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Quantenchemische Untersuchungen von Siliciumverbindungen
(2021)
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Josef Heinrich Wender
- In dieser Arbeit werden die Ergebnisse quantenchemischer Untersuchungen von verschiedenen Siliciumverbindungsklassen vorgestellt, die in weiten Teilen als Begleitung zu experimentellen Arbeiten durchgeführt wurden. Das erste Hauptkapitel befasst sich mit den Chloridkomplexen von Perchlorsilanen, zu denen die inversen Sandwichkomplexe und die Silafullerane mit endohedralem Gast gehören. Der Fokus liegt dabei auf den Bindungseigenschaften zwischen Ligand und Silan. Weiterhin werden thermodynamische Untersuchungen zu Aufbaureaktionen und Eigenschaften der Verbindungen vorgestellt. Mit den durchgeführten Rechnungen kann gezeigt werden, dass durch Wahl geeigneter Substituenten am Siliciumatom ein Wechsel in den Chloridkomplexen von einem hyperkoordinierten Siliciumatom hin zu einem Siliciumatom mit ausgebildeter Tetrelbindung erreicht werden kann. Bei den inversen Sandwichkomplexen sind beide Bindungsmodi möglich, von denen die Tetrelbindung die stärkere darstellt. Neben Chloridionen können hier auch Nitrile und Chlorsubstituenten am eigenen Silangerüst als Liganden fungieren. Die stärksten Tetrelbindungen können bei den endohedral funktionalisierten Silafullerankomplexen gefunden werden. Hier stellt das experimentell isolierte Strukturmotiv mit zwölf äußeren Trichlorsilylsubstituenten das thermodynamisch stabilste Substitutionsmuster dar. Im folgenden Kapitel werden die generellen physikalischen Ursachen für die beobachteten thermodynamischen Trends zwischen Perchlorsilanisomeren sowie Disproportionierungsreaktionen behandelt und ein direkter Vergleich mit Alkanhomologen angestellt. Bei den Perchlorsilanen und den meisten Homologen ist bei den untersuchten Systemen eine energetische Präferenz von verzweigteren Strukturen zu erkennen. Die Ursache hierfür liegt hauptsächlich bei stärkeren attraktiven Wechselwirkungen durch Korrelationseffekte, Hyperkonjugation sowie elektrostatische Effekte, welche stärkere repulsive Wechselwirkungen wie die Pauli-Repulsion überkompensieren. Im letzten Kapitel kommen zu den bisher behandelten Reaktionen unter Si-Cl- und Si-Si-Bindungsbeteiligung noch Reaktionen unter Si-C-Bindungsbeteiligungen hinzu. Dort werden die auch wegen ihrer Elektronentransporteigenschaften interessanten Silacyclopentadiene (Silole) hinsichtlich ihrer Isomerisierung, Dimerisierung und weiteren pericyclischen Reaktivität untersucht. Gegenüber dem verwandten Cyclopentadien zeigen diese eine deutlich erhöhte Reaktivität, was zu verschiedenen Dimerisierungsreaktionen führt, solange keine Abfangreagenzien im Überschuss zugegen sind.
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Kardiovaskuläres Risiko bei Typ 1 Diabetes : Vitamin D Effekte auf inflammatorische Profile und zytotoxische T-Lymphozyten
(2021)
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Julian Michael Cron
- Einleitung: Der Typ 1 Diabetes (T1D) ist eine Autoimmunendokrinopathie, die mit zahlreichen Langzeitkomplikationen assoziiert ist. Kardiovaskuläre Erkrankungen (CVD) stellen hierbei den zentralen Grund für Morbidität und Mortalität dar. Ihre Pathogenese wird zunehmend im Kontext autoimmunologischer Prozesse diskutiert. Wir konnten bereits zeigen, dass Vitamin D (VD) sowohl immunmodulatorische als auch gefäßprotektive Effekte vermittelt. Daher untersuchten wir, ob durch VD die inflammatorische Aktivität CD8+ zytotoxischer T-Zellen (CTL) von Patienten mit T1D ohne und mit kardiovaskulärer Komplikation beeinflusst werden kann.
Methoden: Primär isolierte CTLs von sowohl Patienten mit T1D ohne (T1D Ø CVD, n = 20) und mit CVD (T1D + CVD, n = 20) als auch von gesunden Kontrollprobanden (HCs , n = 20) wurden über 72 h in An- bzw. Abwesenheit (+/-VD) von VD (1,25(OH)2D3) kultiviert. Die relative mRNA-Transkriptmenge der Zytokine IL-2, TNF-α, IFN-γ, IL-4, IL-6 und IL-10 sowie der Zelloberflächen- und Seneszenzmarker CD28, CD57 und CD95 wurde mittels RTqPCR analysiert. Zudem wurde die Proteinkonzentration der sezernierten Zytokine mittels CBA quantifiziert.
Ergebnisse: Die VD-Behandlung in vitro reduzierte die relative mRNA-Transkriptmenge von IL-2 (p = 0.01 und p = 0.02 resp.) und IFN-γ (p = 2x10-6 resp.) in CTLs von Patienten und HCs während die Genexpression von IL-4 (p = 2x10-6 und p = 2x10-3 resp.) und IL-6 (p = 2x10-6 und p = 4x10-6 resp.) erhöht wurde. Überdies war der VD-Effekt (ΔVDbehandelt-unbehandelt) auf die IL-4 Genexpression bei T1D + CVD stärker ausgeprägt als in der Kontrollgruppe (1.7 vs. 1.1; p = 0.03). Subgruppenanalysen zeigten zudem eine reduzierte IL-2 Genexpression durch die Behandlung mit VD in vitro bei T1D + CVD bei manifester diabetischer Nephropathie (142 vs. 97; p = 0.04) wohingegen dies bei erhaltener Nierenfunktion nicht beobachtet werden konnte (62 vs. 56; p = 0.31).
Schlussfolgerung: Die breite Modifikation der Genexpressionslevel untersuchter Zytokine bestätigt den immunmodulatorischen Effekt von VD bei Patienten mit T1D und kardiovaskulärer Komplikation. Die stark reduzierte Genexpression des pro-inflammatorischen IFN-γ legt hierbei einen potenziellen Effekt von VD in der Prävention chronisch-inflammatorischer Prozesse nahe. Die gruppenübergreifend unterschiedlich ausgeprägten VD-Effekte auf die Genexpression von IL-4 sowie die Subgruppenanalysen deuten jedoch auf eine relevante Heterogenität der immunmodulatorischen VD-Effekte hin: sowohl der individuelle klinische Zustand unter Einbeziehung assoziierter Komorbiditäten wie der diabetischen Nephropathie als auch die genetischen Variationen des VD-Systems müssen in groß angelegten Follow-up-Studien weiter untersucht werden, um optimale VD-Dosis-Effekte für klinisch relevante Subgruppen zu identifizieren.
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Function and regulation of novel phosphoribosyl-ubiquitination catalyzed by legionella pneumophila effectors
(2021)
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Yaobin Liu
- Protein ubiquitination is a post-translational modification that typically involves the conjugation of ubiquitin to substrate proteins via a three-enzyme cascade and regulates a wide variety of cellular processes. Recent studies have revealed that SidE family of Legionella effectors such as SdeA catalyzes novel phosphoribosyl-linked ubiquitination (PR-ubiquitination) of serines in host substrate proteins utilizing NAD+, without the need of E2, E3. The catalytic core of SdeA comprises a mono-ADP-ribosyltransferase (mART) domain that functions to ADP-ribosylate ubiquitin, and a phosphodiesterase (PDE) domain that processes ADP-ribosylated ubiquitin and transfers the resulting phosphoribosylated ubiquitin to serines of substrates.
To date, extensive efforts have been made to study the function of SdeA and mechanism of SdeA mediated PR-ubiquitination, however, the cellular effects of this novel ubiquitination and phosphoribosylation of ubiquitin remained poorly understood. In our study, using biochemical and cell biological approaches, we explored the biological effect of phosphoribosylation of ubiquitin caused by SdeA in cells. We found that phosphoribosylated ubiquitin is not available for conventional ubiquitination, thereby phosphoribosylation of ubiquitin impairs numerous classical ubiquitination related cellular processes including mitophagy, TNF-α signaling and proteasomal degradation.
The precise temporal regulation of the functions of bacterial effectors during Legionella infection by other effectors with antagonizing activities has been well studied so far. Not surprisingly, PR-ubiquitination catalyzed by SidE family effecters is tightly controlled as well, it has been long known that effector SidJ counteracts the toxicity of SdeA to yeast cells. Interestingly, in an experiment for verifying the activity of SidJ, we found that Legionella lysate lacking SidJ was still able to remove ubiquitin from PR-ubiquitinated substrates. Using biochemical approach we identified DupA and DupB, two Legionella bacterial effectors that specifically reverse the novel serine PR-ubiquitination catalyzed by SdeA. We found that DupA and DupB possess a highly homologous PDE domain that removes ubiquitin from PR-ubiquitinated substrates by cleaving the phosphodiester bond between the phosphoribosylated-ubiquitin and serines of substrates. Catalytically deficient mutant DupA H67A strongly binds to PR-ubiquitinated proteins but not capable of cleaving PR-ubiquitin, using it as a trapping bait we identified over 180 substrates of PR-ubiquitination, including a number of ER and Golgi proteins.
In particular, we found that exogenously expressed SdeA localizes to the Golgi apparatus via its C-terminal region and disrupts the Golgi. We validated the identified potential substrates of SidE effectors and found that SdeA modifies Golgi tethering proteins GRASP55 and GRASP65. Using mass spectrometry analyses we identified four serine targets (S3, S408, S409, S449) of GRASP55 PR-ubiquitinated by SdeA in vitro. Ubiquitination of GRASP55 serine mutant in cells co-expressing SdeA or infected with Legionella was markedly decreased, compared with that of the wild-type GRASP55. In addition, with co-immunoprecipitation analyses we found that SdeA-catalyzed ubiquitination regulates the function of GRASP55. PR-ubiquitinated GRASP55 exhibited reduced self-interaction compared to unmodified GRASP55, expression of GRASP55 serine mutant in cells in part rescued Golgi damage caused by SdeA. Furthermore, our study reveals that Golgi structure disruption caused by SdeA does not result in the recruitment of Golgi membranes to the Legionella-containing vacuoles. Instead, it affects cellular secretory pathway including cytokine secretion in cells.
Taken all together, this work expands the understanding of this unconventional PR-ubiquitination catalyzed by Legionella effectors and sheds light on the functions of PR-ubiquitination by which Legionella regulates the Golgi function and secretion pathway during bacterial infection.
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Vergleich der Wirksamkeit zweier orthopädischer Therapieverfahren – der verhaltensmedizinisch-orthopädischen Rehabilitation mit der klassisch-orthopädischen Rehabilitation – eine retrospektive Analyse
(2021)
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Omar Zabar
- Ziel der Studie: Eine psychische Komorbidität spielt im Kontext mit weiteren persönlichen, sozialen und beruflichen Faktoren bei der Ermittlung des spezifischen Rehabilitationsbedarfs der Patienten in Deutschland eine immer bedeutendere Rolle. Um die Zuweisung von Patienten zu einer Rehabilitationsform besser ausdifferenzieren zu können, soll im Rahmen dieser retrospektiven Analyse ermittelt werden, von welchem der beiden untersuchten Rehabilitationskonzepte (OR/VMO) Patienten mit psychischer Komorbidität unter Berücksichtigung von Geschlecht, Erwerbsstatus und orthopädischer Hauptdiagnose stärker profitieren.
Methodik: Mittels der Screening-Fragebögen HADS-A, HADS-D, SIMBO und BPI sowie eines Klinikfragebogens zu Beginn der Rehabilitation wurden Angaben von 913 Probanden (529 m/384 w) ausgewertet. Hiervon wurden 43 % der OR und 57 % der VMO zugewiesen. So wurde die Häufigkeitsverteilung der Faktoren psychische Komorbidität, Geschlecht, Erwerbsstatus und orthopädische Hauptdiagnose festgestellt. Mittels HADS wurde am Ende der Therapie der Benefit durch Vergleich der Scorewert-Mediane ermittelt.
Ergebnisse: Häufigkeitsverteilungen und die Entwicklung der HADS-Scores zeigen, dass die im Vorfeld erfolgte Einteilung gemäß psychischer Komorbidität korrekt war. Frauen waren häufiger von einer psychischen Komorbidität betroffen und erzielten in der VMO größere Erfolge. Bezüglich der orthopädischen Hauptdiagnose ergab sich eine hohe Prävalenz von HWS- und LWS-Beschwerden. Beim Erwerbsstatus (Arbeits(un)fähigkeit, Arbeitslosigkeit, berufliche Problemlage) zeigte sich ein diffuseres Bild, das keine generalisierende Aussage bezüglich der arbeitsweltbezogenen Faktoren zulässt.
Schlussfolgerungen: Das Vorliegen einer psychischen Komorbidität stellt einen zielführenden Indikator dar, der als eines der Hauptzuweisungskriterien zur VMO beizubehalten ist. Auch das weibliche Geschlecht in Verbindung mit dem Vorliegen einer psychischen Komorbidität ist als adäquates Kriterium anzusehen. Bezüglich der orthopädischen Hauptdiagnose können insbesondere HWS-Beschwerden als Zuweisungskriterium geeignet sein. Aufgrund der sehr heterogenen Ergebnisse hinsichtlich der Aspekte des Erwerbsstatus lässt sich festhalten, dass diesbezüglich eine Zuweisung zu einem arbeitsweltbezogenen Therapiekonzept (z. B. MBOR) zielführender erscheint.
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Using fingerprints and machine learning tools for the prediction of novel dual active compounds for leukotriene A4 hydrolase and soluble epoxide hydrolase
(2021)
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Lena Hefke
- The aim of this work was to establish a new way of predicting novel dual active compounds by combining classical fingerprint representation with state-of-the-art machine learning algorithms. Advantages and disadvantages of the applied 2D- and 3D-fingerprints were investigated. Further, the impact of various machine learning algorithms was analyzed. The new method developed in this work was used to predict compounds, which inhibit two different targets (LTA4H and sEH) involved in the same disease pattern (inflammation). The development of multitarget drugs has become more important in recent years. Many widespread diseases like metabolic syndrome, or cancer are of a multifactorial nature, which makes them hard to be treated effectively with a single drug. The new in silico method presented in this work can help to accelerate the design and development of multitarget drugs, saving time and efforts.
The nowadays readily available access to a large number of 3D-structures of biological targets and published activity data of millions of synthesized compounds enabled this study and was used as a starting point for this work. Four different data sets were compiled (crystalized ligands from the PDB, active and inactive compounds from ChEMBL23, newly designed compounds using a combinatorial library). Those data sets were collected and processed using an automated KNIME workflow. This automation has the advantage of allowing easy change and update of compound sources and adapted processing ways.
In a next step, the compounds from the compiled data sets were represented using a variety of well-established 2D- and 3D-fingerprints (PLIF, AtomPair, Morgan, FeatMorgan, MACCS). All those fingerprints share the same underlying bit string scheme but vary in the way they describe the molecular structure. Especially the difference between 2D- and 3D-fingerprints was investigated. 2D-fingerprints are solely based on ligand information. 3D-fingerprints, on the other hand, are based on X-ray structure information of protein-ligand complexes. One major difference between 2D- and 3D-fingerprints usage is the need for a 3D-conformation (pose) of the compound in the targets of interest when using 3D-fingerprints. This additional step is time-consuming and brings further uncertainties to the method.
Based on the calculated fingerprints state-of-the-art machine learning algorithms (SVC, RF, XGB and ADA) were used to predict novel dual active compounds. The models were evaluated by 10-fold cross validation and accuracy as the primary measure of model performance was maximized. Second, individual parameters of the four machine learning algorithms were optimized in a grid search to achieve maximal accuracy using the optimized partitioning scheme. Overall accuracies, regardless of fingerprint and machine learning algorithm, are slightly better for LTA4H than for sEH.
The goal to predict dual active compounds was realized by comparing the set of predicted to be active compounds for LTA4H and sEH. For the 3D-fingerprint PLIF the machine learning algorithm Random Forest was chosen, from which compounds for synthesis and testing were selected. Of 115 predicted to be active compounds, six compounds were cherry picked. Two compounds showed very good/moderate dual inhibitory activity. Of the 2D-fingerprints, the AtomPair fingerprint in combination with the machine learning algorithm Random Forest was chosen from which compounds were selected for synthesis and testing. 116 compounds were predicted to be dual active against LTA4H and sEH. One of those compounds showed good dual inhibitory activity.
In this work it was possible to show advantages and disadvantages of using 2D- and 3D-fingerprints in combination with machine learning algorithms. Both strategies (2D: ligand-based, 3D: structure-based) lead to the prediction of novel dual active compounds with moderate to very good inhibitory activity. The method developed in this work is able to predict dual active compounds with very good inhibitory activity and novel (previously unknown) scaffolds inhibiting the targets LTA4H and sEH. This contribution to in silico drug design is promising and can be used for the prediction of novel dual active compounds. Those compounds can further be optimized regarding binding affinity, solubility and further pharmacological and physicochemical properties.
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Empathie im Lehramtsstudium : welchen Einfluss kann Service Learning haben?
(2021)
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Kathrin Kuchta
- Empathie ist ein mehrdimensionales psychologisches Konstrukt, das aus verschiedenen Facetten besteht (Decety & Ickes, 2011). Es ist anzunehmen, dass Empathie ein wichtiger Mechanismus ist, um Menschen miteinander zu verbinden und eine Gruppenkohäsion möglich zu machen (Rameson & Lieberman, 2009). Neben der Fähigkeit die Erlebenswelt des Gegenübers mit eigenen mentalen Repräsentationen nachzuvollziehen, werden dadurch Emotionen ausgelöst, die denen des Gegenübers sehr ähnlich sind. Gleichzeitig unterscheidet sich dieses Gefühlserleben aber beispielsweise von reiner Gefühlsansteckung, da eine Selbst-Andere Differenzierung stattfindet und in einer empathischen Episode immer im Vordergrund steht, dass man sich aufgrund der Gefühle des anderen so fühlt (Altmann, 2015). Hier spielt Imitation eine wichtige Rolle, wenn es darum geht, die Erlebenswelt der anderen Person zu erfassen (Meltzoff & Decety, 2003). Besonders auch bei Lehrkräften zeigt sich eine Wichtigkeit von empathischem Handeln und Verstehen (Tausch & Tausch, 2008). In verschiedenen Studien zeigten sich positive Effekte von Empathie auf die Schülerschaft und die Unterrichtsqualität. Die SchülerInnen trauen sich mehr, es herrscht weniger Angst im Klassenzimmer und die Qualität der Unterrichtsbeiträge steigt (vgl. Tausch & Tausch, 1998). Empathie selbst besteht aus State- und Trait-Anteilen, so dass zumindest Teile davon trainierbar sind (Butters, 2010). Eine potentielle Möglichkeit um Empathie zu fördern scheint das Lehr-Lern-Format Service Learning (SL) darzustellen. Hierbei handelt es sich um ein Veranstaltungskonzept, bei dem ein meist fachlicher, akademischer Inhalt mit einem ehrenamtlichen Engagement außerhalb der Universität verknüpft wird (Reinders, 2016). Forschung aus dem angloamerikanischen Raum weist darauf hin, dass Empathie durch derartige Formate gefördert werden kann (Lundy, 2007; Wilson, 2011). Da die meisten Messverfahren von Empathie auf Selbstauskunft basieren und damit nur indirekt Anteile wie das affektive Mitschwingen abbilden können, war es Teil dieser Arbeit im ersten Schritt einen objektiven, videobasierten Test zu entwickeln, der dann mit anderen Verfahren zur Messung eingesetzt werden sollte. In zwei ExpertInnen-Befragungen wurden aus einem Pool von Videosequenzen mit Unterrichtssituationen insgesamt zehn Videoclips mit jeweils vier Items und zugehörigen Antwortoptionen extrahiert. In einer darauf folgenden Validierung mit Studierenden der Goethe-Universität (N = 112) wurden diese Vignetten mit verschiedenen Verfahren zur Messung von Empathie gemeinsam erhoben und die Zusammenhänge analysiert. Die Reliabilitäten der drei Testscores bewegten sich in den beiden gebildeten Testversionen zwischen Cronbachs α = .53 (Verhaltens-Score der Testversion 1) und α = .76 (Intensitäts-Score der Testversion 2). Es zeigten sich zu allen Fragebögen erwartungskonforme Zusammenhänge von kleinen bis mittleren Effekten. Die Itemschwierigkeiten bei den meisten Items lagen zwischen 50 und 65, die Trennschärfen zwischen .18 und .70.
Im nächsten Entwicklungsschritt wurden die Vignetten in neu zusammengestellten Testversionen nur Lehramtsstudierenden (N = 41) vorgelegt und zusätzlich Videoaufnahmen der Gesichter der ProbandInnen gemacht, um sie mit Face-Reader zu analysieren und die Facette Mitschwingen abzubilden. Die Reliabilitäten der Testversionen lagen mit einem neuen Scoring nun zwischen α = .24 (Emotionserkennungs-Score Prä-Testversion) und
α = .57 (Intensitäts-Score Prä-Testversion) sowie zwischen α = .10 (Emotionserkennungs-Score Post-Testversion) und α = .77 (Intensitäts-Score Post-Testversion). Auch die Schwierigkeiten und Trennschärfen änderten sich nach Adaptieren des Scorings und bewegten sich in beiden Testversionen nun von 30 bis 89 (Schwierigkeit) und von .0 bis .5 (Trennschärfe). Die Face-Reader Analysen zeigten nur in Teilen kongruente Emotionen mit den Selbstauskunftsdaten bzw. den eingeschätzten Intensitäten in den Videosequenzen, dann allerdings mittlere bis große Effekte, so dass in Teilen von einem affektiven Mitschwingen ausgegangen werden kann. Da sich die internen Konsistenzen im Vergleich zur Validierung verschlechterten, wurden die Zusammensetzungen der Testversionen für den Praxiseinsatz wieder auf die Validierungs-Versionen umgestellt.
Im Praxiseinsatz wurden Lehramtsstudierende in SL und Non-SL-Veranstaltungen rekrutiert und miteinander verglichen. Insgesamt nahmen N = 68 Personen an drei Messzeitpunkten teil (n = 30 in SL und n = 38 in Non-SL-Seminaren). Die Analysen zeigten, dass es zwischen den Gruppen keine signifikanten Unterschiede in den genutzten Instrumenten gab. Auch über die Zeit gab es nach der Bonferroni-Korrektur nur einen signifikanten Effekt (F (2,52) = 6.57, p = .003, η2 = .20). Es ist anzunehmen, dass diese Ergebnisse vor allem auf methodische Einschränkungen und Verbesserungsmöglichkeiten des entwickelten Testverfahrens zurückzuführen sind. Weitere Möglichkeiten werden diskutiert.
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Phylogeny and species delimitation of himalopsyche (trichoptera, rhyacophilidae)
(2020)
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Anna Emilia Hjalmarsson
- Freshwater is one of the most fundamental resources for life and is the habitat for a wide diversity of species. One of the most diverse aquatic insect taxa is Trichoptera Kirby, 1813, caddisflies. These semi-aquatic insects have aquatic larvae and terrestrial adults and are found all around the globe in freshwater habitats. Water is also one of the most important natural resources for the human population, but alarmingly, freshwaters are among the most threatened natural habitats. Thus, the monitoring and preservation of the quality of freshwater habitats should have a high priority. In order to track changes in the biota a baseline reference is necessary, but freshwater biodiversity is under-studied in many parts of the Earth such as the biodiversity hotspots of the Himalaya and the Hengduan Mountains. This thesis treats the trichopteran genus Himalopsyche Banks, 1940 (Rhyacophilidae) which has its diversity center in the Himalayas and the Hengduan Mountains. Himalopsyche larvae are large and conspicuous and only occur in clean, unpolluted streams. This makes Himalopsyche potentially suited as indicator organisms for freshwater quality monitoring, but taxonomic knowledge is yet insufficient. Based on samples from a field survey in the Hengduan Mountains targeting both larvae and adults I uncovered three new Himalopsyche species which are described in this thesis (Chapter II), and with the aid of molecular data I associated larvae of Himalopsyche to adult species (Chapter I). The molecular association enabled the first comparative morphological study of Himalopsyche species in the larval stage, and the morphological study in Chapter II revealed that there are four distinct larval types of Himalopsyche. However, no diagnostic characters to identify Himalopsyche larvae to species level were found. To understand Himalopsyche larval morphology from an evolutionary perspective, I reconstructed the first molecular phylogeny of the genus (Chapter III). This demonstrated that each larval type corresponds to a deep phylogenetic split, indicating that larval types evolved early in Himalopsyche evolution and remained constant since. Based on the phylogenetic results as well as larval and adult morphology, I re-defined five species groups of Himalopsyche: H. kuldschensis Group, H. lepcha Group, H. navasi Group, H. phryganea Group, and H. tibetana Group. The species groups differ with respect to their diversity centers. The monotypic H. lepcha Group resides in the Himalayas, and the monotypic H. phryganea Group inhabits Western Nearctic. The H. kuldschensis and H. tibetana Groups are geographically overlapping with distributions in the Himalayas, but the distribution of H. kuldschensis Group stretches more to the west to include the Tian Shan, and the H. tibetana Group is more concentrated around the eastern Himalayas and the Hengduan Mountains. The H. navasi Group has a more eastern distribution than most Himalopsyche including isolated areas such as Japan and Indonesia. The earliest split in Himalopsyche divides the H. navasi Group from remaining Himalopsyche, suggesting a more eastern area of origin of Himalopsyche than its current diversity center, with subsequent radiations in the Himalayas and Hengduan Mountains. In addition to the three chapters, in this thesis I discuss further aspects of Himalopsyche biology including genital evolution, species complexes, and Himalopsyche ecology.
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Target identification of peptides from Xenorhabdus and Photorhabdus
(2020)
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Tien Duy Vo
- Xenorhabdus and Photorhabdus are bacterial genera that live in symbiosis with entomopathogenic nematodes of the genera Steinernema and Heterorhabditis, respectively. These nematodes infect insect larvae through the trachea and then enter the hemocoel. Once inside the hemocoel, the nematodes release the bacteria through their intestine. Thereafter, the bacteria become active and kill the larvae within 48 h. During this process, the immune system of the insect host is compromised by molecules produced and secreted by the bacteria. This illustrates that the bacteria possess not only a large arsenal of biological weaponry such as antibiotics and fungicides but also lipases, proteases, etc. Therefore, they are not only able to kill the insect but also protect the cadaver from other food competitors.
During the past decades, a large number of natural products have been identified from Xenorhabdus and Photorhabdus. However, the targets and functions for many of these biological molecules are still unknown. Therefore, the goal of the doctoral thesis is to elucidate the modes of action of these natural products from Xenorhabdus and Photorhabdus with the main focus on non-ribosomal peptides (NRPs). The work can be divided into two parts. Initially, it starts with the synthesis of natural compounds and various chemically modified derivatives. Besides that, a number of peptides were synthesized for other projects to either verify their structures or quantify the amount produced by the bacteria. Then, secondary analysis methods are applied and provide additional insight into the modes of action of these compounds.
During the thesis, I carried out peptide synthesis either manually or with an automatic synthesizer system from Biotage. Here, the Fmoc-protecting group strategy was preferred in most cases. Natural products, such as silathride, xenoautoxin, phenylethylamide, tryptamide, rhabdopeptide, 3-hydroxyoctanoic acid, and PAX, were produced during this process. Furthermore, new peptide derivatives derived from synthetic NRPS approaches using the XU concept or SYNZIP were generated as standards.
Most of these natural compounds were experimentally verified by MIC tests (broth microdilution, plate diffusion) to be biologically active. For example, silathride, phenylethylamide, and tryptamide showed quorum quenching effects when tested against Chromobacterium violaceum. Initial results from collaborators (PD Dr. Nadja Hellmann/Mainz) showed that tryptamide and phenylethylamide interact with membrane or membrane proteins.
(R)-3-hydroxyoctanoic acid was synthesized to verify the molecule structure of phototemtide A, a cyclic lipopeptide with antiprotozoal activity. The rhabdopeptides are another class, which showed remarkable antiprotozoal effects. However, their mode of action was unknown. These compounds are relatively short peptide sequences, which contain hydrophobic residues, such as valine, leucine, or phenylalanine. Moreover, they possess N methylation, resulting in a rod-shaped highly hydrophobic structure. In this work, I synthesized eight new derivatives of rhabdopeptides for photo-affinity labeling (PAL). These molecules should react covalently under UV-light irradiation with the biological target of the peptides. In addition, these derivatives can be enriched in a pull-down assay using click chemistry. Afterward, analytic methods such as mass detection (proteome analysis) can be applied to elucidate the protein targets.
The PAX peptides derivatives are well-known to have anti-microbial activities and believed to be secreted into the environment by the producing bacteria. However, I found that the majority of these peptides are located in the cell pellet fraction and not in the supernatant. This has been shown through quantification using HPLC MS. New PAX derivatives were synthesized, which carry a moiety suitable for covalent modification using click-chemistry, therefore being functionalizable with a fluorescence dye. In collaboration with Dr. Christoph Spahn (Prof. Dr. Mike Heilemann group), we used confocal, as well as super-resolution microscopy, in particular, single-molecule localization microscopy (SMLM) to investigate the spatial distribution of clickable PAX molecules and revealed that they localize at the bacterial membrane. Furthermore, bioactivity assays revealed that the promotor exchanged X. doucetiae PAX mutants, which do not produce PAX molecules without chemical induction (hereby termed as pax-), were more susceptible to several insect AMPs tested. Based on these findings, a new dual mechanism of action for PAX was proposed. Besides the previously shown antimicrobial activity, these molecules with a positive net charge of +5 (pH = 7) would bind to the negatively charged bacterial surface. Hereby, the surface charge (typically negative) would be inversed resulting in a protective effect for Xenorhabdus against other positively charged AMPs. Furthermore, PAX was investigated as AMP against E. coli to study its antimicrobial mechanism of action. Here, the results show that PAX can disrupt the E. coli membrane at higher concentrations (> 30 µg/ml), enter the cytosol, and lead to reorganization of subcellular structures, such as the nucleoid during this process.
Another aspect of secondary analysis is the application of proteomic analysis. Therefore, I induced X. nematophila, X. szentirmaii, and P. luminescens with insect lysate. These samples were analyzed using HPLC-MS/MS (Q Exactive) together with a database approach (Maxquant/Andromeda). The results showed that in all strains the lipid degradation and the glyoxylate pathway were induced. This is in line with the given insect lysate diet, which mostly contained lipids. Moreover, several interesting unknown peptides and proteins were also upregulated and might get into the focus of future research.
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Structure, assembly and dynamics of H/ACA-Ribonucleoproteins
(2020)
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Gerd Werner Günter Hanspach
- H/ACA-RNPs are involved in RNA guided pseudouridylation of rRNAs and snRNAs. In this thesis I reconstituted active and labeled archaeal as well as eukaryotic H/ACA-RNPs and studied the structural dynamics of complex assembly and pseudouridine formation. Single molecule FRET spectroscopy was used as method of analysis to study structure, assembly and dynamics of these important complexes.
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Gene flow, population structure and genetic specification of giraffe have implications for their conservation
(2020)
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Sven Winter
- The genus Giraffa likely evolved around seven million years ago in Indo-Asia and spread over the Arabian-African land bridge into Eastern Africa. The oldest fossil of the African lineage was found in Kenya and dated to 7-5.4 Mya. Beside modern giraffe, four additional African species have likely existed (G. gracilis, G. pygmaea, G. stillei, and G. jumae). Based on their morphological similarities, G. gracilis is often considered to be the closest relative of the modern giraffe. Nevertheless, the phylogeny within the genus Giraffa is largely unresolved.
Modern giraffe (Giraffa sp.) have been neglected by the scientific community for a long time and still very little is known about their biology. Traditionally, present-day giraffe have been considered a single species (G. camelopardalis) which is divided into six to eleven subspecies, with nine subspecies being the most accepted classification. This classification was based on morphological differences and geographic ranges. However, recent genetic analyses found hidden diversity within Giraffa and proposed four genetically distinct giraffe species (G. camelopardalis, G. reticulata, G. tippelskirchi, G. giraffa) with presumably little gene flow among them.
Gene flow on a population level is the exchange of genetic information among populations facilitated by the migration of individuals between populations. Additionally, it is an important criterion to delineate species, because many species concepts, especially the Biological Species Concept, rely on the concept of reproductive isolation. Yet, new genetic methods are identifying an increasing number of species that show signs of introgressive hybridization or gene flow among them. Therefore, strict reproductive isolation cannot always be applied to delineate species, especially in young, probably still diverging, species such as giraffe.
Therefore, giraffe are ideal study organisms to investigate the level of gene flow in recently diverged species with adjacent or potentially overlapping ranges. Furthermore, their recent classification as “Vulnerable” by the IUCN and their unreliable distribution maps require the genetic evaluation of their population structure, distribution and conservation status.
In Publication 1 (Winter et al. (2018a), Ecological Genetics and Genomics, 7–8, 1–5), I studied the distribution and matrilineal population structure of Angolan giraffe (G. giraffa angolensis) using sequences from the cytochrome b gene (1,140 bp) and the mitochondrial control region for individuals from across their known range and beyond, and additionally including individuals from all known giraffe species and subspecies. The reconstruction of a phylogenetic tree and a mitochondrial haplotype network allowed to identify the most easterly known natural population of Angolan giraffe, a population that was previously assigned to their sister-subspecies South African giraffe (G. giraffa giraffa), indicating the limit of classification by morphology and geography. Furthermore, the analyses show that Namibia’s iconic desert-dwelling giraffe population is genetically distinct, even from the nearest population at Etosha National Park, suggesting very limited, if any, natural exchange of matrilines. Yet, no geographic barriers are known for this region that would prevent genetic exchange. Therefore, the two populations are likely on different evolutionary trajectories. Limited individuals with an Etosha haplotype further suggest that translocation of Etosha giraffe into the desert population had only a minor impact on the local population. Two separate haplogroups within Etosha National Park suggest an “out of Etosha” radiation of Angolan giraffe to the East followed by a later back-migration.
In Publication 2 (Winter et al. (2018b), Ecology and Evolution, 8(20), 10156–10165), I investigated the genetic population structure of giraffe across their range (n = 137) with focus on the amount of gene flow among the proposed giraffe species with a 3-fold increased set of nuclear introns (n = 21). Limited gene flow of less than one effective migrant per generation, even between the closely related northern (G. camelopardalis) and reticulated giraffe (G. reticulata) further supports the existence of four giraffe species by a different methodology, gene flow. This is significant because most species concepts build on reproductive isolation. Furthermore, this result is corroborated by four distinct major clades in a phylogenetic tree analysis, and distinct clusters in Principal Component Analysis and STRUCTURE analysis. All these analyses suggest a low level of genetic exchange among the four giraffe species and, therefore, a high degree of reproductive isolation in accordance with the Biological Species Concept (BSC). In Addition, only a single individual in 137 was identified as being potential of natural hybrid origin, which promotes the four-species concept further. ...
