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Using walls to navigate the room: egocentric representations of borders for spatial navigation
(2021)
Spatial navigation forms one of the core components of an animal’s behavioural repertoire. Good navigational skills boost survival by allowing one to avoid predators, to search successfully for food in an unpredictable world, and to be able to find a mating partner. As a consequence, the brain has dedicated many of its resources to the processing of spatial information. Decades of seminal work has revealed how the brain is able to form detailed representations of one’s current position, and use an internal cognitive map of the environment to traverse the local space. However, what is much less understood is how neural computations of position depend on distance information of salient external locations such as landmarks, and how these distal places are encoded in the brain.
The work in this thesis explores the role of one brain region in particular, the retrosplenial cortex (RSC), as a key area to implement distance computations in relation to distal landmarks. Previous research has shown that damage to the RSC results in losses of spatial memory and navigation ability, but its exact role in spatial cognition remains unclear. Initial electrophysiological recordings of single cells in the RSC during free exploration behaviour of the animal resulted in the discovery of a new population of neurons that robustly encode distance information towards nearby walls throughout the environment. Activity of these border cells was characterized by high firing rates near all boundaries of the arena that were available to the animal, and sensory manipulation experiments revealed that this activity persisted in the absence of direct visual or somatosensory detection of the wall.
It quickly became apparent that border cell activity was not only modulated by the distance to walls, but was contingent on the direction the animal was facing relative to the boundary. Approximately 40% of neurons displayed significant selectivity to the direction of walls, mostly in the hemifield contra-lateral to the recorded hemisphere, such that a neuron in left RSC is active whenever a wall occupies proximal space on the right side of the animal. Using a cue-rotation paradigm, experiments initially showed that this egocentric direction information was invariant to the physical rotation of the arena. Yet this rotation elicited a corresponding shift in the preferred direction of local head-direction cells, as well as a rotation in the firing fields of spatially-tuned cells in RSC. As a consequence, position and direction encoding in RSC must be bound together, rotating in unison during the environmental manipulations, as information about allocentric boundary locations is integrated with head-direction signals to form egocentric border representations.
It is known that the RSC forms many anatomical connections with other parts of the brain that encode spatial information, like the hippocampus and para-hippocampal areas. The next step was to establish the circuit mechanisms in place for RSC neurons to generate their activity in respect to the distance and direction of walls. A series of inactivation experiments revealed how RSC activity is inter-dependent with one of its communication partners, the medial entorhinal cortex (MEC). Together they form a wider functional network that encodes precise spatial information of borders, with information flowing from the MEC to RSC but not vice versa. While the conjunction between distance and heading direction relative to the outer walls was the main driver of neural activity in RSC, border cells displayed further behavioural correlates related to movement trajectories. Spiking activity in either hemisphere tended to precede turning behaviour on a short time-scale in a way that border cells in the right RSC anticipated right-way turns ~300 ms into the future.
The interpretation of these results is that the RSC’s primary role in spatial cognition is not necessarily on the early sensory processing stage as suggested by previous studies. Instead, it is involved in computations related to the generation of motion plans, using spatial information that is processed in other brain areas to plan and execute future actions. One potential function of the RSC’s role in this process could be to act correctly in relation to the nearby perimeter, such that border cells in one hemisphere are involved in the encoding of walls in the contralateral hemifield, after which the animal makes an ipsilateral turn to avoid collision. Together this supports the idea that the MEC→RSC pathway links the encoding of space and position in the hippocampal system with the brain’s motor action systems, allowing animals to use walls as prominent landmarks to navigate the room.
Non-ribosomal peptide synthetase docking domains : structure, function and engineering strategies
(2021)
Non-ribosomal peptide synthetases (NRPSs) are known for their capability to produce a wide range of natural compounds and some of them possess interesting bioactivities relevant for clinical application like antibiotics, anticancer, and immunosuppressive drugs. The diverse bioactivity of non-ribosomal peptides (NRPs) originates from their structural diversity, which results not only from the incorporation of non-proteinogenic amino acids into the growing peptide chain, but also the formation of heterocycles or further peptide modifications like methylation, hydroxylation and acetylation.
The biosynthesis of NRPs is achieved via the orchestrated interplay of distinct catalytic domains, which are grouped to modules that are located on one or more polypeptide chains. Each cycle starts with the selection and activation of a specific amino acid by the adenylation (A) domain, which catalyzes the aminoacyl adenylate formation under ATP consumption. This activated amino acid is then bound via a thioester bond to the 4’-phosphopantetheine cofactor (PPant-arm) of the following thiolation (T) domain. Before substrate loading, the PPant-arm is post-translationally added to the T domain by a phosphopantetheinyl transferase (PPTase), which converts the inactive apo-T domain in its active holo-form. In the last step of the catalytic cycle, two T domain bound peptide building blocks are connected by the condensation (C) domain, resulting in peptide bond formation and transfer of the nascent peptide chain to the following module. Each catalytic cycle is performed by a C-A-T elongation module until the termination module with a C-terminal thioesterase (TE) domain is reached. Here, the peptide product is released by hydrolysis or intramolecular cyclisation.
In comparison to single-protein NRPSs, where all modules are encoded on a single polypeptide chain, multi-protein NRPS systems must also maintain a specific module order during the peptide biosynthesis. Therefore, small C-terminal and N-terminal communication-mediating (COM) domains/docking domains (DD) were identified in the C- and N-terminal regions of multi-protein NRPSs. It was shown that these domains mediate specific and selective non-covalent protein-protein interaction, even though DD interactions are generally characterized by low affinities.
The first publication of this work focuses on the Peptide-Antimicrobial-Xenorhabdus peptide-producing NRPS called PaxS, which consists of the three proteins PaxA, PaxB and PaxC. Here, in particular the trans DD interface between the C-terminal attached DD of PaxB and N-terminal attached DD of PaxC was structurally investigated and thermodynamically characterized by isothermal titration calorimetry (ITC), yielding a dissociation constant (KD) of ~25 µM, which is a DD typical affinity known from further characterized DD pairs. The artificial linking of the PaxB/C C/NDD pair via a glycine-serine (GS) linker facilitated the structure determination of the DD complex by solution nuclear magnetic resonance (NMR) spectroscopy. In comparison to known docking domain structures, this DD complex assembles in a completely new fold which is characterized by a central α-helix of PaxC NDD wrapped in two V-shaped α-helices of PaxB CDD.
The first manuscript of this work focuses on the application of synthetic zippers (SZ) to mimic natural docking domains, enabling the easy assembly of NRPS building blocks encoded on different plasmids in a functional way. Here, the high-affinity interaction of SZs unambiguously defines the order of the synthetases derived from single-protein NRPSs in the engineered NRPS system and allows the recombination in a plug-and-play manner. Notably, the SZ engineering strategy even facilitates the functional assembly of NRPSs derived from Gram-positive and Gram-negative bacteria. Furthermore, the functional incorporation of SZs into NRPS modules is not limited to a specific linker region, so we could introduce them within all native NRPS linker regions (A-T, T-C, C-A).
The second publication and the second manuscript of this thesis again focus on the multi-protein PaxS, in particular on the trans interface between the proteins PaxA and PaxB on a molecular level by solution NMR. Therefore, the PaxA CDD adjacent T domain was included into the structural investigation besides the native interaction partner PaxB NDD. Before a three-dimensional structure could be obtained from NMR data, the NH groups located in the peptide bonds had to be assigned to the respective amino acids of the proteins (backbone assignment). Based on these backbone assignments, the secondary structure of PaxA T1-CDD and PaxB NDD in the absence and presence of the respective interaction partner were predicted.
The structural and functional characterization of the PaxA T1-CDD:PaxB NDD complex is summarized in manuscript two. The thermodynamic analysis of this complex by ITC determined a KD value of ~250 nM, whereas the discrete DDs did not interact at all. The high-affinity interaction allowed to determine the solution NMR structure of the PaxA T1-CDD:PaxB NDD complex without the covalent linkage of the interaction partners and an extended docking domain interface could be determined. This interface comprises on the one hand α-helix 4 of the PaxA T1 domain together with the α-helical CDD, and on the other hand the PaxB NDD, which is composed of two α-helices separated by a sharp bend.
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Standard biorelevant media reflect the average gastrointestinal (GI) physiology in healthy volunteers. The use of biorelevant media in in vitro experiments has become an important strategy to predict drug behaviour in vivo and is often combined with in silico tools in order to simulate drug plasma profiles over time. In addition to the healthy population, the effects of disease state or co-administration of other drugs on plasma profiles must be considered to assure drug efficacy and safety. Thus, there is a need for a more accurate representation of the human GI physiology when it is altered by disease or co-administered drugs in in vitro dissolution experiments.
This thesis focused on the development of biorelevant media and dissolution tests reflecting GI physiology in circumstances where the gastric pH is elevated. Diseases linked to an elevated gastric pH are hypochlorhydria and achlorhydria, but these days treatment with acid-reducing agents (ARAs) is the single greatest cause of elevation in gastric pH. pH-dependent drug-drug interactions (DDIs) with ARAs are frequent, as the ARAs are used in a number of diseases using a variety of drugs. As the drugs currently on the market are often poorly soluble and ionisable, their dissolution is highly dependent on the pH of the GI tract, especially the gastric pH.
The thesis research consisted of several steps. In the first step, physiological changes in the human GI tract during the therapy with ARAs were identified. Parameters of the standard biorelevant gastric medium FaSSGF were adjusted to the identified changes to reflect the impact of ARA co-administration on the gastric physiology. The media aim to assess the potential extent of the ARA impact on gastric physiology by introducing biorelevant media pairs, ARA pH 4 and pH 6 media, of which one reflects a lesser, and the other a stronger impact of ARAs.
In the second step these ARA media were implemented in in vitro dissolution set-ups.
The dissolution of poorly soluble ionisable drugs was assessed using one-stage, two-stage and transfer model set-ups, as well as using a more evolved in vitro system TIM-1. Comparison of results from dissolution set-ups using the standard, low pH, gastric biorelevant medium FaSSGF (pH 1.6 or 2), and the same set-ups using ARA pH 4 and pH 6 media, shows a decrease in dissolution rate and extent for weakly basic compounds PSWB 001 and dipyridamole, and an increase in rate and extent of dissolution for the weakly acidic compound raltegravir potassium, when the gastric pH is elevated. Due to different physicochemical properties, the extent of the impact of physiological changes during ARA therapy (when either ARA pH 4 or pH 6 medium is selected) on dissolution varied among the model drugs. Thus, the bracketing approach, which considers a range of the possible ARA co-administration impact on drug dissolution, was confirmed to be best practice in assessing the impact of ARAs.
In the third step, dissolution data from in vitro experiments with ARA media was implemented into in silico models. The predictions using various in silico model approaches in Simcyp™ Simulator (minimal and full PBPK model, dissolution input using DRM and DLM) successfully bracketed in vivo data on drug administration during ARA therapy and correctly predicted an overall decrease in plasma concentration for the two model weakly basic compounds and an increase in plasma concertation for the model weakly acidic compound.
In all assessed scenarios, the ARA methods proved to be an essential part of evaluating and predicting the impact of ARAs on drug pharmacokinetics, and appropriately predicted the extent of a possible impact of ARAs on the drug plasma profiles. Thus, the ARA biorelevant media and dissolution tests were demonstrated to be valuable tools reflecting administration of drugs when the gastric pH is elevated and able to predict the impact of ARA therapy on drug administration.
The ability to evaluate the impact of human (patho) physioloy on drug behaviour in the gastrointestinal tract is of great importance, as the GI conditions play a significant role in drug release and absorption. Thus, there is great interest on the part of the pharmaceutical industry and regulatory agencies to develop best practices in this field, especially for pH-dependent DDIs. The media and dissolution tests developed in this thesis are biorelevant methods appropriate for evaluation of the impact of elevated gastric pH on drug efficacy and safety. Such methods, used as a risk assessment tool, in connection with evaluation of the efficacy window and potential toxicity, may help to increase confidence about decisions as to whether a pH-effect will occur and whether it is relevant or not, prior to conducting clinical studies. They may also enable changes in inclusion/exclusion criteria during recruiting for large-scale efficacy trials. In fact, the biopharmaceutic approach to drug development is becoming standard practice on a number of fronts, including metabolic DDIs, renal and hepatic insufficiency, powering decision-making process and possibly even waiving certain types of clinical studies.
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We provide extensions of the dual variational method for the nonlinear Helmholtz equation from Evéquoz and Weth. In particular we prove the existence of dual ground state solutions in the Sobolev critical case, extend the dual method beyond the standard Stein Tomas and Kenig Ruiz Sogge range and generalize the method for sign changing nonlinearities.
Photorhabdus and Xenorhabdus are Gram-negative, entomopathogenic bacteria, living in endosymbiosis with the soil-dwelling nematode of the genera Steinernema and Heterorhabditis. The life cycle of these nematodes consists of non-feeding infective juvenile (IJ) stage, which actively searches for insects in the soil. After penetrating the insect prey, Photorhabdus and Xenorhabdus bacteria are released from the nematode gut. The bacteria proliferate and produce toxins to kill the insect. Photorhabdus and Xenorhabdus support nematode development throughout the life cycle and to get rid of food competitors by providing a wide variety of specialized metabolites (SMs). However, little is known about which SMs function as so called “food signals” to trigger the development process.
The IJs develop into adult, self-fertilizing hermaphrodites in a process called recovery, while feeding on cadaver and bacterial biomass. Heterorhabditis and Steinernema proceed to breed until nutrients are exhausted. Next generation IJs (NG-IJs) develop and leave the cadaver to search for another insect prey.
Photorhabdus and Xenorhabdus can be cultivated in defined medium under laboratory conditions. By placing IJs on a plate containing their respective bacterial symbiont, the complete life cycle of the nematodes can be observed in vitro. The in vitro nematode bioassay was used as a tool to investigate the development of the nematode.
The aim of this study was to find the food signals responsible for nematode development. Different Photorhabdus deletion strains unable to produce one or several SMs were co-cultivated with nematodes in the nematode bioassay. Subsequently, two aspects of the life cycle were investigated: recovery and NG-IJ development.
As isopropyl stilbene (IPS) is postulated to function as a food signal to support nematode recovery, it was used as a starting point for investigations. This study was focused on the biosynthetic pathway of IPS, including intermediates, side products and derivatives to investigate which one is in fact responsible for supporting nematode development.
The biosynthesis of IPS requires two precursors, phenylalanine and leucine (Figure 5). The first topic was focused on the phenylalanine derived pathway. Photorhabdus laumondii deletion mutants, defective in intermediate steps of this pathway, were created. The deletion of the genes coding for the phenylalanine ammonium lyase (stlA), converting phenylalanine into cinnamic acid (CA), the coenzyme A (CoA) ligase (stlB) and the operon coding for a ketosynthase and aromatase (stlCDE), were used. These strains were used for nematode bioassay including complementation of mutant phenotypes by feeding experiments. Recovery of nematodes grown on the deletion strains was always lower than recovery of nematodes grown on wild type bacteria. Feeding IPS to a deletion strain did not restore wild type level nematode recovery, thus IPS cannot be the food signal. Instead, the food signal must be another compound derived from this part of biosynthetic pathway. Lumiquinone and 2,5-dihydrostilbene are suggested to function as food signals and need to be investigated in future work.
The second part of this study was focused on the leucine derived pathway, which involved the Bkd complex forming the iso-branched part of IPS. A deletion of bkd was created and phenotypically analysed, subsequently performed with the nematode bioassay. Not only IPS but also other branched SMs, like photopyrones and phurealipids are synthetised by the Bkd complex. Deletions strains defective in producing photopyrones and phurealipids were also performed in nematode bioassays to investigate effects of these SMs individually. Branched SMs did not have an impact on nematode development, but nematodes grown on the ΔbkdABC strain showed a reduced nematode recovery and almost diminished NG-IJs development. As the Bkd complex also produces branched chain fatty acids (BCFAs), feeding experiments were performed with lipid extracts of wild type and mutant strain. All lipid extracts improved recovery, but only wild type lipids could complement NG-IJ development. This strongly indicates that BCFAs play an important role in NG-IJ development, which needs to be proven with purified BCFA feeding. This is an interesting finding, which could improve nematode production for biocontrol agent usage.
The role of IPS derived to epoxy stilbene (EPS) for nematode development, was another focus in the nematode life cycle. Recently it was demonstrated that EPS does not support nematode development. However, EPS forms adducts with amino acids. In my thesis, novel adducts containing the amino acid phenylalanine or a tetrapeptide were characterized. Another adduct, most likely being an EPS dimer, was also characterized. The biological role of such adducts was discussed to be potentially important for insect weakening and the structure of the novel compounds need to be structure elucidated and tested for bioactivity.
Specialized transporter proteins facilitate controlled uptake and extrusion of molecules across biological membranes that would otherwise be impermeable to them. The superfamily of solute carriers (SLC) comprises the second largest group of membrane proteins in humans, acting on a variety of small polar and non-polar molecules and ions. Because of their central role in metabolism, malfunctioning of these proteins often is pathogenic. The interest in SLC transporters as drug targets – as well as for drug delivery – has therefore increased in the past years. For many SLC subfamilies, however, structural and functional information remains scarce to date.
The here presented data provides important insights into different aspects of the transport mechanism of the SLC23 and SLC26 protein families. Importantly, we show that SLC23 nucleobase transporters, in contrast to what was been previously reported, work as uniporters rather than as proton-coupled symporters. In order to do so, we developed the first and only in vitro transport assay for the SLC23 family, which enables investigation of protein function in a defined environment. Moreover, we provide a hypothesis on the role of the extremely conserved negative charged substrate binding site residue found not only in the SLC23, but also SLC4 and SLC26 families. Based on a detailed analysis of binding and transport we conclude that this conserved negative charged has a relevance for protein stability rather than for substrate binding, which explains its conservation for all three protein families that otherwise differ in their substrate specificities and modes of transport. Lastly, we investigated the relevance of oligomerization for the SLC23 and SLC26 families, highlighting the importance of the STAS domain for forming active dimers in the SLC26 anion transporter family.
The vascular endothelium is a monolayer of endothelial cells that builds the inner lining of the blood vessels and constitutes a regulatory organ within the physiological system to sustain homeostasis. Endothelial cells participate in physiological processes including inflammation and angiogenesis. Dysregulation of these processes, however, can evoke or maintain pathological disorders, including cardiovascular and chronic inflammatory diseases or cancer. Although pathological inflammation and angiogenesis represent treatable conditions, current pharmacotherapeutic approaches are frequently not satisfying since their long-term application can evoke therapy resistance and thus reduced clinical efficacy. Consequently, there is an ongoing demand for the discovery of new therapeutic targets and drug leads. Considering that endothelial cells play a critical role in both angiogenesis and inflammation, the vascular endothelium represents a promising target for the treatment of diseases.
Vioprolide A is a secondary metabolite isolated from the myxobacterium Cystobacter violaceus Cb. vi35. Recently, vioprolide A was identified to interact with NOP14, a nucleolar protein involved in ribosome biogenesis. Ribosome biogenesis is an indispensable cellular event that ensures adequate homeostasis. Abnormal alterations in the ribosome biogenesis, referred to as ribosomopathies, however, can lead to an overall increase in the risk of developing cancer. Accordingly, several studies have outlined the involvement of NOP14 in cancer progression and metastasis, and vioprolide A has been demonstrated to exert anti-cancer effects in vitro. However, the impact of vioprolide A and NOP14 on the endothelium has been neglected so far, although endothelial cells are crucially involved in inflammation and angiogenesis under both physiological and pathological conditions.
In the present study, the effect of vioprolide A on inflammatory and angiogenic actions was analysed. In vivo, the laser-induced choroidal neovascularization (CNV) assay outlined a strong inhibitory effect of vioprolide A on both inflammation and angiogenesis. Furthermore, intravital microscopy of the cremaster muscle in mice revealed that vioprolide A strongly impaired the TNF-induced leukocyte-endothelial cell interaction in vivo.
In further experiments, the specific effect of vioprolide A on activation processes of primary human umbilical vein endothelial cells (HUVECs) was examined. According to the in vivo results, vioprolide A decreased the leukocyte-endothelial cell interaction in vitro through downregulating the cell surface expression and total protein expression of ICAM-1, VCAM-1 and E-selectin. Vioprolide A evoked its anti-inflammatory actions via a dual mechanism: On the one hand, the expression of pro-inflammatory proteins, including TNFR1 and cell adhesion molecules, was lowered through a general downregulation of de novo protein synthesis. The inhibition of de novo protein synthesis is most likely linked to the interaction with and inhibition of NOP14 by vioprolide A in HUVECs. On the other hand, the natural product prevented the nuclear translocation and promotor activity of the pro-inflammatory transcription factor NF-ĸB. Interestingly, most anti-inflammatory compounds that interfere with the NF-ĸB signaling pathway prevent NF-ĸB nuclear translocation through recovering or stabilizing the inhibitory IĸB proteins. Vioprolide A, however, decreased rather than stabilized the IĸB proteins and prevented NF-ĸB nuclear translocation through interfering with its importin-dependent nuclear import. By performing siRNA-mediated knockdown experiments, we evaluated the role of NOP14 in inflammatory processes in HUVECs and could establish a causal link between the anti-inflammatory actions of vioprolide A and the deletion of NOP14.
Besides exerting anti-inflammatory actions, we found that vioprolide A potently decreased the angiogenic key features proliferation, migration and sprouting of endothelial cells. Mechanistically, the natural product interfered with pro-angiogenic signaling pathways. Vioprolide A reduced the protein level of growth factor receptors, including VEGFR2, which is the most prominent receptor responsible for angiogenic signaling in endothelial cells. This effect was based on the general inhibition of de novo protein synthesis by the natural product. Downregulation of growth factor receptors impaired the activation of downstream signaling intermediates, including the MAPKs ERK, JNK and p38. To our surprise, however, activation of Akt, another downstream effector of VEGFR2, was increased rather than decreased. Furthermore, vioprolide A lowered the nuclear translocation of the transcriptional coactivator TAZ, which is regulated by the evolutionary conserved Hippo signaling pathway. Interestingly, however, and in contrast to NF-ĸB, TAZ nuclear translocation in mammalian cells seems to be independent of importins. In this context, we found that vioprolide A reduced both the protein level and nuclear localization of MAML1, which is needed to retain TAZ in the nucleus after its successful translocation.
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Das Projekt anan ist ein Werkzeug zur Fehlersuche in verteilten Hochleistungsrechnern. Die Neuheit des Beitrags besteht darin, dass die bekannten Methoden, die bereits erfolgreich zum Debuggen von Soft- und Hardware eingesetzt werden, auf Hochleistungs-Rechnen übertragen worden sind. Im Rahmen der vorliegenden Arbeit wurde ein Werkzeug namens anan implementiert, das bei der Fehlersuche hilft. Außerdem kann es als dynamischeres Monitoring eingesetzt werden. Beide Einsatzzwecke sind
getestet worden.
Das Werkzeug besteht aus zwei Teilen:
1. aus einem Teil namens anan, der interaktiv vom Nutzer bedient wird
2. und aus einem Teil namens anand, der automatisiert die verlangten Messwerte erhebt und nötigenfalls Befehle ausführt.
Der Teil anan führt Sensoren aus — kleine mustergesteuerte Algorithmen —, deren Ergebnisse per anan zusammengeführt werden. In erster Näherung lässt anan sich als Monitoring beschreiben, welches (1) schnell umkonfiguriert werden (2) komplexere Werte messen kann, die über Korrelationen einfacher Zeitreihen hinausgehen.
In this thesis, molecular dynamics (MD) simulations are used to study the interaction of different proteins with lipid bilayers. MD simulations can be used as a “computational microscope” to gain atomistic insights into the interactions between proteins and lipids that can barely be accessed in such detail by experimental methods. The different chapters of this thesis address the lipid sensing functionality of amphipathic helices (AHs) when bound to membranes, the folding of AHs at lipid-water interfaces as well as the conformational dynamics of the HIV-1 Env glycoproteins in viral-like and experimental bilayers. In the last chapter the possibilities to enhance the performance of MD simulations are explored, leading to a more efficient usage of computational resources.
Die Funktion nukleärer Rezeptoren (NR) beruht auf einem empfindlichen Zusammenspiel zwischen ihren Domänen, Coregulatoren und Liganden. Die meisten Rezeptoren binden die DNA als Homo- oder Heterodimere und transregulieren die Gentranskription in Folge von Ligandenbindung. Klassische Assay-Systeme, die sich auf die Untersuchung der NR-Funktion oder auf die Charakterisierung von Substanzen richten, bilden nur die Coregulator-Rekrutierung zu isolierten NR-Ligandenbindungsdomänen (LBDs) ab und vernachlässigen dabei die NR:NR-Interaktion. Damit klammern sie die NR:NR-Wechselwirkung aus, obwohl die Rekrutierung von Cofaktoren durch allosterischen Crosstalk mit der Oligomerisierung verbunden ist. Dies war die Motivation dafür, Assay-Systeme zu entwickeln, welche die Untersuchung von NR-Interaktionen,
insbesondere der NR-Dimerisierung, und deren Modulation durch verschiedene Arten von Liganden ermöglichen. Im Rahmen dieser Doktorarbeit wird ein vielfältiges modulares Set von Assays für die Untersuchung der NR-Dimerisierung und NR-Coregulator-Rekrutierung vorgestellt und deren Anwendbarkeit auf eine Vielzahl von NRs demonstriert. Die Verwendung einer
rekrutierungsunfähigen RXRα-Variante mit einer mutierten AF-2-Domäne ermöglichte den spezifischen Nachweis der Coaktivatorrekrutierung durch PPARγ im Kontext des Heterodimers mit seinem obligatorischen Dimerpartner RXRα. Außerdem konnte gezeigt werden, dass die Aktivierung der RXRα LBD mit ihrem Agonisten SR11237 zu einer Destabilisierung des RXRα-Homodimers, aber zu einer Förderung der Bildung des Heterodimers mit der PPARγ LBD führte.
Ein zentrales Ergebnis war das Phänomen, dass der Einbau von PPARγ in das Heterodimer zu einem erheblichen Anstieg an Affinität gegenüber Coaktivatoren führt, auch in Abwesenheit von Liganden. Somit fördert die RXRα-Aktivierung die Coaktivator-Rekrutierung von PPARγ indirekt durch eine Verschiebung der Oligomerisierungspräferenz von RXRα in Richtung des Heterodimers. Zusätzlich wurde die Wirkung von Tetrac, einem nicht-klassischen Schilddrüsenhormon, auf PPARγ und RXRα untersucht und dessen Aktivierungsvermögen gegenüber beiden Rezeptoren mit einer deutlich vervielfachten Wirkung auf das Heterodimer demonstriert. Mit Hilfe des neu etablierten Cofaktor-Rekrutierungsscreens konnte die Dynamik
zwischen dem Nurr1 NR und 29 kanonischen Coregulatoren, von denen einige ligandenabhängig hohe Affinitäten zum Rezeptor aufwiesen, beleuchtet werden. Diese Interaktionen wurden
bidirektional durch eine Reihe von strukturell unterschiedlichen nicht-steroidalen Antirheumatika moduliert, die auch die Affinitäten sowohl des Nurr1-Homodimers als auch des Heterodimers mit der RXRα LBD beeinflussen konnten. Die Nurr1-Dimere zeigten zudem auch eine hohe Empfindlichkeit gegenüber dem Endocannabinoid Anandamid. Zusätzlich zu PPARγ, RXRα und Nurr1 wurden erste Schritte zur Untersuchung der TLX NR-Funktion unternommen. Unter Anwendung der entwickelten Assays konnte die Heterodimerbildung der TLX und der RXRα LBD
beschrieben und die ligandenabhängige Rekrutierung des Corepressors SMRT beobachtet werden.
Zusammenfassend beschreibt diese Arbeit einen Satz von Werkzeugen für die Untersuchung von ligandenabhängiger NR-Coregulator-Interaktion und Oligomerisierung. Auf diese Weise trug sie zu einer umfassenderen Identifizierung und Charakterisierung von NR-Liganden bei und stellt eine valide Basis für die weitere Assayentwicklung und Ligandendesign dar.
Octanoic acid (C8 FA) is a medium-chain fatty acid which, in nature, mainly occurs in palm kernel oil and coconuts. It is used in various products including cleaning agents, cosmetics, pesticides and herbicides as well as in foods for preservation or flavoring. Furthermore, it is investigated for medical treatments, for instance, of high cholesterol levels. The cultivation of palm oil plants has surged in the last years to satisfy an increasing market demand. However, concerns about extensive monocultures, which often come along with deforestation of rainforest, have driven the search for more environmentally friendly production methods. A biotechnological production with microbial organisms presents an attractive, more sustainable alternative.
Traditionally, the yeast Saccharomyces cerevisiae has been utilized by mankind in bread, wine, and beer making. Based on comprehensive knowledge about its metabolism and genetics, it can nowadays be metabolically engineered to produce a plethora of compounds of industrial interest. To produce octanoic acid, the cytosolic fatty acid synthase (FAS) of S. cerevisiae was utilized and engineered. Naturally, the yeast produces mostly long-chain fatty acids with chain lengths of C16 and C18, and only trace amounts of medium-chain fatty acids, i.e. C8-C14 fatty acids. To generate an S. cerevisiae strain that produces primarily octanoic acid, a mutated version of the FAS was generated (Gajewski et al., 2017) and the resulting S. cerevisiae FASR1834K strain was utilized in this work as a starting strain.
The goal of this thesis was to develop and implement strategies to improve the production level of this strain. The current mode of quantification of octanoic acid includes labor-intensive, low-throughput sample preparation and measurement – a main obstacle in generating and screening for improved strain variants. To this end, a main objective of this thesis was the development of a biosensor. The biosensor was based on the pPDR12 promotor, which is regulated by the transcription factor War1. Coupling pPDR12 to GFP as the reporter gene on a multicopy plasmid allowed in vivo detection via fluorescence intensity. The developed biosensor enabled rapid and facile quantification of the short- and medium-chain fatty acids C6, C7 and C8 fatty acids (Baumann et al., 2018). This is the first biosensor that can quantify externally supplied octanoic acid as well as octanoic acid present in the culture supernatant of producer strains with a high linear and dynamic range. Its reliability was validated by correlation of the biosensor signal to the octanoic acid concentrations extracted from culture supernatants as determined by gas chromatography. The biosensor’s ability to detect octanoic acid in a linear range of 0.01-0.75 mM (≈1-110 mg/L), which is within the production range of the starting strain, and a response of up to 10-fold increase in fluorescence after activation was demonstrated.
A high-throughput FACS (fluorescence-activated cell sorting) screening of an octanoic acid producer strain library was performed with the biosensor to detect improved strain variants (Baumann et al., 2020a). For this purpose, the biosensor was genomically integrated into an octanoic acid producer strain, resulting in drastically reduced single cell noise. The additional knockout of FAA2 successfully prevented medium-chain fatty acid degradation. A high-throughput screening protocol was designed to include iterative enrichment rounds which decreased false positives. The functionality of the biosensor on single cell level was validated by adding octanoic acid in the range of 0-80 mg/L and subsequent flow cytometric analysis. The biosensor-assisted FACS screening of a plasmid overexpression library of the yeast genome led to the detection of two genetic targets, FSH2 and KCS1, that in combined overexpression enhanced octanoic acid titers by 55 % compared to the parental strain. This was the first report of an effect of FSH2 and KCS1 on fatty acid titers. The presented method can also be utilized to screen other genetic libraries and is a means to facilitate future engineering efforts.
In growth tests, the previously reported toxicity of octanoic acid on S. cerevisiae was confirmed. Different strategies were harnessed to create more robust strains. An adaptive laboratory evolution (ALE) experiment was conducted and several rational targets including transporter- (PDR12, TPO1) and transcription factor-encoding genes (PDR1, PDR3, WAR1) as well as the mutated acetyl-CoA carboxylase encoding gene ACC1S1157A were overexpressed or knocked out in producer or non-producer strains, respectively. Despite contrary previous reports for other strain backgrounds, an enhanced robustness was not observable. Suspecting that the utilized laboratory strains have a natively low tolerance level, four industrial S. cerevisiae strains were evaluated in growth assays with octanoic acid and inherently more robust strains were detected, which are suitable future production hosts.
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The role of orthographic knowledge for reading performance in German elementary school children
(2021)
Reading is crucial for successful participation in the modern world. However, 3-8% (e.g., Moll et al., 2014) of children in elementary school age show reading difficulties, which can lead to limited education and enhance risks of social and financial disadvantages (Valtin, 2017). Therefore, it is important to identify reading relevant components (Tippelt & Schmidt-Hertha, 2018). In this context, especially phonological awareness (i.e., awareness of the sound structure of the language) and naming speed (i.e., fast and automatized retrieval of information) were identified as significant components for reading skills (e.g., Georgiou et al., 2012; Landerl & Thaler, 2006; Vellutino, Fletcher, Snowling, & Scanlon, 2004). One further component, which is of growing interest to the recent research, is orthographic knowledge. It comprises the knowledge about the spelling of specific words (word-specific orthographic knowledge) and about legal letter patterns (general orthographic knowledge; Apel, 2011).
Previous research focused predominantly on examining the role of orthographic knowledge on basic reading level, including word identification and word meaning (Conrad et al., 2013; Rothe et al., 2015). The relationship between orthographic knowledge and reading comprehension as the core objective of reading, including understanding of the relationship between words within a sentence as well as building a coherence between sentences (Perfetti et al., 2005), was on the contrary scarcely the object of research. The first goal of this dissertation is, therefore, to provide a remedy by investigating the role of orthographic knowledge on higher reading processes (sentence- and text-level). The scarce body of research investigating children with reading difficulties provide a mixed result pattern (e.g., Ise et al., 2014). Therefore, this dissertation aims at clarifying the influence of orthographic knowledge on word-, sentence-, and text-level in children without and with reading difficulties.
A thorough understanding of reading relevant components is also important for conception of interventions aiming at individual reading performance improvements in order to prevent school failure. One promising approach to help children to overcome their reading difficulties is a text-fading based reading training. During this procedure, reading material is faded out letter by letter in reading direction (i.e., in German from left to right; Breznitz & Nevat, 2006). The aim of this manipulation is to prompt the individual to read faster than usual, resulting in reading rate and comprehension improvements (e.g., Nagler et al., 2015). However, the underlying mechanisms leading to improvements of reading performance are still unclear. Considering previous findings showing orthographic skills to influence training outcomes (Berninger et al., 1999), and also word reading performance after a reading intervention (Stage et al., 2003), it seems plausible to include orthographic knowledge when investigating potential training effects. Therefore, this dissertation aims at investigating the predictive value of orthographic knowledge for comprehension performance during the text-fading based reading training.
In order to answer the first research question, two empirical papers are implemented (see Appendix A: Zarić et al., 2020 and Appendix B: Zarić & Nagler, 2021), which investigate the role of orthographic knowledge for reading at word-, sentence-, and text-level in German school children without and with reading difficulties. The study by Zarić et al. (2020) examines the incremental predictive value for explained reading variance of both word-specific and general orthographic knowledge in relation to variance amount explained by general intelligence and phonological awareness. For this purpose, data from 66 German third-graders without reading difficulties were analyzed. Correlation and multiple regression analyses have shown that word-specific and general orthographic knowledge contribute a unique significant amount to the variance of reading comprehension on word-, sentence-, and text-level, over and above the explained variance by general intelligence and phonological awareness. In order to answer the question whether word-specific and general orthographic knowledge also explain variance in children with poor reading proficiency, in addition to established predictors phonological awareness and naming speed, the data from 103 German third-graders with reading difficulties were analyzed in a second study (Zarić & Nagler, 2021). The analyses revealed that word-specific and general orthographic knowledge explain a unique significant amount of the variance of reading on word- and sentence-level. On text-level, these two components did not explain a significant amount of unique variance. Here, only phonological awareness was shown to be a significant predictor. The results indicate that the knowledge about the spelling of specific words (word-specific orthographic knowledge) and the knowledge about legal letter patterns (general orthographic knowledge) contribute to reading comprehension on word-level. Following the assumptions, for instance, of the Lexical Quality Hypothesis (Perfetti & Hart, 2002) high-quality orthographic representations are considered to be important for higher reading processes, such as comprehension.
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An investigation of photoelectron angular distributions and circular dichroism of chiral molecules
(2021)
The present work demonstrates the capability of several type of molecular frame photoelectron angular distributions (MFPADs) and their linked chiroptical phenomenon the photoelectron circular dichroism (PECD) to map in great detail the molecular geometry of polyatomic chiral molecules as a function of photoelectron energy. To investigate the influence of the molecular potential on the MFPADs, two chiral molecules were selected, namely 2-(methyl)oxirane (C3H6O, MOx, m = 58,08 uma) and 2-(trifluoromethyl)oxirane (C3H3F3O, TFMOx, m = 112,03 uma). The two molecules differs in one substitutional group and share an oxirane group where the O(1s) electron was directly photoionized with the use of synchrotron radiation in the soft X-ray regime. The direct photoionization of the K-shell electron is well localized in the molecule and it induces the ejection of two or more electrons; the excited system separates into several charged (and eventually neutral) fragments which undergo Coulomb explosion due to their charges. The electrons and the fragments were detected using the COLd Target Recoil Ion Momentum Spectroscopy (COLTRIMS) and the momentum vectors calculated for each fragment belonging from a single ionization. The former method gives the possibility to post-orient molecules in space, giving access to the molecular frame, thus the MFPAD and its related PECD for multiple light propagation direction.
Stereochemistry (from the Greek στερεο- stereo- meaning solid) refers to chemistry in three dimensions. Since most molecules show a three-dimensional structure (3D), stereochemistry pervades all fields of chemistry and biology, and it is an essential point of view for the understanding of chemical structure, molecular dynamics and molecular reactions. The understanding of the chemistry of life is tightly bounded with major discoveries in stereochemistry, which triggered tremendous technical advancements, making it a flourishing field of research since its revolutionary introduction in late 18th century. In chemistry, chirality is a brunch of stereochemistry which focuses on objects with the peculiar geometrical property of not being superimposable to their mirror-images. The word chirality is derived from the Greek χειρ for “hand”, and the first use of this term in chemistry is usually attributed to Lord Kelvin who called during a lecture at the Oxford University Junior Scientific Club in 1893 “any geometrical figure, or group of points, “chiral”, and say that it has chirality if its image in a plane mirror, ideally realized, cannot be brought to coincide with itself.”. Although the latter is usually considered as the birth of the word chirality, the concept underlying it was already present in several fields of science (above all mathematics), already proving the already multidisciplinary relevance of chirality across many field of science and beyond. Nature shows great examples of chiral symmetry on all scales. Empirically, it is possible to observe it at macroscopic scale (e.g. distribution of rotations of galaxies), down to the microscopic scale (e.g. structure of some plankton species), but it is at the molecular level where the number gets remarkable: most of the pharmaceutical drugs, food fragrances, pheromones, enzymes, amino acids and DNA molecules, in fact, are chiral. Moreover, the concept of chirality goes far beyond the mere spatial symmetry of objects being crucially entangled with the fundamental properties of physical forces in nature. The symmetry breaking, namely the different physical behaviour of a two chiral systems upon the same stimuli, is considered to be one of the best explanation for the long standing questions of homochirality in biological life, and ultimately to the chemical origin of life on Earth as we know it. Our organism shows high enantio-selectivity towards specific compounds ranging from drugs, to fragrances. Over 800 odour molecules commonly used in food and fragrance industries have been identified as chiral and their enantiomeric forms are perceived to have very different smells, as the well-know example of D- and L- limonene. Similarly, responses to pharmaceuticals drugs can be enantiomer specific, and in fact about 60 % the drugs currently on the market are chiral compounds, and nearly 90 % of them are sold as racemates. The same degree of enantio-selectivity is observed in the communications systems of plants and insects. Plants produce lipophilic liquids with high vapour pressure called plant volatiles (PVs) which are synthesized via different enzymes called tarpene synthases that are usually chiral. Chiral molecules and chiral effects have a strong impact on all the fields of science with exciting developments ranging from stereo-selective synthesis based on heterogeneous enantioselective catalysis, to optoelctronics, to photochemical asymmetric synthesis, and chiral surface science, just to cite a few.
Chiral molecules come in two forms called enantiomers. Their almost identical chemical and physical properties continue to pose technical challenges concerning the resolution of racemic mixtures, the determination of the enantiomeric excess, and the direct determination of the absolute configuration of an enantiomer. ...
Für jeden Betroffenen ist die Diagnose Krebs ein schwerwiegender Einschnitt in der Lebensqualität und -führung, da die Behandlung oftmals mit langen Chemotherapien einhergeht. Moderne Durchbrüche in der Krebsbehandlung stammen aus dem Forschungsbereich der zielgerichteten Molekulartherapie oder aus dem Gebiet der Immuntherapien, die zu beachtlichen Erfolgen bei der Behandlung von Krebspatienten führten. Trotzdem bleiben auf dem Gebiet der Onkologie weiterhin Fragen zu den grundlegenden biologischen Prozessen unbeantwortet.
Zu den Onkoproteinen, die das Tumorwachstum in Leukemiezellen stark beeinflussen, gehören die Proteine der Klasse der mixed lineage leukemia (MLL) Histonmethyltransferasen. Genetische Fusionen des mll Gens, sogenannte Rearragments, führen zu MLL-fusion Produkten, die erheblich zum Verlauf der aggressiven akuten myeloischen Leukämie (AML) beitragen. Ein weiteres Onkoprotein, das für den Krankheitsverlauf vieler Krebsarten relevant ist, ist die Transkriptionsfaktorfamilie MYC. Überexprimierung von MYC wurde in einem Drittel aller humanen Tumore beobachtet. Zahlreiche Studien belegen, dass hohe MYC Level die Expression von Genen regulieren, die essentiell für den Transformationsprozess und somit das Tumorwachstum sind. Da der Transkriptionsfaktor weder eine sabile tertiäre Proteinstruktur noch eine für Inhibitoren adressierbare Bindetasche aufweist, gilt MYC bis heute als undruggable.
Sowohl die Histonmethyltransferase MLL1, als auch der Transkriptionsfaktor MYC interagieren mit einem ca. 37 kDa Protein namens WD40-repeat containing Protein 5 (WDR5), das durch seine propellerförmige Struktur eine Oberfläche mit insgesamt zwei Bindestellen aufweist. Mehrere Studien zeigten, dass WDR5 die Stabilität und somit die Funktion epigenetischer Proteinkomplexe wie SET/ MLL und NSL gewährleistet. In diesem Kontext wurde WDR5 als relevantes Target für die MLL-rearragend akute lymphatische Leukämie (ALL) postuliert. Weitere Studien zeigten zusätzliche Rollen von WDR5, wie die Interaktion zwischen WDR5 und dem Onkoprotein MYC sowie dessen Rekrutierung zum Chromatin. Seit 2015 wurden erfolgreich mehrere niedermolekulare Wirkstoffe für die Inhibierung von WDR5 entwickelt. Dabei zielten die meisten der literaturbekannten Inhibitoren auf die Argininmotiv-erkennende WDR5-interacting (Win) Bindestelle, eine große, hydrophobe Bindetasche im Zentrum des WDR5-Propellers. Die Resultate der besser erforschten Win Inhibitoren zeigten, dass WDR5 ein erfolgsversprechendes Target zur Inhibierung von leukämischen (MLL-r-abhängigen) und neuroblastomatischen (MYC-abhängigen) Zellwachstum ist.
Da beide Bindestellen des WDR5 Proteins Interaktionen mit onkologisch bedeutsamen Faktoren eingehen, würde eine einseitige Inhibierung nur die Effekte der jeweiligen Bindestelle aufzeigen. Diese Limitierung könnte jedoch durch die Entwicklung von WDR5 PROTACs (Proteolysis targeting chimeras) aufgehoben werden, da alle Gerüstfunktionen des Proteins und Protein-Protein-Interaktionen durch die Degradierung von WDR5 entfernt werden würden. Dabei induzieren die heterobifunktionellen Moleküle den Abbau des Zielproteins über das zelleigene Ubiquitin-Proteasom-System, statt die Enzymfunktion zu inhibieren. Nach dem zelleigenen Abbau des Zielproteins wird der PROTAC freigesetzt und kann einen neuen Zyklus der Proteindegradation einleiten, was die erforderliche Menge an Wirkstoff verringert.
Diese Dissertation beschäftigte sich mit dem Design, der Synthese sowie der biophysikalischen und biologischen Evaluierung von WDR5 PROTACs. Ausgehend von literaturbekannten WDR5 Liganden wurden zwei verschiedene PROTAC Typen entworfen. Diese beiden Molekültypen besitzen einen unterschiedlichen geometrischen Austrittswinkel, wodurch die Chance auf eine erfolgreiche Komplexbildung zwischen WDR5, PROTAC und E3 Ligase erhöht wird. Als Leitstruktur fungierten die Verbindungen OICR-9429 sowie DDO-2117 und ausgehend von Ligand (6d) wurden heterobifunktionelle Moleküle mit verschiedenen Linkersystemen ([PEG]- und alkyl-basiert, sowie aromatisch verbrückt) und verschiedenen E3 Ligase Liganden (Cereblon, VHL und MDM2) synthetisiert. Die anschließenden biochemischen und biophysikalischen Evaluierungen der verschiedenen PROTACs durch Thermofluor (DSF) und ITC zeigten eine hohe in vitro Affinität einiger Moleküle. Die zelluläre Permeabilität der großen Moleküle wurde in einem hier etablierten BRET Assay untersucht. Zur Assay-Etablierung wurden drei Tracer (21a-c), basierend auf BODIPY Konjugaten, synthetisiert und getestet, bevor die PROTACs in intakten und lysierten Zellen vermessen wurden. Während die zellulären Affinitäten von Cereblon- und VHL-adressierenden PROTACs sich im niedrigen μM Bereich bewegten, wurden die nicht zellgängigen MDM2 PROTACs von weiteren Experimenten ausgeschlossen.
Die Degradierungeffizienz der WDR5 PROTACs (7a-e) und (8a-j) wurden in der Leukämie Zellinie MV4-11 untersucht, da diese die am meisten auftretende MLL fusion Mutation AF4 birgt. Dabei wurde der Proteinabbau von WDR5 über den HiBiT Assay sowie Western Blots nachgewiesen. ...
Paläoklimarekonstruktionen, die es sich zum Ziel gesetzt haben, Klima-Mensch Interaktionen auf lange Zeitreihen betrachtet zu erforschen, nehmen begünstigt durch die aktuell intensiv geführte Klimadebatte, einen immer größer werdenden Stellenwert in der öffentlichen und wissenschaftlichen Wahrnehmung ein. Denn trotz aller wissenschaftlicher Fortschritte, die in den vergangenen Jahrzehnten im Bereich der modernen Klimaforschung gemacht wurden, bleibt die zuverlässige Vorhersage und Modellierung von zukünftigen Klimaveränderungen noch immer eine der größten Herausforderungen unser heutigen Zeit. Betrachtet man die Karibik exemplarisch in diesem Rahmen, dann prognostizieren viele Modellrechnungen, infolge steigender Ozeantemperaturen, ein deutlich häufigeres Auftreten von tropischen Stürmen und Hurrikanen sowie eine Verschiebung hin zu höheren Sturmstärken. Dieser Trend stellt für die Karibik und viele daran angrenzende Staaten eine der größten Gefahren des modernen Klimawandels dar, den es wissenschaftlich über einen langen Zeitrahmen zu erforschen gilt.
Klimaprognosen stützen sich meist vollständig auf hoch-aufgelöste instrumentelle Datensätze. Diese sind aber alle durch einen wesentlichen Aspekt limitiert. Aufgrund ihrer eingeschränkten Verfügbarkeit (~150 Jahre) fehlt ihnen die erforderliche Tiefe, um die auf langen Zeitskalen operierenden Prozesse der globalen Klimadynamik adäquat abbilden zu können. Betrachtet man das Holozän in seiner Gesamtheit, so wurde die globale Klimadynamik über die vergangenen ~11,700 Jahre von periodisch auftretenden Prozessen und Abläufen gesteuert. Diese wirken grundsätzlich über Zeiträume von mehreren Jahrzehnten, teilweise Jahrhunderten und in einigen Fällen sogar Jahrtausenden. Viele dieser natürlichen Prozesse, können in der kurzen Instrumentellen Ära nicht gänzlich identifiziert und angemessen in Klimamodellen berücksichtig werden. Die alleinige Berücksichtigung der Instrumentellen Ära bietet daher nur eine eingeschränkte Perspektive, um die Ursachen und Abläufe von vergangenen sowie mögliche Folgen von zukünftigen Klimaveränderungen zu verstehen. Um diese Einschränkung zu überwinden, ist es somit erforderlich, dass die geowissenschaftliche Forschung mit Proxymethoden ein zusammenfassendes und mechanistisches Verständnis über alle Holozänen Klimaveränderungen erlangt.
Wenn man sich diese Limitierung, die ansteigenden Ozeantemperaturen und das in der Karibik in den vergangen 20 Jahren vermehrte Auftreten von starken tropischen Zyklonen ins Gedächtnis ruft, ist es nachvollziehbar, dass im Rahmen dieser Doktorarbeit ein zwei Jahrtausende langer und jährlich aufgelöster Klimadatensatz erarbeitet werden soll, der spät Holozäne Variationen von Ozeanoberflächenwasser-temperaturen (SST) und daraus resultierende lang-zeitliche Veränderungen in der Häufigkeit tropischer Zyklone widerspiegelt. In Zentralamerika wird das Ende der Maya Hochkultur (900-1100 n.Chr.) mit drastischen Umweltveränderungen (z.B. Dürren) assoziiert, die während der Mittelalterlichen Warmzeit (MWP; 900-1400 n.Chr.) durch eine globale Klimaveränderung hervorgerufen wurde. Die aus einem „Blue Hole“ abgeleiteten Informationen über Klimavariationen der Vergangenheit können als Referenz für die gegenwärtige Klimakriese verwendet werden.
Als „Blue Hole“ wird eine Karsthöhle bezeichnet, die sich subaerisch während vergangener Meeresspiegeltiefstände im karbonatischen Gerüst eines Riffsystems gebildet hat und in Folge eines Meeresspiegelanstiegs vollständig überflutet wurde. In einigen wenigen marinen „Blue Holes“ treten anoxische Bodenwasserbedingungen auf. Die in diesen anoxischen Karsthöhlen abgelagerten Abfolgen mariner Sedimente können als einzigartiges Klimaarchiv verwendet werden, da sie aufgrund des Fehlens von Bioturbation eine jährliche Schichtung (Warvierung) aufweisen.
In dieser kumulativen Dissertation über das „Great Blue Hole“ werden die Ergebnisse eines 3-jährigen Forschungsprojekts vorgestellt, dass das Ziel verfolgte einen wissenschaftlich herausragenden spät Holozänen Klimadatensatz für die süd-westliche Karibik zu erzeugen. Beim „Great Blue Hole“ handelt es sich um ein weltweit einzigartiges marines Sedimentarchiv für diverse spät Holozäne Klima-veränderungen, das im Zuge dieser Dissertation sowohl nach paläoklimatischen als auch nach sedimentologischen Fragestellungen untersucht wurde. Die vorliegende Doktorarbeit befasst sich im Einzelnen mit (1) der Ausarbeitung eines jährlich aufgelösten Archives für tropische Zyklone, (2) der Entwicklung eines jährlich aufgelösten SST Datensatzes und (3) einer kompositionellen Quantifizierung der sedimentären Abfolgen sowie einer faziell-stratigraphischen Charakterisierung von Schönwetter-Sedimenten und Sturmlagen. Zu jedem dieser drei Aspekte, wurde jeweils ein Fachartikel bei einer anerkannten wissenschaftlichen Fachzeitschrift mit „peer-review“ Verfahren veröffentlicht.
Der insgesamt 8.55 m lange Sedimentbohrkern („BH6“), der für diese Dissertation untersucht wurde, stammt vom Boden des 125 m tiefen und 320 m breiten „Great Blue Holes“, das sich in der flachen östlichen Lagune des 80 km vor der Küste von Belize (Zentralamerika) gelegenen „Lighthouse Reef“ Atolls befindet. Durch seine besondere Geomorphologie wirkt das, innerhalb des atlantischen „Hurrikan Gürtels“ positionierte, „Great Blue Hole“ wie eine gigantische Sedimentfalle. Die unter Schönwetter-Bedingungen kontinuierlich abgelagerten Abfolgen feinkörniger karbonatischer Sedimente, werden von groben Sturmlagen unterbrochen, die auf „over-wash“ Prozesse von tropischen Zyklonen zurückzuführen sind.
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Taxa under scrutiny in this thesis are Halophytophthora-like oomycetes. The genus Halophytophthora, proposed in 1990, is an assemblage of unrelated species grouped together on the basis habitat preference, i.e. the mangrove or saltmarsh biome, and morphological similarity to Phytophthora. The premise “Phytophthora-like species from the mangrove environment” became the genus concept for Halophytophthora and lasted for almost 2 decades which resulted to the addition of several species (i.e. H. elongata, H. exoprolifera, H. porrigovesica, H. kandeliae, H. masteri, and H. tartarea). At the onset of molecular phylogenetics, Halophytophthora was inferred as a highly polyphyletic taxon and the genus concept was found to be unsuitable. This thesis adds to this, since six Phytophthora spp. were isolated from the mangrove environment, two of which were found in the Philippines (Phytophthora elongata and Phytophthora insolita). After a thorough assessment of the morphologic and phylogenetic data of taxa included in this thesis, several taxonomic novelties were introduced – a new family (Salispinaceae), a new genus (Calycofera), new species (Calycofera cryptica, Phytopythium dogmae, Phytopythium leanoi, Salisapilia coffeyi, and Salispina hoi), and new combinations (Calycofera operculata, Salisapilia bahamensis, S. elongata, S. epistomia, S. masteri, S. mycoparasitica). In addition, Salisapiliaceae and Salisapilia were emended.
The specific and precise arrangement of proteins and biomolecules in 3D is an important prerequisite for the study of cell migration, cellular signal transduction and the production of artificial tissue. In a variety of research approaches, proteins have been immobilized on rigid surfaces such as glass or gold to observe protein-protein or protein-cell interactions. While these commonly used analytical platforms offer advantages such as rapid washing steps and easy use, due to their rigidity and two-dimensionality, they cannot replicate the extracellular matrix (ECM) the native environment of cells. This severe deviation from the natural environment results in significant changes in cell structure and cellular processes such as the polarization of the cell, its morphology, and signal transduction. In order to maintain the functionality of the immobilized proteins, it is also enormously important that the proteins are oriented and anchored in the material under mild conditions.
An immobilization strategy that makes this possible is bioaffinity. For this, the specific interaction of a biomolecule with an interaction partner anchored on a surface is used to immobilize the biomolecule. Such an interaction is for example the nitrilotriacetic acid (NTA)/His-tag binding. NTA is a chelator molecule that, when bound to divalent metal ions such as Ni(II), forms an octahedral complex with oligohistidines. The oligo histidine-tag can be competed out of the complex by free histidine or imidazole due to structural similarity. This is exploited in immobilized metal affinity chromatography (IMAC). The binding of a monoNTA/His-tag complex (KD=10 µM) is not stable enough to be used for immobilizations. Therefore, multivalent variants of the chelator were developed, like trisNTA which has a high affinity for His6 tagged proteins (KD= 10 nM). The PA-trisNTA developed in a preliminary work was the first light-activatable system based on the trisNTA chelator head.
The aim of this work was to synthesize a new two-photon (2P) activatable trisNTA (TPA trisNTA) interaction molecule, to analyze its photophysical characteristics and to apply it for two- and three dimensional (2D/3D) biomolecule patterning. The final goal was to use TPA trisNTA for cellular applications in order to manipulate membrane protein organization. Therefore, TPA trisNTA was designed to maintain a stable autoinhibition enabling the immobilization of proteins under physiological conditions with high precision in the x/y, as well as z dimension only upon light activation. 2P activation brings some outstanding advantages: i) the use of near-infrared (NIR) light is less harmful to cells compared to ultraviolet (UV) light, ii) the longer wavelength allows the radiation to penetrate deeper into tissues, iii) the precision of focal irradiation is more accurate because only a focal volume (about 1 fL) is excited and, unlike UV light, scattered light does not lead to activation.
Several backbones for TPA-trisNTA were considered as 2P cleavable groups due to their 2P absorption ability and small size: 3 nitrodibenzofuran (NDBF), 6 bromo 7 hydroxycoumarin (Bhc), and 7 diethylaminocoumarin (DEAC). Initially, suitable synthetic routes were developed for the respective carbaldehydes, since these represented an important intermediate for both the construction of amino acid (aa) derivatives as well as ß hydroxy acids. ß Hydroxy acids were important intermediates because their photocleavage differs from aa derivatives. To establish the conversion from carbaldehydes to hydroxy acids via Reformatsky reaction, commercially available carbaldehydes of the nitroveratral (NV) or nitropiperonal (NP) group were used in addition. The conversion of NDBF, NV, NP proved to be difficult, whereas the ß-hydroxy acid was successfully synthesized from Bhc as well as from DEAC.
Starting from DEAC ß hydroxy acid, a Fmoc protected amino acid derivative was synthesized. To ensure high cleavage efficiency, the DEAC ß hydroxy acid was linked to monoFmoc ethylenediamine through a carbamate linker. Subsequently, the photocleavable group was successfully incorporated into the linker of TPA-trisNTA by solid-phase peptide synthesis (SPPS).
The functional principle of TPA-trisNTA, similar to PA-trisNTA, is based on the autoinhibition of the multivalent chelator head trisNTA, which is linked to an intramolecular oligohistidine sequence by a peptide linker. In presence of Ni(II) ions, trisNTA forms a metal ion-mediated complex with histidine, causing TPA-trisNTA to self-inactivate. The cleavage site is the DEAC based photocleavable amino acid. In contrast to PA-trisNTA, the incorporation of two photocleavable amino acids was omitted. Instead, only one photocleavable DEAC was incorporated in front of the His tag. To avoid a second DEAC group within the His tag, a His5 tag was used instead of an His6 tag. It is known from preliminary work that a His5 tag is sufficient to maintain autoinhibition in the presence of His6-tagged proteins of interest (POIs), but can be displaced from the complex after light-driven cleavage of the peptide backbone. Placement of a cysteine in the peptide linker between the trisNTA and the DEAC group allowed for permanent surface anchoring after photocleavage of the linker.
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This thesis deals with the phenomenology of QCD matter, its aspects in heavy ion collisions and in neutron stars. The first half of the work focuses on the hadronic phase of QCD matter. One focus is on how the hadronic phase shows itself in heavy ion collisions and how its dynamics can be simulated. The role of hadronic interactions is considered in the context of the lattice QCD data. The second part of this thesis presents a unified approach to QCD matter, the CMF model. The CMF model incorporates many aspects of QCD phenomenology which allows for a consistent description of the hadron-quark transition, making it applicable to the entire QCD phase diagram, i.e., to the cold nuclear matter and to the hot QCD matter. It is shown that a description of both the hot matter created in heavy ion collisions and the cold dense matter in neutron star interiors is possible within one single approach, the CMF model.
Despite constant progress in basic and translational research, cancer is still one of the leading cause of death. In particular, tumors of the central nervous system (CNS) are usually associated with dismal prognosis. Although about 100 distinct subtypes of primary CNS tumors have been classified molecularly, metastases derived from primaries outside the CNS (= brain metastases, BrM) are more frequently observed across brain tumor patients. It is estimated that approximately 20 - 40 % of all cancer patients will develop BrM during their course of disease, and basically every tumor type is able to metastasize to the brain. Nevertheless, BrM are most frequently derived from primaries of the lung, breast, and skin (melanoma). Treatment options for patients with BrM are very limited, and standard of care therapies include surgery, ionizing radiation (e.g. whole brain radio-therapy, WBRT), and some systemic and immuno-therapeutic approaches.
The brain represents a unique organ, which in part is due to the presence of the blood-brain barrier, a unit of the neuro-vascular interface ensuring tightly regulated exchange of nutrients, molecules, and cells. Furthermore, apart from microglia the brain parenchyma does not harbor other immune cells. Those cells however can be found at the borders of the CNS residing in the meninges, for instance. Based on recent insight on the immune landscape in the CNS, a paradigm shift occurred after which the brain is no longer regarded as immune-privileged but rather immune distinct. The phenomenon of immune cell infiltration has been described before in the context of neurological disorders including Multiple Sclerosis, as well as in brain tumors.
Since the development of immune-therapeutic approaches for tumors outside the CNS that aim to evoke sustainable anti-tumor effects, it became increasingly interesting to understand and harness the immune landscape (= tumor microenvironment, TME) of brain tumors, as well. Interestingly, most of the knowledge about the TME is based on studies of primary brain tumors. However, it is known that BrM compared to primary brain tumors induce a different TME like e.g. the recruitment of much more lymphocytes, which is one of the reasons primary brain tumors are considered immunologically “cold” and poorly respond to immuno-therapies. Previous insight into the functional contribution of tumor-associated cells in BrM progression revealed for example that brain-resident cell types (e.g. astrocytes or microglia) promote BrM development and outgrowth. However, until recently a comprehensive view on the cellular composition and functional role of the brain metastases-associated TME was missing and little was known how it changes during tumor progression or standard therapy.
Hence, within this thesis it was sought to describe novel aspects of the TME of preclinical BrM models, which include two xenograft and one syngeneic mouse model. BrM was induced via intra-cardiac injection of tumor cells with a high brain tropism. Both xenograft models were based on immuno-compromised nude mice (Balb/c nude) and included the melanoma-to-brain (M2B) model H1_DL2, and the lung-to-brain (L2B) model H2030. In addition the breast-to-brain model 99LN-BrM was used in wild-type mice (BL6), and therefore represented an immuno-competent, syngeneic model. First BrMs could be detected in the xenograft models at 3 weeks after injection, whereas first 99LN BrMs were detected at 5 weeks. BrM development and progression were monitored by bioluminescence imaging once per week in the xenograft models. Tumor progression in the 99LN model was examined by magnetic resonance imaging. Based on the measurement methods, and for further histologic and cytometric experiments, mice were stratified into groups with small or large BrMs, respectively. Some initial immuno-stainings confirmed previous findings, showing that brain-resident cells like astrocytes and microglia become activated in the presence of tumor cells, whereas neurons for example rather give the impression of passive bystanders. Importantly, an accumulation of IBA1+ cells was observed during BrM progression. IBA1 is a pan-macrophage marker that stains all tumor-associated macrophages (TAMs). However previous work suggested that the TAM population consists of at least two main subpopulations in BrM as well: the resident-infiltrating microglia (MG, TAM-MG), as well as the peripheral and monocytic-derived macrophages (TAM-MDM). Since both cell types within the tumor share morphological traits, and due to the lack of markers to distinguish them, an exact discrimination of both cell types was complicated in the past. Recently, an integrative lineage-tracing-based study identified the integrin CD49d as MDM-specific in the context of brain tumor-associated myeloid cells, hence enabling a reliable dissection of both TAM populations in e.g. flow cytometric experiments.
One of the main aims of this thesis was to dissect the myeloid TME in the three different BrM models during tumor progression. Using a 5-marker flow cytometry (FCM) (CD45/CD11b/Ly6C/Ly6G/CD49d) approach, the following cell populations were examined in more detail: granulocytes, inflammatory monocytes, MDM, and MG.
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Endolysosomal effectors and their relevance for antiviral activity against the Hepatitis E virus
(2021)
Mit über 20 Millionen registrierter Fälle pro Jahr, repräsentiert das Hepatitis-E-Virus (HEV) eine Hauptursache einer viralen Hepatitis weltweit und stellt ein erhebliches Risiko insbesondere für Schwangere und Immunsupprimierte dar. Jedoch sind Behandlungsoptionen stark limitiert und mit teils schweren Nebenwirkungen verbunden. Neue Erkenntnisse des Wechselspiels zwischen Wirtszelle und HEV werden deshalb benötigt, um neue antivirale Wirkstoffe zu entwickeln. Der Fokus der Arbeit wurde hierbei auf Effektoren des endosomalen Systems gesetzt, welches von HEV zur Freisetzung von Virionen genutzt wird.
Eine virale Infektion führt in der Zelle zur Produktion von Interferonen (IFNs) und weiters zu einer IFN-Antwort. Ein essenzielles Effektormolekül, welches HEV nachweislich effizient repressiert, ist die GTPase guanylate binding protein 1 (GBP1). In dieser Studie wurde beleuchtet, dass Letztere durch eine HEV-Infektion induziert wird. Zusätzlich reduziert die ektopische Expression von GBP1 sowohl die intrazelluläre Menge des HEV Kapsidproteins als auch die Menge freigesetzter Virionen. Mechanistisch liegt diesem Sachverhalt die GBP1-induzierte Inkorporation von Virionen in Lysosomen zugrunde, was schlussendlich deren Abbau nach sich zieht. Erkenntnisse über die Rolle verschiedener GBP1 Proteindomänen innerhalb des Mechanismus wurden unter Verwendung ektopischer Expression von GBP1-Mutanten erlangt. Inkorporation der Mutation R48A führt zum Verlust der GTPase-Aktivität. Andererseits führt eine Inkorporation der Mutation S73A zum Verlust der Homodimerisierung, was die nachfolgende Farnesylierung und gekoppelte Membranassoziation reduziert. Hierbei behält GBP1-R48A Fähigkeiten zur Induktion lysosomalen Abbaus von HEV bei, GBP1-S73A jedoch nicht. Dies wiederum bedeutet, dass eine GBP1 Homodimerisierung notwendig für den antiviralen Mechanismus ist, was eine Adapterfunktion des Moleküls für lysosomale Inkorporation nahelegt. Die Relevanz von GBP1 während einer IFNγ-Antwort wurde deshalb mittels siRNA-basiertem Silencing untersucht. Ähnlich der ektopischen Expression von GBP1 induziert IFNγ die lysosomale Degradation von HEV. In Abwesenheit von GBP1 jedoch, ist dieser Effekt signifikant geringer ausgeprägt, was zu einem Effizienzverlust von IFNy in Bezug auf dessen antiviralen Effekt bedeutet. Dies führte schlussendlich zur Identifizierung von GBP1 als essenziellen Restriktionsfaktor gegen HEV, was seine Rolle in Abhängigkeit seiner Homodimerisierung via Induktion lysosomalen Abbaus erfüllt.
Nebst der Induktion von GBP1, konnte eine Akkumulation von Cholesterin in Lysosomen durch IFNy nachgewiesen werden. Da dieses Lipid einen essenziellen Faktor für endosomale Reifung, Transport und Funktionalität darstellt, wurden Cholesterinspiegel und verbundene transkriptionelle Fußabdrücke im Kontext einer HEV Infektion untersucht. Letztere führt zu einer Dysregulation Cholesterin-assoziierter Genexpression, was eine Reduktion intrazellulären Cholesterins nach sich zieht. Auch in HEV infizierten Patienten liegt eine Abnahme des Serumcholesterins vor. Unter Modulation intrazellulären Cholesterins, wurde deutlich, dass die Inhibition der Cholesterinsynthese durch Simvastatin eine verstärkte Freisetzung von Virionen nach sich zieht, was ebenso in HEV infizierten Patienten nachweisbar war. Im Gegensatz hierzu zieht eine Erhöhung intrazellulären Cholesterins via Supplementierung von Lipoproteinpartikeln niedriger Dichte (LDL) oder 25-Hydroxycholesterin eine signifikante Reduktion des viralen Kapsidproteins und freigesetzter Virionen nach sich. Dem liegt eine verstärkte Inkorporation von HEV in Lysosomen mit anschließender Degradation zugrunde. Ob dieser Mechanismus pharmakologisch nutzbar ist, wurde mittels eines Screenings Lipid modulatorischer Medikamente untersucht. Der p-Glykoprotein Inhibitor PSC833 und besonders der PPARα-Agonist Fenofibrat stellten sich als äußerst effiziente Inhibitoren des HEV heraus. Beide führen zu einer Erhöhung und Akkumulation zellulären Cholesterins in vesikulären Strukturen. Dies zieht eine dramatische Erhöhung lysosomaler Lokalisation von HEV nach sich und führt letzten Endes zu einer signifikanten Reduktion freigesetzter Virionen.
Zusammenfassend konnten in dieser Studie essenzielle Funktionen von GBP1 in Bezug auf dessen restriktiven Effekt gegen HEV identifiziert werden. Weiters wurde dieses als entscheidender Wirtsfaktor für die IFNγ-Antwort gegen das Virus identifiziert. Andererseits legt diese Studie nahe, dass HEV niedrige Cholesterinspiegel innerhalb infizierter Zellen für die Freisetzung von Virionen benötigt. Andererseits sind erhöhte intrazelluläre Cholesterinspiegel schädlich für die virale Freisetzung, da der lysosomale Abbau von Virionen induziert wird. Dies führte zur erfolgreichen Entdeckung eines neuartigen antiviralen Wirkstoffes, welcher diesen cholesterinabhängigen Effekt effizient induziert: Fenofibrat.