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In der vorliegenden Dissertationsarbeit wurden die kardialen Effekte des C-Typ natriuretischen Peptids (CNP) an wildtypischen Mäusen (Studie 1) und an einem neuen genetischen Mausmodell, mit einer Kardiomyozyten-spezifischen Deletion des Guanylyl-Cyclase B (GC-B) Rezeptors (Studie 2) untersucht.
In Studie 1 wurden die Wirkungen von exogenem, synthetischem CNP auf eine durch Druckbelastung-induzierte Herzinsuffizienz in wildtypischen Mäusen (C57Bl6 Hintergrund) untersucht. Dafür wurde CNP parallel zu einer operativen transversen Aortenkonstriktion (TAC) über osmotische Minipumpen in einer Dosierung von 50 ng/kg/min über 14 Tage appliziert. Die 14 Tage TAC führten zu einer ausgeprägten Linksherzhypertrophie. Diese wurde durch exogenes CNP auf zellulärer (verringerte Kardiomyozytenflächen) und molekularer (verringerte BNP mRNA Expression) Ebene signifikant gehemmt. Auch die durch TAC-induzierte linksventrikuläre Dilatation wurde durch exogenes CNP fast vollständig verhindert. Diese kardialen protektiven Effekte von CNP traten ohne eine wesentliche Veränderung des arteriellen Blutdrucks auf. Mögliche mechanistische Ursachen für die schützende Wirkung von CNP könnte die PKG-abhängige Phosphorylierung des sarkomerischen Proteins Titin sein. Eine gesteigerte Phosphorylierung von Titin an der elastischen N2B-Domäne verringert die Steifigkeit der Kardiomyozyten und verbessert somit deren Relaxationsfähigkeit (Hudson 2011). Die erhöhten linksventrikulären Volumina nach TAC (end-diastolische und end-systolische Volumina) wurden möglicherweise durch eine erhöhte Steifigkeit der Kardiomyozyten provoziert. Dies könnte durch den akuten IL-6 mRNA Anstieg nach TAC begünstigt werden, da Kruger et al. einen Zusammenhang zwischen passiver Steifigkeit der Kardiomyozyten und IL-6-Expression postulierten (Kotter 2016, Kruger 2009). Diese Veränderungen wurden durch exogenes CNP verhindert. Es ist wahrscheinlich, dass die CNP-induzierte Phosphorylierung von Titin an Serin 4080 in die Relaxationsfähigkeit der Kardiomyozyten und somit die diastolische Funktion des linken Ventrikels verbesserte.
Aufgrund dieser Beobachtungen wurde in Studie 2 untersucht, ob auch endogenes CNP als parakrines Hormon im Herzen eine TAC-induzierte Herzhypertrophie und die kontraktile Funktion von Kardiomyozyten bei einer hypertensiven Herzerkrankung beeinflussen kann. Dafür wurde ein neues genetisches Mausmodell mit einer Kardiomyozyten-spezifischen Deletion des GC-B Rezeptors generiert (CM GC-B KO). Da vorangegangene Studien in unserer Arbeitsgruppe zeigten, dass die basale CNP-Expression im Herzen sehr gering ist, nach 3-tägiger TAC aber akut ansteigt und nach 14-tägiger TAC wieder abfällt, haben wir CM GC-B KO Mäuse und deren Geschwister-Kontrolltiere an beiden Zeitpunkten nach TAC untersucht. Die TAC führte Genotyp-unabhängig zu einem Anstieg der kardialen Nachlast nach 3 Tagen und weiter nach 14 Tagen. Diese Druckbelastung provozierte eine progressive, signifikante Linksherzhypertrophie.
Allerdings reagierten die CM GC-B KO Mäuse im Vergleich zu den Kontrolltieren bereits nach 3-tägiger TAC mit einer ausgeprägten Kardiomyozyten-Hypertrophie. Zudem beobachteten wir nach 3-tägiger TAC in den Knockout-Mäusen eine Abnahme der Ejektionsfraktion und gleichzeitig eine signifikante Zunahme der beiden linksventrikulären Volumina (end-diastolische und end-systolische Volumen). Diese frühe linksventrikuläre Dilatation wurde in den Kontrolltieren nicht beobachtet. Daraus schlussfolgerten wir, dass endogenes kardiales CNP, dessen Expression zu frühen Zeitpunkten nach Druckbelastung ansteigt, das Herz vor kontraktiler Dysfunktion und Dilatation schützen kann. Um mögliche Mechanismen für die protektive Wirkung von endogenem CNP zu erklären, untersuchten wir die IL-6 mRNA Expression sowie die Titin-Phosphorylierung im Herzen. Der akute Anstieg der IL-6 mRNA Expression nach 3-tägiger TAC in den CM GC-B KO Mäusen korreliert mit der verminderten Phosphorylierung von Titin an der PGK-spezifischen Phosphorylierungsstelle (Serin 4080). Somit könnte der CNP/GC-B/cGMP-Signalweg zu einer Inhibition pro-inflammatorischer Gene beitragen, da der akute IL-6 mRNA Anstieg in den Kontrollen nicht beobachtet wurde. Auch die gesteigerte NOX4 Expression 3 Tage nach TAC, könnte zu der frühen dilatativen Kardiomyopathie in den Knockout-Mäusen beigetragen haben. Die verringerte STAT3 Aktivierung in den CM GC-B KO Mäusen würde laut Literatur zu vermehrter Apoptose führen, indem pro-apoptotische Gene wie Bcl oder Bax vermehrt transkribiert werden. Auch die erhöhte Cxcl-1 mRNA Expression in den Knockout-Mäusen deutet zusammen mit dem IL-6 Anstieg auf vermehrte Entzündungsreaktionen 3 Tage nach TAC hin. Zusammengenommen deuten die Ergebnisse dieser Dissertationsarbeit darauf hin, dass der CNP/GC-B/cGMP-Signalweg in frühen Stadien einer erhöhten kardialen Druckbelastung und der Entstehung einer dilatativen Kardiomyopathie entgegenwirken kann. Die Phosphorylierung des sarkomerischen Proteins Titin und die Hemmung der Expression pro-inflammatorischer Zytokine (speziell IL-6) könnten zu diesem protektiven Effekt beitragen.
Symbiotic microbes help a myriad of insects acquire nutrients. Recent work suggests that insects also frequently associate with actinobacterial symbionts that produce molecules to help defend against parasites and predators. Here we explore a potential association between Actinobacteria and two species of fungus-farming ambrosia beetles, Xyleborinus saxesenii and Xyleborus affinis. We isolated and identified actinobacterial and fungal symbionts from laboratory reared nests, and characterized small molecules produced by the putative actinobacterial symbionts. One 16S rRNA phylotype of Streptomyces (XylebKG-1) was abundantly and consistently isolated from the galleries and adults of X. saxesenii and X. affinis nests. In addition to Raffaelea sulphurea, the symbiont that X. saxesenii cultivates, we also repeatedly isolated a strain of Nectria sp. that is an antagonist of this mutualism. Inhibition bioassays between Streptomyces griseus XylebKG-1 and the fungal symbionts from X. saxesenii revealed strong inhibitory activity of the actinobacterium toward the fungal antagonist Nectria sp. but not the fungal mutualist R. sulphurea. Bioassay guided HPLC fractionation of S. griseus XylebKG-1 culture extracts, followed by NMR and mass spectrometry, identified cycloheximide as the compound responsible for the observed growth inhibition. A biosynthetic gene cluster putatively encoding cycloheximide was also identified in S. griseus XylebKG-1. The consistent isolation of a single 16S phylotype of Streptomyces from two species of ambrosia beetles, and our finding that a representative isolate of this phylotype produces cycloheximide, which inhibits a parasite of the system but not the cultivated fungus, suggests that these actinobacteria may play defensive roles within these systems.
Objective
The biological interpretation of gene expression measurements is a challenging task. While ordination methods are routinely used to identify clusters of samples or co-expressed genes, these methods do not take sample or gene annotations into account. We aim to provide a tool that allows users of all backgrounds to assess and visualize the intrinsic correlation structure of complex annotated gene expression data and discover the covariates that jointly affect expression patterns.
Results
The Bioconductor package covRNA provides a convenient and fast interface for testing and visualizing complex relationships between sample and gene covariates mediated by gene expression data in an entirely unsupervised setting. The relationships between sample and gene covariates are tested by statistical permutation tests and visualized by ordination. The methods are inspired by the fourthcorner and RLQ analyses used in ecological research for the analysis of species abundance data, that we modified to make them suitable for the distributional characteristics of both, RNA-Seq read counts and microarray intensities, and to provide a high-performance parallelized implementation for the analysis of large-scale gene expression data on multi-core computational systems. CovRNA provides additional modules for unsupervised gene filtering and plotting functions to ensure a smooth and coherent analysis workflow.
Over the last decade life sciences have made an enormous leap forward. The development of complex analytical instruments, in particular in fluorescence microscopy, has played a decisive role in this. Scientist can now rely on a wide range of imaging techniques that offer different advantages in terms of optical resolution, recording speed or living cell compatibility. With the help of these modern microscopy techniques, multi-protein complexes can be resolved, membrane receptors can be counted, cellular pathways analysed or the internalisation of receptors can be tracked. However, there is currently no universal technique for comprehensive experiment execution that includes dynamic process capture and super resolution imaging on the same target object. In this work, I built a microscope that combines two complementary imaging techniques and enables correlative experiments in living and fixed cells. With an image scanning based laser spot confocal microscope, fast dynamics in several colors with low photodamage of the cells can be recorded. This novel system also has an improved resolution of 170 nm and was thoroughly characterized in this work. The complementary technique is based on single molecule localization microscopy, which can achieve a structural resolution down to 20-30 nm. Furthermore I implemented a microfluidic pump that allows direct interaction with the sample placed on the microscope. Numerous processes such as living cell staining, living cell fixation, immunostaining and buffer exchange can be observed and performed directly on the same cell. Thus, dynamic processes of a cell can be frozen and the structures of interest can be stained and analysed with high-resolution microscopy. Furthermore, I have equipped the detection path of the single molecule technique with an adaptive optical element. With the help of a deformable mirror, imaging functions can be shaped and information on the 3D position of the individual molecules can be extracted.
Cooperative Breeding in the Ambrosia Beetle Xyleborus affinis and Management of Its Fungal Symbionts
(2020)
Fungus-farming is known from attine ants, macrotermites, and ambrosia beetles (Scolytinae, Platypodinae). Farming ant and termite societies are superorganismal and grow fungal cultivars in monocultures. Social organization of ambrosia beetle groups and their farming systems are poorly studied, because of their enigmatic life within tunnel systems inside of wood. Ambrosia beetle-fungus symbioses evolved many times independently in both the beetles and their fungal cultivars. Observations suggest that there is evolutionary convergence between these lineages, but also a high variation in the degree of sociality and the modes of fungiculture. Using a laboratory observation technique, I here tried to give insights into the social system and fungus symbiosis of the sugar-cane borer, Xyleborus affinis Eichhoff (Scolytinae: Curculionidae), a currently poorly studied ambrosia beetle. The study revealed a cooperatively breeding system characterized by delayed dispersal of adult daughters, alloparental brood care by larvae and adults, and about half of the totipotent adult daughters laying eggs within the natal nest. Most interesting, there was a tendency of egg-laying females to engage more commonly in mutually beneficial behaviors than non-egg-layers. Fungus gardens covering gallery walls composed of five different filamentous fungi. A Raffaelea isolate was predominant and together with an unidentified fungus likely served as the main food for adults and larvae. Three isolates, a Mucor, a Fusarium and a Phaeoacremonium isolate were most abundant in the oldest gallery part close to the entrance; Mucor, Fusarium and the Raffaelea isolate in diseased individuals. Additionally, there was correlative evidence for some fungal isoaltes influencing beetle feeding and hygienic behaviors. Overall, X. affinis is now the second ambrosia beetle that can be classified as a cooperative breeder with division of labor among and between adults and larvae.
To improve and focus preclinical testing, we combine tumor models based on a decellularized tissue matrix with bioinformatics to stratify tumors according to stage-specific mutations that are linked to central cancer pathways. We generated tissue models with BRAF-mutant colorectal cancer (CRC) cells (HROC24 and HROC87) and compared treatment responses to two-dimensional (2D) cultures and xenografts. As the BRAF inhibitor vemurafenib is—in contrast to melanoma—not effective in CRC, we combined it with the EGFR inhibitor gefitinib. In general, our 3D models showed higher chemoresistance and in contrast to 2D a more active HGFR after gefitinib and combination-therapy. In xenograft models murine HGF could not activate the human HGFR, stressing the importance of the human microenvironment. In order to stratify patient groups for targeted treatment options in CRC, an in silico topology with different stages including mutations and changes in common signaling pathways was developed. We applied the established topology for in silico simulations to predict new therapeutic options for BRAF-mutated CRC patients in advanced stages. Our in silico tool connects genome information with a deeper understanding of tumor engines in clinically relevant signaling networks which goes beyond the consideration of single drivers to improve CRC patient stratification.
Comprehensive bioinformatics identifies key microRNA players in ATG7-deficient lung fibroblasts
(2020)
Background: Deficient autophagy has been recently implicated as a driver of pulmonary fibrosis, yet bioinformatics approaches to study this cellular process are lacking. Autophagy-related 5 and 7 (ATG5/ATG7) are critical elements of macro-autophagy. However, an alternative ATG5/ATG7-independent macro-autophagy pathway was recently discovered, its regulation being unknown. Using a bioinformatics proteome profiling analysis of ATG7-deficient human fibroblasts, we aimed to identify key microRNA (miR) regulators in autophagy. Method: We have generated ATG7-knockout MRC-5 fibroblasts and performed mass spectrometry to generate a large-scale proteomics dataset. We further quantified the interactions between various proteins combining bioinformatics molecular network reconstruction and functional enrichment analysis. The predicted key regulatory miRs were validated via quantitative polymerase chain reaction. Results: The functional enrichment analysis of the 26 deregulated proteins showed decreased cellular trafficking, increased mitophagy and senescence as the major overarching processes in ATG7-deficient lung fibroblasts. The 26 proteins reconstitute a protein interactome of 46 nodes and miR-regulated interactome of 834 nodes. The miR network shows three functional cluster modules around miR-16-5p, miR-17-5p and let-7a-5p related to multiple deregulated proteins. Confirming these results in a biological setting, serially passaged wild-type and autophagy-deficient fibroblasts displayed senescence-dependent expression profiles of miR-16-5p and miR-17-5p. Conclusions: We have developed a bioinformatics proteome profiling approach that successfully identifies biologically relevant miR regulators from a proteomics dataset of the ATG-7-deficient milieu in lung fibroblasts, and thus may be used to elucidate key molecular players in complex fibrotic pathological processes. The approach is not limited to a specific cell-type and disease, thus highlighting its high relevance in proteome and non-coding RNA research.
Comparison of the central human and mouse platelet signaling cascade by systems biological analysis
(2020)
Background
Understanding the molecular mechanisms of platelet activation and aggregation is of high interest for basic and clinical hemostasis and thrombosis research. The central platelet protein interaction network is involved in major responses to exogenous factors. This is defined by systemsbiological pathway analysis as the central regulating signaling cascade of platelets (CC).
Results
The CC is systematically compared here between mouse and human and major differences were found. Genetic differences were analysed comparing orthologous human and mouse genes. We next analyzed different expression levels of mRNAs. Considering 4 mouse and 7 human high-quality proteome data sets, we identified then those major mRNA expression differences (81%) which were supported by proteome data. CC is conserved regarding genetic completeness, but we observed major differences in mRNA and protein levels between both species. Looking at central interactors, human PLCB2, MMP9, BDNF, ITPR3 and SLC25A6 (always Entrez notation) show absence in all murine datasets. CC interactors GNG12, PRKCE and ADCY9 occur only in mice. Looking at the common proteins, TLN1, CALM3, PRKCB, APP, SOD2 and TIMP1 are higher abundant in human, whereas RASGRP2, ITGB2, MYL9, EIF4EBP1, ADAM17, ARRB2, CD9 and ZYX are higher abundant in mouse. Pivotal kinase SRC shows different regulation on mRNA and protein level as well as ADP receptor P2RY12.
Conclusions
Our results highlight species-specific differences in platelet signaling and points of specific fine-tuning in human platelets as well as murine-specific signaling differences.
Aim:
Temperature, food resources and top‐down regulation by antagonists are considered as major drivers of insect diversity, but their relative importance is poorly understood. Here, we used cavity‐nesting communities of bees, wasps and their antagonists to reveal the role of temperature, food resources, parasitism rate and land use as drivers of species richness at different trophic levels along a broad elevational gradient.
Location:
Mt. Kilimanjaro, Tanzania.
Taxon:
Cavity‐nesting Hymenoptera (Hymenoptera: Apidae, Colletidae, Megachilidae, Crabronidae, Sphecidae, Pompilidae, Vespidae).
Methods:
We established trap nests on 25 study sites that were distributed over similar large distances in terms of elevation along an elevational gradient from 866 to 1788 m a.s.l., including both natural and disturbed habitats. We quantified species richness and abundance of bees, wasps and antagonists, parasitism rates and flower or arthropod food resources. Data were analysed with generalized linear models within a multi‐model inference framework.
Results:
Elevational species richness patterns changed with trophic level from monotonically declining richness of bees to increasingly humped‐shaped patterns for caterpillar‐hunting wasps, spider‐hunting wasps and antagonists. Parasitism rates generally declined with elevation but were higher for wasps than for bees. Temperature was the most important predictor of both bee and wasp host richness patterns. Antagonist richness patterns were also well predicted by temperature, but in contrast to host richness patterns, additionally by resource abundance and diversity. The conversion of natural habitats through anthropogenic land use, which included biomass removal, agricultural inputs, vegetation structure and percentage of surrounding agricultural habitats, had no significant effects on bee and wasp communities.
Main conclusions:
Our study underpins the importance of temperature as a main driver of diversity gradients in ectothermic organisms and reveals the increasingly important role of food resources at higher trophic levels. Higher parasitism rates at higher trophic levels and at higher temperatures indicated that the relative importance of bottom‐up and top‐down drivers of species richness change across trophic levels and may respond differently to future climate change.