert werden, während das Protokoll für die biolistische Transformation optimiert wurde. Die Elektroporation erbrachte die höchste Transformationseffizienz. Molekularbiologische Unterfangen eines Lhcx6_1-Knockdowns mittels Antisense-RNA erzielten zunächst, aufgrund der starken Gegenregulation der Diatomee, keinen Erfolg...
Im Rahmen dieser Arbeit wurden sRNAs des halophilen Archaeons Haloferax volcanii hinsichtlich ihrer biologischen und ihrer regulatorischen Funktion charakterisiert.
Um einen Überblick über die biologischen Funktionen archaealer sRNAs zu erhalten, wurde eine umfassende phänotypische Charakterisierung von 27 sRNA-Deletionsmutanten im Vergleich zum Wildtyp ausgewertet. Im Zuge dieser phänotypischen Charakterisierungen wurden zehn verschiedene Wachstumsbedingungen, morphologische Unterschiede und Veränderungen in der Zellmotilität untersucht. Hierbei zeigten nahezu alle Deletionsmutanten unter mindestens einer der getesteten Bedingungen phänotypische Unterschiede. Durch den Verlust von sRNAs wurden sowohl sogenannte Gain-of-function als auch Loss-of-function Phänotypen beobachtet. Haloarchaeale sRNAs spielen eine wichtige Rolle beim Wachstum mit verschiedenen Salzkonzentrationen, mit verschiedenen Kohlenstoffquellen und beim Schwärmverhalten, sind jedoch weniger in die Adaptation an diverse Stressbedingungen involviert.
Zur näheren Charakterisierung der regulatorischen Funktion archaealer sRNAs wurden sRNA362, sRNAhtsf468 und sRNA479 mittels molekulargenetischer Methoden wie Northern Blot-Analyse und DNA-Mikroarray sowie bioinformatischer in silico-Analyse untersucht. Das Expressionslevel von sRNA362 konnte bestimmt und potentielle Zielgene für sRNAhtsf468 und sRNA479 identifiziert werden.
Eine vorangegangene Studie zeigte den Einfluss von sRNA30 unter Hitzestress und führte zur Identifikation differentiell produzierter Proteine in Abwesenheit der sRNA. In dieser Arbeit wurde mittels Northern Blot-Analysen die Expression der sRNA30 charakterisiert. Das Wachstum in An- und Abwesenheit von sRNA30 wurde bei 42°C und 51°C phänotypisch charakterisiert und der regulatorische Einfluss der sRNA auf die mRNA differentiell regulierter Proteine durch Northern Blot-Analyse überprüft. Eine Transkriptomanalyse mittels DNA-Mikroarray nach Hitzeschock-Induktion führte zur Identifikation differentiell regulierter Gene involviert in Transportprozesse, Metabolismus, Transkriptionsregulation und die Expression anderer sRNAs. Die differentielle Regulation des Proteoms nach Hitzeschockinduktion in An- und Abwesenheit von sRNA30 konnte bestätigt werden.
Desweiteren wurde in dieser Arbeit sRNA132 und deren phosphatabhängige Regulation der Ziel-mRNA HVO_A0477-80 näher charakterisiert. Eine Induktionskinetik nach Phosphatentzug bestätigte die Bedeutung von sRNA132 für die verstärkte Expression des Operons HVO_A0477-80 unter Phosphatmangel-Bedingungen und verwies auf die Existenz weiterer Regulationsmechanismen. Während vor und nach Phosphatentzug kein Unterschied bezüglich der Zellmorphologie von Wildtyp und Deletionsmutante zu erkennen war, führte das Wachstum mit einem starken Phosphatüberschuss von 5 mM zu einer Zellverlängerung der Deletionsmutante. Die Kompetition der nativen 3‘-UTR des Operons HVO_A0477-80 mit einer Vektor-kodierten artifiziellen 3‘-UTR legt eine Regulation über die Bindung von sRNA132 an die 3‘-UTR nahe. Der Transkriptomvergleich nach Phosphatentzug in An- und Abwesenheit von sRNA132 führte zur Identifikation des Phosphoregulons der sRNA. Zu diesem Phosphoregulon gehören unter anderem zwei Glycerinphosphat-Dehydrogenasen, Transkriptionsregulatoren, eine Polyphosphatkinase und eine Glycerolphosphodiesterase. Zudem waren die Transkriptlevel der beiden ABC-Transporter HVO_A0477-80 und HVO_2375-8 für anorganisches Phosphat und des Transporters HVO_B0292-5 für Glycerinaldehyd-3-Phosphat in Abwesenheit der sRNA verringert. Die beiden ABC-Transportsysteme für anorganisches Phosphat wurden im Rahmen dieser Arbeit deletiert und weiter charakterisiert. Es konnte gezeigt werden, dass das ABC-Transportsystem HVO_2375-8 bei geringen Phosphatkonzentrationen leicht induziert wird und das Transkriptlevel in Anwesenheit von sRNA132 erhöht ist. Wachstumsversuche der jeweiligen Deletionsmutante in direkter Konkurrenz mit dem Wildtyp zeigten, dass keiner der beiden ABC-Transporter den anderen vollständig ersetzen kann und der Wildtyp mit beiden intakten ABC-Transportern unter phosphatlimitierenden Bedingungen einen Wachstumsvorteil besitzt. In silico-Analysen der Promotorbereiche von sRNA und ABC-Transporter legen zudem die Existenz von P-Boxen nahe.
Der erste Teil der vorliegenden Arbeit beinhaltet die funktionelle Analyse von fünf Oberflächenproteinen von B. recurrentis die die Fähigkeit besitzen, die Aktivierung von humanen Komplement zu inhibieren und Borrelien vor Bakteriolyse zu schützen. Im zweiten Teil der Arbeit wurden zwei immunologische Testverfahren mit hoher Sensitivität sowie Spezifität entwickelt und mit zahlreichen Patientenseren evaluiert. Die entwickelten Tests könnten in Zukunft als zuverlässige Instrumente für eine gesicherte Diagnose von LRF eingesetzt werden.
Eine Sequenzanalyse führte zur Identifizierung eines neuen Proteinclusters, welches die fünf untersuchten Komplement-inhibierenden Proteine als „Cluster of Complement-targeting and Host-interacting Proteins“ oder „Chi-Gencluster“, zusammenfasst. Diese Oberflächenproteine wurden als ChiA, ChiB, ChiC, ChiD und ChiE bezeichnet. Weiterführende Sequenzanalysen ergaben, dass das Chi-Gencluster extrem hoch konserviert ist und sowohl in den ersten B. recurrentis-Isolaten aus den 1990er Jahren als auch in B. recurrentis-Stämmen nachgewiesen werden konnte, die 2015 aus Patienten isoliert wurden.
Durch funktionelle Analysen konnte gezeigt werden, dass alle fünf Chi-Proteine in der Lage sind den alternativen und terminalen Komplementweg zu inhibieren. Ebenfalls konnte für die Proteine ChiB, ChiD sowie ChiE nachgewiesen werden, dass die Interaktion mit der Komplementkomponente C5 dosisabhängig verläuft.
Die strukturelle Aufklärung des Proteins ChiB ermöglichte es Aminosäuren zu identifizieren, von denen angenommen wurde, dass sie für die Interaktion mit Komplement eine Rolle spielen könnten. Durch in vitro Mutagenese konnten insgesamt fünf verschiedene Varianten von ChiB generiert werden, die jedoch keine Veränderungen in ihrem Komplement-inhibierenden Potential gegenüber dem unveränderten ChiB-Protein aufwiesen. Weder in der Inhibition des alternativen oder des terminalen Komplementweges, noch in der Interaktion mit den untersuchten Komplementkomponenten C3b, C5 und C9.
Weiter konnte gezeigt werden, dass die lytische Aktivität von Humanserum durch Vorinkubation mit ChiB, ChiC, ChiD und ChiE drastisch reduziert werden konnte, sodass Serum-sensible Borrelienzellen in Gegenwart von Komplement überlebten. „Gain-of-function“ B. garinii-Transformanten, welche mit dem entsprechendem Chi-kodierenden Gen transformiert wurden, bestätigten die mit den gereinigten Proteinen erhobenen Ergebnisse.So konnte nachgewiesen werden, dass ChiB-, ChiC- oder ChiD-produzierende „Gain-of-function“ B. garinii Transformanten, nicht jedoch ChiE- produzierende Zellen, in der Lage waren einen Serum-resistenten Phänotypen auszubilden. Für Transformanten, die zwei-, drei- oder vier Chi-Proteine in verschiedenen Kombinationen gleichzeitig produzierten, konnte allerdings die Fähigkeit in Gegenwart von Humanserum zu überleben nicht bestätigt werden.
Molekulare Analysen mit verschiedenen RF-Borrelienstämmen führten zum Nachweis, dass die fünf Chi-kodierenden Gene bei allen Isolaten vorhanden sind und unter in vitro Bedingungen exprimiert werden. Im Gegensatz zu B. recurrentis PAbJ, ließ sich das HcpA kodierende Gen in B. duttonii LAI nicht nachweisen, jedoch alle dem Chi-Cluster zugehörigen Gene. Bei B. duttoni V fehlte das gesamte Chi-Cluster sowie die für CihC- und HcpA-kodierenden Gene. Durch eine Western Blot-Analyse konnte mit spezifischen Antikörpern bestätigt werden, dass die Proteine CihC, HcpA und ChiB in B. recurrentis A17 unter in vitro Bedingungen produziert wurden.
Im zweiten Teil der vorliegenden Arbeit wurden durch die Analyse der IgM- und IgG-Immunreaktivitäten der LRF-Patientenseren zwei Proteine identifiziert, CihC und GlpQ, die als potenzielle Antigene für die Serodiagnostik des LRF evaluiert wurden. Eine initiale Evaluierung des IgM Lineblot-Immmunoassays zeigte jedoch nur eine geringe Sensitivität für die beiden Antigene, während der IgG Lineblot-Immunoassay eine sehr hohe Sensitivität aufwies. Der ELISA hingegen zeigte bei einer Kombination beider Antigene sehr gute Sensitivitäten und Spezifitäten. Um die starke Hintergrundfärbung bei den Lineblot-Immunoassays, welche eine korrekte Bewertung der Reaktivitäten gegenüber CihC erheblich erschwerten, zu minimieren, wurde ein „Epitop-Mapping“ durchgeführt, um immunogene Regionen innerhalb des CihC-Proteins zu lokalisieren. Eine zweite Evaluierung mit dem immunreaktiven N-terminalen CihC-Fragment CihC-N führte zu einer deutlichen Verbesserung der IgG Lineblot-Immunoassays mit einer Sensitivität von 100 % und einer starken Reduktion der Hintergrundfärbung. Zusätzlich konnte die Sensitivität der IgM-ELISA deutlich verbessert werden. Die Verwendung von CihC-N führte beim IgG-ELISA zur Herabsetzung des Cut-off-Wertes und zu einer besseren Unterscheidung zwischen den positiven LRF-Seren und den verwendeten Kontrollseren. Im Rahmen dieser Arbeit konnten somit zwei serologische in vitro Diagnostika entwickelt werden, die als zuverlässige Point-of-Care-Diagnostik in klinischen Studien eingesetzt werden könnten. Zur Steigerung der Sensitivität des IgM-Lineblot-Immunoassays sollten allerdings weiterführende Untersuchungen mit weiteren immunreaktiven Antigenen, wie z.B. den Vmp-Proteinen von B. recurrentis, angestrebt werden.
Seit Jahrzehnten finden Kunststoffe aufgrund ihrer vorteilhaften Materialeigenschaften wie z. B. Formbarkeit und im Vergleich zu Glas oder Metall geringe Kosten und leichtes Gewicht, vermehrt Anwendung in allen Bereichen des täglichen Lebens. Einhergehend gelangen Kunststoffe zunehmend in die Umwelt, und reichern sich dort an. Besondere Aufmerksamkeit erfahren Partikel im Größenbereich von 1-1000 µm, sogenanntes Mikroplastik (MP), welches entweder direkt eingetragen wird oder in der Umwelt durch Fragmentierung größerer Plastikteile entsteht. Lange Zeit fokussierte sich die MP Forschung vorrangig auf aquatische Ökosysteme, obwohl Schätzungen davon ausgehen, dass die Kunststoffeinträge in terrestrischen Ökosystemen um ein Vielfaches höher sind. Besonders relevante Eintragspfade sind neben der unsachgemäßen Entsorgung von Abfällen, die landwirtschaftliche Klärschlamm- und Kompostdüngung und der zunehmende Einsatz von Mulchfolien, sowie der im Straßenverkehr generierte Reifenabrieb.
Für eine Abschätzung und Bewertung der MP-Belastung in Böden sind analytische Messungen von MP in Umweltproben essenziell, derzeit jedoch kaum existent, da MP im Boden partikulär und heterogen verteilt vorliegt und deshalb nur schwierig zu detektieren ist. Die für viele Analyseverfahren notwendige Isolation der Kunststoffpartikel, sowie die für repräsentative Messungen erforderliche Aufbereitung großer Probenvolumina stellen besondere analytische Herausforderungen mit großem Kosten- und Zeitaufwand dar. Chromatografische Verfahren finden wenig Anwendung, bieten aber vorteilhafte Voraussetzungen als Screeningverfahren für die Untersuchung von Böden, da sie nicht zwangsweise eine Partikelisolation verlangen, und zudem als Ergebnis einen Massegehalt liefern.
Diese Dissertation zeigt drei Anwendungen Chromatografie basierter Analyseverfahren zur Charakterisierung von MP im Boden. Erstmalig wurde die Thermo-Extraktion-Desorption-Gaschromatografie-Massenspektrometrie (TED-GC/MS) für die Analytik von Reifenabrieb in realen Umweltproben angewandt bei minimaler Probenaufbereitung. Dafür wurde ein Straßenrandboden umfangreich beprobt und analysiert, und es konnte neben der Eignung der analytischen Methode auch eine repräsentative Probenahmestrategie und räumliche Verteilungsmuster von Reifenabrieb im Boden demonstriert werden.
Der zweite Forschungsschwerpunkt lag auf der Methodenentwicklung und validierung eines neuartigen chemischen Extraktionsverfahrens für die Bestimmung von Polyestern in Bodenproben. Das Verfahren basiert auf der hydrolytischen Spaltung von Polyestern in ihre Monomere, deren flüssigchromatografische Abtrennung von Matrixbestandteilen und der Detektion mittels UV-Absorption. Das Verfahren verlangt neben der Extraktion keine weiteren Probenaufbereitungsschritte, ist für unterschiedliche Umweltmatrizes geeignet und ist damit z. B. prädestiniert für den Nachweis von Polyesterfasern auf gedüngten landwirtschaftlichen Flächen.
MP ist nicht nur aufgrund seiner Persistenz problematisch, sondern auch, weil es hydrophobe organische Schadstoffe aus dem Umweltmedium anreichern und transportieren kann. Maßgeblich für das Sorptionsverhalten sind die Materialeigenschaften des zugrunde liegenden Kunststoffes, welche Änderungen durch Alterungsprozessen unterliegen. Der Zusammenhang zwischen Materialalterung und Sorptionsverhalten wurde in früheren Studien kontrovers diskutiert und ist der dritte Teil dieser Arbeit. In einem Sorptionsexperiment konnte mittels Headspace-Gaschromatografie mit Flammenionisations-Detektion die Aufnahme von Aromaten an den Kunststoffen Polypropylen und Polystyrol quantifiziert werden. Die Kunststoffe wurden materialwissenschaftlich charakterisiert, teilweise künstlich gealtert und die daraus resultierende Änderungen der Materialeigenschaften sowie einhergehenden Änderungen des Sorptionsverhaltens erfasst. Dadurch war es möglich den Einfluss einzelner Materialeigenschaften auf das Sorptionsverhalten zu bewerten, Rückschlüsse auf zugrunde liegende Sorptionsmechanismen zu treffen und zu zeigen, dass in vorliegendem Experiment die Polymeralterung bei MP nicht zu einer erhöhten Schadstoffsorption führte.
Sleep is one of the fundamental requirements of all animals from nematodes to humans. It appears in different formats with shared features such as reduced muscle activities and reduced responsiveness to the environment. Despite the long history of sleep research, why a brain must be taken offline for a large portion of each day remains unknown. Moreover, sleep research focused on mammals and birds reveals two stages, rapid-eye-movement (REM) and slow-wave (SW) sleep, alternating during sleep. Whether these two stages of sleep exist in other vertebrates, particularly reptiles, is debated, as is the evolution of sleep in general.
Recordings from the brain of a lizard, the Australian bearded dragon Pogona vitticeps, indicate the presence of two electrophysiological states and provides a better picture of their sleep. Local field potential (LFP) signals, head velocity, eye movements, and heart rate during sleep match the pattern of REM and SW sleep in mammals. The SW and REM sleep patterns that we observed in lizards oscillated continuously for 6 to 10 hours with a period of 80-100 seconds when the ambient temperature was ~27°C. Lizard SW dynamics closely resemble those observed in rodent hippocampal CA1, yet originated from a brain area, the dorsal ventricular ridge (DVR), that does not correspond anatomically or transcriptomically to the mammalian hippocampus. This finding pushes back the probable evolution of these dynamics to the emergence of amniotes, at least 300 million years ago.
Unlike mammals and birds, REM and SW sleep in lizards occupy an almost equal amount of time during sleep. The clock-like alternation between these two sleep states was found initially by measuring the power modulation of two frequency bands, delta and beta. I recorded the full-band LFP and found an infra-slow oscillation (ISO) in the frequency range between 5 and 20 milli-Hz during sleep. The magnitude of ISO increased during sleep and decreased during both wakefulness and arousal during sleep. The up- and down-states of ISO were synchronized with the sleep state alternating rhythm but with a significant time lag dependent on the locations of the recording electrodes. Multi-site LFP recordings indicated that this ISO is a putative propagation wave sweeping extremely slowly, 30-67 µm/sec, from the posterior-dorsal pole to the anterior-ventral pole of the DVR.
Previous studies in other animals showed that brainstem areas such as the locus coeruleus, laterodorsal tegmentum, and periaqueductal gray are involved in sleep states regulation. It is sadly impossible to carry out in vivo recordings in the lizard brainstem without severely affecting them and their quality of life. I thus carried out ex vivo recordings in both DVR and brainstem. Pharmacological stimulation of the brainstem could reversibly silence one distinct EEG pattern characteristic of SW sleep, the sharp-wave and ripple complex, in DVR. An ISO could be recorded simultaneously in both DVR and brainstem. From data collected in both intact and split ex vivo brains, I concluded that there are independent ISO generators in at least two areas, the brainstem and the telencephalon. Their signals may normally be synchronized by long-range connections. The DVR ISO leads the brainstem ISO by ~29 sec. Optogenetic stimulation of brainstem neurons was able to disrupt the ISO in DVR reversibly.
In conclusion, the lizard brain offers a relatively simple model system to study sleep. Despite a diversity of results in different lizard species, my results revealed a number of new findings. Relevant for sleep research in general: 1) REM and SW sleep exist in a reptile. Since they also exist in birds and mammals, they probably existed in their common amniote ancestor, if not earlier. 2) REM and SW occupy equal amounts of time during sleep (50% duty cycle), a unique feature among all described sleep electrophysiological patterns, suggesting the possible existence of a simple central pattern generator of sleep, possibly ancestral. 3) I discovered the existence, in the local field potential, of an infra slow oscillation with extremely slow propagation, locked to the SW-REM alternating rhythm. The causes and mechanisms of this ISO remain to be understood. To my knowledge, the correlation between sleep states and a slow rhythm has only been reported in human scalp EEG recordings so far.
Climate and subsequent environmental changes are regarded as one driver of species evolution. Against this background the present study investigates the evolutionary history of the mammalian family Bovidae (Cetartiodactyla, Mammalia), today the most species-rich family of large herbivores on the African continent. Temporal and spatial patterns in that group’s evolution are the focus of the present study and were investigated using methods and data deriving from multiple disciplines (palaeontology, genetics, climatology, conservation biology). The results serve as a validation of macroevolutionary hypotheses of species evolution.
A major proportion of African mammalian fossils can be assigned to that family. Due to their morphological adaptations, bovid species are highly indicative of their habitats. Hence, bovids are of great importance for paleontology. However, a strong taphonomic bias is present in the fossil record of bovids, favoring large and arid- adapted species. Molecular phylogenies of extant species and species distribution modelling combined with climate reconstructions can help to overcome these limitations.
A molecular phylogeny, based on the cytochrome b gene of 136 bovid species served as basis for analysis of temporal patterns. Divergence events were dated using the relaxed molecular clock approach. The tree was time calibrated at 30 nodes using information inferred from the fossil record. Lineage-Through-Time plots and the respective statistical analyses reveal detailed temporal patterns in the evolutionary history of tribes and groups combining arid- and humid-adapted tribes. The resulting pattern shows three distinct phases. Phase 1 (P1) is dominated by speciation events within the humid group, while the second phase (P2) is marked by a dominance of speciation within the arid group. The switch in diversification rates (BDS) from P1 to P2 is dated to 2.8 million years ago. The third phase (P3) shows low diversification rates for all groups, starting around 1.4 million year ago and culminates in a significantly reduced diversification rate for the complete family at 0.8 million years ago. Both transitions are contemporaneous with global climate changes and turnover events in fossil faunal communities.
To investigate the impact of climate changes onto the habitat availability within the last 3 million years and its putative influence on diversification rates, the species distribution modeling method was applied. For 85 African species and subspecies the climate niches were established and grouped into 5 climate-groups based on their climate preferences. For each group the available habitat for the period before and after the BDS was calculated on continental scale using reconstructed climate scenarios. To evaluate the modeled habitat distributions, regional analyses were performed in test areas surrounding well studied fossil sites (Laetoli, Olduvai, Chiwondo Beds, Lothagam, Koobi Fora, West Turkana, Swartkrans, Sterkfontain und Toros-Menalla). Habitat profiles (HP) permitted the comparison of the model based habitat reconstruction with the interpretations of classic paleontological reconstruction. The validity of the habitat modeling has been shown in particular for East African test areas. The reconstructions for the northern and southern fossil sites does not support the modeled habitats in these areas. Yet, the method of habitat- profiling may serve as suitable tool for environmental reconstruction of areas lacking sufficient paleontological material. A comparison of habitat availability before and after the BDS on continental scale identified a significant loss of habitat for humid adapted groups (7-22%) and habitat gain for arid adapted groups (19-173%). The climatically intermediate group experiences a tremendous gain of habitat (3366%). The greatest environmental change was modeled for East Africa, initiated by a progressive regional aridification.
In addition to the distribution modeling for past climate conditions, the geographical distribution was modeled for the future, i.e. for climate scenarios representing the years 2050 and 2080 under a putative climate change scenario (global surface warming). It was shown that in particular the arid groups have to expect a remarkable loss of habitat (41-76%), while a gain of available habitat can be expected for the humid adapted groups (114-577%). The climatically intermediate group suffers the strongest habitat loss (85%). Regions with locally stable climate conditions were detected and may serve as potential refugia and are already today known as Africa’s hot spots of biodiversity.
The results show a positive correlation of high diversification rates and increasing habitat availability. None of the tested speciation hypotheses taken alone explains the observations (e.g., Turnover-pulse Hypothesis, Relay Model). A major element in these hypotheses is the passive fragmentation of populations induced by unfavorable climate changes. In contrast, the Periodic Model (Grubb 1999) considers natural, periodically recurring climate changes and moreover, the active dispersal of individuals and resulting founder events. I added the effect of a superimposed directed climate trend – like the progressive aridification since the late Pliocene in Africa – which leads to a bias in the proportion and probability towards leading edge effects. This Directed Periodic Model explains the patterns found in the evolution of Bovidae.
The combination of a molecular phylogeny and species distribution modeling, together with information inferred from the fossil record, reveals remarkable temporal and spatial patterns in the evolution of bovids, and helps overcome the limitations of the fossil record. The present study highlights the importance of active dispersal and founder populations in speciation processes. A point widely unattended in speciation hypotheses. The fully dated molecular phylogeny is the most densely sampled tree for the family Bovidae to date and may serve as a framework for a connection of present and future population studies, permitting the connection of medium-scale with long- term effects induced by climate and environmental changes.
Gravitropism is a fundamental process in plants that allows shoots to grow upward and roots to grow downward. Protein phosphorylation has been postulated to participate in the intricate signaling cascade of gravitropism. In order to elucidate the underlying mechanisms governing the gravitropic signaling and unearth novel protein constituents, an exhaustive investigation employing microgravity-induced phosphoproteomics was undertaken. The significantly phosphorylated proteins unraveled in this study can be effectively divided into two groups through clustering analysis. Furthermore, the elucidation of Gene Ontology (GO) enrichment analysis disclosed the conspicuous overrepresentation of these clustered phosphoproteins in cytoskeletal organization and in hormone-mediated responses intimately intertwined with the intricate phenomenon of gravitropism. Motif enrichment analysis unveiled the overrepresentation of [-pS-P-] and [-R-x-x-pS-] motifs. Notably, the [-pS-P-] motif has been suggested as the substrate for the Casein kinase II (CK II) and Cyclin-dependent kinase (CDK). Kinase-inhibitor assays confirmed the pivotal role played by CK II and CDK in root gravitropism. Mutant gravitropism assays validated the functional significance of identified phosphoproteins, with some mutants exhibiting altered bending kinetics using a custom-developed platform. The study also compared phosphoproteomics data from different platforms, revealing variations in the detected phosphopeptides and highlighting the impact of treatment differences. Furthermore, the involvement of TOR signaling in microgravity-induced phosphorylation changes was uncovered, expanding the understanding of plant gravitropism responses.
To fulfill the large-scale verification of interesting candidates from the phosphoproteomics study, a novel root and hypocotyl gravitropism phenotyping platform was developed. This platform integrated cost-effective hardware, including Raspberry Pi, a high-quality camera, an Arduino board, a rotation stage (obtained from Prof. Dr. Maik Böhmer), and programmable green light (modified by Sven Plath). In addition, through collaboration with a software developer, machine-learning-based software was developed for data analysis. This platform tested the gravitropic response of candidate mutants identified in the phosphoproteomics study. Furthermore, the capabilities of this platform were expanded to investigate tropisms in other species and organs. To find novel proteins that might act as partners of a key protein that is involved in gravitropism signaling, ALTERED RESPONSE TO GRAVITY 1 (ARG1), immunoprecipitation coupled with Mass Spectrometry (IP-MS) was performed and identified ARG1-LIKE1 (ARL1) as a potential interacting protein with ARG1. This interaction was further confirmed through in vivo pull-down assays and bimolecular fluorescence complementation assays. In addition, the interaction between ARG1 and HSP70-1 was also validated.
Overall, this thesis sheds light on the molecular components and signaling events involved in plant gravitropism. It contributes to existing knowledge and opens up new ways to investigate this fascinating area of plant biology.
The continuous conversion of natural wildlife habitats into agricultural areas, as well as the fragmentation of the last wildlife refuges, is increasing the interface between people and wildlife. When wildlife negatively impacts on people and vice versa, we speak about human-wildlife conflicts (HWCs). This definition includes losses on both sides and takes into consideration the rooting of most of these conflicts between different groups of interest, such as advocates for nature conservation and economic groups. The centres of highest biodiversity are located in developing countries, which are also characterized by poverty. In African and Asian countries, people living in the vicinity of national parks and other conservation areas mostly receive only little support through the government or conservation organisations. Especially for those people who are dependent on agriculture, damage to fields and harvests can have catastrophic consequences. If the species causing damage is protected by national or even international law, the farmer is not allowed to use lethal methods, but has to approach the authority in charge. If this agency, however, cannot offer appropriate support, resentment, anger or even hate develops, and the support for wildlife conservation activities declines. For this reason, HWCs were declared as one of the most important conservation topics today, being particularly relevant for large and threatened species such as the African and Asian elephant, hippopotamus and the greater one-horned rhino, as well as for large predators. Up to today, no general assessment scheme has been recommended for damage caused by protected wildlife species.
In my study, HWCs in Asia and Africa are compared, focussing on all herbivorous species identified which damaged crops. For the French NGO Awely, des animaux et des hommes, I developed a detailed assessment scheme suitable for all terrestrial ecosystems, and any type of HWCs and any species (Chapter 2). This HWC assessment scheme was used in four different study areas located in two African countries (South Luangwa/Zambia (SL), Tarangire/Tanzania (TA)) and two Asian countries (Bardia/Nepal (BA) and Manas/India (MA)). This scheme ran for six consecutive years (2009 to 2014) for Zambia, Nepal and India and two years (2010 to 2011) for Tanzania. To carry out the assessments, I trained local HWC officers (Awely Red Caps) to assess HWCs by field observations (measurement of damage, identification of species through signs of presence, landscape attributes etc.) and interviews with aggrieved parties (socio economic data). Results of this assessment are presented in Chapters 2-4.
To determine whether elephants prefer or avoid specific crop species, two field experiments were carried out, one in SL and one in BA (Chapter 5 and 6). For this, two test plots were set up and damage by elephants (and other herbivores) were quantified.
Within this doctoral thesis, 3306 damage events of 7408 aggrieved parties were analysed. In three out of the four study areas (SL, BA, MA), elephants caused the highest number of damage events compared to all other wildlife species, however, in TA, most fields were damaged by zebra. Furthermore, the greater one-horned rhino, hippopotamus, wild boar, bushpig, deer and antelope, as well as primates, caused damage to fields and harvests. Damage to houses and other property were nearly exclusively caused by elephants.
With this doctoral thesis I was able to show that season, crop availability, type and the phenological stage of the crop played an important role for crop damaging behavior of herbivores (Chapter 2). Elephants especially damaged rice, maize and wheat and preferred all crop types in a mature stage of growth. In contrast, rhinos preferred wheat to rice and similar to antelope and deer, they preferred crops at earlier stages of growth, before ripening. Crop damage by wildlife species varied strongly in size; most damages fell below 40% of the total harvest per farmer, but in several cases (3 to 8% depending on the study area), harvests were completely destroyed. Interestingly, during times of low nutritional availability in the natural habitat (dry season), crop damages in all four study areas were significantly less than during other seasons.
In all four study areas, crop protection strategies, such as active guarding in the fields, chasing wildlife with noise or fire torches or erecting barriers, were used. In some cases protection strategies were combined. Analysis of data revealed that traditional protection strategies did not reduce the costs of damage (Chapter 3). In some cases, costs of damage, on protected fields were even higher than for unprotected fields. Only in MA did strategic and cohesive guarding significantly reduce crop damage by wildlife species.
Besides damage in the fields, elephants also caused damage to properties in the villages. In search for stored staple crops, they damaged houses, grain stores and kitchens. Such damage was analysed in three study areas (SL, BA, MA) (Chapter 4). Although property damage occurred less frequently compared to crop damage in the fields, the mean cost of this damage was found to be double in BA/MA and four times higher in SL, compared to the costs of crop damage in the fields. It is further remarkable that property damage significantly increased towards the dry season, when the harvest was brought into the villages.
The findings of this study underpin the assumption that wildlife herbivores, especially elephants, are lured to fields and crops because the highly nutritional food (crop) being readily available. Traditional crop protection is cost and labour intensive and does not reduce the costs of damage. For this reason, crop types, which are thought to be not consumed by elephants were systematically tested on their attractiveness in field experiments in SL and BA (Chapter 5 and 6). In SL, lemon grass, ginger and garlic were proven to be less attractive to African elephants than maize and in BA, basil, turmeric, chamomile, coriander, mint, citronella and lemon grass were found to be less attractive to Asian elephants than rice.
The results of this doctoral thesis are relevant for the management of wildlife conservation as they can lead to new approaches to the mitigation of HWCs in African and Asian countries. Finally, specific needs for more scientific research in this field have been identified.
The fruit fly Drosophila melanogaster is one of the most important biological model organisms, but only the comparative approach with closely related species provides insights into the evolutionary diversification of insects. Of particular interest is the live imaging of fluorophores in developing embryos. It provides data for the analysis and comparison of the threedimensional morphogenesis as a function of time. However, for all species apart from Drosophila, for example the red flour beetle Tribolium castaneum, essentially no established standard operation procedures are available and the pool of data and resources is sparse. The goal of my PhD project was to address these limitations. I was able to accomplish the following milestones:
- Development of the hemisphere and cobweb mounting methods for the non-invasive imaging of Tribolium embryos in light sheet-based fluorescence microscopes and characterization of most crucial embryogenetic events.
- Comprehensive documentation of methods as protocols that describe (i) beetle rearing in the laboratory, (ii) preparation of embryos, (ii) calibration of light sheet-based fluorescence microscopes, (iv) recording over several days, (v) embryo retrieval as a quality control as well as (vi) data processing.
- Adaption of the methods to record and analyze embryonic morphogenesis of the Mediterranean fruit fly Ceratitis capitata and the two-spotted cricket Gryllus bimaculatus as well as integration of the data into an evolutionary context.
- Further development of the hemisphere method to allow the bead-based / landmark-based registration and fusion of three-dimensional images acquired along multiple directions to compensate the shadowing effect.
- Development of the BugCube, a web-based computer program that allows to share image data, which was recorded by using light sheet-based fluorescence microscopy, with colleagues.
- Invention and experimental proof-of-principle of the (i) AGameOfClones vector concept that creates homozygous transgenic insect lines systematically. Additionally, partial proof-of-principle of the (ii) AClashOfStrings vector concept that creates double homozygous transgenic insect lines systematically, as well as preliminary evaluation of the (iii) AStormOfRecords vector concept that creates triple homozygous transgenic insect lines systematically.
- Creation and performance screening of more than fifty transgenic Tribolium lines for the long-term imaging of embryogenesis in fluorescence microscopes, including the first Lifeact and histone subunit-based lines.
My primary results contribute significantly to the advanced fluorescence imaging approaches of insect species beyond Drosophila. The image data can be used to compare different strategies of embryonic morphogenesis and thus to interpret the respective phylogenetic context. My technological developments extend the methodological arsenal for insect model organisms considerably.
Within my perspective, I emphasize the importance of non-invasive long-term fluorescence live imaging to establish speciesspecific morphogenetic standards, discuss the feasibly of a morphologic ontology on the cellular level, suggest the ‘nested linearly decreasing phylogenetic relationship’ approach for evolutionary developmental biology, propose the live imaging of species hybrids to investigate speciation and finally outline how light sheet-based fluorescence microscopy contributes to the transition from on-demand to systematic data acquisition in developmental biology.
During my PhD project, I wrote a total of ten manuscripts, six of which were already published in peer-reviewed scientific journals. Additionally, I supervised four Master and two Bachelor projects whose scientific questions were inspired by the topic of my PhD work.
Alternative splicing (AS) is a co- or post-transcriptional process by which one gene gives rise to multiple isoforms. This ‘split and combine’ step multiplies eukaryotic proteome diversity several fold and is implicated in several diseases given its pervasive impact. Control of alternative splicing is brought about by cis-regulatory elements, such as RNA sequence and structure, which recruit trans-acting RNA-binding proteins (RBPs). Although several of these interactions are already described in detail, we lack a comprehensive understanding of the regulatory code that underlies a splicing decision.
Here, we have established a high-throughput screen to comprehensively identify and characterise cis-regulatory elements that control a specific splicing decision. A cancer-relevant splicing event in proto-oncogene RON was picked as a minigene prototype for initialising the screening approach. Then, we transfected a library of thousands of randomly mutagenised minigene variants as a pool into human cells, and subsequently quantified the spliced isoforms by RNA sequencing. Importantly, we used a barcode sequence to tag the minigene variants and thereby linked mutations to their corresponding spliced products. By using a linear regression-based modelling approach, we were able to determine the effects of single mutations on RON AS. In total, more than 700 mutations were found to significantly affect the splicing regulation of the RON alternative exon. In addition, mutation effects quantified from the screening approach correlate with RON alternative splicing in cancer patients. We discovered numerous previously unknown cis-regulatory elements in both introns and exons, and found that the RBP heterogeneous nuclear ribonucleoprotein H (HNRNPH) extensively regulates RON AS at multiple levels in both cell lines and cancer. Furthermore, the large number of RBPs involved in the process, point to a complex splicing regulatory network involved in the control of RON splicing. iCLIP and synergy analysis between mutations and HNRNPH knockdown data pinpointed the most relevant HNRNPH binding sites across RON. Finally, cooperative HNRNPH binding was shown to mediate a splicing switch of RON alternative exon. In summary, our results provide an unprecedented view on the complexity of splicing regulation of an alternative exon. The novel screening approach introduces a tool to study the relationship of RNA sequence variants along with trans-acting regulators to their impact on the splicing outcome, offering insights on alternative splicing regulation and the relevance of mutations in human disease.
Most cellular processes are regulated by RNA-binding proteins (RBPs). These RBPs usually use defined binding sites to recognize and directly interact with their target RNA molecule. Individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) experiments are an important tool to de- scribe such interactions in cell cultures in-vivo. This experimental protocol yields millions of individual sequencing reads from which the binding spec- trum of the RBP under study can be deduced. In this PhD thesis I studied how RNA processing is driven from RBP binding by analyzing iCLIP-derived sequencing datasets.
First, I described a complete data analysis pipeline to detect RBP binding sites from iCLIP sequencing reads. This workflow covers all essential process- ing steps, from the first quality control to the final annotation of binding sites. I described the accurate integration of biological iCLIP replicates to boost the initial peak calling step while ensuring high specificity through replicate re- producibility analysis. Further I proposed a routine to level binding site width to streamline downstream analysis processes. This was exemplified in the re- analysis of the binding spectrum of the U2 small nuclear RNA auxiliary factor 2 (U2AF2, U2AF65). I recaptured the known dominance of U2AF65 to bind to intronic sequences of protein-coding genes, where it likely recognizes the polypyrimidine tract as part of the core spliceosome machinery.
In the second part of my thesis, I analyzed the binding spectrum of the serine and arginine rich splicing factor 6 (SRSF6) in the context of diabetes. In pancreatic beta-cells, the expression of SRSF6 is regulated by the transcription factor GLIS3, which encodes for a diabetes susceptibility gene. It is known that SRSF6 promotes beta-cell death through the splicing dysregulation of genes essential to beta-cell function and survival. However, the exact mechanism of how these RNAs are targeted by SRSF6 remains poorly understood. Here, I applied the defined iCLIP processing pipeline to describe the binding landscape of the splicing factor SRSF6 in the human pancreatic beta-cell line EndoC-H1. The initial binding sites definition revealed a predominant binding to coding sequences (CDS) of protein-coding genes. This was followed up by extensive motif analysis which revealed a so far, in human, unknown purine-rich binding motif. SRSF6 seemed to specifically recognize repetitions of the triplet GAA. I also showed that the number of contiguous triplets correlated with increasing binding site strength. I further integrated RNA-sequencing data from the same cell type, with SRSF6 in KD and in basal conditions, to analyze SRSF6- related splicing changes. I showed that the exact positioning of SRSF6 on alternatively spliced exons regulates the produced transcript isoforms. This mechanism seemed to control exons in several known susceptibility genes for diabetes.
In summary, in my PhD thesis, I presented a comprehensive workflow for the processing of iCLIP-derived sequencing data. I applied this pipeline on a dataset from pancreatic beta-cells to unveil the impact of SRSF6-mediated splicing changes. Thus, my analysis provides novel insights into the regulation of diabetes susceptibility genes.
Die Funktion der äußeren Haarsinneszellen geht weit über die normale Rezeptoreigenschaft der Kategorie Mechanorezeptor hinaus. Äußere Haarzellen mit ihrer reichhaltigen efferenten Innervierung sind nicht nur für die sensorische Aufnahme mechanischer Bewegung zuständig, sondern ermöglichen aufgrund ihrer motorischen Funktionen die mechanische Verstärkung der Wanderwelle in der Cochlea. Äußere Haarzellen sind eine maßgebliche Komponente des ´cochleären Verstärkers` und ihr Ausfall führt zur Schwerhörigkeit. Beiprodukte des cochleä-ren Verstärkers sind otoakustische Emissionen, deren Messung Aufschluss über aktive mechanische Prozesse im Innenohr gibt.
Die äußeren Haarsinneszellen bilden Synapsen mit dem olivo-cochleären efferenten System, welches im Zentrum der vorliegenden Untersuchung steht. Es vermittelt den Einfluss des Zentralnervensystems auf das Corti-Organ des Innenohrs. Über die akustische Reizung des olivo-cochleären Reflexbogens ist man in der Lage, das efferente System zu aktivieren und gleichzeitig die Antworteigenschaften der Cochlea zu verändern. Efferente Modulationen des cochleären Verstärkers können sich z. B. in einer Veränderung des Emissionspegels bemerk-bar machen. Die Fledermausspezies Carollia perspicillata ist aufgrund ihres Echoortungs-systems mit einem sehr sensitiven und hochauflösenden Hörvermögen ausgestattet und eignet sich hervorragend als Modelltier in der Hörforschung, insbesondere auch deshalb, da oto-akustische Emissionen sehr gut messbar sind.
Das efferente System von C. perspicillata wurde in dieser Untersuchung durch akustische Stimulation der kontralateralen Cochlea angeregt. Die Stimuli, die nicht nur in ihrem Pegel sondern auch in ihrer Bandbreite und in der Mittelfrequenz in Relation zu den ipsilateralen Stimulusfrequenzen variierten, beeinflussten dabei die Generierung der otoakustischen Emis-sionen (DPOAE, engl: distortion product otoacoustic emissions) im ipsilateralen Ohr: akustische Stimulation der kontralateralen Cochlea bewirkte zuverlässig eine Änderung der DPOAE- Amplitude im kontralateralen Ohr. Vor allem eine Suppression des cochleären Verstärkers in Form von DPOAE-Pegelverminderungen wurde beobachtet. Die supprimieren-den Effekte erreichten trotz leiser bis moderater kontralateraler Rauschpegel (bis maximal 54 dB SPL) Werte von bis zu 14, 17.1 und 13.9 dB SPL (bei f2 = 20, 40 und 60 kHz und effek-tivstem kontralateralen Rauschstimulus) und waren damit deutlich größer als in vorangegang-enen Studien an anderen Spezies. Die DPOAE-Pegelverminderungen waren positiv mit dem x Pegel der kontralateralen akustischen Stimulation, ebenso wie seiner Bandbreite und der Mittelfrequenzen in Relation zu den ipsilateralen Stimulusfrequenzen korreliert. Es gab keinen absoluten Frequenzbereich, in dem die efferenten Effekte am größten gewesen wären. Vielmehr traten maximale Effekte immer durch etwas oberhalb der ipsilateralen Stimulusfre-quenzen gelegene kontralaterale Rauschstimuli auf. Die Effekte waren auch abhängig von der Bandbreite des kontralateralen Rauschstimulus und maximal bei einer relativen Bandbreite von 1.5 Oktaven. Die Verschiebung des efferenten Effekts hin zu hohen Frequenzen und die Bandbreitenabhängigkeit sind vereinbar mit den anatomischen Eigenschaften der Projektio-nen der medialen olivo-cochleären Efferenzen in der Säugetiercochlea. Kontralaterale akusti-sche Reizung bewirkte auch eine Verschiebung der Wachstumsfunktionen der 2f1-f2 -DPOAE in einen unsensitiven Bereich und außerdem eine Verformung der Wachstumsfunktion. Bei-des könnte durch Beeinträchtigung des cochleären Verstärkers verursacht sein. Eine Beteili-gung des Mittelohrmuskels an den Effekten kann nahezu ausgeschlossen werden und die beobachteten Effekte sind höchstwahrscheinlich dem olivo-cochleären System zuzuschreiben.
Funktionell ist denkbar, dass bei C. perspicillata das mediale olivo-cochleäre System im Kontext einer Frequenzverschärfung bei der cochleären Verstärkung der Basilarmembranbe-wegung aktiv wird. Aus diesem Grund wurden ipsilateral sogenannte DPOAE-Suppressions- Abstimmkurven gemessen, welche die mechanische Abstimmschärfe im Innenohr beschrei-ben. Während und nach kontralateraler Reizung kam es zu Veränderungen der Abstimmkur-ven. Signifikante Effekte konnten allerdings nicht festgestellt werden, da die Veränderungen der Suppressions-Abstimmkurven variabel und schlecht kategorisierbar war.
Die vorliegenden Ergebnisse unterstützen weit verbreitete Hypothesen zur Funktion der medialen olivo-cochleären Effernzen in Bezug auf mechanische Suppression, Verbesserung des cochleären Signal-Rauschverhältnisses und einer generellen frequenzspezifischen Wirkung.
Deciphering the ecological functions of fungal root endophytes based on their natural occurrence
(2017)
Plants are colonized by a large diversity of fungi, some residing on the surface and others penetrating the plant tissues, the latter referred to as fungal endophytes (endon Gr., within; phyton, plant; de Bary 1879). Despite the saprotrophic potential of fungal endophytes, they are not found to cause visible disease symptoms to the host. Plants are colonized simultaneously by various fungal species, which form rich and diverse endophytic assemblages. Although it is hypothesized that fungal endophytes contribute to the fitness of their hosts and to the functioning of ecosystems, the ecological function of fungal endophytic assemblages remains cryptic. The aims of this doctoral thesis are to gain insight to the ecological functions of root fungal endophytes, by deciphering their roles in ecosystems based on their natural occurrence and the structure of their assemblages. The thesis focuses on studying the diversity and structure of the endophytic mycobiome within roots of two annual and widespread plant hosts Microthlapsi perfoliatum and M. erraticum (Brassicaceae) in several locations across northern Mediterranean and central Europe. The thesis is composed by six Chapters, with a primary focus on Chapter 1, 2 and 3.
Chapter 1 (Glynou et al., 2016) aimed at characterizing the diversity of fungal endophytes in roots at a continental scale and at assessing the factors affecting the structure of endophytic assemblages with the use of cultivation-based methods. For that, root samples were collected from 52 plant populations, along with a collection of soil, bioclimatic, geographic and host data. Cultivation of surface-sterilized root samples on culture media and isolation of fungal colonies in pure culture generated 1,998 fungal colonies. Grouping of sequences into Operational Taxonomic Units (OTUs), based on the 97% similarity of the isolates’ rDNA Internal Transcribed Spacer (ITS) sequence, generated in total 296 OTUs, representing taxa mostly within the phylum Ascomycota with a minor representation of Basidiomycota. Endophytic assemblages were mostly correlated with variation in bioclimatic conditions. Interestingly, despite the large diversity revealed, the assemblages were dominated by only six OTUs related to the orders Hypocreales, Pleosporales and Helotiales, which had a widespread distribution across populations but with some following patterns of ecological preferences.
Chapter 2 aimed at characterizing the uncultivable fraction of the root fungal endophytic diversity, which was not possible to capture in Chapter 1. High-throughput sequencing via the
Illumina Miseq platform was implemented in 43 of the 52 original populations and mostly in the same root samples. In comparison with the cultivation-based approach, the HTS managed to cover the overall diversity within samples. It revealed a large non-cultivated endophytic diversity but the same cultivable fungi dominated assemblages. Moreover, the endophytic diversity was grouped mostly within fungal orders with demonstrated ability to grow in culture and taxonomically related groups were found to have divergent ecological preferences.
The genetic identity of the most abundant OTUs was further investigated in Chapter 3 (Glynou et al., 2017), aiming to unravel genotypic variability, which was possibly overlooked due to the use of lTS, as a universal genetic marker, and could explain their high abundance and widespread distribution. Multi-locus gene sequencing and AFLP profiling for the five most abundant OTUs suggested a low within-OTU genetic variability and show that these fungi have ubiquitous distribution and are not limited by environmental conditions within the ecological ranges of the study. A selection of endophytes frequently isolated in Chapter 1 was functionally characterized in Chapter 4 (Kia et al., 2017) based on the isolates’ traits and interactions with plants. In Chapter 5 (Cheikh-Ali et al., 2015) fungal cultures of Exophiala sp. with differential colony structure where investigated for their production of secondary metabolites. Moreover, Chapter 6 (Maciá-Vicente et al., 2016) comprises the description of the new species Exophiala radicis based on morphological and molecular characteristics.
Compilation of all results shows that the fungal endophytic diversity in roots of Microthlaspi spp. is high but few widespread OTUs dominate the assemblages, and have unlimited dispersal ability. These fungi seem also to have a wide niche breadth and are not affected by environmental filtering. The findings indicate that the local environment but also processes of competitive exclusion determine the structure of endophytic assemblages. In addition, the fungal endophytes associated with Microthlapsi spp. likely have saprotrophic activity however the interactions with plants are likely context-dependent. Further research is needed to assess the biotic interactions among endophytes and their effect on the structure of fungal endophytic assemblages. Ultimately, the findings of this thesis are useful to shed light on the processes underlying the structure of endophytic assemblages. They also upraise the need to describe diversity by combining genetic, metabolic and physiological data, in order to disentangle the elusive ecological roles of the endophytic mycobiome.
Der DNA-Translokator von T. thermophilus HB27, ebenso wie Typ-IV-Pili (T4P), sind Multiproteinkomplexe, die die Membranen und das Periplasma durchspannen. Sie sind ähnlich aufgebaut und enthalten identische Proteine. Der DNA-Translokator vermittelt Transport von DNA in das Zellinnere während der natürlichen Transformation. T4P sind filamentöse Zellorganellen, die an der inneren Membran assembliert werden und bis zu mehrere Mikrometer aus der Zelle hinausragen. Sie dienen der Anhaftung und Fortbewegung der Zellen auf Oberflächen.
Das Ziel dieser Arbeit war es, die Funktionen einzelner Komponenten der Komplexe und ihrer Proteindomänen bei der natürlichen Transformation, der T4P-Assemblierung und den durch T4P vermittelten Funktionen Adhäsion und „twitching motility“ aufzuklären.
Es sind neun Proteine bekannt, die eine duale Rolle als Komponenten des DNA-Translokators und des T4P spielen. Eines dieser Proteine ist die Assemblierungs-ATPase PilF, die Hexamere bildet. Diese cytoplasmatischen ATPase-Komplexe stellen die Energie für die Assemblierung der T4P bereit, ebenso wie für die Aufnahme freier DNA. Es ist jedoch bisher nicht geklärt, wie die durch PilF bereitgestellte Energie auf die anderen Komponenten des DNA-Translokators/T4P übertragen wird.
In dieser Arbeit konnte gezeigt werden, dass PilF an das cytoplasmatische Protein PilM des T4P und DNA-Translokators bindet. Zudem konnten Proteinkomplexe bestehend aus den Proteinen PilM, PilN und PilO heterolog produziert und aus Zellmembranen koisoliert werden. PilF interagierte mit diesen PilMNO-Komplexen via PilM. Diese Interaktionen führt zur Stimulierung der ATPase-Aktivität von PilF. Dies deutet an, dass PilM ein Kupplungsprotein ist, welches die Assemblierungs-ATPase PilF physisch und funktionell mit dem T4P/DNA-Translokator über den PilMNO-Komplex verbindet.
Neben PilF standen Präpiline von T. thermophilus im Fokus dieser Arbeit. Präpiline sind Vorläuferproteine, die zu Pilinen prozessiert werden und als solche dann die Untereinheiten der Pilus-Strukturen bilden.
Zusammenfassend konnten die Rollen einzelner Präpilin-ähnlicher Proteine bei T4P-assoziierten Funktionen geklärt werden und es konnten erste Analysen zur Charakterisierung des weitestgehend unbekannten Proteins ComZ durchgeführt werden. Desweiteren liefert diese Arbeit Hinweise darauf, dass die membranassoziierten Proteine PilM, PilN und PilO Kupplungsproteine sind, die PilF mit den periplasmatischen Komponenten des T4P/DNA-Translokators verbinden und dadurch die ATPase-Aktivität von PilF stimulieren. Die Rollen einzelner Proteindomänen von PilF und PilM bei der Protein-Protein-Interaktion und der Bindung von Liganden wurden aufgeklärt, sowie ihre Funktionen bei den T4P-vermittelten Funktionen und der natürlichen Transformation.