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New experimental methods have drastically accelerated the pace and quantity at which biological data is generated. High-throughput DNA sequencing is one of the pivotal new technologies. It offers a number of novel applications in various fields of biology, including ecology, evolution, and genomics. However, together with those opportunities many new challenges arise. Specialized algorithms and software are required to cope with the amount of data, often requiring substantial training in bioinformatic methods. Another way to make those data accessible to non-bioinformaticians is the development of programs with intuitive user interfaces.
In my thesis I developed analyses and programs to tackle current problems with high-throughput data in biology. In the field of ecology this covers the establishment of the bioinformatic workflow for pollen DNA meta-barcoding. Furthermore, I developed an application that facilitates the analysis of ecological communities in the context of their traits. Information from multiple public databases have been aggregated and can now be mapped automatically to existing community tables for interactive inspection. In evolution the new data are used to reconstruct phylogenetic trees from multiple genes. I developed the tool bcgTree to automate this process for bacteria. Many plant genomes have been sequenced in current years. Sequencing reads of those projects also contain data from the chloroplasts. The tool chloroExtractor supports the targeted extraction and analysis of the chloroplast genome. To compare the structure of multiple genomes specialized software is required for calculation and visualization of the relationships. I developed AliTV to address this. In contrast to existing programs for this task it allows interactive adjustments of produced graphics. Thus, facilitating the discovery of biologically relevant information. Another application I developed helps to analyze transcriptomes even if no reference genome is present. This is achieved by aggregating the different pieces of information, like functional annotation and expression level, for each transcript in a web platform. Scientists can then search, filter, subset, and visualize the transcriptome.
Together the methods and tools expedite insights into biological systems that were not possible before.
The transcription factor Myc interacts with several co-factors to regulate growth and proliferationand thereby enables normal animal development. Deregulation of Myc is associated witha wide range of human tumors. Myc binds to DNA together with its dimerization partner Max, preferentially to canonical E-box motifs, but this sequence-specific interaction is probably not sufficient for Myc’s binding to target genes.
In this work, the PAF1 complex was characterized as a novel co-factor of Myc in Drosophila melanogaster. All components of the complex are required for Myc’s recruitment to chromatin, but the subunit Atu has the strongest effect on Myc's binding to target genes through ist direct physical interaction with Myc. Unexpectedly, the impact of Atu depletion on the Expression of Myc target genes was weak compared to its effect on Myc binding. However, the influence of Atu becomes more prominent in situations of elevated Myc levels in vivo . Mycrepressed as well as Myc-activated targets are affected, consistent with the notion that Myc
recruitment is impaired.
An independent set of analyses revealed that Myc retains substantial activity even in the complete absence of Max. The overexpression of Myc in Max0 mutants specifically blocks their pupariation without affecting their survival, which raised the possibility that Myc might
affect ecdysone biosynthesis. This connection was studied in the second part of this Thesis which showed that Myc inhibits the expression of ecdysteroidogenic genes and thereby the production of ecdysone. Myc most likely affects the signaling pathways (PTTH and insulin
signaling) upstream of the PG, the organ where ecdysone is produced. By combining existing ChIPseq, RNAseq and electronic annotation data, we identified five potential Maxindependent Myc targets and provided experimental data that they might be involved in Myc's effect on Max mutant animals. Together our data confirm that some Myc functions are Max-independent and they raise the possibility that this effect might play a role during replication.
The high infection rates and recent emergence of extremely drug resistant forms of
Mycobacterium tuberculosis pose a significant challenge for global health. The NADH-
dependent enoyl-ACP-reductase InhA of the type II mycobacterial fatty acid biosynthesis
pathway is a well-validated target for inhibiting mycobacterial growth. InhA has been
shown to be inhibited by a variety of compound series. Prominent classes of InhA
inhibitors from literature include diaryl ethers, pyrrolidine carboxamides and arylamides
which can be subjected to further development. Despite the progress in this area, very
few compounds are in clinical development phase. The present work involves a detailed
computational investigation of the binding modes and structure-based optimisation of
pyrrolidine carboxamides as InhA inhibitors.
With substituents of widely varying bulkiness, the pyrrolidine carboxamide dataset
presented a challenge for prediction of binding mode as well as affinity. Using advanced
docking protocols and in-house developed pose selection procedures, the binding modes
of 44 compounds were predicted. The poses from docking were used in short molecular
dynamics (MD) simulations to ascertain the dominant binding conformations for the
bulkier members of the series. Subsequently, an activity-based classification strategy
could be developed to circumvent the affinity prediction problems observed with this
dataset. The prominent motions of the bound ligand and the active site residues were
then ascertained using Essential Dynamics (ED). The information from ED and literature
was subsequently used to design a total of 20 compounds that were subjected to extensive
in-silico evaluations. Finally, the molecular determinants of rapid-reversible binding of
pyrrolidine carboxamides were investigated using long MD simulations.
This work considered the frequency-modulated balanced steady-state free precession (fm-bSSFP) sequence as a tool to provide banding free bSSFP MR images. The sequence was implemented and successfully applied to suppress bandings in various in vitro and in vivo examples. In combination with a radial trajectory it is a promising alternative for standard bSSFP applications. First, two specialized applications were shown to establish the benefits of the acquisition strategy in itself. In real time cardiac imaging, it was shown that the continuous shift in frequency causes a movement of the bandings across the FOV. Thus, no anatomical region is constantly impaired, and a suitable timeframe can be found to examine all important structures. Furthermore, a combination of images with different artifact positions, similar to phase-cycled acquisitions is possible. In this way, fast, banding-free imaging of the moving heart was realized. Second, acquisitions with long TR were shown. While standard bSSFP suffers from increasing incidence of bandings with higher TR values, the frequency-modulated approach provided banding free images, regardless of the TR.
A huge disadvantage of fm-bSSFP, in combination with the radial trajectory, is the decrease in signal intensity. In this work a specialized reconstruction method, the multifrequency reconstruction for frequency-modulated bSSFP (Muffm), was established, which successfully compensated that phenomena. The application of Muffm to several anatomical sites, such as inner ear, legs and cardiac acquisitions, proofed the advantageous SNR of the reconstruction.
Furthermore, fm-bSSFP was applied to the clinically highly relevant task of water-fat separation. Former approaches of a phase-sensitive separation procedure in combination with standard bSSFP showed promising results but failed in cases of high inhomogeneity or high field strengths where banding artifacts become a major issue. The novel approach of using the fm-bSSFP acquisition strategy with the separation approach provided robust, reliable images of high quality. Again, losses in signal intensity could be regained by Muffm, as both approaches are completely compatible.
Opposed to conventional banding suppression techniques, like frequency-scouts or phase-cycling, all reconstruction methods established in this work rely on a single radial acquisition, with scan times similar to standard bSSFP scans. No prolonged measurement times occur and patient time in the scanner is kept as short as possible, improving patient comfort, susceptibility to motion or physiological noise and cost of one scan.
All in all, the frequency-modulated acquisition in combination with specializes reconstruction methods, leads to a completely new quality of images with short acquisition times.
The work presented in this thesis covers the effects of early-life adversity in the context of altered serotonin (5-HT; 5-hydroxytryptamine) system functioning in mice. The main body is focussing on a screening approach identifying molecular processes, potentially involved in distinct behavioural manifestations that emerge from or are concomitant with early adversity and, with regard to some behavioural manifestations, dependent on the functioning of the 5-HT system.
The obligate intracellular pathogen Chlamydia trachomatis is the causative agent of
trachoma related blindness and the sexually transmitted pelvic inflammatory disease.
Being an obligate intracellular pathogen, C. trachomatis has an intricate dependency
on the survival of the host cell. This relationship is indispensible owing to the fact that
the pathogen spends a considerable fraction of its biphasic lifecycle within a
cytoplasmic vacuole inside the host cell, the so-called chlamydial inclusion. The
cellular apoptotic-signalling network is governed by several finely tuned regulatory
cascades composed of pro- and anti-apoptotic proteins that respond to changes in
the cellular homeostasis. In order to facilitate its intracellular survival, Chlamydia has
been known to inhibit the premature apoptosis of the host cell via the stabilization of
several host anti-apoptotic proteins such as cIAP2 and Mcl-1. While the pro- and
anti-apoptotic proteins are the major regulators of the host apoptotic signalling
network, a class of the small non-coding RNAs called microRNAs (miRNAs) has
increasingly gained focus as a new level of regulatory control over apoptosis.
This work investigates the changes in the host miRNA expression profile post
Chlamydia infection using a high throughput miRNA deep sequencing approach.
Several miRNAs previously associated with the modulation for apoptotic signalling
were differentially expressed upon Chlamydia infection in human endothelial cells. Of
the differentially regulated miRNAs, miR-30c-5p was of particular interest since it had
been previously shown to target the tumor suppressor protein p53. Our lab and
others have previously demonstrated that Chlamydia can downregulate the levels of
p53 by promoting its proteasomal degradation. This work demonstrates that
Chlamydia infection promotes p53 downregulation by increasing the abundance of
miR-30c-5p and a successful infection cycle is hindered by a loss of miR-30c-5p.
Over the last decade, dedicated research aimed towards a better understanding of
apoptotic stimuli has greatly improved our grasp on the subject. While extrinsic
stress, deprivation of survival signals and DNA damage are regarded as major
proponents of apoptotic induction, a significant responsibility lies with the
mitochondrial network of the cell. Mitochondrial function and dynamics are crucial to
cell fate determination and dysregulation of either is decisive for cell survival and
pathogenesis of several diseases. The ability of the mitochondrial network to perform
its essential tasks that include ATP synthesis, anti-oxidant defense, and calcium
homeostasis amongst numerous other processes critical to cellular equilibrium is tied
closely to the fission and fusion of individual mitochondrial fragments. It is, thus,
8
unsurprising that mitochondrial dynamics is closely linked to apoptosis. In fact, many
of the proteins involved regulation of mitochondrial dynamics are also involved in
apoptotic signalling. The mitochondrial fission regulator, Drp1 has previously been
shown to be transcriptionally regulated by p53 and is negatively affected by a miR-
30c mediated inhibition of p53. Our investigation reveals a significant alteration in the
mitochondrial dynamics of Chlamydia infected cells affected by the loss of Drp1. We
show that loss of Drp1 upon chlamydial infection is mediated by the miR-30c-5p
induced depletion of p53 and results in a hyper-fused architecture of the
mitochondrial network.
While it is widely accepted that Chlamydia depends on the host cell metabolism for
its intracellular growth and development, the role of mitochondria in an infected cell,
particularly with respect to its dynamic nature, has not been thoroughly investigated.
This work attempts to illustrate the dependence of Chlamydia on miR-30c-5p induced
changes in the mitochondrial architecture and highlight the importance of these
modulations for chlamydial growth and development.
Neurobiology is widely supported by bioinformatics. Due to the big amount of data generated from the biological side a computational approach is required. This thesis presents four different cases of bioinformatic tools applied to the service of Neurobiology.
The first two tools presented belong to the field of image processing. In the first case, we make use of an algorithm based on the wavelet transformation to assess calcium activity events in cultured neurons. We designed an open source tool to assist neurobiology researchers in the analysis of calcium imaging videos. Such analysis is usually done manually which is time consuming and highly subjective. Our tool speeds up the work and offers the possibility of an unbiased detection of the calcium events. Even more important is that our algorithm not only detects the neuron spiking activity but also local spontaneous activity which is normally discarded because it is considered irrelevant. We showed that this activity is determinant in the calcium dynamics in neurons and it is involved in important functions like signal modulation and memory and learning.
The second project is a segmentation task. In our case we are interested in segmenting the neuron nuclei in electron microscopy images of c.elegans. Marking these structures is necessary in order to reconstruct the connectome of the organism. C.elegans is a great study case due to the simplicity of its nervous system (only 502 neurons). This worm, despite its simplicity has taught us a lot about neuronal mechanisms. There is still a lot of information we can extract from the c.elegans, therein lies the importance of reconstructing its connectome. There is a current version of the c.elegans connectome but it was done by hand and on a single subject which leaves a big room for errors. By automatizing the segmentation of the electron microscopy images we guarantee an unbiased approach and we will be able to verify the connectome on several subjects.
For the third project we moved from image processing applications to biological modeling. Because of the high complexity of even small biological systems it is necessary to analyze them with the help of computational tools. The term in silico was coined to refer to such computational models of biological systems. We designed an in silico model of the TNF (Tumor necrosis factor) ligand and its two principal receptors. This biological system is of high relevance because it is involved in the inflammation process. Inflammation is of most importance as protection mechanism but it can also lead to complicated diseases (e.g. cancer). Chronic inflammation processes can be particularly dangerous in the brain. In order to better understand the dynamics that govern the TNF system we created a model using the BioNetGen language. This is a rule based language that allows one to simulate systems where multiple agents are governed by a single rule. Using our model we characterized the TNF system and hypothesized about the relation of the ligand with each of the two receptors. Our hypotheses can be later used to define drug targets in the system or possible treatments for chronic inflammation or lack of the inflammatory response.
The final project deals with the protein folding problem. In our organism proteins are folded all the time, because only in their folded conformation are proteins capable of doing their job (with some very few exceptions). This folding process presents a great challenge for science because it has been shown to be an NP problem. NP means non deterministic Polynomial time problem. This basically means that this kind of problems cannot be efficiently solved. Nevertheless, somehow the body is capable of folding a protein in just milliseconds. This phenomenon puzzles not only biologists but also mathematicians. In mathematics NP problems have been studied for a long time and it is known that given the solution to one NP problem we could solve many of them (i.e. NP-complete problems). If we manage to understand how nature solves the protein folding problem then we might be able to apply this solution to many other problems. Our research intends to contribute to this discussion. Unfortunately, not to explain how nature solves the protein folding problem, but to explain that it does not solve the problem at all. This seems contradictory since I just mentioned that the body folds proteins all the time, but our hypothesis is that the organisms have learned to solve a simplified version of the NP problem. Nature does not solve the protein folding problem in its full complexity. It simply solves a small instance of the problem. An instance which is as simple as a convex optimization problem. We formulate the protein folding problem as an optimization problem to illustrate our claim and present some toy examples to illustrate the formulation. If our hypothesis is true, it means that protein folding is a simple problem. So we just need to understand and model the conditions of the vicinity inside the cell at the moment the folding process occurs. Once we understand this starting conformation and its influence in the folding process we will be able to design treatments for amyloid diseases such as Alzheimer's and Parkinson's.
In summary this thesis project contributes to the neurobiology research field from four different fronts. Two are practical contributions with immediate benefits, such as the calcium imaging video analysis tool and the TNF in silico model. The neuron nuclei segmentation is a contribution for the near future. A step towards the full annotation of the c.elegans connectome and later for the reconstruction of the connectome of other species. And finally, the protein folding project is a first impulse to change the way we conceive the protein folding process in nature. We try to point future research in a novel direction, where the amino code is not the most relevant characteristic of the process but the conditions within the cell.
Analysis of the mechanism and the regulation of histatin 5 resistance in \(Candida\) \(albicans\)
(2018)
Antimycotics such as fluconazole are frequently used to treat C. albicans infections of the oral mucosa. Prolonged treatment of the fungal infection with fluconazole pose a risk to resistance development. C. albicans can adapt to these stressful environmental changes by regulation of gene expression or by producing genetically altered variants that arise in the population. Adapted variants frequently carry activating mutations in zinc cluster transcription factors, which cause the upregulation of their target genes, including genes encoding efflux pumps that confer drug resistance. MDR1, regulated by the zinc cluster transcription factor Mrr1, as well as CDR1 and CDR2, regulated by the zinc cluster transcription factor Tac1, are well-known examples of genes encoding efflux pumps that extrude the antimycotic fluconazole from the fungal cell and thus contribute to the survival of the fungus.
In this study, it was investigated if C. albicans can develop resistance to the antimicrobial peptide histatin 5, which serves as the first line of defence in the oral cavity of the human host. Recently, it was shown that C. albicans transports histatin 5 outside of the Candia cell via the efflux pump Flu1. As efflux pumps are often regulated by zinc cluster transcription factors, the Flu1 efflux pump could also be regulated by a zinc cluster transcription factor which could in a hyperactive form upregulate the expression of the efflux pump, resulting in increased export of histatin 5 and consequently in histatin 5 resistance.
In order to find a zinc cluster transcription factor that upregulates FLU1 expression, a comprehensive library of C. albicans strains containing artificially activated forms of zinc cluster transcription factors was screened for suitable candidates. The screening was conducted on medium containing mycophenolic acid because mycophenolic acid is also a substrate of Flu1 and a strain expressing a hyperactive zinc cluster transcription factor that upregulates FLU1 expression should exhibit an easily recognisable mycophenolic acid-resistant phenotype. Further, FACS analysis, quantitative real-time RT-PCR analysis, broth microdilution assays as well as histatin 5 assays were conducted to analyse the mechanism and the regulation of histatin 5 resistance.
Several zinc cluster transcription factors caused mycophenolic acid resistance and upregulated FLU1 expression. Of those, only hyperactive Mrr1 was able to confer increased histatin 5 resistance. Finding Mrr1 to confer histatin 5 resistance was highly interesting as fluconazole-resistant strains with naturally occurring Mrr1 gain of function mutations exist, which were isolated from HIV-infected patients with oral candidiasis. These Mrr1 gain of function mutations as well as artificially activated Mrr1 cause fluconazole resistance by upregulation of the efflux pump MDR1 and other target genes. In the course of the study, it was found that expression of different naturally occurring MRR1 gain-of-function mutations in the SC5314 wild type background caused increased FLU1 expression and increased histatin 5 resistance. The same was true for fluconazole-resistant clinical isolates with Mrr1 gain of function mutations, which also caused the overexpression of FLU1. Those cells were less efficiently killed by histatin 5 dependent on Mrr1. Surprisingly, FLU1 contributed only little to histatin 5 resistance, rather, overexpression of MDR1 mainly contributed to the Mrr1-mediated histatin 5 resistance, but also additional Mrr1-target genes were involved. These target genes are yet to be uncovered. Moreover, if a link between the yet unknown Mrr1-target genes contributing to fluconazole resistance and increased histatin 5 resistance can be drawn remains to be discovered upon finding of the responsible target genes.
Collectively, this study contributes to the understanding of the impact of prolonged antifungal exposure on the interaction between host and fungus. Drug therapy can give rise to resistance evolution resulting in strains that have not only developed resistance to fluconazole but also to an innate host mechanism, which allows adaption to the host niche even in the absence of the drug.
Transsexualität ist gekennzeichnet durch die dauerhafte Gewissheit, in einem Körper des falschen Geschlechts geboren worden zu sein. Bei Mann-zu-Frau-Transsexualität ist die Stimme ein oft unterschätzter Bestandteil der ganzheitlichen Therapie. Kann mit konservativer Therapie kein zufriedenstellend weiblicher Stimmklang erreicht werden, ist Phonochirurgie die Methode der Wahl. In Würzburg wird hierzu die Glottoplastik nach Wendler modifiziert durch Hagen angewendet.
An der vorliegenden Studie zur Qualitätsüberprüfung des operativen Verfahrens nahmen insgesamt 21 auf diese Art operierte Patientinnen teil, von denen 18 zu einer Nachuntersuchung in Würzburg erschienen und 3 die zugsandten Fragebögen ausfüllten. Erwartet wurden eine Anhebung der mittleren Sprechstimmlage sowie eine Veränderung weiterer objektiver Stimmparameter. Mit einer angehobenen Sprechstimmlage wurde auch eine höhere Zufriedenheit der Patientinnen mit ihrer Stimme vermutet. Nach Erfahrungsberichten vieler Patientinnen blieben Probleme beim Telefonieren jedoch weiterhin bestehen. Diese für den subjektiven Therapieerfolg sehr wichtige Situation wurde mit einer Perzeptionsstudie gezielt untersucht.
Insgesamt zeigte sich die Operation als risikoarme und effektive Therapieoption, um die mittlere Sprechstimmlage anzuheben. So lag die mittlere Sprechstimmlage der Patientinnen postoperativ im Median bei 170 Hz und somit im ausschließlich weiblichen Stimmlagenbereich. Die Anhebung der mittleren Sprechstimmlage ging mit einem leichten Verlust des Dynamikumfangs einher, der jedoch nur von ca. einem Drittel der Patientinnen als störend empfunden wurde. Zur subjektiven Erfolgskontrolle wurden Daten aus den standardisierten Fragebögen „Voice Handicap Index“ sowie „Fragebogen zur Lebenszufriedenheit“ und dem eigenen „Würzburger Fragebogen“ erhoben und ausgewertet. Die Ergebnisse dieser Fragebögen zeigten, abweichend von den guten objektiven Messwerten, deutliche Einschränkungen gegenüber einer stimmgesunden Vergleichsgruppe aus der Literatur. Diese Defizite betrafen sowohl die stimmbezogenen Fragengebiete des Voice Handicap Index, als auch die allgemeine Lebenszufriedenheit. Dennoch gaben die Patientinnen an, durch die Stimmoperation ein selbstsichereres Auftreten gegenüber fremden Personen gewonnen zu haben. Die subjektive Stimmzufriedenheit korrelierte sowohl mit der mittleren Sprechstimmlage als auch mit der Selbsteinschätzung der Weiblichkeit der Stimme. Bei Frequenz- und Dynamikumfang zeigten sich starke Differenzen zwischen objektiven Messergebnissen und subjektiver Zufriedenheit.
Für die Perzeptionsstudie zur Telefonsituation wurden von 18 Patientinnen sowie jeweils im Alter gepaarten männlichen und weiblichen Kontrollsprechern identische Sprachaufnahmen angefertigt und in der Frequenz entsprechend der Übertragungs-bandbreite am Telefon bearbeitet. Diese Stimmproben wurden 50 männlichen und 50 weiblichen zufällig ausgewählten Laienjuroren zur Bewertung hinsichtlich des Sprechergeschlechts vorgespielt. Gemessen wurde neben dem Urteil männlich oder weiblich auch die Zeitspanne von Beginn der Wiedergabe bis zur Urteilseingabe. Ungefähr 40 % der transsexuellen Patientinnen wurden mehrheitlich, also in über 50 % der Urteile als weiblich bewertet. Die Urteilszeit lag für die Sprachproben der transsexuellen Patientinnen signifikant über der Urteilszeit für männliche und weibliche Kontrollsprecher. Bezogen auf die Juroren zeigten sich Unterschiede zwischen männlicher und weiblicher Jurorengruppe: Männer ordneten die Sprachproben häufiger einem weiblichen Sprecher zu. Weibliche Juroren fällten ihr Urteil hingegen signifikant schneller als männliche Juroren. Es zeigte sich eine positive Korrelation der Geschlechtszuordnung mit der mittleren Sprechstimmlage. Die unabhängig von der Sprechstimmlage deutlich verlängerte Urteilszeit für transsexuelle Sprecherinnen zeigte jedoch, dass neben der mittleren Sprechstimmlage auch noch andere Faktoren die Geschlechtszuordnung beeinflussen. Dementsprechend existierte keine klare Grenzfrequenz, oberhalb derer Stimmen regelhaft als weiblich wahrgenommen wurden. Auch in einem in der Literatur mehrfach als ausschließlich weiblich definierten Sprechbereich wurden die Stimmen einzelner Patientinnen mehrheitlich als männlich wahrgenommen. Es konnte kein Zusammenhang der Formantfrequenzen F1 – F3 mit der Geschlechtszuordnung gefunden werden.
Zusammenfassend zeigten diese aus objektiven Stimmdaten, Eigen- und Fremd-bewertung bestehenden Ergebnisse, dass durch alleinige Operation zwar eine höhere Stimmlage, jedoch kein vollständig weiblicher Stimmklang erreicht wurde. Deswegen muss die Phonochirurgie zukünftig stärker in ein umfassendes Behandlungskonzept aus logopädischem Stimmtraining, Übungen für eine weibliche Gestik und Mimik sowie Alltagstraining eingebunden werden. Hierzu wurde in dieser Arbeit ein neuer Behandlungsalgorithmus für die Univ.-HNO-Klinik Würzburg erstellt.
Kürzlich wurden bei immunvermittelten Neuropathien Autoantikörper gegen Proteine
des paranodalen axoglialen Komplexes beschrieben. Deren Charakteristika,
Prävalenzen, pathophysiologische Relevanz sowie Bedeutung für Diagnostik
und Therapie sind jedoch noch nicht abschließend erforscht.
In dieser Studie wurden daher Seren und Plasmapheresematerial (PE-Material)
von 150 Patienten mit inflammatorischen Neuropathien, nämlich 105 mit chronisch
inflammatorischer demyelinisierender Polyneuropathie (CIDP), 21 mit Guillain-
Barré-Syndrom (GBS) und 24 mit multifokaler motorischer Neuropathie
(MMN), welche etablierte diagnostische Kriterien der jeweiligen Krankheit erfüllen,
sowie 74 Kontrollen mittels immunhistochemischen Färbungen an murinen
Zupfnervenpräparaten und/oder ELISA (Enzyme-linked Immunosorbent Assay)
auf Autoantikörper gegen die paranodalen Proteine Caspr, Contactin-1 und Neurofascin-
155 untersucht. Bei positivem Ergebnis wurde deren Spezifität mittels
immunhistochemischen Färbungen an transfizierten HEK (Human embryonic kidney)-
293-Zellen und Präinkubationsversuchen bestätigt. Es wurden die IgG-Subklassen
und die Antikörpertiter bestimmt und das Komplementbindungsverhalten
unter Zugabe von intravenösen Immunglobulinen (IVIG) mit zellbasierten und
ELISA-basierten Methoden analysiert. Klinische Merkmale und das Therapieansprechen
Antikörper-positiver Patienten wurden ermittelt und mit den experimentellen
Ergebnissen in Zusammenhang gesetzt.
IgG-Autoantikörper gegen Contactin-1 konnten bei vier Patienten mit CIDP nachgewiesen
werden, IgG-Autoantikörper gegen Caspr bei einem Patienten mit
CIDP und einer Patientin mit GBS. Es konnten keine weiteren Autoantikörper bei
CIDP-Patienten, GBS-Patienten, MMN-Patienten oder bei den Kontrollen detektiert
werden. Die Prävalenz von Autoantikörpern gegen axogliale paranodale Proteine
liegt somit in dieser Studie bei jeweils 4,76% bei CIDP und GBS und 0%
bei MMN. Die Antikörper gehörten bei Patienten in der akuten Erkrankungsphase
(zwei der CIDP-Patienten mit Anti-Contactin-1-Autoantikörpern und eine GBS-Patientin mit Anti-Caspr-Autoantikörpern) hauptsächlich den Subklassen IgG1
und IgG3 an, bei Patienten in der chronischen Phase (zwei der CIDP-Patienten
mit Anti-Contactin-1-Autoantikörpern, ein CIDP-Patient mit Anti-Caspr-Autoantikörpern)
überwog die Subklasse IgG4. Experimentell kam es zur Komplementbindung
und -aktivierung abhängig vom Gehalt der Subklassen IgG1-3, nicht
aber IgG4; diese konnte durch die Zugabe von IVIG dosisabhängig gemindert
werden. Alle Autoantikörper-positiven CIDP-Patienten zeigten einen GBS-artigen
Beginn mit einer schweren motorischen Beteiligung. Anti-Contactin-1-positive
Patienten kennzeichnete klinisch zusätzlich das Vorkommen einer Ataxie und eines
Tremors, Anti-Caspr-positive Patienten das Vorkommen starker neuropathischer
Schmerzen. Elektrophysiologisch standen neben Hinweisen auf eine Leitungsstörung
Zeichen einer axonalen Schädigung im Vordergrund. Als histopathologisches
Korrelat lagen eine nodale Architekturstörung und ein Axonverlust
vor. Die Patienten zeigten nur in der Anfangsphase der Erkrankung ein Ansprechen
auf IVIG. Bei drei CIDP-Patienten mit IgG4-Autoantikörpern (zwei Patienten
mit Anti-Contactin-1-Antikörpern und ein Patient mit Anti-Caspr-Antikörpern)
wurde eine Therapie mit Rituximab durchgeführt. Diese führte zu einer Titerreduktion
und zur zeitgleichen klinischen und elektrophysiologischen Befundbesserung
bei zwei Patienten.
Die in dieser Arbeit angewandten Screeningmethoden führten zum erfolgreichen
Nachweis von Autoantikörpern gegen paranodale axogliale Proteine. Die Patienten
mit positivem Autoantikörpernachweis definieren eine kleine Untergruppe mit
ähnlichen klinischen Merkmalen im Kollektiv der Patienten mit inflammatorischen
Polyneuropathien. Histopathologische Merkmale sowie das Therapieansprechen
auf antikörperdepletierende Therapie sprechen in Kombination mit den Ergebnissen
weiterer Studien zu paranodalen Autoantikörpern für eine pathogenetische
Relevanz der Autoantikörper. Mit einem charakteristischen, am Schnürring ansetzenden
Pathomechanismus könnten Neuropathien mit Nachweis von paranodalen
Autoantikörpern der kürzlich eingeführten Entität der Nodo-Paranodopathien
angehören. Die Komplementaktivierung und das Therapieansprechen der Patienten auf IVIG stehen möglicherweise in Zusammenhang mit der prädominanten
IgG-Subklasse. Diese könnte auch in Bezug auf die Chronifizierung eine
Rolle spielen. Der Nachweis von Autoantikörpern gegen paranodale Proteine hat
wohlmöglich in Zukunft direkte Konsequenzen auf das diagnostische und therapeutische
Prozedere bei Patienten mit CIDP und GBS; weitere klinische und experimentelle
Daten aus größeren, prospektiven Studien sind jedoch zum weiteren
Verständnis und zur Charakterisierung dieser Entität notwendig.
The pancreas and the small intestine are pivotal organs acting in close synergism to regulate glucose metabolism. After absorption and processing of dietary glucose within the small intestine, insulin and glucagon are released from pancreatic islet cells to maintain blood glucose homeostasis. Malfunctions affecting either individual, organ-specific functions or the sophisticated interplay of both organs can result in massive complications and pathologic conditions. One of the most serious metabolic diseases of our society is diabetes mellitus (DM) that is hallmarked by a disturbance of blood glucose homeostasis. Type 1 (T1DM) and type 2 (T2DM) are the main forms of the disease and both are characterized by chronic hyperglycemia, a condition that evokes severe comorbidities in the long-term. In the past, several standard treatment options allowed a more or less adequate therapy for diabetic patients. Albeit there is much effort to develop new therapeutic interventions to treat diabetic patients in a more efficient way, no cure is available so far. In view of the urgent need for alternative treatment options, a more systemic look on whole organ systems, their biological relation and complex interplay is needed when developing new therapeutic strategies for DM.
T1DM is hallmarked by an autoimmune-mediated destruction of the pancreatic β-cell mass resulting in a complete lack of insulin that is in most patients restored by applying a life-long recombinant insulin therapy. Therefore, novel regenerative medicine-based concepts focus on the derivation of bioartificial β-like cells from diverse stem cell sources in vitro that survive and sustain to secrete insulin after implantation in vivo. In this context, the first part of this thesis analyzed multipotent intestinal stem cells (ISCs) as alternative cell source to derive bioartificial, pancreatic β-like cells in vitro. From a translational perspective, intestinal stem cells pose a particularly attractive cell source since intestinal donor tissues could be obtained via minimal invasive endoscopy in an autologous way. Furthermore, intestinal and pancreatic cells both derive from the same developmental origin, the endodermal gut tube, favoring the differentiation process towards functional β-like cells. In this study, pancreas-specific differentiation of ISCs was induced by the ectopic expression of the pancreatic transcription factor 1 alpha (Ptf1a), a pioneer transcriptional regulator of pancreatic fate. Furthermore, pancreatic lineage-specific culture media were applied to support the differentiation process. In general, ISCs grow in vitro in a 3D Matrigel®-based environment. Therefore, a 2D culture platform for ISCs was established to allow delivery and ectopic expression of Ptf1a with high efficiency. Next, several molecular tools were applied and compared with each other to identify the most suitable technology for Ptf1a delivery and expression within ISCs as well as their survival under the new established 2D conditions. Success of differentiation was investigated by monitoring changes in cellular morphology and induction of pancreatic differentiation-specific gene expression profiles. In summary, the data of this project part suggest that Ptf1a harbors the potential to induce pancreatic differentiation of ISCs when applying an adequate differentiation media. However, gene expression analysis indicated rather an acinar lineage-determination than a pancreatic β-cell-like specification. Nevertheless, this study proved ISCs not only as interesting stem cell source for the generation of pancreatic cell types with a potential use in the treatment of T1DM but alsoPtf1a as pioneer factor for pancreatic differentiation of ISCs in general.
Compared to T1DM, T2DM patients suffer from hyperglycemia due to insulin resistance. In T2DM management, the maintenance of blood glucose homeostasis has highest priority and can be achieved by drugs affecting the stabilization of blood glucose levels. Recent therapeutic concepts are aiming at the inhibition of the intestinal glucose transporter Na+-D-Glucose cotransporter 1 (SGLT1). Pharmacological inhibition of SGLT1 results in reduced postprandial blood glucose levels combined with a sustained and increased Glucagon-like peptide 1 (GLP-1) secretion. So far, systemic side effects of this medication have not been addressed in detail. Of note, besides intestinal localization, SGLT1 is also expressed in various other tissues including the pancreas. In context of having a closer look also on the interplay of organs when developing new therapeutic approaches for DM, the second part of this thesis addressed the effects on pancreatic islet integrity after loss of SGLT1. The analyses comprised the investigation of pancreatic islet size, cytomorphology and function by the use of a global SGLT1 knockout (SGLT1-/-) mouse model. As SGLT1-/- mice develop the glucose-galactose malabsorption syndrome when fed a standard laboratory chow, these animals derived a glucose-deficient, fat-enriched (GDFE) diet. Wildtype mice on either standard chow (WTSC) or GDFE (WTDC) allowed the discrimination between diet- and knockout-dependent effects. Notably, GDFE fed mice showed decreased expression and function of intestinal SGLT1, while pancreatic SGLT1 mRNA levels were unaffected. Further, the findings revealed increased isled sizes, reduced proliferation- and apoptosis rates as well as an increased α-cell and reduced β-cell proportion accompanied by a disturbed cytomorphology in islets when SGLT1 function is lost or impaired. In addition, pancreatic islets were dysfunctional in terms of insulin- and glucagon-secretion. Moreover, the release of intestinal GLP-1, an incretin hormone that stimulates insulin-secretion in the islet, was abnormal after glucose stimulatory conditions. In summary, these data show that intestinal SGLT1 expression and function is nutrient dependent. The data obtained from the islet studies revealed an additional and new role of SGLT1 for maintaining pancreatic islet integrity in the context of structural, cytomorphological and functional aspects. With special emphasis on SGLT1 inhibition in diabetic patients, the data of this project indicate an urgent need for analyzing systemic side effects in other relevant organs to prove pharmacological SGLT1 inhibition as beneficial and safe.
Altogether, the findings of both project parts of this thesis demonstrate that focusing on the molecular and cellular relationship and interplay of the small intestine and the pancreas could be of high importance in context of developing new therapeutic strategies for future applications in DM patients.
The present study was conducted on the rOCT1, a member of SLC22 family. Structurally, it consists of 12 membrane spanning α-helices with both N- and C-termini intracellular. Studies done so far, through tracer uptake and inhibition, reconstitution of rOCT1 in nanodiscs and proteoliposomes and voltage-clamp fluorometry, have identified the main amino acids in the cleft of rOCT1 that interact in a critical manner with the substrates/inhibitors either directly or indirectly. Homology modeling studies have also supported these observations. In the present study we aimed at measuring the binding of substrates MPP+ and TEA+ to rOCT1 at 0oC in order to establish the amino acids in the cleft region that interact with the substrate when the transporter is frozen in the outward-open conformation. Previously identified crucial amino acids (Asp475, Phe160, Leu447, Arg440, Trp218 and Tyr222) were selected for the study. rOCT1 wild-type and its mutants were stably expressed in HEK293 cells and these cells were used for the binding measurements with the radioactive substrate (MPP+ or TEA+) at 0°C in Mg-Ca-PBS buffer as described in “Materials and Methods” section in detail. rOCT1 wild-type revealed for MPP+-binding a KD which was not significantly different from the corresponding Km value. Also, after addition of 10 nM non-radioactive MPP+, an initial increase of about 20% in bound MPP+ was observed. The results indicate that the Km for transport is dependent on the binding of MPP+ to the outward-open conformation and hints at the possibility of allosteric interaction between the binding sites. Mutations at position Trp218, Phe160 and Asp475 resulted in a change in the KD value. Trp218 mutations also showed an allosteric increase similar to the rOCT1 wild-type. This study suggests that these amino acids are located at a critical position in the outward-open conformation for MPP+ transport. TEA+-binding could not be observed in rOCT1 wild-type, indicating that the binding site is perhaps inaccessible for TEA+ in frozen outward-open state. The mutants D475E, F160A, L447F, R440K and Y222F showed a very low affinity binding with a very high KD value as compared to the corresponding Km values indicating that the transporter might have different affinities for extra-cellular binding alone and for the complete transport process especially if temperature is the limiting factor. Substrate inhibition studies done using both MPP+ and TEA+ have confirmed the existence of overlapping binding sites for these two ligands. This study has confirmed the direct interaction of Trp218, Phe160, Asp475 with MPP+ and Phe160, Asp475, Leu447, Arg440 and Tyr222 with TEA+ in the outward-open conformation.
Coffin-Lowry syndrome is a rare syndromic form of X-linked mental retardation caused by heterogeneous loss-of-function mutations in the gene RPS6KA3 that encodes the RSK2 protein. Clinical features are delayed motor development, small height, progressive skeletal malformations and mental retardation.
Rsk2 deficiency affects behavioral, cellular and molecular functions. To characterize and investigate how this deficiency affects these functions, we made a series of experiments using Rsk2-deficient mice as the animal model for Coffin-Lowry syndrome.
We applied a battery of behavioral tests and included the use of the IntelliCage for the first time as a behavioral paradigm to study anxiety-like behavior and depression-like behavior in Rsk2-deficient mice. Results from the conventional behavioral tests and from the IntelliCage indicate that Rsk2-deficient mice may have an anti-anxiety and anti-depressive phenotype.
We evaluated in Rsk2 deficient mice the relative gene expression of a set of genes coding for proteins related to RSK2 which are involved in fear memory, synaptic plasticity, neurogenesis, learning, emotional behavior and stress. We found gene expression alterations in the prefrontal cortex and striatum. These results suggest that RSK2 may be involved in the expression of the genes.
RSK2 is known to be related to monoamine neurotransmitter function. We measured the levels of dopamine, serotonin and noradrenaline/norepinephrine and their metabolites in different brain regions of Rsk2-deficient mice. We found differences in the dopaminergic and noradrenergic systems suggesting an increased or decreased activity of these neurotransmission systems as a result of Rsk2 deficiency.
Adult neurogenesis is a form of neuronal plasticity and a multi-step process of cell development. We explored if this form of neuronal plasticity was affected by Rsk2-deficiency. Our results indicate that adult hippocampal neurogenesis is not influenced by lifelong Rsk2 deficiency. It would be worth to analyze in the future other aspects of neuroplasticity.
We have confirmed, that behavioral characteristics of Rsk2-deficient mice make them an interesting model to study the Coffin-Lowry syndrome by extending the behavioral characterization on the emotional level. Furthermore, we have extended the characterization of the model on a molecular level, opening new opportunities to study and understand the pathophysiological basis of the Coffin-Lowry syndrome.
For cellular viability, transcription is a fundamental process. Hereby, the DNA plays the most elemental and highly versatile role. It has long been known that promoters contain conserved and often well-defined motifs, which dictate the site of transcription initiation by providing binding sites for regulatory proteins. However, research within the last decade revealed that it is promoters lacking conserved promoter motifs and transcribing constitutively expressed genes that constitute the majority of promoters in eukaryotes. While the process of transcription initiation is well studied, whether defined DNA sequence motifs are required for the transcription of constitutively expressed genes in eukaryotes remains unknown. In the highly divergent protozoan parasite Trypanosoma brucei, most of the proteincoding genes are organized in large polycistronic transcription units. The genes within one polycistronic transcription unit are generally unrelated and transcribed by a common transcription start site for which no RNA polymerase II promoter motifs have been identified so far. Thus, it is assumed that transcription initiation is not regulated but how transcription is initiated in T. brucei is not known. This study aimed to investigate the requirement of DNA sequence motifs and chromatin structures for transcription initiation in an organism lacking transcriptional regulation. To this end, I performed a systematic analysis to investigate the dependence of transcription initiation on the DNA sequence. I was able to identify GT-rich promoter elements required for directional transcription initiation and targeted deposition of the histone variant H2A.Z, a conserved component during transcription initiation. Furthermore, nucleosome positioning data in this work provide evidence that sites of transcription initiation are rather characterized by broad regions of open and more accessible chromatin than narrow nucleosome depleted regions as it is the case in other eukaryotes. These findings highlight the importance of chromatin during transcription initiation. Polycistronic RNA in T. brucei is separated by adding an independently transcribed miniexon during trans-splicing. The data in this work suggest that nucleosome occupancy plays an important role during RNA maturation by slowing down the progressing polymerase and thereby facilitating the choice of the proper splice site during trans-splicing. Overall, this work investigated the role of the DNA sequence during transcription initiation and nucleosome positioning in a highly divergent eukaryote. Furthermore, the findings shed light on the conservation of the requirement of DNA motifs during transcription initiation and the regulatory potential of chromatin during RNA maturation. The findings improve the understanding of gene expression regulation in T. brucei, a eukaryotic parasite lacking transcriptional Regulation.
Fluorescence microscopy has become one of the most important techniques for the imaging of biological cells and tissue, since the technique allows for selective labeling with fluorescent molecules and is highly suitable for low-light applications down to the single molecule regime. The methodological requirements are well-defined for studying membrane receptors within a highly localized nanometer-thin membrane. For example, G-protein-coupled receptors (GPCRs) are an extensively studied class of membrane receptors that represent one of the most important pharmaceutical targets. Ligand binding and GPCR activation dynamics are suspected to take place at the millisecond scale and may even be far faster. Thus, techniques that are fast, selective, and live-cell compatible are required to monitor GPCR dynamics. Fluorescence resonance energy transfer (FRET) and total internal reflection fluorescence microscopy (TIRF-M) are methods of choice to monitor the dynamics of GPCRs selectively within the cell membrane.
Despite the remarkable success of these modalities, there are limitations. Most importantly, inhomogeneous illumination can induce imaging artifacts, rendering spectroscopic evaluation difficult. Background signal due to scattering processes or imperfect labeling can hamper the signal-to-noise, thus limiting image contrast and acquisition speed. Careful consideration of the internal physiology is required for FRET sensor design, so that ligand binding and cell compatibility are well-preserved despite the fluorescence labeling procedures. This limitation of labeling positions leads to very low signal changes in FRET-based GPCR analysis. In addition, microscopy of these systems becomes even more challenging in single molecule or low-light applications where the accuracy and temporal resolution may become dramatically low. Fluorescent labels should therefore be brighter, protected from photobleaching, and as small as possible to avoid interference with the binding kinetics. The development of new fluorescent molecules and labeling methods is an ongoing process. However, a complete characterization of new labels and sensors takes time. So far, the perfect dye system for GPCR studies has not been found, even though there is high demand.
Thus, this thesis explores and applies a different approach based on improved illumination schemes for TIRF-M as well as metal-coated coverslips to enhance fluorescence and FRET efficiency. First, it is demonstrated that a 360° illumination scheme reduces typical TIRF artifacts and produces a much more homogenously illuminated field of view. Second, membrane imaging and FRET spectroscopy are improved by metal coatings that are used to modulate the fluorescent properties of common fluorescent dyes. Computer simulation methods are used to understand the underlying photophysics and to design the coatings. Third, this thesis explores the operational regime and limitations of plasmonic approaches with high sectioning capabilities. The findings are summarized by three publications that are presented in the results section of this work. In addition, the theory of fluorescence and FRET is explained, with particular attention to its emission modulations in the vicinity of metal-dielectric layers. Details of the instrumentation, computer simulations, and cell culture are described in the method section. The work concludes with a discussion of the findings within the framework of recent technological developments as well as perspectives and suggestions for future approaches complete the presented work.
Kritische Knochendefekte stellen heutzutage ein ungelöstes Problem in der klinischen Praxis dar, da die verfügbaren prothetischen Optionen oft die mechanische Anpassung an das Gewebe nicht gewährleisten oder zu wichtigen immunologischen und Implantat-bedingten Komplikationen führen.
In diesem Kontext ermöglichen Tissue Engineering-Ansätze neue Strategien, um in vitro Zell-Material Interaktionen zu untersuchen und so die Implantatmaterialien zu optimieren.
In dieser Arbeit habe ich Zell-Material Interaktionen eines neuen Kollagen-basierten Scaffolds untersucht, das langfristig als Trägerstruktur für eine zellbasierte Therapie für kritische Knochendefekte entwickelt werden soll. Im Rahmen der Dissertation konnte ich belegen, dass die Kollagen-basierten makroporöse Mikrocarrier für die Zellvermehrung humaner mesenchymaler Stammzellen (MSC) und deren osteogene Differenzierung unter GMP Bedingungen verwendet werden können. Außerdem habe ich die die Kokultur von hämatopoietischen Stammzellen des Knochenmarks und multiplen Myelomzellen funktionell charakterisiert. Ich konnte erstmals Kulturbedingungen etablieren, die die Langzeitkultur ohne die Verwendung von Zytokinen ermöglicht. Mittels dieser Kokultur konnte ich ein Knochenmarknischen-Modell etablieren und die Untersuchung der Expression von zentralen Signalkaskaden der Homöostase dieser Nische untersuchen. Ich konnte die Expression von zwei verschiedenen Isoformen von Osteopontin nachweisen, die in Tiermodellen nicht gefunden werden. Diese Isoformen des Osteopontins habe ich kloniert und die rekombinanten Isoformen exprimiert und ihre Rollen in der Homöostase der Knochenmarknische untersucht.
Critical size bone defects represent nowadays an unresolved problem in the clinical practice, where the available prosthetic options often lack adequate mechanical matching to the host tissue or lead to important immunological and implant-related complications.
In this context, Tissue Engineering approaches promise more effective strategies to study cell-material interactions in vitro and consequently optimize implant materials.
In this work, I investigated the cell-scaffold interactions of a new collagen-based scaffold for a putative cell-based therapy for critical size defects to be developed. In the context of this thesis, I could demonstrate that the collagen-based macroporous microcarriers could be employed for the expansion and osteogenic differentiation of human mesenchymal stromal cells (MSCs) under GMP-compliant conditions. Moreover, I functionally characterized the co-culture of bone marrow hematopoietic stem cells and multiple myeloma cells. I was for the first time able to establish culture conditions allowing their long-term culture in absence of externally supplemented cytokines. Using this co-culture, I was able to establish a bone marrow niche model to investigate the expression of key signaling pathways involved in the niche´s homeostasis. I was able to demonstrate the expression of two different isoforms of Osteopontin, that could not previously be detected in animal models. Finally, I cloned these Osteopontin isoforms, expressed recombinant versions of the isoforms, and investigated their roles in the homeostasis of the bone marrow niche.
The transcription factor MYC is deregulated in over 70% of all human tumors and, in its oncogenic form, plays a major role in the cancer metabolic reprogramming, promoting the uptake of nutrients in order to sustain the biosynthetic needs of cancer cells.
The research presented in this work aimed to understand if MYC itself is regulated by nutrient availability, focusing on the two major fuels of cancer cells: glucose and glutamine.
Initial observations showed that endogenous MYC protein levels strongly depend on the availability of glutamine, but not of glucose. Subsequent analysis highlighted that the mechanism which accounts for the glutamine-mediated regulation of MYC is dependent on the 3´-untranslated region (3´-UTR) of MYC. Enhanced glutamine utilization by tumors has been shown to be directly linked to MYC oncogenic activity and MYC-dependent apoptosis has been observed under glutamine starvation. Such effect has been described in experimental systems which are mainly based on the use of MYC transgenes that do not contain the 3´-UTR. It was observed in the present study that cells are able to survive under glutamine starvation, which leads to cell cycle arrest and not apoptosis, as previously reported. However, enforced expression of a MYC transgene, which lacks the 3´-UTR, strongly increases the percentage of apoptotic cells upon starvation. Evaluation of glutamine-derived metabolites allowed to identify adenosine nucleotides as the specific stimulus responsible for the glutamine-mediated regulation of MYC, in a 3´-UTR-dependent way. Finally, glutamine-dependent MYC-mediated effects on RNA Polymerase II (RNAPII) function were evaluated, since MYC is involved in different steps of global transcriptional regulation. A global loss of RNAPII recruitment at the transcriptional start site results upon glutamine withdrawal. Such effect is overcome by enforced MYC expression under the same condition.
This study shows that the 3´UTR of MYC acts as metabolic sensor and that MYC globally regulates the RNAPII function according to the availability of glutamine. The observations presented in this work underline the importance of considering stress-induced mechanisms impinging on the 3´UTR of MYC.
Immunologische Gedächtnisreaktionen sind die Grundlage um wiederkehrende Erreger schnell und effizient zu bekämpfen und um einen Impfschutz zu generieren. Das zellvermittelte Gedächtnis wird unter anderem durch CD8 Gedächtnis-T-Zellen aufgebaut, welche vor allem im Kontext von Immunreaktionen gegen intrazellulärer Erreger vonnöten sind, um bei Reinfektion mit den Erregerstämmen einen schnellen Schutz zu gewährleisten. Ein detailliertes Wissen über die Generierung, Kontrolle und Reaktivierung der Gedächtniszellen ist nützlich, um Gedächtnisreaktionen verstehen und lenken zu können. Durch die Entdeckung des TZR und CD28 wurden Meilensteine für das Verständnis der T-Zellaktivierung gelegt und die Grundlage geschaffen, CD8 Gedächtnisreaktionen zu verstehen. Auch wenn für primäre Immunreaktionen die „2-Signal-Theorie“ lange als erwiesen gilt, so blieb die Rolle der Kostimulation für Gedächtnisreaktionen lange umstritten. In dieser Arbeit wurden verschiedene methodische Herangehensweisen verwendet, mit denen durchgehend die Bedeutung von CD28 vermittelter Kostimulation für immunologische CD8 T-Zell-Gedächtnisreaktionen nachgewiesen wurde. CD28 blockierende Antikörper und CD28 induzierbar deletierbare Mauslinien wurden im Modellinfektionssystem mit Ovalbumin produzierenden Listeria monocytogenes zur Analyse der Primär- und Sekundärantworten verwendet. Mit diesen Methoden konnte eine Beeinträchtigung der Expansion von CD8 Gedächtniszellen in Abwesenheit von CD28 bewiesen werden. Weiterhin werden Effektorfunktionen wie Degranulation und Produktion von IFN-γ während der Sekundärinfektion in Abwesenheit von Kostimulation eingeschränkt. Mit Hilfe von Experimenten, bei denen CD28 suffizienten Mäusen eine geringe Anzahl an naiven, antigenspezifischen, CD28 deletierbaren CD8 T-Zellen transferiert wurden, wurde die Bedeutung der Kostimulation für die Expansion von Gedächtniszellen bestätigt, jedoch konnte überraschenderweise auch ein Anstieg der Effektorfunktionen in Abwesenheit von CD28 sowohl während der Primär- als auch der Sekundärantwort dokumentiert werden. Diese zur globalen Blockade bzw. Deletion widersprüchlichen Ergebnisse lassen eine Beteiligung anderer CD28 abhängiger Zelltypen an der Induktion der Effektorfunktionen der CD8 T-Zellen plausibel erscheinen, wie zum Beispiel Einflüsse von T-Helferzellen, welche die Effektorfunktionen positiv verstärken, solange sie selbst Kostimulationssignale empfangen können. Weiterhin konnte gezeigt werden, dass sich Gedächtniszellen an den CD28 defizienten Phänotyp – eine CD28 intakte immunologische Umgebung vorausgesetzt – adaptieren können, wenn ausreichend Zeit nach Deletion und vor Sekundärinfektion verstreichen konnte.
Cardiovascular diseases represent the leading cause of death worldwide, with myocardial infarction and strokes being the most common complications. In both cases, the appearance of an enlarged artery wall as a consequence of a growing plaque is responsible for the disturbance of the blood flow. The formation of plaques is driven by a chronic inflammatory condition known as atherosclerosis, characterized by an initial step of endothelial cell (EC) dysfunction followed by the recruitment of circulating immune cells into the tunica intima of the vessel. Accumulation of lipids and cells lead to the formation of atheromatous plaques that will define the cardiovascular outcome of an individual.
The role of the immune system in the progression of atherosclerosis has been widely recognized. By far, macrophages constitute the most abundant cell type in lesions and are known to be the major source of the lipid-laden foam cell pool during the course of the disease. However, other immune cells types, including T cells, dendritic cells (DCs) or mast cells, among others, have been described to be present in human and mouse plaques. How these populations can modulate the atherogenic process is dependent on their specialized function.
DCs constitute a unique population with the ability to bridge innate and adaptive immune responses, mainly by their strong capacity to present antigens bound to a major histocompatibility complex (MHC) molecule. Given their ability to polarize T cells and secrete cytokines, their role in atherosclerosis has gained attention for the development of new therapeutic approaches that could impact lesion growth. Hence, knowing the effect of a specific subset is an initial key step to evaluate its potential for clinical purposes. For example, the basic leucine zipper ATF-like 3 transcription factor (Batf3) controls the development of conventional dendritic cells type 1 (cDCs1), characterized by the expression of the surface markers CD8 and CD103. Initially, they were described to promote both T-helper 1 (Th1) and regulatory T cell (Treg) responses, known to accelerate and to protect against atherosclerosis, respectively. The first part of this thesis aimed to elucidate the potential role of Batf3-dependent DCs in atherosclerosis and concluded that even though systemic immune responses were mildly altered they do not modify the course of the disease and may not represent an attractive candidate for clinical studies.
DCs also have the ability to impact lesion growth through the release of a broad range of cytokines, which can either directly impact atherosclerotic plaques by modulating resident cells, or by further polarizing T cell responses. Among others, interleukin (IL) 23, a member of the IL-12 family of cytokines, has received much attention during the past year due to its connection to autoimmunity.
IL-23 is known to induce pathogenicity of Th17 cells and is responsible for the development of several autoimmune diseases including multiple sclerosis, psoriasis or rheumatoid arthritis. Interestingly, these patients often present with an accelerated course of atherosclerosis and thus, are at higher risk of developing cardiovascular events. Several epidemiological studies have pointed toward a possible connection between IL-23 and its receptor IL-23R in atherosclerosis, although their exact contribution remains to be elucidated. The second part of this thesis showed that resident antigen-presenting cells (APCs) in the aorta produced IL-23 during the steady state but this secretion was greatly enhanced after incubation with oxidized low-density lipoprotein (oxLDL). Furthermore, disruption of the IL-23R signaling led to decreased relative necrotic plaque area in lesions of Ldlr-/-Il23r-/- mice fed a high-fat diet (HFD) for 6 and 12 weeks compared to Ldlr-/- controls. A proposed mechanism involves that increased IL-23 production in the context of atherosclerosis may promote the pathogenicity of IL-23-responding T cells, especially IL-23R+ γδ T cells in the aortic root. Response to IL-23 might increase the release of granulocyte-macrophage colony-stimulating factor (GM-CSF) and IL-17 and alter the pro- and anti-inflammatory balance of cytokines in the aortic root. Altogether, these data showed that the IL-23 / IL-23R axis play a role in plaque stability.
Bei der Entstehung und Aufrechterhaltung von Furcht und Angsterkrankungen stellt, neben der Furchtkonditionierung, die Generalisierung der konditionierten Furcht einen wesentlichen Mechanismus dar. Die der Generalisierung zugrunde liegenden psychologischen und biologischen Prozesse sind jedoch beim Menschen bisher nur wenig untersucht.
Ziel dieser Arbeit war, anhand eines neu entwickelten experimentellen Paradigmas den Einfluss eines psychometrisch bestimmbaren angstspezifischen Faktors sowie der mit Furcht und Angst assoziierten Genotypen Stathmin1, COMT Val158Met und BDNF Val66Met auf die Furchtkonditionierung und Generalisierung konditionierter Furcht zu untersuchen und somit mögliche Risikofaktoren für die Entstehung von Angsterkrankungen zu bestimmen. Hierfür wurden N = 126 gesunde Versuchspersonen (n = 69 weiblich; mittleres Alter M = 23.05, SD = 3.82) für die genannten Polymorphismen genotypisiert und zu ängstlichen und affektiven Symptomen befragt. In einer Akquisitionsphase wurden den Probanden zwei neutrale weibliche Gesichter präsentiert (CS), von denen eines mit einem Schrei sowie einem ängstlichen Gesichtsausdruck (UCS) gepaart wurde. Der sich anschließende Generalisierungstest erfolgte anhand von vier Gesichtern, die in der Ähnlichkeit zwischen den beiden CS schrittweise übergingen. Die Furchtreaktion wurde über die Bewertung von Valenz, Arousal und Kontingenzerwartung sowie über die Hautleitfähigkeitsreaktion (SCR) erfasst.
Die Analyse der Fragebögen anhand einer Hauptachsenanalyse und anhand von Strukturgleichungsmodellen erbrachte eine zweifaktorielle Lösung, die die Konstrukte Depression und Angst abbildete. Nur der Faktor Angst war mit einer veränderten Furchtkonditionierung und Furchtgeneralisierung assoziiert: Hoch Ängstliche zeigten eine stärkere konditionierte Furchtreaktion (Arousal) und wiesen eine stärkere Generalisierung der Valenzeinschätzung und Kontingenzerwartung auf. Für den Stathmin1 Genotyp ergaben sich geschlechtsspezifische Effekte. Bei den männlichen Versuchspersonen zeigte sich in Folge der Akquisition ein stärkerer Abfall der Valenz für den CS+ in der Gruppe der Stathmin1 T Allelträger, die ebenfalls eine stärkere Generalisierung der Furchtreaktion, abgebildet in allen verbalen Maßen, aufwiesen. Ein gegenteiliger Befund ergab sich für die Gruppe der Frauen, insofern eine mit dem Stathmin1 C Allel assoziierte höhere Generalisierung der Valenz, des Arousals und der Kontingenzerwartung festgestellt werden konnte. Für den COMT Val158Met Genotyp ergaben sich keine Einflüsse auf die Akquisition der konditionierten Furcht. Für Träger des COMT 158Val Allels zeigte sich jedoch eine stärkere Generalisierung der Valenz und der Kontingenzerwartung. Auch für den BDNF Val66Met Genotyp konnte keine Veränderung der Furchtakquisition beobachtet werden. Es ergaben sich jedoch Hinweise auf eine erhöhte Generalisierung der Kontingenzerwartung in der Gruppe der BDNF 66Val Homozygoten. Für keinen der beschriebenen Faktoren konnte ein Einfluss auf die Furchtkonditionierung oder deren Generalisierung anhand der SCR abgebildet werden.
Unsere Ergebnisse weisen auf einen psychometrisch erfassbaren Faktor und genetische Einflüsse hin, die über den Prozess einer stärkeren Generalisierung der konditionierten Furcht das Risiko für die Entstehung von Angsterkrankungen erhöhen können. Jedoch sollten die Befunde in größeren Stichproben repliziert werden. Neben der frühzeitigen Identifikation von Risikofaktoren sollten in zukünftigen Studien darüber hinaus wirksame Maßnahmen zur Prävention und Intervention entwickelt werden, um diesem Risiko entgegen zu wirken.
Der Tumorsupressor APC ist in der Mehrzahl aller Fälle kolorektaler Karzinome bereits in
der initialen Phase der Karzinogenese mutiert. Diese Mutationen führen zu einer aberranten Aktivierung des Wnt-Signalweges sowie zu weiteren die Karzinogenese vorrantreibenden Aktivitäten, beispielsweise einem veränderten Migrationsverhalten. Dieser Dissertation
zu Grunde liegt die Idee, dass durch die Trunkierung des APC-Proteins aber auch Abhängigkeiten von Genaktivitäten entstehen, die zuvor entbehrlich waren. Solche synthetisch
letalen Gene sollten in einem high-content shRNA-Screen gefunden werden.
Für die Durchführung des Screens wurde ein von der SW480 Kolonkarzinomzelllinie
abgeleitetes, isogenes Zellsystem generiert, welches durch Induktion mit Doxyzyklin das
vollständige APC-Allel (FL-APC) exprimiert. Infolge dieser Expression zeigen die Zellen
einen weniger malignen Phänotyp. Dies spiegelt sich darin wider, dass die Zellen durch
FL-APC Expression in ihrer Wnt-Signalwegsaktivität eingeschränkt werden. Doxyzyklininduzierte Zellen sind schlechter in der Lage ohne Adhäsion zu proliferieren als nicht induzierte Zellen. Andererseits ist ihre Fähigkeit einem FKS-gradienten entlang zu migrieren
verbessert.
Der shRNA-Screen wurde mit der Decipher shRNA-Bibliothek durchgeführt. Diese
enthält 27.500 verschiedene shRNAs mit Interferenzaktivität gegen 5.000 mRNAs, die potentiell pharmakologisch inhibierbare Proteine kodieren. Die besten zwei Kandidaten für
eine synthetisch letale Interaktion mit trunkiertem APC, BCL2L1 und EIF2B5 wurden im
Verlauf einer Masterarbeit bzw. direkt in dieser Disseration validiert. EIF2B5 zeigte in vitro nach Depletion durch unterschiedliche shRNAs einen di erentiellen Proliferationse ekt
bei FL-APC induzierten im Vergleich zu kontrollbehandelten Zellen. Dieser di erentielle
E ekt konnte in einem weiteren Modellsystem, SW480 Zellen mit konstitutiver FL-APC
Expression, ebenfalls validiert werden.
Durch Expression einer shRNA mit Aktivität gegen EIF2B5 werden in beiden Zellsystem die unfolded protein response (UPR) Gene DDIT3 und splXBP1 aktiviert. Interessanterweise werden durch die Expression von FL-APC diese Gene reprimiert. Im Promotor
der EIF2B5-mRNA be ndet sich eine Bindestelle für MYC. Es ist denkbar, dass durch die
Expression von FL-APC eine globale Veränderung der Genexpression vorgenommen wird,
die einerseits eine Repression von EIF2B5 nach sich zieht aber andererseits eine hierdurch
ausgelöste ER-Stress Antwort verhindert. Eine Inhibition von EIF2B5 ohne diese Adaption
andererseits führt nach diesem Model zu einer UPR-aktivierten Apoptose.
In einem zweiten Projekt wurde das überraschende Verhalten von Kolonkarzinomzellen untersucht, die nach Zugabe von BEZ235, einem dualen PI3K/mTOR Inhibitor, trotz
gegenteiliger Erwartungen MYC-Proteinmengen erhöhen. Eine Repression wurde erwar-
tet, weil die Inhibition von PI3K einerseits zu einer proteasomalen Destabiliserung und
andererseits die mTOR Inhibition zu einer verringerten Synthese von MYC führen sollte.
Während bereits gezeigt werden konnte, dass durch einen FOXO-vermittelten Mechanismus MAPK-abhängig die MYC-Expression verstärkt wird, wurde in dieser Dissertation
die erwartete Translationsinhibition untersucht. BEZ235 inhibiert zwar CAP-abhängige
Translation, das MYC Protein wird jedoch aufgrund einer IRES-vermittelten Translation
weiterhin exprimiert. Silvestrol, ein Inhibitor der Helikase eIF4A andererseits interveniert
mit CAP- und IRES-abhängiger Translation und kann die MYC-Proteinkonzentrationen
verringern. Wir konnten zudem feststellen, dass die Applikation von Silvestrol auch in vivo
möglich und wirksam ist und zudem tolleriert wird. Dies gibt Anlass zur Ho nung, dass
eine Intervention der Translation auch im Menschen eine valide Strategie zur Behandlung
MYC-getriebener Tumore sein könnte.
The human-bacterial pathogen interaction is a complex process that results from
a prolonged evolutionary arms race in the struggle for survival. The pathogen employs
virulence strategies to achieve host colonization, and the latter counteracts using defense
programs. The encounter of both organisms results in drastic physiological changes
leading to stress, which is an ancient response accompanying infection. Recent evidence
suggests that the stress response in the host converges with the innate immune pathways
and influences the outcome of infection. However, the contribution of stress and the exact
mechanism(s) of its involvement in host defense remain to be elucidated. Using the model
bacterial pathogen Shigella flexneri, and comparing it with the closely related pathogen
Salmonella Typhimurium, this study investigated the role of host stress in the outcome of
infection.
Shigella infection is characterized by a pronounced pro-inflammatory response
that causes intense stress in host tissues, particularly the intestinal epithelium, which
constitutes the first barrier against Shigella colonization. In this study, inflammatory
stress was simulated in epithelial cells by inducing oxidative stress, hypoxia, and cytokine
stimulation. Shigella infection of epithelial cells exposed to such stresses was strongly
inhibited at the adhesion/binding stage. This resulted from the depletion of sphingolipidrafts
in the plasma membrane by the stress-activated sphingomyelinases. Interestingly,
Salmonella adhesion was not affected, by virtue of its flagellar motility, which allowed the
gathering of bacteria at remaining membrane rafts. Moreover, the intracellular replication
of Shigella lead to a similar sphingolipid-raft depletion in the membrane across adjacent
cells inhibiting extracellular bacterial invasion.
Additionally, this study shows that Shigella infection interferes with the host stress
granule-formation in response to stress. Interestingly, infected cells exhibited a nuclear
depletion of the global RNA-binding stress-granule associated proteins TIAR and TIA-1
and their accumulation in the cytoplasm.
Overall, this work investigated different aspects of the host stress-response in the
defense against bacterial infection. The findings shed light on the importance of the host
stress-pathways during infection, and improve the understanding of different strategies
in host-pathogen interaction.
Aktivierung des MEK5/ Erk5-Signalwegs durch inhibitorische Substanzen des Mevalonatstoffwechsels
(2018)
Die Osteoporose ist eine Erkrankung, die durch verminderte Dichte und erhöhte Fragilität des Knochens gekennzeichnet ist. Sie zählt zu den häufigsten Erkrankungen weltweit und geht mit erheblicher Einschränkung der Lebensqualität und erhöhter Mortalität einher. Eine Behandlungsmöglichkeit dieses schwerwiegenden Krankheitsbilds ist die Therapie mit Bisphosphonaten. Diese hemmen mit ihren antiresorptiven Eigenschaften den Knochenabbau und fördern vermutlich gleichzeitig den Knochenaufbau. Obwohl schon lange die Wirkungsweise der Bisphosphonate erforscht wird, ist noch nicht sicher geklärt, wie beispielsweise osteoanabole oder antitumoröse Effekte vermittelt werden. Einen Erklärungsansatz bietet der MEK5/ Erk5-Signalweg. Diesem werden unter anderem antiangiogenetische, antiinflammatorische und antiproliferative Eigenschaften zugesprochen. In früheren Studien konnte gezeigt werden, dass Statine Erk5 und Erk5-abhängige Gene aktivieren können. Statine wiederum inhibieren ebenfalls den Mevalonatstoffwechsel, jedoch weiter upstream als Bisphosphonate. Da Statine zudem osteoanabole Effekte aufweisen, lag die These nahe, dass auch Bisphosphonate ihre Wirkung über den MEK5/Erk5-Signalweg vermitteln könnten. Die These konnte im Rahmen dieser Arbeit bestätigt werden: Stickstoffhaltige, nicht aber stickstofffreie Bisphosphonate aktivieren Erk5 sowohl in Endothelzellen als auch in Osteoblasten. Es gilt jedoch zu bedenken, dass eine Weiterentwicklung der Substanzen mit verbesserter Aufnahme in die Zelle zur Vermeidung von Apoptose-Induktion anzustreben ist.
Des Weiteren konnte gezeigt werden, dass ein Knock-down der FDPS, dem Angriffspunkt der Bisphosphonate im Mevalonatstoffwechsel, ebenfalls eine Erk5-Phosphorylierung zur Folge hat. Durch Inhibition der FDPS wird die Prenylierung kleiner G-Proteine wie Cdc42 unterbunden, was eine veränderte Funktion der Proteine zur Folge hat. Ein Knock-down von Cdc42 mittels siRNA führt wiederum zu einer Aktivierung von Erk5. Auf diese Weise wurde nicht nur ein neuer Wirkungsweg der Bisphosphonate identifiziert, sondern auch ein möglicher Aktivierungsmechanismus der MEK5/ Erk5-Signalkaskade aufgedeckt.
Erk5 wandert nach seiner Aktivierung in den Zellkern und beeinflusst dort die Genexpression. Im Rahmen dieser Arbeit wurden knochenrelevante Gene identifiziert, die durch Zoledronat-Stimulation induziert werden konnten. Zu diesen zählen INPP4B, das die Osteoklastogenese inhibiert, und PTHLH sowie FOSL1, welche die Osteoblastogenese fördern. Somit kann davon ausgegangen werden, dass die Aktivierung des MEK5/ Erk5-Signalwegs durch Zoledronat eine Geninduktion zur Folge hat, die sowohl die osteoanabole Wirkung unterstützt, als auch die katabolen Effekte hemmt. Auf diese Weise konnte neben den bereits bekannten Wirkungswegen der Bisphosphonate ein neuer identifiziert werden, der auch einen möglichen Ansatz für weitere, bisher ungeklärte Effekte von Bisphosphonaten darstellt.
Anxiety and depressive disorders result from a complex interplay of genetic and environmental factors and are common mutual comorbidities. On the level of cellular signaling, regulator of G protein signaling 2 (Rgs2) has been implicated in human and rodent anxiety as well as rodent depression. Rgs2 negatively regulates G protein-coupled receptor (GPCR) signaling by acting as a GTPase accelerating protein towards the Gα subunit.
The present study investigates, whether mice with a homozygous Rgs2 deletion (Rgs2-/-) show behavioral alterations as well as an increased susceptibility to stressful life events related to human anxiety and depressive disorders and tries to elucidate molecular underlying’s of these changes.
To this end, Rgs2-/- mice were characterized in an aversive-associative learning paradigm to evaluate learned fear as a model for the etiology of human anxiety disorders. Spatial learning and reward motivated spatial learning were evaluated to control for learning in non-aversive paradigms. Rgs2 deletion enhanced learning in all three paradigms, rendering increased learning upon deletion of Rgs2 not specific for aversive learning. These data support reports indicating increased long-term potentiation in Rgs2-/- mice and may predict treatment response to conditioning based behavior therapy in patients with polymorphisms associated with reduced RGS2 expression. Previous reports of increased innate anxiety were corroborated in three tests based on the approach-avoidance conflict. Interestingly, Rgs2-/- mice showed novelty-induced hypo-locomotion suggesting neophobia, which may translate to the clinical picture of agoraphobia in humans and reduced RGS2 expression in humans was associated with a higher incidence of panic disorder with agoraphobia. Depression-like behavior was more distinctive in female Rgs2-/- mice. Stress resilience, tested in an acute and a chronic stress paradigm, was also more distinctive in female Rgs2-/- mice, suggesting Rgs2 to contribute to sex specific effects of anxiety disorders and depression.
Rgs2 deletion was associated with GPCR expression changes of the adrenergic, serotonergic, dopaminergic and neuropeptide Y systems in the brain and heart as well as reduced monoaminergic neurotransmitter levels. Furthermore, the expression of two stress-related microRNAs was increased upon Rgs2 deletion. The aversive-associative learning paradigm induced a dynamic Rgs2 expression change. The observed molecular changes may contribute to the anxious and depressed phenotype as well as promote altered stress reactivity, while reflecting an alter basal stress level and a disrupted sympathetic tone. Dynamic Rgs2 expression may mediate changes in GPCR signaling duration during memory formation.
Taken together, Rgs2 deletion promotes increased anxiety-like and depression-like behavior, altered stress reactivity as well as increased cognitive function.
The plant cuticle is a continuous extracellular protective layer covering the outermost surfaces of higher plants that are in contact with the surrounding atmosphere. The primary function of the cuticular lipid membrane, which is mainly composed of biopolymer cutin and cuticular waxes, is to protect the plant organs against uncontrolled water loss. The chemical composition and the biophysical properties of cuticular waxes affect the rate of water diffusion across the cuticle. Fruit transpiration plays an important role in the development and the maintenance of fruit quality. The fruit has been suggested to present better dehydration stress tolerance than the leaf. However, the differences in transpiration and the chemical composition of cuticular waxes between fruit and leaf have yet to be comprehensively investigated.
The present study aims to investigate the water permeability and cuticular wax composition of fruit and leaf cuticles of a wide range of plant species and to elucidate the different roles of the cuticular wax components in the transpiration barrier. To address these objectives, fruit and leaf samples from 17 species were investigated. The cuticular transpiration of intact fruits and astomatous adaxial leaf surfaces and the minimum leaf conductance obtained by leaf drying curves for intact leaves were gravimetrically determined for a variety of plant species. The chemical composition of cuticular waxes of fruits and leaves was thoroughly analysed by gas chromatography with flame ionization and mass spectrometry.
The water permeability of fruits ranged from 3.7 x 10-5 m s-1 (Prunus domestica subsp. syriaca) to 37.4 x 10-5 m s-1 (Coffea arabica), whereas permeability for leaves varied between 1.6 x 10-5 m s-1 (Cornus officinalis) and 4.5 x 10-5 m s-1 (Prunus domestica subsp. syriaca (L.)). The interspecies range of water permeability of fruits was significantly higher than that of leaves. Chemical analyses of the cuticular waxes demonstrated that fatty acids, primary alcohols, n-alkanes, aldehydes and alkyl esters were the predominant very-long-chain aliphatic compound classes of fruit and leaf surfaces. Sterols, such as β-sitosterol and campesterol, and triterpenoids, such as oleanolic acid, ursolic acid, α-amyrin and ß-amyrin, were the major cyclic compound classes in the cuticular wax membrane.
The amount and composition of cuticular waxes of both fruits and leaves varied at an intraspecific level. There were no significant correlations between the total cuticular wax load or the individual cuticular wax composition and the water permeability of fruits or leaves independently or together. After combining the fruit and leaf data set, a significant correlation between the average chain length of very-long-chain aliphatic compounds and permeabilities was detected, i.e. the longer the average chain length, the lower the water permeability.
Interestingly, n-Nonacosane (C29) was abundantly detected in fruit waxes of Rosaceae species. These fruits exhibited a relatively low transpiration level, which was very close to their leaf cuticular permeability. The present study suggests that the lower cuticular permeability of leaves, in comparison to that of fruits, may be attributed to the longer average chain length of aliphatic compounds. The accumulation of total wax, triterpenoids and aliphatic compounds may not contribute to the transpiration barrier directly. The present results are highly consistent with the previous model assumptions for the cuticular structure and transport barrier. Furthermore, this comparative study on leaf and fruit cuticles provides further insights linking the cuticular wax chemistry to the physiological properties of the plant cuticle.
Als Hämostase bezeichnet man die Gesamtheit der Reaktionen, die zu einer effektiven Blutgerinnung beitragen. Sie lässt sich in die primäre (thrombozytäre) Hämostase, in die sekundäre (plasmatische) Hämostase und in das Fibrinolysesystem einteilen. Thrombozyten, oder auch Plättchen genannt, spielen hierbei eine entscheidende Rolle. Sie binden an die durch eine Verletzung einer Blutgefäßwand freigelegten Faktoren, werden so aktiviert und aggregieren mit weiteren Thrombozyten, wodurch ein Thrombus entsteht, der die Verletzung verschließt. Zudem besitzen Thrombozyten Immunokompetenz und können mit anderen Immunzellen interagieren, über Rezeptoren Pathogene erkennen und sie direkt angreifen. Einer dieser Pathogene ist der opportunistische Pilz Aspergillus fumigatus. Dieser bildet im Verlauf seines Lebenszyklus 2,5 -3 µm kleine Konidien aus, die mit dem Wind verbreitet werden und bis tief in die Alveolen der menschlichen Lunge eingeatmet werden können. Während diese Konidien im gesunden Menschen durch das Immunsystem und andere Abwehrmechanismen eliminiert werden, können sie im immunsupprimierten Patienten, z. B. bei Patienten nach einer hämatopoietischen Stammzelltransplantation, auskeimen und verschiedene Krankheiten, sogenannte Aspergillosen, auslösen mit der Invasiven Aspergillose (IA) als schwerwiegendste Form. Diese ist assoziiert mit Gewebezerstörungen, Blutungen und Thrombenbildung am Ort der Infektion. Diese Komplikationen könnten auf einer überhöhten Immunantwort des Wirtes, auf dem mechanischen Eindringen des Pilzes in das Gewebe und die Blutgefäße oder auf einer Änderung der lokalen Hämostase durch sezernierte hydrolytische Enzyme (Proteasen) oder Sekundärmetabolite von A. fumigatus beruhen.
Um diese Änderung der Hämostase im Verlauf einer IA zu analysieren, wurde der Einfluss von Morphologien (Konidien, geschwollene Konidien, Keimschläuche und Hyphen), deren Überstände, sowie von proteolytisch aktivem Überstand und von verschiedenen Sekundärmetaboliten von A. fumigatus auf die sekundäre Hämostase und die Aggregation und Aktivität von humanen Thrombozyten untersucht. Bei der Analyse der sekundären Hämostase konnte für keinen dieser eingesetzten Effektoren ein Einfluss festgestellt werden. Bei der Analyse der primären Hämostase und dem Einsatz von Morphologien und ihrer Überstände konnte für Hyphen und ihren ankonzentrierten Überstand eine aggregationssteigernde Wirkung auf Thrombozyten beobachtet werden, die möglicherweise auf Bestandteile der Zellwand von A. fumigatus, wie z. B. β-Galactosaminogalactan (GAG) zurückzuführen ist. Proteolytisch aktiver Überstand führte zu einer Aktivierung der Thrombozyten, die zum Teil auf die PrtT-abhängige proteolytische Spaltung und damit die Aktivierung der Thrombinrezeptoren PAR1 und/oder PAR4 auf der Thrombozytenoberfläche, zum Teil aber auch auf GAG zurückzuführen sein kann. Von den hier verwendeten Mykotoxinen Gliotoxin, Fumagillin, Citrinin, Verruculogen und Deoxynivalenol konnte für Gliotoxin ein negativer Einfluss auf die Thrombozytenaktivität nachgewiesen werden. Dieses Toxin inhibierte die Aggregation und die Aktivität der Thrombozyten, möglicherweise durch die Bildung von Disulfid-Brückenbindungen oder auch durch die Bildung von reaktiven Sauerstoffspezies. Zudem wurde im Verlauf dieser Arbeit eine direkte Interaktion von Gliotoxin mit den ADP-Rezeptoren P2Y1 und P2Y12 sowie mit dem Integrin αIIbβ3 postuliert, die so zwar nicht bestätigt, aber auch nicht vollständig wiederlegt werden konnte.
Die hier dargestellten Ergebnisse zeigen deutlich zwei Wirkungen von A. fumigatus auf humane Thrombozyten: zum einen eine Aktivierung oder auch verstärkte Aggregation durch sezernierte Proteasen oder Zellwandbestandteile, zum anderen eine Hemmung durch Gliotoxin, was die bei einer IA beobachtete Thrombenbildung sowie die Blutungen erklären kann. Die Interaktion der aktivierten Thrombozyten mit den Zellen des Immunsystems sowie die zytotoxischen Eigenschaften von Gliotoxin könnten zudem für die beobachtete Gewebezerstörung verantwortlich sein. Dennoch ist weitere Forschung in diesem Gebiet unabdingbar, um die pathophysiologische Änderung der lokalen Hämostase durch A. fumigatus und seine Wirkung auf humane Thrombozyten besser zu verstehen und so eine schnellere Erkennung und Behandlung von Aspergillosen zu ermöglichen.
G protein-coupled receptors (GPCRs) form the biggest receptor family that is encoded in the human genome and represent the most druggable target structure for modern therapeutics respectively future drug development. Belonging to aminergic class A GPCRs muscarinic Acetylcholine receptors (mAChRs) are already now of clinical relevance and are also seen as promising future drug targets for treating neurodegenerative diseases like Alzheimer or Parkinson. The mAChR family consist of five subtypes showing high sequence identity for the endogenous ligand binding region and thus it is challenging until now to selectively activate a single receptor subtype. A well accepted method to study ligand binding, dynamic receptor activation and downstream signaling is the fluorescence resonance energy transfer (FRET) application. Here, there relative distance between two fluorophores in close proximity (<10 nm) can be monitored in a dynamic manner. The perquisite for that is the spectral overlap of the emission spectrum of the first fluorophore with the excitation spectrum of the second fluorophore. By inserting two fluorophores into the molecular receptor structure receptor FRET sensors can serve as a powerful tool to study dynamic receptor pharmacology.
Dualsteric Ligands consist of two different pharmacophoric entities and are regarded as a promising ligand design for future drug development. The orthosteric part interacts with high affinity with the endogenous ligand binding region whereas the allosteric part binds to a different receptor region mostly located in the extracellular vestibule. Both moieties are covalently linked. Dualsteric ligands exhibit a dynamic ligand binding. The dualsteric binding position is characterized by a simultaneous binding of the orthosteric and allosteric moiety to the receptor and thus by receptor activation. In the purely allosteric binding position no receptor activation can be monitored.
In the present work the first receptor FRET sensor for the muscarinic subtype 1 (M1) was generated and characterized. The M1-I3N-CFP sensor showed an unaltered physiological behavior as well as ligand and concentration dependent responses. The sensor was used to characterize different sets of dualsteric ligands concerning their pharmacological properties like receptor activation. It was shown that the hybrids consisting of the synthetic full agonist iperoxo and the positive allosteric modulator of BQCA type is very promising. Furthermore, it was shown for orthosteric as well as dualsteric ligands that the degree of receptor activation is highly dependent on the length of and the chemical properties of the linker moiety. For dualsteric ligands a bell-shaped activation characteristic was reported for the first time, suggesting that there is an optimal linker length for dualsteric ligands. The gained knowledge about hybrid design was then used to generate and characterize the first photo-switchable dualsteric ligand. The resulting hybrids were characterized with the M1-I3N-CFP sensor and were described as photo-inactivatable and dimmable. In addition to the ligand characterization the ligand application methodology was further developed and improved. Thus, a fragment-based screening approach for dualsteric ligands was reported in this study for the first time. With this approach it is possible to investigate dualsteric ligands in greater detail by applying either single ligand fragments alone or in a mixture of building blocks. These studies revealed the insights that the effect of dualsteric ligands on a GPCR can be rebuild by applying the single building blocks simultaneously. The fragment-based screening provides high potential for the molecular understanding of dualsteric ligands and for future screening approaches. Next, a further development of the standard procedure for measuring FRET by sensitized emission was performed. Under normal conditions single cell FRET is measured on glass coverslips. After coating the coverslips surface with a 20 nm thick gold layer an increased FRET efficiency up to 60 % could be reported. This finding was validated in different approaches und in different configurations. This FRET enhancement by plasmonic surfaces was until yet unreported in the literature for physiological systems and make FRET for future projects even more powerful.
Genetic foundation of unrivaled survival strategies - Of water bears and carnivorous plants -
(2018)
All living organisms leverage mechanisms and response systems to optimize reproduction, defense, survival, and competitiveness within their natural habitat. Evolutionary theories such as the universal adaptive strategy theory (UAST) developed by John Philip Grime (1979) attempt to describe how these systems are limited by the trade-off between growth, maintenance and regeneration; known as the universal three-way trade-off. Grime introduced three adaptive strategies that enable organisms to coop with either high or low intensities of stress (e.g., nutrient deficiency) and environmental disturbance (e.g., seasons). The competitor is able to outcompete other organisms by efficiently tapping available resources in environments of low intensity stress and disturbance (e.g., rapid growers). A ruderal specism is able to rapidly complete the life cycle especially during high intensity disturbance and low intensity stress (e.g., annual colonizers). The stress tolerator is able to respond to high intensity stress with physiological variability but is limited to low intensity disturbance environments. Carnivorous plants like D. muscipula and tardigrades like M. tardigradum are two extreme examples for such stress tolerators. D. muscipula traps insects in its native habitat (green swamps in North and South Carolina) with specialized leaves and thereby is able to tolerate nutrient deficient soils. M. tardigradum on the other side, is able to escape desiccation of its terrestrial habitat like mosses and lichens which are usually covered by a water film but regularly fall completely dry. The stress tolerance of the two species is the central study object of this thesis. In both cases, high througput sequencing data and methods were used to test for transcriptomic (D. muscipula) or genomic adaptations (M. tardigradum) which underly the stress tolerance. A new hardware resource including computing cluster and high availability storage system was implemented in the first months of the thesis work to effectively analyze the vast amounts of data generated for both projects. Side-by-side, the data management resource TBro [14] was established together with students to intuitively approach complex biological questions and enhance collaboration between researchers of several different disciplines. Thereafter, the unique trapping abilities of D. muscipula were studied using a whole transcriptome approach. Prey-dependent changes of the transcriptional landscape as well as individual tissue-specific aspects of the whole plant were studied. The analysis revealed that non-stimulated traps of D. muscipula exhibit the expected hallmarks of any typical leaf but operates evolutionary conserved stress-related pathways including defense-associated responses when digesting prey. An integrative approach, combining proteome and transcriptome data further enabled the detailed description of the digestive cocktail and the potential nutrient uptake machinery of the plant. The published work [25] as well as a accompanying video material (https://www.eurekalert.org/pub_releases/ 2016-05/cshl-fgr042816.php; Video credit: Sönke Scherzer) gained global press coverage and successfully underlined the advantages of D. muscipula as experimental system to understand the carnivorous syndrome. The analysis of the peculiar stress tolerance of M. tardigradum during cryptobiosis was carried out using a genomic approach. First, the genome size of M. tardigradum was estimated, the genome sequenced, assembled and annotated. The first draft of M. tardigradum and the workflow used to established its genome draft helped scrutinizing the first ever released tardigrade genome (Hypsibius dujardini) and demonstrated how (bacterial) contamination can influence whole genome analysis efforts [27]. Finally, the
M. tardigradum genome was compared to two other tardigrades and all species present in the current release of the Ensembl Metazoa database. The analysis revealed that tardigrade genomes are not that different from those of other Ecdysozoa. The availability of the three genomes allowed the delineation of their phylogenetic position within the Ecdysozoa and placed them as sister taxa to the nematodes. Thereby, the comparative analysis helped to identify evolutionary trends within this metazoan lineage. Surprisingly, the analysis did not reveal general mechanisms (shared by all available tardigrade genomes) behind the arguably most peculiar feature of tardigrades; their enormous stress tolerance. The lack of molecular evidence for individual tardigrade species (e.g., gene expression data for M. tardigradum) and the non-existence of a universal experimental framework which enables hypothesis testing withing the whole phylum Tardigrada, made it nearly impossible to link footprints of genomic adaptations to the unusual physiological capabilities. Nevertheless, the (comparative) genomic framework established during this project will help to understand how evolution tinkered, rewired and modified existing molecular systems to shape the remarkable phenotypic features of tardigrades.
Die Synthese der mRNA durch die RNA-Polymerase II ist der zentrale und kritische Prozess im Rahmen
der Transkriptionsregulation Protein-kodierender Gene. Viele Jahrzehnte der intensiven Erforschung brachten viele Details über diesen Mechanismus zu Tage, der von einer unglaublichen Komplexität und Dynamik geprägt ist. Dabei stellte sich heraus, dass der Mediatorkomplex eine zentrale Rolle bei der Regulation der Polymerase II-abhängigen Transkription spielt, im Besonderen der Initiation. In der Funktion einer Schnittstelle verknüpft er die allgemeine Transkriptionsmaschinerie mit den Gen- spezifischen Transkriptionsregulatoren. Durch die Interaktion des Schwanzmoduls mit diesen Regulatoren und der Interaktion des Kopfmoduls mit der Polymerase II verbindet er wie eine Brücke die oberhalb des Promotors liegenden Aktivatorsequenzen mit dem Kernpromotor und initiiert so die Ausbildung des Pre-Initiationskomplexes. Darüber hinaus mehren sich gerade in den letzten Jahren die Hinweise darauf, dass der Mediator auch noch an anderen Prozessen der Transkription beteiligt ist. Zu diesen gehören z.B. die Elongation, die Ausbildung von Genschlaufen oder auch der Umbau der Chromatinstruktur. In Anbetracht der Tatsachen, dass der Mediator (a) aus bis zu 25 Untereinheiten mit flexibler Zusammensetzung besteht, (b) eine flexible Struktur besitzt und (c) umfassend und dynamisch über posttranslationale Modifikationen modifiziert ist, erscheint es durchaus möglich, dass der Mediator all diese Funktionen ausfüllt und die Rolle einer allgemeinen Transkriptionsplattform einnimmt. Im Zusammenhang mit dieser Dissertationsschrift ist es gelungen, den Mediator innerhalb all dieser Funktionen „abzubilden“ und die bisher umfassendste Interaktomanalyse dieses Komplexes zu präsentieren. Durch die optimierten Bedingungen der Zelllyse und Co-Immunopräzipitation, gelang es auch transiente Interaktionspartner zu isolieren. Durch das metabolische Markieren der Wildtypkontrolle konnten außerdem unspezifische und spezifische Interaktionen eindeutig voneinander unterschieden werden. Über 400 Proteine wurden als signifikante Interaktionspartner des Mediators identifiziert. Viele dieser Proteine konnten als vollständige Komplexe zusammengefasst werden, z.B die RNA-Polymerase II, alle allgemeinen Transkriptionsfaktoren, der SAGA-Komplex, viele Komplexe des Chromatin Remodelings und stark acetylierte Histone. Viele weitere Interaktionspartner spielen zudem eine Rolle bei der co-transkriptionalen Prozessierung der mRNA, wie z.B dem Splicing, dem mRNA-decapping oder Abbau. Darüber hinaus gibt es starke Hinweise darauf, dass der Mediator auch mit der Polymerase I und III interagiert und an der ribosomalen Biogenese beteiligt ist. Weitere
Analysen zeigten, dass das Interaktom zudem hochdynamisch ist
RNA sequencing (RNA-seq) has in recent years become the preferred method for gene expression analysis and whole transcriptome annotation. While initial RNA-seq experiments focused on eukaryotic messenger RNAs (mRNAs), which can be purified from the cellular ribonucleic acid (RNA) pool with relative ease, more advanced protocols had to be developed for sequencing of microbial transcriptomes. The resulting RNA-seq data revealed an unexpected complexity of bacterial transcriptomes and the requirement for specific analysis methods, which in many cases is not covered by tools developed for processing of eukaryotic data.
The aim of this thesis was the development and application of specific data analysis methods for different RNA-seq-based approaches used to gain insights into transcription and gene regulatory processes in prokaryotes.
The differential RNA sequencing (dRNA-seq) approach allows for transcriptional start site (TSS) annotation by differentiating between primary transcripts with a 5’-triphosphate (5’-PPP) and processed transcripts with a 5’-monophosphate (5’-P). This method was applied in combination with an automated TSS annotation tool to generate global trancriptome maps for Escherichia coli (E. coli) and Helicobacter pylori (H. pylori).
In the E. coli study we conducted different downstream analyses to gain a deeper understanding of the nature and properties of transcripts in our TSS map. Here, we focused especially on putative antisense RNAs (asRNAs), an RNA class transcribed from the opposite strand of known protein-coding genes with the potential to regulate corresponding sense transcripts. Besides providing a set of putative asRNAs and experimental validation of candidates via Northern analysis, we analyzed and discussed different sources of variation in RNA-seq data.
The aim of the H. pylori study was to provide a detailed description of the dRNA-seq approach and its application to a bacterial model organism. It includes information on experimental protocols and requirements for data analysis to generate a genome-wide TSS map. We show how the included TSS can be used to identify and analyze transcriptome and regulatory features and discuss challenges in terms oflibrary preparation protocols, sequencing platforms, and data analysis including manual and automated TSS annotation.
The TSS maps and associated transcriptome data from both H. pylori and E. coli were made available for visualization in an easily accessible online browser.
Furthermore, a modified version of dRNA-seq was used to identify transcriptome targets of the RNA pyrophosphohydrolase (RppH) in H. pylori. RppH initiates 5’-end-dependent degradation of transcripts by converting the 5’-PPP of primary transcripts to a 5’-P. I developed an analysis method, which uses data from complementary DNA (cDNA) libraries specific for transcripts carrying a 5’-PPP, 5’-P or both, to specifically identify transcripts modified by RppH. For this, the method assessed the 5’-phosphorylation state and cellular concentration of transcripts in rppH deletion in comparison to strains with the intact gene. Several of the identified potential RppH targets were further validated via half-life measurements and quantification of their 5’-phosphorylation state in wild-type and mutant cells. Our findings suggest an important role for RppH in post-transcriptional gene regulationin H. pylori and related organisms.
In addition, we applied two RNA-seq -based approaches, RNA immunoprecipitation followed by sequencing (RIP-seq) and cross-linking immunoprecipitation followed by sequencing (CLIP-seq), to identify transcripts bound by Hfq and CsrA, two RNA-binding proteins (RBPs) with an important role in post-transcriptional regulation.
For RIP-seq -based identification of CsrA binding regions in Campylobacter jejuni(C. jejuni), we used annotation-based analysis and, in addition, a self-developed peak calling method based on a sliding window approach. Both methods revealed flaA mRNA, encoding the major flagellin, as the main target and functional analysis of identified targets showed a significant enrichment of genes involved in flagella biosynthesis. Further experimental analysis revealed the role of flaA mRNA in post-transcriptional regulation. In comparison to RIP-seq, CLIP-seq allows mapping of RBP binding sites with a higher resolution. To identify these sites an approach called “block-based peak calling” was developed and resulting peaks were used to identify sequence and structural constraints required for interaction of Hfq and CsrA with Salmonella transcripts.
Overall, the different RNA-seq-based approaches described in this thesis together with their associated analyis pipelines extended our knowledge on the transcriptional repertoire and modes of post-transcriptional regulation in bacteria. The global TSS maps, including further characterized asRNA candidates, putative RppH targets, and identified RBP interactomes will likely trigger similar global studies in the same or different organisms or will be used as a resource for closer examination of these features.
LOX-catalyzed collagen stabilization is a proximal cause for intrinsic resistance to chemotherapy
(2018)
The potential of altering the tumor ECM to improve drug response remains fairly unexplored. To identify targets for modification of the ECM aiming to improve drug response and overcome resistance, we analyzed expression data sets from pre-treatment patient cohorts. Cross-evaluation identified a subset of chemoresistant tumors characterized by increased expression of collagens and collagen-stabilizing enzymes. We demonstrate that strong collagen expression and stabilization sets off a vicious circle of self-propagating hypoxia, malignant signaling, and aberrant angiogenesis that can be broken by an appropriate auxiliary intervention: Interfering with collagen stabilization by inhibition of lysyl oxidases significantly enhanced response to chemotherapy in various tumor models, even in metastatic disease. Inhibition of collagen stabilization by itself can reduce or enhance tumor growth depending on the tumor type. The mechanistical basis for this behavior is the dependence of the individual tumor on nutritional supply on one hand and on high tissue stiffness for FAK signaling on the other.
The regulation of immune cell migration throughout the body is essential to warrant immunosurveillance and to maintain immune homeostasis. Marking and tracking of these cells has proven important to study mechanisms of immune cell trafficking and cell interaction in vivo. Photoconversion is a well-suited technique for intravital application because it enables contactless time- and location-specific marking of cells in the tissue without surgically manipulating the microenvironment of the cells in question. However, in dividing cells the converted fluorescent protein may decline quickly. Here, we provide a detailed description of the photoconversion technique and its applicability to tracking highly proliferating T cells from the priming site of T cell activation to peripheral target organs of effector function in a preclinical model. Dendra2+ T cells were photoconverted in the Peyer’s patches during the initiation phase of acute graft-versus-host disease (GvHD) and tracked through the mesenteric lymph nodes and the peripheral blood to the small intestine with flow cytometry and intravital two-photon microscopy. Photoconverted alloreactive T cells preserved the full proliferative capacity, homing, and migration of alloreactive T cells in the intestinal lamina propria. We conclusively proved that photoconversion of highly proliferative alloreactive T cells in the Peyer’s patches is an effective tool to study trafficking of alloreactive T cells under physiologic conditions and to GvHD target tissues. This technique can also be applied to the study of immune cell tracking under inflammatory and non-inflammatory conditions.