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One of the fascinating features of meiotic prophase I, is the highly conserved
vigorous movements of homologous chromosomes. These movements are
critical for the success of essential events as homologs alignment, synapsis and
recombination. Several organisms studied so far, including mammals, worms,
yeast and plants achieve these movements by anchoring the chromosome ends
to specialized sites in the nuclear envelope (NE). This attachment requires
telomere adaptor proteins which have to date been identified in fission yeast
and mice.
The mouse meiosis-specific telomere adaptor proteins TERB1, TERB2, and
MAJIN are involved in the attachment of ubiquitous shelterin telomere to the
LINC complex, in an analogous mechanism as those described in fission yeast.
Despite the essential role of meiosis-specific telomere adaptor proteins, the
precise mechanism of anchorage of telomeres to the nuclear envelope, as well
as their evolutionary history, are still not well understood. Therefore, the main
aim of this thesis is to investigate the organization of the mouse meiosis-specific
telomere adaptor complex TERB1-TERB2-MAJIN and its evolutionary history.
In the first part of this thesis high-resolution Structured Illumination Microscopy
(SIM), indirect immunofluorescence and Telo-FISH on mouse spermatocytes
were used to determine precisely how the telomere complex proteins are
localized with relation to the shelterin telomeric TRF1 protein and telomeric
DNA. During zygotene and pachytene stages staining patterns revealed
extensively overlapping of meiotic telomere complex proteins distributions in
which TERB2 organization is more heterogeneous than TERB1 and MAJIN at
the chromosome ends. Further, TRF1 localization was shown at the side of
lateral elements (LEs) ends with grasp-like distribution surrounding the TERB1
and MAJIN signals in zygotene and pachytene stages. Interestingly, telomeric
DNA was shown to be laterally distributed and partially overlapping with the
more central distribution displayed by meiotic telomere complex proteins of LEs
ends. The combination of these results allowed to describe an alternative model
of the telomere attachment to the NE during meiotic prophase I. The second part of this thesis, analyses mouse TERB1, TERB2, and MAJIN
evolutionary history. The lack of similarity between mouse and fission yeast
meiotic-specific telomere adaptor proteins has raised the question about the
origin of this specific complex through evolution. To identify mouse TERB1,
TERB2, and MAJIN putative orthologues, computational approaches and
phylogenetic analyses were performed. Besides, to test their potential function
during meiosis, expression studies were conducted. From these analyses, it was
revealed that mouse meiosis-specific telomere complex is ancient, as it
originated as early as eumetazoans pointing to a single origin. The absence of
any homologs in Nematoda and only a few candidates detected in Arthropoda
for meiosis-specific telomere complex, seemed, that these proteins have been
lost/replaced or highly diversified in these lineages. Remarkably, TERB1, TERB2,
and MAJIN protein domains involved in the formation of the complex as well as
those required for the interaction with the telomere shelterin protein and the
LINC complexes revealed high sequence similarity across all clades. Finally,
gene expression in the cnidarian Hydra Vulgaris provided evidence that the
TERB1-TERB2-MAJIN complex is selectively expressed in the germline
suggesting conservation of meiotic functions across metazoan evolution.
In summary, this thesis provides significant insights into the meiosis-specific
telomere complex mechanism to engage telomeres to the nuclear envelope and
the elucidation of its origin in metazoans.
Neuroblastoma is the most abundant, solid, extracranial tumor in early childhood and the leading cause of cancer-related childhood deaths worldwide. Patients with high-risk neuroblastoma often show MYCN-amplification and elevated levels of Aurora-A. They have a low overall survival and despite multimodal therapy options a poor therapeutic prognosis. MYCN-amplified neuroblastoma cells depend on Aurora-A functionality. Aurora-A stabilizes MYCN and prevents it from proteasomal degradation by competing with the E3 ligase SCFFBXW7. Interaction between Aurora-A and MYCN can be observed only in S phase of the cell cycle and activation of Aurora-A can be induced by MYCN in vitro. These findings suggest the existence of a profound interconnection between Aurora-A and MYCN in S phase. Nevertheless, the details remain elusive and were investigated in this study.
Fractionation experiments show that Aurora-A is recruited to chromatin in S phase in a MYCN-dependent manner. Albeit being unphosphorylated on the activating T288 residue, Aurora-A kinase activity was still present in S phase and several putative, novel targets were identified by phosphoproteomic analysis. Particularly, eight phosphosites dependent on MYCN-activated Aurora-A were identified. Additionally, phosphorylation of serine 10 on histone 3 was verified as a target of this complex in S phase. ChIP-sequencing experiments reveal that Aurora-A regulates transcription elongation as well as histone H3.3 variant incorporation in S phase. 4sU-sequencing as well as immunoblotting demonstrated that Aurora-A activity impacts splicing. PLA measurements between the transcription and replication machinery revealed that Aurora-A prevents the formation of transcription-replication conflicts, which activate of kinase ATR.
Aurora-A inhibitors are already used to treat neuroblastoma but display dose-limiting toxicity. To further improve Aurora-A based therapies, we investigated whether low doses of Aurora-A inhibitor combined with ATR inhibitor could increase the efficacy of the treatment albeit reducing toxicity. The study shows that the combination of both drugs leads to a reduction in cell growth as well as an increase in apoptosis in MYCN-amplified neuroblastoma cells, which is not observable in MYCN non-amplified neuroblastoma cells. This new approach was also tested by a collaboration partner in vivo resulting in a decrease in tumor burden, an increase in overall survival and a cure of 25% of TH-MYCN mice. These findings indicate indeed a therapeutic window for targeting MYCN-amplified neuroblastoma.
Die Regulation der Genexpression steht am Anfang vieler zellbiologischer Prozesse wie beispielsweise dem Zellwachstum oder der Differenzierung. Gene werden an Promotoren transkribiert, wobei ein Promotor selbst aus vielen logischen Einheiten aufgebaut ist, den Transkriptionsfaktorbindestellen (TFBSs). Diese können sehr nah beieinander liegen, aber auch weit entfernt voneinander sein. Sie werden spezifisch von Transkriptionsfaktoren (TFs) gebunden, die die Transkritptionsrate z.B. verstärken (Enhancer) oder schwächen (Silencer) können. Zwei oder mehr dieser TFBSs mit bestimmtem Abstand werden als "Module" zusammengefasst, die über Spezies hinweg konserviert sein können. Typischerweise findet man Module in Zellen mit einem Zellkern. Spezies mit gemeinsamen Modulen können ein Hinweis auf die gemeinsame phylogenetische Abstammung darstellen, aber auch gemeinsame Funktionsmechanismen von TFs über Gene hinweg aufdecken. Heutzutage sind verschiedene Anwendungen verfügbar, mit denen nach TFBSs in DNA gesucht werden kann. Zum Zeitpunkt des Verfassens dieser Arbeit sind aber nur zwei kommerzielle Produkte bekannt, die nicht nur TFBSs, sondern auch Module erkennen. Deshalb stellen wir hier die freie und quelloffene Lösung "AIModules" vor, die diese Lücke füllt und einen Webservice zur Verfügung stellt, der es erlaubt nach TFBSs sowie nach Modulen auf DNA- und auf RNA-Abschnitten zu suchen. Für die Motivesuche werden entweder Matrizen aus der Jaspar Datenbank oder Matrizen vom Anwender verwendet. Darüberhinaus zeigen wir, dass unser Tool für die TF Suche nur Sekunden benötigt, wohingegen conTraV3 mindestens eine Stunde für dieselbe Analyse braucht. Zusätzlich kann der Anwender bei unserem Tool den Grad der Konserviertheit für TFs mit angeben und wir zeigen, dass wir mit unserer Lösung, die die Jaspar Datenbank heranzieht, mehr Module finden, als ein kommerziell verfügbares Produkt. Weiterhin kann mit unserer Lösung auch auf RNA-Sequenzen nach regulatorischen Motiven gesucht werden, wenn der Anwender die dafür nötigen Matrizen liefert. Wir zeigen dies am Beispiel von Polyadenylierungsstellen. Zusammenfassend stellen wir ein Werkzeug vor, das erstens frei und quelloffen ist und zweitens entweder auf Servern veröffentlicht werden kann oder On-Site auf einem Notebook läuft. Unser Tool erlaubt es Promotoren zu analysieren und nach konservierten Modulen sowie TFBSs in Genfamilien sowie nach regulatorischen Elementen in mRNA wie z.B. Polyadenylierungsstellen oder andere regulatorische Elemente wie beispielsweise Enhancern oder Silencern in genomischer DNA zu suchen.
Im Zuge der Bemühungen um neue, tumorspezifische Therapieansätze für die Myelomerkrankung hat sich der C-X-C-Chemokinrezeptor 4 (CXCR4) aufgrund seiner zentralen Rolle in der Tumorgenese als vielversprechender Angriffspunkt hervorgetan. Im Sinne eines theranostischen Konzepts wird der Rezeptor mithilfe eines radioaktiv markierten Liganden quantifiziert und anschließend von rezeptorspezifischen Radiotherapeutika als Zielstruktur genutzt. Die CXCR4-Expression ist allerdings ein höchst dynamischer Prozess mit großer inter- und intraindividueller Heterogenität, der u.a. durch eine begleitende Chemotherapie beeinflusst werden kann. Ob sich therapieinduzierte Veränderungen der Rezeptorexpression gezielt nutzen lassen, um die CXCR4-Expression zu optimieren und so die Effektivität der CXCR4-gerichteten Strategien zu steigern, wurde bislang nicht untersucht.
Vor diesem Hintergrund wurden in der vorliegenden Arbeit verschiedene, in der Myelomtherapie etablierte Substanzen sowohl einzeln als auch in Kombination hinsichtlich ihres Einflusses auf die CXCR4-Expression von MM-Zelllinien und primären MM-Zellen unter in vitro Bedingungen analysiert.
In den durchgeführten Experimenten zeigte sich eine hohe Variabilität der CXCR4-Expression der MM-Zellen nach Therapieinduktion, die sich als substanz-, dosis- und zeitabhängig herausstellte. Die Ergebnisse bestätigten das große Potenzial der therapieinduzierten Modulation der CXCR4-Expression. Im weiteren Verlauf sind translationale Forschungsansätze gerechtfertigt, die die Übertragbarkeit der in vitro gewonnenen Ergebnisse auf die komplexen Vorgänge im lebenden Organismus überprüfen. Langfristiges Ziel ist der Entwurf eines patientenzentrierten, multimodalen Therapiekonzepts, welches das CXCR4-gerichtete theranostische Konzept mit einer individuell angepassten, medikamentösen MM-Therapie kombiniert.
The nuclear envelope serves as important mRNA surveillance system. In yeast and humans, several control mechanisms act in parallel to prevent nuclear export of unprocessed mRNAs. However, trypanosomes lack homologues to most of the proteins involved. In addition, gene expression in trypanosomes relies almost completely on post-transcriptional regulation as they transcribe mRNAs as long polycistrons, which are subsequently processed into individual mRNA molecules by trans-splicing. As trans-splicing is not error-free, unspliced mRNAs may be recognized and prevented from reaching the cytoplasm by a yet unknown mechanism.
When trans-splicing is inhibited in trypanosomes, the formation of a novel RNA granule type at the cytoplasmic periphery of the nucleus, so called nuclear periphery granules (NPGs) was previously observed. To identify potential regulators of nuclear export control, changes in protein localization which occur when trans-splicing is inhibited, were globally analyzed during this work. For this, trypanosome nuclei were purified under conditions maintaining NPG attachment to the nucleus, in the absence and presence of trans-splicing. Mass spectrometry analyses identified 128 proteins which are specifically enriched in nuclear preparations of cells inhibited for trans-splicing. Amongst them are proteins, which change their localization to the nucleus or to the nuclear pores as well as many proteins that move into NPGs. Some of these proteins are promising candidates for nuclear export control proteins, as the changes in localization (to the nucleus or nuclear pores) were specific to the accumulation of unspliced mRNAs. The NPG proteome almost exclusively contains proteins involved in mRNA metabolism, mostly unique to trypanosomes, notably major translation initiation factors were absent. These data indicate that NPGs are RNP complexes which have started or completed nuclear export, but not yet entered translation. As a byproduct of these proteomic studies, a high-quality dataset of the yet unknown T. brucei nuclear proteome is provided, closing an important gap in knowledge to study trypanosome biology, in particular nuclear related processes.
NPGs were characterized in more detail by microscopy. The granules are cytoplasmic and present in at least two different trypanosome life cycle stages. There are at least two distinct granule subsets, with differences in protein composition. A closer analysis of NPGs by electron microscopy revealed that the granules are electron dense structures, which are connected to nuclear pores by string-like structures.
In order to approach the function of NPGs, on the one hand, the hypothesis that NPGs might be related to perinuclear germ granules of adult gonads of C. elegans was tested: we found no relation between the two granule types. On the other hand, initial single molecule mRNA FISH experiments performed in trypanosomes showed no accumulation of unspliced transcripts in NPGs, arguing against an involvement of the granules in mRNA quality control.
ERK1/2 are known key players in the pathophysiology of heart failure, but the members of the ERK cascade, in particular Raf1, can also protect the heart from cell death and ischemic injury. An additional autophosphorylation (ERK1 at Thr208, ERK2 at Thr188) empowers ERK1/2 translocation to the nucleus and phosphorylation of nuclear targets which take part in the development of cardiac hypertrophy. Thereby, targeting this additional phosphorylation is a promising pharmacological approach.
In this thesis, an in silico model of ERK cascade in the cardiomyocyte is introduced. The model is a semi-quantitive model and its behavior was tested with different softwares (SQUAD and CellNetAnalyzer). Different phosphorylation states of ERK1/2 as well as different stimuli can be reproduced. The different types of stimuli include hypertrophic as well as non-hypertrophic stimuli. With the introduced in-silico model time courses and synergistic as well as antagonistic receptor stimuli combinations can be predicted. The simulated time courses were experimentally validated. SQUAD was mainly used to make predictions about time courses and thresholds, whereas CNA was used to analyze steady states and feedback loops.
Furthermore, new targets of ERK1/2 which partially contribute, also in the formation of cardiac hypertrophy, were identified and the most promising of them were illuminated. Important further targets are Caspase 8, GAB2, Mxi-2, SMAD2, FHL2 and SPIN90.
Cardiomyocyte gene expression data sets were analyzed to verify involved components and to find further significantly altered genes after induced hypertrophy with TAC (transverse aortic constriction). Changes in the ultrastructure of the cardiomyocyte are the final result of induced hypertrophy.
The transcription factor NRF2 is considered as the master regulator of cytoprotective and ROS-detoxifying gene expression. Due to their vulnerability to accumulating reactive oxygen species, melanomas are dependent on an efficient oxidative stress response, but to what extent melanomas rely on NRF2 is only scarcely investigated so far. In tumor entities harboring activating mutations of NRF2, such as lung adenocarcinoma, NRF2 activation is closely connected to therapy resistance. In melanoma, activating mutations are rare and triggers and effectors of NRF2 are less well characterized.
This work revealed that NRF2 is activated by oncogenic signaling, cytokines and pro-oxidant triggers, released cell-autonomously or by the tumor microenvironment. Moreover, silencing of NRF2 significantly reduced melanoma cell proliferation and repressed well-known NRF2 target genes, indicating basal transcriptional activity of NRF2 in melanoma. Transcriptomic analysis showed a large set of deregulated gene sets, besides the well-known antioxidant effectors. NRF2 suppressed the activity of MITF, a marker for the melanocyte lineage, and induced expression of epidermal growth factor receptor (EGFR), thereby stabilizing the dedifferentiated melanoma phenotype and limiting pigmentation markers and melanoma-associated antigens. In general, the dedifferentiated melanoma phenotype is associated with a reduced tumor immunogenicity. Furthermore, stress-inducible cyclooxygenase 2 (COX2) expression, a crucial immune-modulating gene, was regulated by NRF2 in an ATF4-dependent manner. Only in presence of both transcription factors was COX2 robustly induced by H2O2 or TNFα. COX2 catalyzes the first step of the prostaglandin E2 (PGE2) synthesis, which was described to be associated with tumor immune evasion and reduction of the innate immune response.
In accordance with these potentially immune-suppressive features, immunocompetent mice injected with NRF2 knockout melanoma cells had a strikingly longer tumor-free survival compared to NRF2-proficient cells. In line with the in vitro data, NRF2-deficient tumors showed suppression of COX2 and induction of MITF. Furthermore, transcriptomic analyses of available tumors revealed a strong induction of genes belonging to the innate immune response, such as RSAD2 and IFIH1. The expression of these genes strongly correlated with immune evasion parameters in human melanoma datasets and NRF2 activation or PGE2 supplementation limited the innate immune response in vitro.
In summary, the stress dependent NRF2 activation stabilizes the dedifferentiated melanoma phenotype and facilitates the synthesis of PGE2. As a result, NRF2 reduces gene expression of the innate immune response and promotes the generation of an immune-cold tumor microenvironment. Therefore, NRF2 not only elevated the ROS resilience, but also strongly contributed to tumor growth, maintenance, and immune control in cutaneous melanoma.
How diversity of life is generated, maintained, and distributed across space and time is the central question of community ecology. Communities are shaped by three assembly processes: (I) dispersal, (II) environ-mental, and (III) interaction filtering. Heterogeneity in environmental conditions can alter these filtering processes, as it increases the available niche space, spatially partitions the resources, but also reduces the effective area available for individual species. Ultimately, heterogeneity thus shapes diversity. However, it is still unclear under which conditions heterogeneity has positive effects on diversity and under which condi-tions it has negative or no effects at all. In my thesis, I investigate how environmental heterogeneity affects the assembly and diversity of diverse species groups and whether these effects are mediated by species traits.
In Chapter II, I first examine how much functional traits might inform about environmental filtering pro-cesses. Specifically, I examine to which extent body size and colour lightness, both of which are thought to reflect the species thermal preference, shape the distribution and abundance of two moth families along elevation. The results show, that assemblages of noctuid moths are more strongly driven by abiotic filters (elevation) and thus form distinct patterns in colour lightness and body size, while geometrid moths are driven by biotic filters (habitat availability), and show no decline in body size nor colour lightness along elevation. Thus, one and the same functional trait can have quite different effects on community assembly even between closely related taxonomic groups.
In Chapter III, I elucidate how traits shift the relative importance of dispersal and environmental filtering in determining beta diversity between forests. Environmental filtering via forest heterogeneity had on aver-age higher independent effects than dispersal filtering within and among regions, suggesting that forest heterogeneity determines species turnover even at country-wide extents. However, the relative importance of dispersal filtering increased with decreasing dispersal ability of the species group. From the aspects of forest heterogeneity covered, variations in herb or tree species composition had overall stronger influence on the turnover of species than forest physiognomy. Again, this ratio was influenced by species traits, namely trophic position, and body size, which highlights the importance of ecological properties of a taxo-nomic group in community assembly.
In Chapter IV, I assess whether such ecological properties ultimately determine the level of heterogeneity which maximizes species richness. Here, I considered several facets of heterogeneity in forests. Though the single facets of heterogeneity affected diverse species groups both in positive and negative ways, we could not identify any generalizable mechanism based on dispersal nor the trophic position of the species group which would dissolve these complex relationships.
In Chapter V, I examine the effect of environmental heterogeneity of the diversity of traits itself to evalu-ate, whether the effects of environmental heterogeneity on species richness are truly based on increases in the number of niches. The results revealed that positive effects of heterogeneity on species richness are not necessarily based on an increased number of niches alone, but proposedly also on a spatially partition of resources or sheltering effects. While ecological diversity increased overall, there were also negative trends which indicate filtering effects via heterogeneity.
In Chapter VI, I present novel methods in measuring plot-wise heterogeneity of forests across continental scales via Satellites. The study compares the performance of Sentinel-1 and LiDar-derived measurements in depicting forest structures and heterogeneity and to their predictive power in modelling diversity. Senti-nel-1 could match the performance of Lidar and shows high potential to assess free yet detailed infor-mation about forest structures in temporal resolutions for modelling the diversity of species.
Overall, my thesis supports the notion that heterogeneity in environmental conditions is an important driv-er of beta-diversity, species richness, and ecological diversity. However, I could not identify any general-izable mechanism which direction and form this effect will have.
Summary
Bees, like many other organisms, evolved an endogenous circadian clock, which enables them to foresee daily environmental changes and exactly time foraging flights to periods of floral resource availability. The social lifestyle of a honey bee colony has been shown to influence circadian behavior in nurse bees, which do not exhibit rhythmic behavior when they are nursing. On the other hand, forager bees display strong circadian rhythms. Solitary bees, like the mason bee, do not nurse their offspring and do not live in hive communities, but face the same daily environmental changes as honey bees. Besides their lifestyle mason and honey bees differ in their development and life history, because mason bees overwinter after eclosion as adults in their cocoons until they emerge in spring. Honey bees do not undergo diapause and have a relatively short development of a few weeks until they emerge. In my thesis, I present a comparison of the circadian clock of social honey bees (Apis mellifera) and solitary mason bees (Osmia bicornis and Osmia cornuta) on the neuroanatomical level and behavioral output level.
I firstly characterized in detail the localization of the circadian clock in the bee brain via the expression pattern of two clock components, namely the clock protein PERIOD (PER) and the neuropeptide Pigment Dispersing Factor (PDF), in the brain of honey bee and mason bee. PER is localized in lateral neuron clusters (which we called lateral neurons 1 and 2: LN1 and LN2) and dorsal neuron clusters (we called dorsal lateral neurons and dorsal neurons: DLN, DN), many glia cells and photoreceptor cells. This expression pattern is similar to the one in other insect species and indicates a common ground plan of clock cells among insects. In the LN2 neuron cluster with cell bodies located in the lateral brain, PER is co-expressed with PDF. These cells build a complex arborization network throughout the brain and provide the perfect structure to convey time information to brain centers, where complex behavior, e.g. sun-compass orientation and time memory, is controlled. The PDF arborizations centralize in a dense network (we named it anterio-lobular PDF hub: ALO) which is located in front of the lobula. In other insects, this fiber center is associated with the medulla (accessory medulla: AME). Few PDF cells build the ALO already in very early larval development and the cell number and complexity of the network grows throughout honey bee development. Thereby, dorsal regions are innervated first by PDF fibers and, in late larval development, the fibers grow laterally to the optic lobe and central brain. The overall expression pattern of PER and PDF are similar in adult social and solitary bees, but I found a few differences in the PDF network density in the posterior protocerebrum and the lamina, which may be associated with evolution of sociality in bees.
Secondly, I monitored activity rhythms, for which I developed and established a device to monitor locomotor activity rhythms of individual honey bees with contact to a mini colony in the laboratory. This revealed new aspects of social synchronization and survival of young bees with indirect social contact to the mini colony (no trophalaxis was possible). For mason bees, I established a method to monitor emergence and locomotor activity rhythms and I could show that circadian emergence rhythms are entrainable by daily temperature cycles. Furthermore, I present the first locomotor activity rhythms of solitary bees, which show strong circadian rhythms in their behavior right after emergence. Honey bees needed several days to develop circadian locomotor rhythms in my experiments. I hypothesized that honey bees do not emerge with a fully matured circadian system in the hive, while solitary bees, without the protection of a colony, would need a fully matured circadian clock right away after emergence. Several indices in published work and preliminary studies support my hypothesis and future studies on PDF expression in different developmental stages in solitary bees may provide hard evidence.
These days, treatment of melanoma patients relies on targeted therapy with BRAF/MEK inhibitors and on immunotherapy. About half of all patients initially respond to existing therapies. Nevertheless, the identification of alternative therapies for melanoma patients with intrinsic or acquired resistance is of great importance. In melanoma, antioxidants play an essential role in the maintenance of the redox homeostasis. Therefore, disruption of the redox homeostasis is regarded as highly therapeutically relevant and is the focus of the present work.
An adequate supply of cysteine is essential for the production of the most important intracellular antioxidants, such as glutathione. In the present work, it was investigated whether the depletion of cysteine and glutathione is therapeutically useful. Depletion of glutathione in melanoma cells could be achieved by blocking cysteine supply, glutathione synthesis, and NADPH regeneration. As expected, this led to an increased level of reactive oxygen species (ROS). Surprisingly, however, these changes did not impair the proliferation and survival of the melanoma cells. In contrast, glutathione depletion led to cellular reprogramming which was characterized by the induction of mesenchymal genes and the repression of differentiation markers (phenotypic switch). This was accompanied by an increased migration and invasion potential which was favored by the induction of the transcription factor FOSL1. To study in vivo reprogramming, Gclc, the first and rate-limiting enzyme in glutathione synthesis, was knocked out by CRISPR/Cas9 in murine melanoma cells. The cells were devoid of glutathione, but were fully viable and showed a phenotypic switch, the latter only in MITF-expressing B16F1 cells and not in MITF-deficient D4M3A.781 cells. Following subcutaneous injection into immunocompetent C57BL/6 mice, Gclc knockout B16F1 cells grew more aggressively and resulted in an earlier tumor onset than B16F1 control cells.
In summary, this work demonstrates that inhibition of cysteine supply and thus, glutathione synthesis leads to cellular reprogramming in melanoma. In this context, melanoma cells show metastatic capabilities, promoting a more aggressive form of the disease.
Effects of dopamine on BDNF / TrkB mediated signaling and plasticity on cortico-striatal synapses
(2021)
Progressive loss of voluntary movement control is the central symptom of Parkinson's disease (PD). Even today, we are not yet able to cure PD. This is mainly due to a lack of understanding the mechanisms of movement control, network activity and plasticity in motor circuits, in particular between the cerebral cortex and the striatum. Brain-derived neurotrophic factor (BDNF) has emerged as one of the most important factors for the development and survival of neurons, as well as for synaptic plasticity. It is thus an important target for the development of new therapeutic strategies against neurodegenerative diseases. Together with its receptor, the Tropomyosin receptor kinase B (TrkB), it is critically involved in development and function of the striatum. Nevertheless, little is known about the localization of BDNF within presynaptic terminals in the striatum, as well as the types of neurons that produce BDNF in the cerebral cortex. Furthermore, the influence of midbrain derived dopamine on the control of BDNF / TrkB interaction in striatal medium spiny neurons (MSNs) remains elusive so far. Dopamine, however, appears to play an important role, as its absence leads to drastic changes in striatal synaptic plasticity. This suggests that dopamine could regulate synaptic activity in the striatum via modulation of BDNF / TrkB function. To answer these questions, we have developed a sensitive and reliable protocol for the immunohistochemical detection of endogenous BDNF. We find that the majority of striatal BDNF is provided by glutamatergic, cortex derived afferents and not dopaminergic inputs from the midbrain. In fact, we found BDNF in cell bodies of neurons in layers II-III and V of the primary and secondary motor cortex as well as layer V of the somatosensory cortex. These are the brain areas that send dense projections to the dorsolateral striatum for control of voluntary movement. Furthermore, we could show that these projection neurons significantly downregulate the expression of BDNF during the juvenile development of mice between 3 and 12 weeks.
In parallel, we found a modulatory effect of dopamine on the translocation of TrkB to the cell surface in postsynaptic striatal Medium Spiny Neurons (MSNs). In MSNs of the direct pathway (dMSNs), which express dopamine receptor 1 (DRD1), we observed the formation of TrkB aggregates in the 6-hydroxydopamine (6-OHDA) model of PD. This suggests that DRD1 activity controls TrkB surface expression in these neurons. In contrast, we found that DRD2 activation has opposite effects in MSNs of the indirect pathway (iMSNs). Activation of DRD2 promotes a rapid decrease in TrkB surface expression which was reversible and depended on cAMP. In parallel, stimulation of DRD2 led to induction of phospho-TrkB (pTrkB). This effect was significantly slower than the effect on TrkB surface expression and indicates that TrkB is transactivated by DRD2. Together, our data provide evidence that dopamine triggers dual modes of plasticity on striatal MSNs by acting on TrkB surface expression in DRD1 and DRD2 expressing MSNs. This surface expression of the receptor is crucial for the binding of BDNF, which is released from corticostriatal afferents. This leads to the induction of TrkB-mediated downstream signal transduction cascades and long-term potentiation (LTP). Therefore, the dopamine-mediated translocation of TrkB could be a mediator that modulates the balance between dopaminergic and glutamatergic signaling to allow synaptic plasticity in a spatiotemporal manner. This information and the fact that TrkB is segregated to persistent aggregates in PD could help to improve our understanding of voluntary movement control and to develop new therapeutic strategies beyond those focusing on dopaminergic supply.
Identification of a novel LysR-type transcriptional regulator in \(Staphylococcus\) \(aureus\)
(2021)
Staphylococcus aureus is a facultative pathogen which causes a variety of infections. The treatment of staphylococcal infections is complicated because the bacteria is resistant to multiple common antibiotics. S. aureus is also known to express a variety of virulence factors which modulate the host’s immune response in order to colonize and invade certain host cells, leading to the host cell’s death. Among the virulence factors is a LysR-type transcriptional regulator (lttr) which is required for efficient colonization of secondary organs. In a recent report, which used transposon screening on S. aureus-infected mice, it was found that the amount of a novel lttr852 mutant bacteria recovered from the kidneys was significantly lower compared to the wildtype strains.
This doctoral thesis therefore focused on phenotypical and molecular characterization of lttr852. An assessment of the S. aureus biofilm formation and the hemolysis revealed that lttr852 was not involved in the regulation of these virulence processes. RNA-sequencing for potential target genes of lttr852 identified differentially expressed genes that are involved in branched chain amino-acid biosynthesis, methionine sulfoxide reductase and copper transport, as well as a reduced transcription of genes encoding urease and of components of pyrimidine nucleotides. Promoter fusion with GFP reporters as as well as OmniLog were used to identify conditions under which the lttr852 was active. The promoter studies showed that glucose and high temperatures diminish the lttr852 promoter activity in a time-dependent manner, while micro-aerobic conditions enhanced the promoter activity. Copper was found to be a limiting factor. In addition, the impact on promoter activity of the lttr852 was tested in the presence of various regulators, but no central link to the genes involved in virulence was identified.
The present work, thus, showed that lttr852, a new member of the class of LysR-type transcriptional regulators in S. aureus, has an important role in the rapid adaptation of S. aureus to the changing microenvironment of the host.
Chapter 1 – General Introduction
One of the greatest challenges of ecological research is to predict the response of ecosystems to global change; that is to changes in climate and land use. A complex question in this context is how changing environmental conditions affect ecosystem processes at different levels of communities. To shed light on this issue, I investigate drivers of biodiversity on the level of species richness, functional traits and species interactions in cavity-nesting Hymenoptera. For this purpose, I take advantage of the steep elevational gradient of Mt. Kilimanjaro that shows strong environmental changes on a relatively small spatial scale and thus, provides a good environmental scenario for investigating drivers of diversity. In this thesis, I focus on 1) drivers of species richness at different trophic levels (Chapter 2); 2) seasonal patterns in nest-building activity, life-history traits and ecological rates in three different functional groups and at different elevations (Chapter 3) and 3) changes in cuticular hydrocarbons, pollen composition and microbiomes in Lasioglossum bees caused by climatic variables (Chapter 4).
Chapter 2 – Climate and food resources shape species richness and trophic interactions of cavity-nesting Hymenoptera
Drivers of species richness have been subject to research for centuries. Temperature, resource availability and top-down regulation as well as the impact of land use are considered to be important factors in determining insect diversity. Yet, the relative importance of each of these factors is unknown. Using trap nests along the elevational gradient of Mt. Kilimanjaro, we tried to disentangle drivers of species richness at different trophic levels. Temperature was the major driver of species richness across trophic levels, with increasing importance of food resources at higher trophic levels in natural antagonists. Parasitism rate was both related to temperature and trophic level, indicating that the relative importance of bottom-up and top-down forces might shift with climate change.
Chapter 3 – Seasonal variation in the ecology of tropical cavity-nesting Hymenoptera
Natural populations fluctuate with the availability of resources, presence of natural enemies and climatic variations. But tropical mountain seasonality is not yet well investigated. We investigated seasonal patterns in nest-building activity, functional traits and ecological rates in three different insect groups at lower and higher elevations separately. Insects were caught with trap nests which were checked monthly during a 17 months period that included three dry and three rainy seasons. Insects were grouped according to their functional guilds. All groups showed strong seasonality in nest-building activity which was higher and more synchronised among groups at lower elevations. Seasonality in nest building activity of caterpillar-hunting and spider-hunting wasps was linked to climate seasonality while in bees it was strongly linked to the availability of flowers, as well as for the survival rate and sex ratio of bees. Finding adaptations to environmental seasonality might imply that further changes in climatic seasonality by climate change could have an influence on life-history traits of tropical mountain species.
Chapter 4 – Cryptic species and hidden ecological interactions of halictine bees along an elevational Gradient
Strong environmental gradients such as those occurring along mountain slopes are challenging for species. In this context, hidden adaptations or interactions have rarely been considered. We used bees of the genus Lasioglossum as model organisms because Lasioglossum is the only bee genus occurring with a distribution across the entire elevational gradient at Mt. Kilimanjaro. We asked if and how (a) cuticular hydrocarbons (CHC), which act as a desiccation barrier, change in composition and chain length along with changes in temperature and humidity (b), Lasioglossum bees change their pollen diet with changing resource availability, (c) gut microbiota change with pollen diet and climatic conditions, and surface microbiota change with CHC and climatic conditions, respectively, and if changes are rather influenced by turnover in Lasioglossum species along the elevational gradient. We found physiological adaptations with climate in CHC as well as changes in communities with regard to pollen diet and microbiota, which also correlated with each other. These results suggest that complex interactions and feedbacks among abiotic and biotic conditions determine the species composition in a community.
Chapter 5 – General Discussion
Abiotic and biotic factors drove species diversity, traits and interactions and they worked differently depending on the functional group that has been studied, and whether spatial or temporal units were considered. It is therefore likely, that in the light of global change, different species, traits and interactions will be affected differently. Furthermore, increasing land use intensity could have additional or interacting effects with climate change on biodiversity, even though the potential land-use effects at Mt. Kilimanjaro are still low and not impairing cavity-nesting Hymenoptera so far. Further studies should address species networks which might reveal more sensitive changes. For that purpose, trap nests provide a good model system to investigate effects of global change on multiple trophic levels and may also reveal direct effects of climate change on entire life-history traits when established under different microclimatic conditions. The non-uniform effects of abiotic and biotic conditions on multiple aspects of biodiversity revealed with this study also highlight that evaluating different aspects of biodiversity can give a more comprehensive picture than single observations.
Plasma membrane receptors are the most crucial and most commonly studied components of cells, since they not only ensure communication between the extracellular space and cells, but are also responsible for the regulation of cell cycle and cell division. The composition of the surface receptors, the so-called "Receptome", differs and is characteristic for certain cell types. Due to their significance, receptors have been important target structures for diagnostic and therapy in cancer medicine and often show aberrant expression patterns in various cancers compared to healthy cells. However, these aberrations can also be exploited and targeted by different medical approaches, as in the case of personalized immunotherapy. In addition, advances in modern fluorescence microscopy by so-called single molecule techniques allow for unprecedented sensitive visualization and quantification of molecules with an attainable spatial resolution of 10-20 nm, allowing for the detection of both stoichiometric and expression density differences.
In this work, the single molecule sensitive method dSTORM was applied to quantify the receptor composition of various cell lines as well as in primary samples obtained from patients with hematologic malignancies. The focus of this work lies on artefact free quantification, stoichiometric analyses of oligomerization states and co localization analyses of membrane receptors.
Basic requirements for the quantification of receptors are dyes with good photoswitching properties and labels that specifically mark the target structure without generating background through non-specific binding. To ensure this, antibodies with a predefined DOL (degree of labeling) were used, which are also standard in flow cytometry. First background reduction protocols were established on cell lines prior analyses in primary patient samples. Quantitative analyses showed clear expression differences between the cell lines and the patient cells, but also between individual patients.
An important component of this work is the ability to detect the oligomerization states of receptors, which enables a more accurate quantification of membrane receptor densities compared to standard flow cytometry. It also provides information about the activation of a certain receptor, for example of FLT3, a tyrosine kinase, dimerizing upon activation. For this purpose, different well-known monomers and dimers were compared to distinguish the typical localization statistics of single bound antibodies from two or more antibodies that are in proximity. Further experiments as well as co localization analyses proved that antibodies can bind to closely adjacent epitopes despite their size.
These analytical methods were subsequently applied for quantification and visualization of receptors in two clinically relevant examples. Firstly, various therapeutically relevant receptors such as CD38, BCMA and SLAMF7 for multiple myeloma, a malignant disease of plasma cells, were analyzed and quantified on patient cells. Furthermore, the influence of TP53 and KRAS mutations on receptor expression levels was investigated using the multiple myeloma cell lines OPM2 and AMO1, showing clear differences in certain receptor quantities.
Secondly, FLT3 which is a therapeutic target receptor for acute myeloid leukemia, was quantified and stoichiometrically analyzed on both cell lines and patient cells. In addition, cells that have developed resistance against midostaurin were compared with cells that still respond to this type I tyrosine-kinase-inhibitor for their FLT3 receptor expression and oligomerization state.
L-type voltage-gated calcium channels (LTCC) are heteromultimeric membrane proteins that allow Ca2+ entry into the cell upon plasma membrane depolarization. The β subunit of voltage-dependent calcium channels (Cavβ) binds to the α-interaction domain in the pore-forming α1 subunit and regulates the trafficking and biophysical properties of these channels. Of the four Cavβ isoforms, Cavβ2 is predominantly expressed in cardiomyocytes. This subunit associates with diverse proteins besides LTCC, but the molecular composition of the Cavβ2 nanoenvironments in cardiomyocytes is yet unresolved. Here, we used a protein-labeling technique in living cells based on an engineered ascorbate peroxidase 2 (APEX2). In this strategy, Cavβ2b was fused to APEX2 and expressed in adult rat cardiomyocytes using an adenovirus system. Nearby proteins covalently labeled with biotin-phenol were purified using streptavidin-coated beads and identified by mass spectrometry (MS). Analysis of the in situ APEX2-based biotin labeling by MS revealed 61 proteins located in the nanoenvironments of Cavβ2b, with a high specificity and consistency in all the replicates. These proteins are involved in diverse cellular functions such as cellular trafficking, sarcomere organization and excitation-contraction coupling. Among these proteins, we demonstrated an interaction between the ryanodine receptor 2 (RyR2) and Cavβ2b, probably coupling LTCC and the RyR2 into a supramolecular complex at the dyads. This interaction is mediated by the Src homology 3 (SH3) domain of Cavβ2b and is necessary for an effective pacing frequency‐dependent increase in Ca2+-induced Ca2+ release in cardiomyocytes.
During infection, bacteria need to adapt to a changing environment and have to endure various stress conditions. Small non-coding RNAs are considered as important regulators of bacterial gene expression and so allow quick adaptations by altering expression of specific target genes. Regulation of gene expression in the human-restricted pathogen Neisseria gonorrhoeae, the causative agent of the sexually transmitted disease gonorrhoea, is only poorly understood. The present study aims a better understanding of gene regulation in N. gonorrhoeae by studying small non-coding RNAs.
The discovery of antisense RNAs for all opa genes led to the hypothesis of asRNA-mediated degradation of out-of-frame opa transcripts. Analysis of asRNA expression revealed a very low abundance of the transcripts and inclusion of another phase-variable gene in the study indicates that the asRNAs are not involved in degradation of out-of-frame transcripts.
This doctoral thesis focuses on the analysis of trans-acting sRNAs. The sibling sRNAs NgncR_162 and NgncR_163 were discovered as post-transcriptional regulators altering expression of genes involved in metabolic processes, amino acid uptake and transcriptional regulation. A more detailed analysis by in silico and transcriptomic approaches showed that the sRNAs regulate a broad variety of genes coding for proteins of central metabolism, amino acid biosynthesis and degradation and several transport processes. Expression levels of the sibling sRNAs depend on the growth phase of the bacteria and on the growth medium. This indicates that NgncR_162 and NgncR_163 are involved in the adaptation of the gonococcal metabolism to specific growth conditions.
This work further initiates characterisation of the sRNA NgncR_237. An in silico analysis showed details on sequence conservation and a possible secondary structure. A combination of in silico target prediction and differential RNA sequencing resulted in the identification of several target genes involved in type IV pilus biogenesis and DNA recombination. However, it was not successful to find induction conditions for sRNA expression. Interestingly, a possible sibling sRNA could be identified that shares the target interaction sequence with NgncR_237 and could therefore target the same mRNAs.
In conclusion, this thesis provides further insights in gene regulation by non-coding RNAs in N. gonorrhoeae by analysing two pairs of sibling sRNAs modulating bacterial metabolism or possibly type IV pilus biogenesis.
Bildgebende Zweifarben-Einzelmolekül-PET-Fluoreszenzspektroskopie am molekularen Chaperon Hsp90
(2021)
Im Forschungsfeld der Proteindynamik häufen sich in den letzten Jahren Untersuchungen an einzelnen Molekülen. Damit können molekulare Ereignisse, die in konventioneller Spektroskopie durch stochastische Prozesse unentdeckt bleiben, durch direkte Beobachtung identifiziert und analysiert werden, was zu tieferem mechanistischem Verständnis des untersuchten Systems beitragen kann.
Die Implikation des molekularen Chaperons Hsp90 in die korrekte Faltung und Aktivierung einer Vielzahl davon abhängiger Klientenproteine machen es zu einem zentralen Knotenpunkt der zellulären Proteinhomöostase, allerdings ist der Mechanismus seiner breiten Klientenerkennung und -prozessierung bisher nur lückenhaft untersucht. Mit der Erkenntnis, dass Hsp90 ATP abhängig große, ratenlimitierende Umstrukturierungen erfährt, wurden Reportersysteme entwickelt, die auf dem Förster-Resonanzenergietransfer mit einer räumlichen Auflösung von ca. 2-10 nm basieren. Diese dokumentieren einen Klammerschluss des Chaperons und prognostizieren einen intermediatbbasierten Konformations-Zyklus. Details über den Mechanismus der Umstrukturierungen wurden mit der Entwicklung von Reportersystemen ermittelt, die auf dem photoinduzierten Elektronentransfer zwischen der Aminosäure Tryptophan und einem organischen Farbstoff basieren. Die Technik beruht auf kontaktinduzierter Fluoreszenzlöschung und damit verbundenen digitalen Intensitätsübergängen, dabei ermöglicht die räumliche Sensitivität von < 1 nm die Beobachtung von lokalen Umstrukturierungen. In Hsp90 wurden damit mittels konventioneller Spektroskopie drei kritische lokale Umlagerungen untersucht und daraus ein Modell mit heterogenen apo-Konformationen sowie ein kooperativer Konformationszyklus abgeleitet, der dem intermediatbasierten Modell gegenübersteht.
Im Rahmen dieser Dissertation wurde anhand des Hsp90-Chaperons eine Methode entwickelt, die eine bildgebende PET Fluoreszenzspektroskopie von mehreren Umstrukturierungen gleichzeitig an einzelnen Molekülen erlaubt. Ein umfangreiches Farbstoffscreening führte zur Identifizierung eines Farbstoffpaars, das die PET-basierte simultane Aufzeichnung zweier Konformations-Koordinaten ermöglicht. Über verschiedene Modifikationen des Chaperons konnten einzelmolekültaugliche Oberflächen hergestellt werden, auf denen zweifach markierte Hsp90-Proteine immobilisiert sind. Fluoreszenzintensitätszeitspuren einzelner Chaperone und entsprechende Kontrollkonstrukte bestätigen qualitativ den Erfolg der Methode, für die quantitative Analyse wurde eine Routine in der Programmiersprache Python entwickelt, mit welcher kinetische Informationen ermittelt werden konnten.
Diese legen eine enge wechselseitige Abhängigkeit der drei lokalen Elemente nahe, wobei der Großteil der Konformationsübergänge zweier simultan aufgezeichneter Umstrukturierungen Synchronität innerhalb von zwei Sekunden zeigt. Im Vergleich zur Hydrolyse von einem ATP in mehreren Minuten deutet das auf eine enge Kopplung hin. Weiter konnte eine Beschleunigung der Dynamiken durch aromatische Modifikation des N-Terminus von Hsp90 beobachtet werden, zudem erlaubt der Einzelmolekülansatz die Verwendung des nativen Nukleotids ATP, wodurch auch die lokalen Öffnungsdynamiken zugänglich werden. Die zur Bestimmung der Zeitkonstanten durchgeführte Analyse unterstützt die Ansicht heterogener apo-Zustände und einer einheitlich geschlossenen Konformation.
Die bildgebende Zweifarben-Einzelmolekül-PET-Spektroskopie konnte insgesamt zu einem Komplement der Einzelmolekül-FRET-Spektroskopie entwickelt werden, um damit lokale Konformationsdynamiken zu untersuchen. Der bildgebende Ansatz erlaubt eine einfache Implementierung in einen experimentellen Einzelmolekül-FRET Aufbau bei gleichzeitiger Erweiterung der beobachteten Koordinaten und wird so zu einem breit anwendbaren Werkzeug multidimensionaler Dynamikuntersuchungen einzelner Proteine.
Ionotrope Glutamatrezeptoren (iGluRs) sind ligandengesteuerte Ionenkanäle und vermitteln den Großteil der exzitatorischen Signalweiterleitung im gesamten zentralen Nervensystem. Darüber hinaus spielen iGluRs eine entscheidende Rolle bei der neuronalen Entwicklung und Funktion, einschließlich Lernprozessen und Gedächtnisbildung. Da eine Fehlfunktion dieser Rezeptoren mit zahlreichen neurodegenerativen Erkrankungen verbunden ist, stellen iGluRs zudem wichtige Zielproteine für die pharmakologische Wirkstoffentwicklung dar. Im Allgemeinen wird zwischen drei Untergruppen ionotroper Glutamatrezeptoren unterschieden, welche aufgrund ihrer Selektivität für einen bestimmten Liganden benannt sind: AMPA-, Kainate-, und NMDA-Rezeptoren. Die iGluRs jeder dieser Untergruppen bestehen in der Regel aus vier Untereinheiten, welche wiederum aus vier semiautonomen Domänen aufgebaut sind: (i) die aminoterminale Domäne (ATD), (ii) die Ligandenbindedomäne (LBD), (iii) die Transmembrandomäne (TMD) und (iv) die carboxyterminale Domäne (CTD).
Die Ligandenbindedomäne, welche wiederum aus zwei Lobes (D1 und D2) besteht und in ihrer Struktur einer Muschelschale ähnelt, vollzieht bei Bindung eines Neurotransmitters eine Konformationsänderung, wobei sie sich um den gebundenen Agonisten herumschließt. Diese Konformationsänderung der LBD wird auf die Transmembrandomäne, welche den membranüberspannenden Ionenkanal ausbildet, übertragen, was in einer Umlagerung der Transmembranhelices und infolgedessen der Öffnung des Ionenkanals resultiert. Die Konformationsänderung der LBD ist demnach die treibende Kraft, welche dem Öffnen und Schließen des Ionenkanals zugrunde liegt. Aus diesem Grund stellt die isolierte Ligandenbindedomäne, welche als lösliches Protein hergestellt werden kann, ein etabliertes Modellsystem zur Untersuchung der strukturellen und funktionellen Zusammenhänge innerhalb des Funktionsmechanismus ionotroper Glutamatrezeptoren dar.
Im Rahmen dieser Arbeit wurden die Konformationsdynamiken der in Escherichia coli-Bakterien exprimierten isolierten Ligandenbindedomänen der drei homologen Untergruppen – AMPA-, Kainate- und NMDA-Rezeptoren – sowohl als Monomer als auch als Dimer untersucht. Hierbei wurden im ungebundenen Apo-Zustand der Proteine signifikante Kinetiken im Bereich von Nanosekunden bis Mikrosekunden festgestellt, welche bei Bindung eines Agonisten sowie bei Dimerisierung erheblichen Veränderungen zeigen. Darüber hinaus wurde allosterische Kommunikation zwischen den LBDs der NMDA-Untergruppe untersucht, wobei in der Tat ein deutlicher allosterischer Effekt in Bezug auf die Konformationsdynamiken der Proteine gemessen werden konnte. Weiterhin wurde ein PET-FCS-basiertes Verfahren zur Messung der Dissoziationskonstante der Bindung eines Liganden an die LBD eines AMPA-Rezeptors entwickelt. Zuletzt wurde außerdem ermittelt, ob ein Unterschied zwischen vollen und partiellen Agonisten hinsichtlich ihres Einflusses auf die Konformationsdynamiken einer AMPA-Rezeptor LBD besteht, was nachgewiesenermaßen nicht der Fall ist.
Alle Messungen wurden auf Einzelmolekülebene auf Zeitskalen von Nanosekunden bis Millisekunden basierend auf Fluoreszenzfluktuationen unter Verwendung des photoinduzierten Elektronentransfers (PET) in Kombination mit Korrelationsspektroskopie (PET-FCS) durchgeführt. Zu diesem Zweck wurden PET-basierte Fluoreszenzsonden entwickelt, um Konformationsänderungen auf einer räumlichen Skala von einem Nanometer zu detektieren.
Durch die Experimente innerhalb dieser Arbeit konnte gezeigt werden, dass die PET-FCS-Methode eine vielversprechende Ergänzung zu allen bisher bestehenden Methoden zur Untersuchung der Konformationsdynamiken der Ligandenbindedomäne ionotroper Glutamatrezeptoren darstellt und daher eine aussichtsreiche Möglichkeit zur Erweiterung des zukünftigen Verständnisses der Funktionsweise von iGluRs bietet.
Owing to climate change, natural forest disturbances and consecutive salvage logging are drastically increasing worldwide, consequently increasing the importance of understanding how these disturbances would affect biodiversity conservation and provision of ecosystem services.
In chapter II, I used long-term water monitoring data and mid-term data on α-diversity of twelve species groups to quantify the effects of natural disturbances (windthrow and bark beetle) and salvage logging on concentrations of nitrate and dissolved organic carbon (DOC) in streamwater and α-diversity. I found that natural disturbances led to a temporal increase of nitrate concentrations in streamwater, but these concentrations remained within the health limits recommended by the World Health Organization for drinking water. Salvage logging did not exert any additional impact on nitrate and DOC concentrations, and hence did not affect streamwater quality. Thus, neither natural forest disturbances in watersheds nor associated salvage logging have a harmful effect on the quality of the streamwater used for drinking water. Natural disturbances increased the α-diversity in eight out of twelve species groups. Salvage logging additionally increased the α-diversity of five species groups related to open habitats, but decreased the biodiversity of three deadwood-dependent species groups.
In chapter III, I investigated whether salvage logging following natural disturbances (wildfire and windthrow) altered the natural successional trajectories of bird communities. I compiled data on breeding bird assemblages from nine study areas in North America, Europe and Asia, over a period of 17 years and tested whether bird community dissimilarities changed over time for taxonomic, functional and phylogenetic diversity when rare, common and dominant species were weighted differently. I found that salvage logging led to significantly larger dissimilarities than expected by chance and that these dissimilarities persisted over time for rare, common and dominant species, evolutionary lineages, and for rare functional groups. Dissimilarities were highest for rare, followed by common and dominant species.
In chapter IV, I investigated how β-diversity of 13 taxonomic groups would differ in intact, undisturbed forests, disturbed, unlogged forests and salvage-logged forests 11 years after a windthrow and salvage logging. The study suggests that both windthrow and salvage logging drive changes in between-treatment β-diversity, whereas windthrow alone seems to drive changes in within-treatment β-diversity. Over a decade after the windthrow at the studied site, the effect of subsequent salvage logging on within-treatment β-diversity was no longer detectable but the effect on between-treatment β-diversity persisted, with more prominent changes in saproxylic groups and rare species than in non-saproxylic groups or common and dominant species.
Based on these results, I suggest that salvage logging needs to be carefully weighed against its long-lasting impact on communities of rare species. Also, setting aside patches of naturally disturbed areas is a valuable management alternative as these patches would enable post-disturbance succession of bird communities in unmanaged patches and would promote the conservation of deadwood-dependent species, without posing health risks to drinking water sources.
Genome Wide Association Studies (GWAS) have revolutionized the way on
how genotype-phenotype relations are assessed. In the 20 years long history
of GWAS, multiple challenges from a biological, computational, and statistical
point of view have been faced. The implementation of this technique using
the model plant species Arabidopsis thaliana, has enabled the detection of many
association for multiple traits. Despite a lot of studies implementing GWAS
have discovered new candidate genes for multiple traits, different samples are
used across studies. In many cases, either globally diverse samples or samples
composed of accessions from a geographically restricted area are used. With
the aim of comparing GWAS outcomes between populations from different
geographic areas, this thesis describes the performance of GWAS in different
European samples of A. thaliana. Here, association mapping results for flowering
time were compared. Chapter 2 describes the analyses of random resampling
from this original sample. The aim was to establish reduced subsamples to
later carry out GWAS and compare the outcomes between these subsamples.
In Chapter 3, the European sample was split into eight equally-sized local
samples representing different geographic regions. Next, GWAS was carried
out and an attempt was made to clarify the differences in GWAS outcomes.
Chapter 4 contains the results of a collaboration with Prof. Dr. Wolfgang Dröge-
Laser, in which my mainly task was the analysis of RNAseq data from A.
thaliana plants infected by pathogenic fungi. Finally, Appendix A presents a very
short description of my participation in the GHP Project on Access to Care for
Cardiometabolic Diseases (HPACC) at the university of Heidelberg.
An adequate task allocation among colony members is of particular importance in large insect societies. Some species exhibit distinct polymorphic worker classes which are responsible for a specific range of tasks. However, much more often the behavior of the workers is related to the age of the individual. Ants of the genus Cataglyphis (Foerster 1850) undergo a marked age-related polyethism with three distinct behavioral stages. Newly emerged ants (callows) remain more or less motionless in the nest for the first day. The ants subsequently fulfill different tasks inside the darkness of the nest for up to four weeks (interior workers) before they finally leave the nest to collect food for the colony (foragers).
This thesis focuses on the neuronal substrate underlying the temporal polyethism in Cataglyphis nodus ants by addressing following major objectives:
(1) Investigating the structures and neuronal circuitries of the Cataglyphis brain to understand potential effects of neuromodulators in specific brain neuropils.
(2) Identification and localization of neuropeptides in the Cataglyphis brain.
(3) Examining the expression of suitable neuropeptide candidates during behavioral maturation of Cataglyphis workers.
The brain provides the fundament for the control of the behavioral output of an insect. Although the importance of the central nervous system is known beyond doubt, the functional significance of large areas of the insect brain are not completely understood. In Cataglyphis ants, previous studies focused almost exclusively on major neuropils while large proportions of the central protocerebrum have been often disregarded due to the lack of clear boundaries. Therefore, I reconstructed a three-dimensional Cataglyphis brain employing confocal laser scanning microscopy. To visualize synapsin-rich neuropils and fiber tracts, a combination of fluorescently labeled antibodies, phalloidin (a cyclic peptide binding to filamentous actin) and anterograde tracers was used. Based on the unified nomenclature for insect brains, I defined traceable criteria for the demarcation of individual neuropils. The resulting three-dimensional brain atlas provides information about 33 distinct synapse-rich neuropils and 30 fiber tracts, including a comprehensive description of the olfactory and visual tracts in the Cataglyphis brain. This three-dimensional brain atlas further allows to assign present neuromodulators to individual brain neuropils.
Neuropeptides represent the largest group of neuromodulators in the central nervous system of insects. They regulate important physiological and behavioral processes and have therefore recently been associated with the regulation of the temporal polyethism in social insects. To date, the knowledge of neuropeptides in Cataglyphis ants has been mainly derived from neuropeptidomic data of Camponotus floridanus ants and only a few neuropeptides have been characterized in Cataglyphis. Therefore, I performed a comprehensive transcriptome analysis in Cataglyphis nodus ants and identified peptides by using Q-Exactive Orbitrap mass spectrometry (MS) and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS. This resulted in the characterization of 71 peptides encoded on 49 prepropeptide genes, including a novel neuropeptide-like gene (fliktin). In addition, high-resolution MALDI-TOF MS imaging (MALDI-MSI) was applied for the first time in an ant brain to localize peptides on thin brain cryosections. Employing MALDI-MSI, I was able to visualize the spatial distribution of 35 peptides encoded on 16 genes.
To investigate the role of neuropeptides during behavioral maturation, I selected suitable neuropeptide candidates and analyzed their spatial distributions and expression levels following major behavioral transitions. Based on recent studies, I suggested the neuropeptides allatostatin-A (Ast-A), corazonin (Crz) and tachykinin (TK) as potential regulators of the temporal polyethism. The peptidergic neurons were visualized in the brain of C. nodus ants using immunohistochemistry. Independent of the behavioral stages, numerous Ast-A- and TK-immunoreactive (-ir) neurons innervate important high-order integration centers and sensory input regions with cell bodies dispersed all across the cell body rind. In contrast, only four corazonergic neurons per hemisphere were found in the Cataglyphis brain. Their somata are localized in the pars lateralis with axons projecting to the medial protocerebrum and the retrocerebral complex. Number and branching patterns of the Crz-ir neurons were similar across behavioral stages, however, the volume of the cell bodies was significantly larger in foragers than in the preceding behavioral stages. In addition, quantitative PCR analyses displayed increased Crz and Ast-A mRNA levels in foragers, suggesting a concomitant increase of the peptide levels. The task-specific expression of Crz and Ast-A along with the presence in important sensory input regions, high-order integration center, and the neurohormonal organs indicate a sustaining role of the neuropeptides during behavioral maturation of Cataglyphis workers.
The present thesis contains a comprehensive reference work for the brain anatomy and the neuropeptidome of Cataglyphis ants. I further demonstrated that neuropeptides are suitable modulators for the temporal polyethism of Cataglyphis workers. The complete dataset provides a solid framework for future neuroethological studies in Cataglyphis ants as well as for comparative studies on insects. This may help to improve our understanding of the functionality of individual brain neuropils and the role of neuropeptides, particularly during behavioral maturation in social insects.
The Chimpanzees of the Comoé National Park, Ivory Coast. Status, distribution, ecology and behavior
(2021)
Although wild chimpanzees (Pan troglodytes) have been studied intensely for more than 50 years, there are still many aspects of their ecology and behavior that are not well understood. Every time that a new population of chimpanzees has been studied, new behaviors and unknown aspects of their ecology have been discovered. All this accumulated knowledge is helping us to piece together a model of how could last human and chimpanzee common ancestors have lived and behaved between seven and five million years ago. Comoé chimpanzees had never been studied in depth, until we started our research in October 2014, only a few censuses had been realized. The last surveys prior our work, stated that the population was so decimated that was probably functionally extinct. When we started this research, we had to begin with a new intensive survey, using new methods, to ascertain the real status and distribution of the chimpanzees living in Comoé National Park (CNP). During the last five years, we have realized a deep study aiming to know more about their ecology and behavior. We combined transects and reconnaissance marches (recces) with the use of camera traps, for the first time in CNP, obtaining a wealth of data that is not fully comprised in this dissertation. With this research, we determined that there is a sustainable continuous population of Western chimpanzees (Pan troglodytes verus) in CNP and the adjacent area of Mont Tingui, to the West, with a minimum of 127 weaned chimpanzees living in our main 900 km2 study area, SW of CNP. We found that this population is formed by a minimum of eight different chimpanzee communities, of which we studied seven, four of them more in detail. These chimpanzees spent much more time in the forest than in the savanna habitats.
We also found that Comoé chimpanzees consumed at least 58 different food items in their dit, which they obtained both from forest and savanna habitats. Another finding was that insectivory had an important role in their diet, with at least four species of ants, three of termites and some beetle larvae. These chimpanzees also hunted at least three species of monkeys and maybe rodents and duikers and occasionally consumed the big land snails of genus Achatina. We found that, during the fruit scarcity period in the late rainy season, they intensely consumed the cambium of Ceiba pentandra, as fallback food, much more than the bark or cambium of any other tree species. Another interesting finding was that all the chimpanzees in the studied area realized this particular bark-peeling behavior and had been repeatedly peeling the trees of this species for years. This did not increase tree mortality and the damage caused to the trees was healed in two years, not reducing the growth, thus being a sustainable use of the trees. We found that Comoé chimpanzees produced and used a great variety of tools, mainly from wooden materials, but also from stone and herbaceous vegetation.
Their tool repertory included stick tools to dip for Dorylus burmeisteri ants, to fish for Camponotus and Crematogaster ants, to dip for honey, mainly from Meliponini stingless bees, but sometimes from honey bees (Apis mellifera). It also included the use of stick tools to fish termites of Macrotermes subhyalinus and Odontotermes majus (TFTs), to dip for water from tree holes and investigatory probes for multiple purposes. Additionally, these chimpanzees used leaf-sponges to drink from tree holes and to collect clayish water from salt-licks. They also used stones to hit the buttresses of trees during displays, the so called accumulative stone throwing behavior and probably used stones as hammers, to crack open hard-shelled Strichnos spinosa and Afraegle paniculata fruits and Achatina snails. The chimpanzees also used objects that are not generally accepted as animal tools, for being attached to the substrate, with different purposes: they drummed buttresses of trees with hands and/or feet to produce sound during male displays and they pounded open hard-shelled fruits, Achatina snails and Cubitermes termite mounds on stone or root anvils. We finally measured the stick tools and found significant differences between them suggesting that they were specialized tools made specifically for every purpose. We studied more in detail the differences between apparently similar tools, the honey dipping tools and the water dipping tools, often with brushes made at their tips to collect the fluids. These last tools were exclusive from Comoé and have not been described at any other site. We found that total length, diameter and brush length were significantly different, suggesting that they were specialized tools. We concluded that Comoé chimpanzees had a particular culture, different from those of other populations of Western chimpanzees across Africa. Efficient protection, further research and permanent presence of research teams are required to avoid that this unique population and its culture disappears by the poaching pressure and maybe by the collateral effects of climate change.
The family of trypanosomatid parasites, including the human pathogens Trypanosoma brucei and Leishmania, has evolved sophisticated strategies to survive in harmful host environments. While Leishmania generate a safe niche inside the host’s macrophages, Trypanosoma brucei lives extracellularly in the mammalian bloodstream, where it is constantly exposed to the attack of the immune system. Trypanosoma brucei ensures its survival by periodically changing its protective surface coat in a process known as antigenic variation. The surface coat is composed of one species of ‘variant surface glycoprotein’ (VSG). Even though the genome possesses a large repertoire of different VSG isoforms, only one is ever expressed at a time from one out of the 15 specialized subtelomeric ‘expression sites’ (ES). Switching the coat can be accomplished either by a recombination-based exchange of the actively-expressed VSG with a silent VSG, or by a transcriptional switch to a previously silent ES.
The conserved histone methyltransferase DOT1B methylates histone H3 on lysine 76 and is involved in ES regulation in T. brucei. DOT1B ensures accurate transcriptional silencing of the inactive ES VSGs and influences the kinetics of a transcriptional switch. The molecular machinery that enables DOT1B to execute these regulatory functions at the ES is still elusive, however. To learn more about DOT1B-mediated regulatory processes, I wanted to identify DOT1B-associated proteins.
Using two complementary approaches, specifically affinity purification and proximity-dependent biotin identification (BioID), I identified several novel DOT1B-interacting candidates. To validate these data, I carried out reciprocal co-immunoprecipitations with the most promising candidates. An interaction of DOT1B with the Ribonuclease H2 protein complex, which has never been described before in any other organism, was confirmed. Trypanosomal Ribonuclease H2 maintains genome integrity by resolving RNA-DNA hybrids, structures that if not properly processed might initiate antigenic variation. I then investigated DOT1B’s contribution to this novel route to antigenic variation. Remarkably, DOT1B depletion caused an increased RNA-DNA hybrid abundance, accumulation of DNA damage, and increased VSG switching. Deregulation of VSGs from throughout the silent repertoire was observed, indicating that recombination-based switching events occurred. Encouragingly, the pattern of deregulated VSGs was similar to that seen in Ribonuclease H2-depleted cells. Together these data support the hypothesis that both proteins act together in modulating RNA-DNA hybrids to contribute to the tightly-regulated process of antigenic variation.
The transmission of trypanosomatid parasites to mammalian hosts is facilitated by insect vectors. Parasites need to adapt to the extremely different environments encountered during transmission. To ensure their survival, they differentiate into various specialized forms adapted to each tissue microenvironment. Besides antigenic variation, DOT1B additionally affects the developmental differentiation from the mammalian-infective to the insect stage of Trypanosoma brucei. However, substantially less is known about the influence of chromatin-associated proteins such as DOT1B on survival and adaptation strategies of related Leishmania parasites. To elucidate whether DOT1B’s functions are conserved in Leishmania, phenotypes after gene deletion were analyzed. As in Trypanosoma brucei, generation of a gene deletion mutant demonstrated that DOT1B is not essential for the cell viability in vitro. DOT1B deletion was accompanied with a loss of histone H3 lysine 73 trimethylation (the lysine homologous to trypanosomal H3K76), indicating that Leishmania DOT1B is also solely responsible for catalyzing this post-translational modification. As in T. brucei, dimethylation could only be observed during mitosis/cytokinesis, while trimethylation was detectable throughout the cell cycle in wild-type cells. In contrast to the trypanosome DOT1B, LmxDOT1B was not essential for differentiation in vitro. However, preliminary data indicate that the enzyme is required for effective macrophage infection.
In conclusion, this study demonstrated that the identification of protein networks and the characterization of protein functions of orthologous proteins from related parasites are effective tools to improve our understanding of the parasite survival strategies. Such insights are a necessary step on the road to developing better treatments for the devastating diseases they cause.
Recent progress in nanotechnology has attracted interest to a biomedical application of the carbon nanoparticle C60 fullerene (C60) due to its unique structure and versatile biological activity. In the current study the dual functionality of C60 as a photosensitizer and a drug nanocarrier was exploited to improve the efficiency of chemotherapeutic drugs towards human leukemic cells.
Pristine C60 demonstrated time-dependent accumulation with predominant mitochondrial localization in leukemic cells. C60’s effects on leukemic cells irradiated with high power single chip LEDs of different wavelengths were assessed to find out the most effective photoexcitation conditions. A C60-based noncovalent nanosized system as a carrier for an optimized drug delivery to the cells was evaluated in accordance to its physicochemical properties and toxic effects. Finally, nanomolar amounts of C60-drug nanocomplexes in 1:1 and 2:1 molar ratios were explored to improve the efficiency of cell treatment, complementing it with photodynamic approach.
A proposed treatment strategy was developed for C60 nanocomplexes with the common chemotherapeutic drug Doxorubicin, whose intracellular accumulation and localization, cytotoxicity and mechanism of action were investigated. The developed strategy was revealed to be transferable to an alternative potent anticancer drug – the herbal alkaloid Berberine.
Hereafter, a strong synergy of treatments arising from the combination of C60-mediated drug delivery and C60 photoexcitation was revealed. Presented data indicate that a combination of chemo- and photodynamic treatments with C60-drug nanoformulations could provide a promising synergetic approach for cancer treatment.
Fluorescence microscopy is a form of light microscopy that has developed during the 20th century and is nowadays a standard tool in Molecular and Cell biology for studying the structure and function of biological molecules. High-resolution fluorescence microscopy techniques, such as dSTORM (direct Stochastic Optical Reconstruction Microscopy) allow the visualization of cellular structures at the nanometre scale (10−9 m). This has already made it possible to decipher the composition and function of various biopolymers, such as proteins, lipids and nucleic acids, up to the three-dimensional (3D) structure of entire organelles. In practice, however, it has been shown that these imaging methods and their further developments still face great challenges in order to achieve an effective resolution below ∼ 10 nm. This is mainly due to the nature of labelling biomolecules. For the detection of molecular structures, immunostaining is often performed as a standard method. Antibodies to which fluorescent molecules are coupled, recognize and bind specifcally and with high affnity to the molecular section of the target structure, also called epitope or antigen. The fluorescent molecules serve as reporter molecules which are imaged with the use of a fluorescence microscope. However, the size of these labels with a length of about 10-15 nm in the case of immunoglobulin G (IgG) antibodies, cause a detection of the fluorescent molecules shifted to the real position of the studied antigen. In dense regions where epitopes are located close to each other, steric hindrance between antibodies can also occur and leads to an insuffcient label density. Together with the shifted detection of fluorescent molecules, these factors can limit the achievable resolution of a microscopy technique. Expansion microscopy (ExM) is a recently developed technique that achieves a resolution improvement by physical expansion of an investigated object. Therefore, biological samples such as cultured cells, tissue sections, whole organs or isolated organelles are chemically anchored into a swellable polymer. By absorbing water, this so-called superabsorber increases its own volume and pulls the covalently bound biomolecules isotropically apart. Routinely, this method achieves a magnifcation of the sample by about four times its volume. But protocol variants have already been developed that result in higher expansion factors of up to 50-fold. Since the ExM technique includes in the frst instance only the sample treatment for anchoring and magnifcation of the sample, it can be combined with various standard methods of fluorescence microscopy. In theory, the resolution of the used imaging technique improves linearly with the expansion factor of the ExM treated sample. However, an insuffcient label density and the size of the antibodies can here again impair the effective achievable resolution. The combination of ExM with high-resolution fluorescence microscopy methods represents a promising strategy to increase the resolution of light microscopy. In this thesis, I will present several ExM variants I developed which show the combination of ExM with confocal microscopy, SIM (Structured Illumination Microscopy), STED (STimulated Emission Depletion) and dSTORM. I optimized existing ExM protocols and developed different expansion strategies, which allow the combination with the respective imaging technique. Thereby, I gained new structural insights of isolated centrioles from the green algae Chlamydomonas reinhardtii by combining ExM with STED and confocal microscopy. In another project, I combined 3D-SIM imaging with ExM and investigated the molecular structure of the so-called synaptonemal complex. This structure is formed during meiosis in eukaryotic cells and contributes to the exchange of genetic material between homologous chromosomes. Especially in combination with dSTORM, the ExM method showed its high potential to overcome the limitations of modern fluorescence microscopy techniques. In this project, I expanded microtubules in mammalian cells, a polymer of the cytoskeleton as well as isolated centrioles from C. reinhardtii. By labelling after expansion of the samples, I was able to signifcantly reduce the linkage error of the label and achieve an improved label density. In future, these advantages together with the single molecule sensitivity and high resolution obtained by the dSTORM method could pave the way for achieving molecular resolution in fluorescence microscopy
The right timing of phenological events is crucial for species fitness. Species should be highly synchronized with mutualists, but desynchronized with antagonists. With climate warming phenological events advance in many species. However, often species do not respond uniformly to warming temperatures. Species-specific responses to climate warming can lead to asynchrony or even temporal mismatch of interacting species. A temporal mismatch between mutualists, which benefit from each other, can have negative consequences for both interaction partners. For host-parasitoid interactions temporal asynchrony can benefit the host species, if it can temporally escape its parasitoid, with negative consequences for the parasitoid species, but benefit the parasitoid species if it increases synchrony with its host, which can negatively affect the host species. Knowledge about the drivers of phenology and the species-specific responses to these drivers are important to predict future effects of climate change on trophic interactions. In this dissertation I investigated how different drivers act on early flowering phenology and how climate warming affects the tritrophic relationship of two spring bees (Osmia cornuta & Osmia bicornis), an early spring plant (Pulsatilla vulgaris), which is one of the major food plants of the spring bees, and three main parasitoids of the spring bees (Cacoxenus indagator, Anthrax anthrax, Monodontomerus).
In Chapter II I present a study in which I investigated how different drivers and their change over the season affect the reproductive success of an early spring plant. For that I recorded on eight calcareous grasslands around Würzburg, Germany the intra-seasonal changes in pollinator availability, number of co-flowering plants and weather conditions and studied how they affect flower visitation rates, floral longevity and seed set of the early spring plant P. vulgaris. I show that bee abundances and the number of hours, which allowed pollinator foraging, were low at the beginning of the season, but increased over time. However, flower visitation rates and estimated total number of bee visits were higher on early flowers of P. vulgaris than later flowers. Flower visitation rates were also positively related to seed set. Over time and with increasing competition for pollinators by increasing numbers of co-flowering plants flower visitation rates decreased. My data shows that a major driver for early flowering dates seems to be low interspecific competition for pollinators, but not low pollinator abundances and unfavourable weather conditions.
Chapter III presents a study in which I investigated the effects of temperature on solitary bee emergence and on the flowering of their food plant and of co-flowering plants in the field. Therefore I placed bee cocoons of two spring bees (O. cornuta & O. bicornis) on eleven calcareous grasslands which differed in mean site temperature. On seven of these grasslands the early spring plant P. vulgaris occurred. I show that warmer temperatures advanced mean emergence in O. cornuta males. However, O. bicornis males and females of both species did not shift their emergence. Compared to the bees P. vulgaris advanced its flowering phenology more strongly with warmer temperatures. Co-flowering plants did not shift flowering onset. I suggest that with climate warming the first flowers of P. vulgaris face an increased risk of pollinator limitation whereas for bees a shift in floral resources may occur.
In Chapter IV I present a study in which I investigated the effects of climate warming on host-parasitoid relationships. I studied how temperature and photoperiod affect emergence phenology in two spring bees (O. cornuta & O. bicornis) and three of their main parasitoids (C. indagator, A. anthrax, Monodontomerus). In a climate chamber experiment with a crossed design I exposed cocoons within nest cavities and cocoons outside of nest cavities to two different temperature regimes (long-term mean of Würzburg, Germany and long-term mean of Würzburg + 4 °C) and three photoperiods (Würzburg vs. Snåsa, Norway vs. constant darkness) and recorded the time of bee and parasitoid emergence. I show that warmer temperatures advanced emergence in all studied species, but bees advanced less strongly than parasitoids. Consequently, the time period between female bee emergence and parasitoid emergence decreased in the warm temperature treatment compared to the cold one. Photoperiod influenced the time of emergence only in cocoons outside of nest cavities (except O. bicornis male emergence). The data also shows that the effect of photoperiod compared to the effect of temperature on emergence phenology was much weaker. I suggest that with climate warming the synchrony of emergence phenologies of bees and their parasitoids will amplify. Therefore, parasitism rates in solitary bees might increase which can negatively affect reproductive success and population size.
In this dissertation I show that for early flowering spring plants low interspecific competition for pollinators with co-flowering plants is a major driver of flowering phenology, whereas other drivers, like low pollinator abundances and unfavourable weather conditions are only of minor importance. With climate warming the strength of different drivers, which act on the timing of phenological events, can change, like temperature. I show that warmer temperatures advance early spring plant flowering more strongly than bee emergence and flowering phenology of later co-flowering plants. Furthermore, I show that warmer temperatures advance parasitoid emergence more strongly than bee emergence. Whereas temperature changes can lead to non-uniform temporal shifts, I demonstrate that geographic range shifts and with that altered photoperiods will not change emergence phenology in bees and their parasitoids. In the tritrophic system I investigated in this dissertation climate warming may negatively affect the reproductive success of the early spring plant and the spring bees but not of the parasitoids, which may even benefit from warming temperatures.
The biosphere harbors a large quantity and diversity of microbial organisms that can thrive in all environments. Estimates of the total number of microbial species reach up to 1012, of which less than 15,000 have been characterized to date. It has been challenging to delineate phenotypically, evolutionary and ecologically meaningful lineages such as for example, species, subspecies and strains. Even within recognized species, gene content can vary considerably between sublineages (for example strains), a problem that can be addressed by analyzing pangenomes, defined as the non-redundant set of genes within a phylogenetic clade, as evolutionary units.
Species considered to be ecologically and evolutionary coherent units, however to date it is still not fully understood what are primary habitats and ecological niches of many prokaryotic species and how environmental preferences drive their genomic diversity. Majority of comparative genomics studies focused on a single prokaryotic species in context of clinical relevance and ecology. With accumulation of sequencing data due to genomics and metagenomics, it is now possible to investigate trends across many species, which will facilitate understanding of pangenome evolution, species and subspecies delineation.
The major aims of this thesis were 1) to annotate habitat preferences of prokaryotic species and strains; 2) investigate to what extent these environmental preferences drive genomic diversity of prokaryotes and to what extent phylogenetic constraints limit this diversification; 3) explore natural nucleotide identity thresholds to delineate species in bacteria in metagenomics gene catalogs; 4) explore species delineation for applications in subspecies and strain delineation in metagenomics.
The first part of the thesis describes methods to infer environmental preferences of microbial species. This data is a prerequisite for the analyses performed in the second part of the thesis which explores how the structure of bacterial pangenomes is predetermined by past evolutionary history and how is it linked to environmental preferences of the species. The main finding in this subchapter that habitat preferences explained up to 49% of the variance for pangenome structure, compared to 18% by phylogenetic inertia. In general, this trend indicates that phylogenetic inertia does not limit evolution of pangenome size and diversity, but that convergent evolution may overcome phylogenetic constraints. In this project we show that core genome size is associated with higher environmental ubiquity of species. It is likely this is due to the fact that species need to have more versatile genomes and most necessary genes need to be present in majority of genomes of that species to be highly prevalent. Taken together these findings may be useful for future predictive analyses of ecological niches in newly discovered species.
The third part of the thesis explores data-driven, operational species boundaries. I show that homologous genes from the same species from different genomes tend to share at least 95% of nucleotide identity, while different species within the same genus have lower nucleotide identity. This is in line with other studies showing that genome-wide natural species boundary might be in range of 90-95% of nucleotide identity. Finally, the fourth part of the thesis discusses how challenges in species delineation are relevant for the identification of meaningful within-species groups, followed by a discussion on how advancements in species delineation can be applied for classification of within-species genomic diversity in the age of metagenomics.
Temporal development of communities with a focus on insects, in time series of one to four decades
(2021)
Changes and development are fundamental principles in biocenoses and can affect a multitude of ecological processes. In insect communities phenological and density changes, changes in species richness and community composition, as well as interactions between those changes, are the most important macro processes. However, climate change and other factors like habitat degradation and loss alter these processes leading to shifts and general biodiversity declines. Even though knowledge about insect decline in central Europe increased during the last decades, there are significant knowledge gaps about the development of insect communities in certain habitats and taxa. For example, insect communities in small lentic as well as in forested habitats are under-sampled and reported to be less endangered than communities in other habitats. Furthermore, the changes within habitats and taxa are additionally influenced by certain traits, like host or feeding specialization. To disentangle these influences and to increase the knowledge about the general long-term development of insect communities, comprehensive long-term monitoring studies are needed. In addition, long-term effects of conservation strategies should also be evaluated on large time scales in order to be able to decide on a scientific base which strategies are effective in promoting possibly declining taxa. Hence, this thesis also tackles the effects of an integrative conservation strategy on wood dependent beetle and fungi, beside the development of water beetle and macro moth communities over multiple decades. In Chapter 2 I present a study on the development of water beetle communities (Dytiscidae, Haliplidae, Noteridae) in 33 water bodies in Southern Germany from 1991 to 2018. Time-standardized capture per waterbody was used during three periods: between 1991 and 1995, 2007 and 2008, and 2017 and 2018. Results showed annual declines in both species number (ca. -1%) and abundance (ca. -2%). In addition, community composition shifted over time in part due to changing pH values. Hence, the recorded changes during the 28-year study period partly reflect natural succession processes. However, since also moor-related beetle species decreased significantly, it is likely that water beetles in southern Germany are also threatened by non-successional factors, including desiccation, increased nitrogen input and/or mineralization, as well as the loss of specific habitats. The results suggest, that in small to midsize lentic waterbodies, current development should aim for constant creation of new water bodies and protection of moor waterbodies in order to protect water beetle communities on a landscape scale. In Chapter 3 I present an analysis of the development of nocturnal macro moth species richness, abundance and biomass over four decades in forests of southern Germany. Two local scale data sets featuring a coppiced oak forest as well as an oak high forest were analysed separately from a regional data set representing all forest types in the temperate zone of Central Europe. At the regional scale species richness, abundance and biomass showed annual declines of ca. 1 %, 1.3 % and 1.4 %, respectively. These declines were more pronounced in plant host specialists and in dark coloured species. In contrast, species richness increased by ca. 1.5 % annually in the coppiced forest, while no significant trends were found in the high forest. In contrast to past assumptions, insect decline apparently affects also hyper diverse insect groups in forests. Since host specialists and dark coloured species were affected more heavily by the decline than other groups, habitat loss and climate change seem to be potential drivers of the observed trends. However, the positive development of species richness in the coppiced oak forest indicates that maintaining complex and diverse forest ecosystems through active management might compensate for negative trends in biodiversity. Chapter 4 features a study specifically aiming to investigate the long-term effect of deadwood enrichment as an integrative conservation strategy on saproxylic beetles and fungi in a central European beech forest at a landscape scale. A before–after control–impact design, was used to compare assemblages and gamma diversities of saproxylic organisms (beetles and fungi) in strictly protected old-growth forest areas (reserves) and previously moderately and intensively managed forest areas. Forests were sampled one year before and a decade after starting a landscape-wide strategy of dead-wood enrichment. Ten years after the start of the dead-wood enrichment, neither gamma diversities of saproxylic organisms nor species composition of beetles did reflect the previous management types anymore. However, fungal species composition still mirrored the previous management gradient. The results demonstrated that intentional enrichment of dead wood at the landscape scale can effectively restore communities of saproxylic organisms and may thus be a suitable strategy in addition to permanent strict reserves in order to protect wood dependent organisms in Europe. In this thesis I showed, that in contrast to what was assumed and partly reported so far, also water beetles in lentic water bodies and macro moths in forests decreased in species richness, abundance and biomass during the last three to four decades. In line with earlier studies, especially dark coloured species and specialists decreased more than light-coloured species and generalists. The reasons for these declines could partly be attributed to natural processes and pollution and possibly to climate change. However, further studies, especially experimental ones, will be needed to achieve a better understanding of the reasons for insect decline. Furthermore, analyses of time series data should be interpreted cautiously especially if the number of sampling years is smaller than ten years. In addition, validation techniques such as left- and right- censoring and cross validation should be used in order to proof the robustness of the analyses. However, the lack of knowledge, we are still facing today, should not prevent scientists and practitioners from applying conservation measures. In order to prove the effectiveness of such measures, long-term monitoring is crucial. Such control of success is essential for evidence based and thus adapted conservation strategies of threatened organisms.
Neisseria gonorrhoeae are Gram-negative bacteria with diplococcal shape. As an obligate human pathogen, it is the causative agent of gonorrhoea, a sexually transmitted disease. Gonococci colonize a variety of mucosal tissues, mainly the urogenital tract in men and women. Occasionally N. gonorrhoeae invades the bloodstream, leading to disseminated gonococcal infection. These bacteria possess a repertoire of virulence factors, which expression patterns can be adapted to the environmental conditions of the host. Through the accumulation of antibiotic resistances and in absence of vaccines, some neisserial strains have the potential to spread globally and represent a major public health threat. Therefore, it is necessary to understand the exact molecular mechanisms underlying the successful infection and progression of gonococci within their host. This deeper understanding of neisserial infection and survival mechanisms is needed for the development of new therapeutic agents.
In this work, the role of host-cell sphingolipids on the intracellular survival of N. gonorrhoeae was investigated. It was shown that different classes of sphingolipids strongly interact with invasive gonococci in epithelial cells. Therefore, novel and highly specific clickable sphingolipid analogues were applied to study these interactions with this pathogen. The formation of intra- and extracellular sphingosine vesicles, which were able to target gonococci, was observed. This direct interaction led to the uptake and incorporation of sphingosine into the neisserial membrane. Together with in vitro results, sphingosine was identified as a potential bactericidal reagent as part of the host cell defence. By using different classes of sphingolipids and their clickable analogues, essential structural features, which seem to trigger the bacterial uptake, were detected. Furthermore, effects of key enzymes of the sphingolipid signalling pathway were tested in a neutrophil infection model.
In conclusion, the combination of click chemistry and infection biology made it possible to shed some light on the dynamic interplay between cellular sphingosine and N. gonorrhoeae. Thereby, a possible “catch-and-kill” mechanism could have been observed.
Angesichts des dramatischen, weltweiten Anstiegs der Prävalenz von Demenzerkrankungen und der aktuellen, unzureichenden Therapieansätze ist die Bereitstellung neuer, wirkungsvoller Behandlungsoptionen von größter Bedeutung. Technologische, pharmakologische und verhaltensbasierte Verfahren des Memory Enhancement könnten zur Lösung dieses Problems beitragen: Hierzu zählt die Stammzelltransplantation, die in mehreren Tierstudien zu einer Verbesserung der Gedächtnisfunktion führte. Zudem wird seit Längerem an einer Impfung gegen die Alzheimer-Krankheit mittels β-Amyloid-Antikörpern geforscht. Ein weiterer therapeutischer Ansatz für die Alzheimer-Krankheit besteht in der optogenetischen Stimulation spezifischer hippocampaler Engramm-Zellen, durch die bei einem Maus-Modell verloren gegangene Erinnerungen wiederhergestellt werden konnten. Unkonventionelle Pharmazeutika wie Erythropoetin führten in Tierstudien und bei Patienten mit neuropsychiatrischen Erkrankungen zu einer Verbesserung der kognitiven Fähigkeiten und des Gedächtnisses. Eine Modifikation der Ernährung und der Einsatz von Pro- und Präbiotika beeinflussen das Gedächtnis über eine Manipulation der Darm-Hirn-Achse. Verhaltensbasierte Maßnahmen wie körperliche Aktivität und der Einsatz von Mnemotechniken stellen effektive Ansätze des Memory Enhancement dar, welche bereits heute von gesunden Individuen implementiert werden können. Für die Anwendung von Augmented Reality (AR) konnten kognitionsfördernde Wirkungen beim Lernen neuroanatomischer Themen und dem Zusammenbau von Objekten nachgewiesen werden. Besonders vielversprechend stellt sich die Entwicklung einer Gedächtnisprothese dar, durch die vergessene Informationen bei Personen mit stattgehabtem Schädel-Hirn-Trauma und apoplektischem Insult reaktiviert werden könnten. Memory Enhancement ist prinzipiell bereits heute bei gesunden und kranken Individuen anwendbar und verspricht wirksame zukünftige Präventions- und Therapieoptionen. Ein realer Einsatz in der klinischen Praxis ist in naher Zukunft jedoch noch nicht zu erwarten.
Die Calcineurin/NFAT-Signalkaskade spielt eine wichtige Rolle bei der Entwicklung einer kardialen Hypertrophie. Im Zytoplasma von Kardiomyozyten wird die Phosphatase Calcineurin nach Stimulierung der Zellen, z. B. durch Dehnungsreize, Angiotensin II (Ang II) oder Endothelin I (ET-1), und einen daraus folgenden intrazellulären Ca2+-Strom aktiviert. Dies führt zur Dephosphorylierung von NFAT und zu dessen nukleärer Translokation. In früheren Arbeiten von Ritter et al. wurden sowohl eine nukleäre Lokalisationssequenz (NLS) als auch eine nukleäre Exportsequenz (NES) innerhalb von Calcineurin identifiziert, die den Transport von Calcineurin zwischen dem Zytoplasma und dem Nukleus ermöglichen. Basierend auf diesen Ergebnissen wurde das Import Blocking Peptid (IBP) entwickelt. Dieses Peptid entspricht der NLS von Calcineurin und blockiert die Calcineurin-Bindungsstellen des Shuttleproteins (Karyopherins) Importin β1. So wird die Translokation von Calcineurin in den Nukleus unterbunden und die Signalkaskade zur Aktivierung von Hypertrophie-Genen in Kardiomyozyten unterbrochen. Dabei blieb die Phosphatase-Aktivität von Calcineurin unbeeinflusst. Eines der Ziele dieser Arbeit war, IBP weiter zu optimieren und den „proof of principle“ auch in vivo zu führen. Hierfür wurden u. a. ein geeignetes Lösungsmittel bestimmt (biokompatibel und an die Peptidcharakteristika angepasst), die Peptidstruktur modifiziert (Erhöhung der Spezifität/Wirksamkeit) und die erforderliche Dosis weiter eingegrenzt (Belastungs- und Kostenreduktion). Unter Verwendung einer TAMRA-markierten Wirkstoffvariante konnten der Weg des Peptids in Mäusen nachverfolgt und die Ausscheidung quantifiziert werden.
Aufbauend auf den Ergebnissen von Burkard et al., die die Entstehung einer konstitutiv-aktiven und nukleären Calcineurin-Isoform nach proteolytischer Spaltung durch Calpain nachwiesen, wurde die Rolle von Calcineurin im Zellkern genauer untersucht. Außerdem sollte die Frage beantwortet werden, wie (über Calcineurin?) die Herzmuskelzelle zwischen Calciumschwankungen im Zuge der Exzitations-Kontraktions-Kopplung (ECC) und vergleichsweise schwachen Calciumsignalen zur Transkriptionsteuerung unterscheidet. Mit Hilfe von nukleären Calcineurin-Mutanten, die einen Defekt in der Ca2+-Bindung aufwiesen, konnte die Bedeutung von Calcineurin als Calciumsensor für die NFAT-abhängige Transkription nachgewiesen werden. Im Mausmodell waren unter Hypertrophie-Bedingungen die Ca2+-Transienten in der nukleären Mikrodomäne signifikant stärker als im Zytosol, wodurch die Hypothese, dass die Aktivierung der Calcineurin/NFAT-Signalkaskade unabhängig von zytosolischem Ca2+ erfolgt, gestützt wird. Messungen von nukleären und zytosolischen Ca2+-Transienten in IP3-Sponge-Mäusen zeigten im Vergleich zu Wildtyp-Mäusen keine Erhöhung des Ca2+-Spiegels während der Diastole, was auf eine Rolle von Inositoltrisphosphat (IP3) in der Signalkaskade deutet. Außerdem zeigten isolierte Zellkerne ventrikulärer adulter Kardiomyozyten eine erhöhte Expression des IP3-Rezeptors 2 (IP3R2) nach Ang II-Stimulierung. Diese gesteigerte Expression war abhängig von der Calcineurin/NFAT-Kaskade und bestand sogar
3 Wochen nach Entfernung des Ang II-Stimulus fort. Zusammenfassend lässt sich sagen, dass nukleäres Calcineurin als ein Ca2+-Sensor agiert, dass die lokale Ca2+-Freisetzung im Kern über IP3-Rezeptoren detektiert wird und dass dies im Zusammenspiel mit NFAT die Transkription von Hypertrophiegenen initiiert.
Chlamydia infect millions worldwide and cause infertility and blinding trachoma. Chlamydia trachomatis (C. trachomatis) is an obligate intracellular gram-negative pathogen with a significantly reduced genome. This bacterium shares a unique biphasic lifecycle in which it alternates between the infectious, metabolically inert elementary bodies (EB) and the non-infections, metabolically active replicative reticular bodies (RB).
One of the challenges of working with Chlamydia is its difficult genetic accessibility. In the present work, the high-throughput method TagRNA-seq was used to differentially label transcriptional start sites (TSS) and processing sites (PSS) to gain new insights into the transcriptional landscape of C. trachomatis in a coverage that has never been achieved before. Altogether, 679 TSSs and 1067 PSSs were detected indicating its high transcriptional activity and the need for transcriptional regulation. Furthermore, the analysis of the data revealed potentially new non-coding ribonucleic acids (ncRNA) and a map of transcriptional processing events. Using the upstream sequences, the previously identified σ66 binding motif was detected.
In addition, Grad-seq for C. trachomatis was established to obtain a global interactome of the RNAs and proteins of this intracellular organism. The Grad-Seq data suggest that many of the newly annotated RNAs from the TagRNA-seq approach are present in complexes. Although Chlamydia lack the known RNA-binding proteins (RBPs), e.g. Hfq and ProQ, observations in this work reveal the presence of a previously unknown RBP.
Interestingly, in the gradient analysis it was found that the σ66 factor forms a complex with the RNA polymerase (RNAP). On the other hand, the σ28 factor is unbound. This is in line with results from previous studies showing that most of the genes are under control of σ66. The ncRNA IhtA is known to function via direct base pairing to its target RNA of HctB, and by doing so is influencing the chromatin condensation in Chlamydia. This study confirmed that lhtA is in no complex. On the other hand, the ncRNA ctrR0332 was found to interact with the SNF2 protein ctl0077, a putative helicase. Both molecules co-sedimented in the gradient and were intact after an aptamer-based RNA pull-down. The SWI2/SNF2 class of proteins are nucleosome remodeling complexes. The prokaryotic RapA from E. coli functions as transcription regulator by stimulating the RNAP recycling. This view might imply that the small ncRNA (sRNA) ctrR0332 is part of the global regulation network in C. trachomatis controlling the transition between EBs and RBs via interaction with the SNF2 protein ctl0077.
The present work is the first study describing a global interactome of RNAs and proteins in C. trachomatis providing the basis for future interaction studies in the field of this pathogen.
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.
Background
- Brain-Computer Interfaces (BCI) enable their users to interact and communicate with the environment without requiring intact muscle control. To this end, brain activity is directly measured, digitized and interpreted by the computer. Thus, BCIs may be a valuable tool to assist severely or even completely paralysed patients. Many BCIs, however, rely on neurophysiological potentials evoked by visual stimulation, which can result in usability issues among patients with impaired vision or gaze control. Because of this, several non-visual BCI paradigms have been developed. Most notably, a recent study revealed promising results from a tactile BCI for wheelchair control. In this multi-session approach, healthy participants used the BCI to navigate a simulated wheelchair through a virtual apartment, which revealed not only that the BCI could be operated highly efficiently, but also that it could be trained over five sessions. The present thesis continues the research on this paradigm in order to - confirm its previously reported high performance levels and trainability - reveal the underlying factors responsible for observed performance increases - establish its feasibility among potential impaired end-users
Methods
- To approach these goals, three studies were conducted with both healthy participants and patients with amyotrophic lateral sclerosis (ALS). Brain activity during BCI operation was recorded via electroencephalography (EEG) and interpreted using a machine learning-based linear classifier. Wheelchair navigation was executed according to the classification results and visualized on a monitor. For offline statistical analysis, neurophysiological features were extracted from EEG data. Subjective data on usability were collected from all participants. Two specialized experiments were conducted to identify factors for training.
Results and Discussion
- Healthy participants: Results revealed positive effects of training on BCI performances and their underlying neurophysiological potentials. The paradigm was confirmed to be feasible and (for a non-visual BCI) highly efficient for most participants. However, some had to be excluded from analysis of the training effects because they could not achieve meaningful BCI control. Increased somatosensory sensitivity was identified as a possible mediator for training-related performance improvements. Participants with ALS: Out of seven patients with various stages of ALS, five could operate the BCI with accuracies significantly above chance level. Another ALS patient in a state of near-complete paralysis trained with the BCI for several months. Although no effects of training were observed, he was consistently able to operate the system above chance level. Subjective data regarding workload, satisfaction and other parameters were reported.
Significance
- The tactile BCI was evaluated on the example of wheelchair control. In the future, it could help impaired patients to regain some lost mobility and self-sufficiency. Further, it has the potential to be adapted to other purposes, including communication. Once visual BCIs and other assistive technologies fail for patients with (progressive) motor impairments, vision-independent paradigms such as the tactile BCI may be among the last remaining alternatives to interact with the environment. The present thesis has strongly confirmed the general feasibility of the tactile paradigm for healthy participants and provides first clues about the underlying factors of training. More importantly, the BCI was established among potential end-users with ALS, providing essential external validity.
My dissertation comprises three studies: (1) an assessment of honey bee colony losses in the USA between 2014 and 2015, (2) an exploration of the potential of reclaimed sand mines as bee habitat, and (3) an evaluation of native and non-native pollinator friendly plants in regard to their attraction to bees. While the first study focuses on honey bees, the latter two studies primarily take wild bees or entire bee communities in focus.
The study on honey bee colony losses was conducted within the framework of the Bee Informed Partnership (BIP, beeinformed.org) and aligns with the annual colony loss surveys which have been conducted in the USA since the winter of 2006/2007. It was the fourth year for which summer and annual losses were calculated in addition to winter losses. Among participants, backyard beekeepers were the largest group (n = 5690), although sideline (n = 169) and commercial (n = 78) beekeepers managed the majority (91.7 %) of the 414 267 surveyed colonies. Overall, 15.1 % of the estimated 2.74 million managed colonies in the USA were included in the study. Total honey bee colony losses (based on the entirety of included colonies) were higher in summer (25.3 %) than in winter (22.3 %) and amounted to 40.6 % for the entire 2014/2015 beekeeping year. Average colony losses per beekeeper or operation were higher in winter (43.7 %) than in summer (14.7 %) and amounted to 49 % for the entire 2014/2015 beekeeping year. Due to the dominance of backyard beekeepers among participants, average losses per operation (or unweighted loss) stronger reflected this smaller type of beekeeper. Backyard beekeepers mainly named colony management issues (e.g., starvation, weak colony in the fall) as causes for mortality, while sideline and commercial beekeepers stronger emphasized parasites or factors outside their control (e.g., varroa, nosema, queen failure).
The second study took place at reclaimed sand mines. Sand mines represent anthropogenically impacted habitats found worldwide, which bear potential for bee conservation. Although floral resources can be limited at these habitats, vegetation free patches of open sandy soils and embankments may offer good nesting possibilities for sand restricted and other bees. We compared bee communities as found in three reclaimed sand mines and at adjacent roadside meadows in Maryland, USA, over two years. Both sand mines and roadsides hosted diverse bee communities with 111 and 88 bee species, respectively. Bee abundances as well as richness and Shannon diversity of bee species were higher in sand mines than at roadsides and negatively correlated with the percentage of vegetational ground cover. Species composition also differed significantly between habitats. Sand mines hosted a higher proportion of ground nesters, more uncommon and more ‘sand loving’ bees similar to natural sandy areas of Maryland. Despite the destruction of the original pre-mining habitat, sand mines thus appear to represent a unique habitat for wild bees, particularly when natural vegetation and open sand spots are encouraged. Considering habitat loss, the lack of natural disturbance regimes, and ongoing declines of wild bees, sand mines could add promising opportunities for bee conservation which has hitherto mainly focused on agricultural and urban habitats.
The third study was an experimental field study on pollinator friendly plants. Bees rely on the pollen and nectar of plants as their food source. Therefore, pollinator friendly plantings are often used for habitat enhancements in bee conservation. Non-native pollinator friendly plants may aid in bee conservation efforts, but have not been tested and compared with native pollinator friendly plants in a common garden experiment. In this study, we seeded mixes of 20 native and 20 non-native pollinator friendly plants in two separate plots at three sites in Maryland, USA. For two years, we recorded flower visitors to the plants throughout the blooming period and additionally sampled bees with pan traps. A total of 3744 bees (120 species) were sampled in the study. Of these, 1708 bees (72 species) were hand netted directly from flowers for comparisons between native and non-native plants. Depending on the season, bee abundance and species richness was either similar or lower (early season and for richness also late season) at native plots compared to non-native plots. Additionally, the overall bee community composition differed significantly between native and non-native plots. Furthermore, native plants were associated with more specialized plant-bee visitation networks compared to non-native plants. In general, visitation networks were more specialized in the early season than the later seasons. Four species (Bombus impatiens, Halictus poeyi/ligatus, Lasioglossum pilosum, and Xylocopa virginica) out of the five most abundant bee species (also including Apis mellifera) foraged more specialized on native than non-native plants. Our study showed that non-native plants were well accepted by a diverse bee community and had a similar to higher attraction for bees compared to native plants. However, we also demonstrated alterations in foraging behavior, bee community assemblage, and visitation networks. As long as used with caution, non-native plants can be a useful addition to native pollinator friendly plantings. This study gives a first example of a direct comparison between native and non-native pollinator friendly plants.
Modern agriculture is the basis of human existence, a blessing, but also a curse. It provides nourishment and well-being to the ever-growing human population, yet destroys biodiversity-mediated processes that underpin productivity: ecosystem services such as water filtration, pollination and biological pest control. Ecological intensification is a promising alternative to conventional farming, and aims to sustain yield and ecosystem health by actively managing biodiversity and essential ecosystem services. Here, I investigate opportunities and obstacles for ecological intensification. My research focuses on 1) the relative importance of soil, management and landscape variables for biodiversity and wheat yield (Chapter II); 2) the influence of multi-scale landscape-level crop diversity on biological pest control in wheat (Chapter III) and 3) on overall and functional bird diversity (Chapter IV). I conclude 4) by introducing a guide that helps scientists to increase research impact by acknowledging the role of stakeholder engagement for the successful implementation of ecological intensification (Chapter V).
Ecological intensification relies on the identification of natural pathways that are able to sustain current yields. Here, we crossed an observational field study of arthropod pests and natural enemies in 28 real-life wheat systems with an orthogonal on-field insecticide-fertilizer experiment. Using path analysis, we quantified the effect of 34 factors (soil characteristics, recent and historic crop management, landscape heterogeneity) that directly or indirectly (via predator-prey interactions) contribute to winter wheat yield. Reduced soil preparation and high crop rotation diversity enhanced crop productivity independent of external agrochemical inputs. Concurrently, biological control by arthropod natural enemies could be restored by decreasing average field sizes on the landscape scale, extending crop rotations and reducing soil disturbance. Furthermore, reductions in agrochemical inputs decreased pest abundances, thereby facilitating yield quality.
Landscape-level crop diversity is a promising tool for ecological intensification. However, biodiversity enhancement via diversification measures does not always translate into agricultural benefits due to antagonistic species interactions (intraguild predation). Additionally, positive effects of crop diversity on biological control may be masked by inappropriate study scales or correlations with other landscape variables (e.g. seminatural habitat). Therefore, the multiscale and context-dependent impact of crop diversity on biodiversity and ecosystem services is ambiguous. In 18 winter wheat fields along a crop diversity gradient, insect- and bird-mediated pest control was assessed using a natural enemy exclusion experiment with cereal grain aphids. Although birds did not influence the strength of insect-mediated pest control, crop diversity (rather than seminatural habitat cover) enhanced aphid regulation by up to 33%, particularly on small spatial scales. Crop diversification, an important Greening measure in the European Common Agricultural Policy, can improve biological control, and could lower dependence on insecticides, if the functional identity of crops is taken into account. Simple measures such as ‘effective number of crop types’ help in science communication.
Although avian pest control did not respond to landscape-level crop diversity, birds may still benefit from increased crop resources in the landscape, depending on their functional grouping (feeding guild, conservation status, habitat preference, nesting behaviour). Observational studies of bird functional diversity on 14 wheat study fields showed that non-crop landscape heterogeneity rather than crop diversity played a key role in determining the richness of all birds. Insect-feeding, non-farmland and non-threatened birds increased across multiple spatial scales (up to 3000 m). Only crop-nesting farmland birds declined in heterogeneous landscapes. Thus, crop diversification may be less suitable for conserving avian diversity, but abundant species benefit from overall habitat heterogeneity. Specialist farmland birds may require more targeted management approaches.
Identifying ecological pathways that favour biodiversity and ecosystem services provides opportunities for ecological intensification that increase the likelihood of balancing conservation and productivity goals. However, change towards a more sustainable agriculture will be slow to come if research findings are not implemented on a global scale. During dissemination activities within the EU project Liberation, I gathered information on the advantages and shortcomings of ecological intensification and its implementation. Here, I introduce a guide (‘TREE’) aimed at scientists that want to increase the impact of their research. TREE emphasizes the need to engage with stakeholders throughout the planning and research process, and actively seek and promote science dissemination and knowledge implementation. This idea requires scientists to leave their comfort zone and consider socioeconomic, practical and legal aspects often ignored in classical research.
Ecological intensification is a valuable instrument for sustainable agriculture. Here, I identified new pathways that facilitate ecological intensification. Soil quality, disturbance levels and spatial or temporal crop diversification showed strong positive correlations with natural enemies, biological pest control and yield, thereby lowering the dependence on agrochemical inputs. Differences between functional groups caused opposing, scale-specific responses to landscape variables. Opposed to our predictions, birds did not disturb insect-mediated pest control in our study system, nor did avian richness relate to landscape-level crop diversity. However, dominant functional bird groups increased with non-crop landscape heterogeneity. These findings highlight the value of combining different on-field and landscape approaches to ecological intensification. Concurrently, the success of ecological intensification can be increased by involving stakeholders throughout the research process. This increases the quality of science and reduces the chance of experiencing unscalable obstacles to implementation.
Fanconi-Anämie (FA) ist, mit Ausnahme von Mutationen in FANCR/RAD51, eine autosomal-rezessive oder X-chromosomal vererbte Krankheit, die sich durch eine ausgesprochene klinische als auch genetische Heterogenität auszeichnet. Neben einem fortschreitenden Knochenmarksversagen zählen zu den typischen Merkmalen eine Vielzahl an angeborenen Fehlbildungen, wie beispielsweise Radialstrahlanomalien, Minderwuchs oder Pigmentierungsstörungen. Zudem besteht für FA-Patienten ein überdurchschnittlich hohes Risiko bereits in jungen Jahren an akuter myeloischer Leukämie oder soliden Tumoren zu erkranken. Bislang konnten in 21 FA-Genen (FANCA, -B, -C, - D1, -D2, -E, -F, -G, -I, -J, -L, -M, -N, -O, -P, -Q, -R, -S, -T, -U oder -V) krankheitsverursachende Mutationen identifiziert werden, deren Proteinprodukte maßgeblich an der Aufrechterhaltung der Genomstabilität beteiligt sind und Komponenten des FA/BRCA-DNA-Reparaturweges darstellen. In der klassischen FA-Mutationsanalyse kommen meist Sanger-Sequenzierungen sowie MLPA- und Immunblot-Analysen zum Einsatz. Da im Wesentlichen keine Genotyp-Phänotyp-Korrelation besteht, gestaltet sich, gerade bei seltenen FA-Komplementationsgruppen, der Nachweis von krankheitsverursachenden Mutationen oftmals sehr zeit- und kostenintensiv. Während der letzten Jahre wurden verschiedene Strategien zur Anreicherung und Sequenzierung entwickelt, welche die parallele Sequenzanalyse einzelner ausgewählter Gene, ganzer Exome oder sogar des gesamten Genoms und somit eine kosten- und zeiteffiziente Mutationsanalyse ermöglichen. In der vorliegenden Arbeit wurden unterschiedliche Anreicherungsmethoden mit anschließender Hochdurchsatzsequenzierung auf ihre Anwendbarkeit in der molekulargenetischen FA-Diagnostik getestet, um klassische Mutationsanalyse-Methoden zu ergänzen oder möglicherweise sogar ganz ersetzen zu können.
Der erste Teil der Arbeit befasste sich mit der Etablierung eines FA-spezifischen Genpanels zur Genotypisierung von FA-Patienten. Nachdem die Methode zunächst anhand von FA-Patienten mit bekannten Mutationen optimiert werden musste, erwies sie sich als effizienter Ansatz zum Nachweis krankheitsverursachender Mutationen bei FA-Patienten unbekannter Komplementationsgruppe. Durch die FA-Panelanalyse konnten 37 von 47 unklassifizierten Patienten einer FA-Komplementationsgruppe zugeordnet werden, indem deren kausalen Mutationen bestimmt wurden. In einem weiteren Ansatz sollte die Anwendbarkeit eines kommerziellen Anreicherungspanels zur FA-Diagnostik untersucht werden. Auch hier konnte ein Großteil der krankheitsverursachenden Mutationen von fünf bekannten wie auch 13 nicht zugeordneten FA-Patienten detektiert und somit eine molekulargenetische Diagnose bei neun weiteren, zuvor unklassifizierten FA-Patienten, gestellt werden. Ferner wurden sechs ausgewählte Patienten, zusätzlich zur Panelanreicherung, per Exomanalyse untersucht. Zum einen konnten Mutationen in bekannten FA-Genen bestätigt oder neu identifiziert werden. Zum anderen wurden auch potentiell pathogene Mutationen in DNA-Reparaturgenen außerhalb des FA/BRCA-Signalweges bei zwei Patienten mit unbestätigter Verdachtsdiagnose FA verifiziert. So wurde bei mehreren Mitgliedern einer Familie mit unterschiedlichen Tumorerkrankungen eine zuvor unbeschriebene homozygote Nonsense-Mutation in der BER-Glykosylase NTHL1 nachgewiesen, für welche bislang erst zwei pathogene Mutationen als Auslöser eines neuen Krebssyndroms bekannt sind. Bei einem weiteren Patienten wurden compound-heterozygote Mutationen in RPA1 detektiert, ein Gen für das bislang noch kein Krankheitsbild bekannt ist. Mit Hilfe der drei verschiedenen Anreicherungsstrategien konnten insgesamt 47 von 60 unklassifizierten FA-Patienten 13 verschiedenen Komplementationsgruppen eindeutig zugeordnet werden. Es zeigte sich dabei ein breites Spektrum an neuen, bislang unbeschriebenen FA-Mutationen. Den größten Anteil an der Gesamtzahl der nachgewiesenen Mutationen hatten Spleißmutationen, die auf eine Auswirkung auf das kanonische Spleißmuster untersucht wurden, um einen pathogenen Effekt nachweisen zu können.
Weiterhin schloss die Arbeit die Charakterisierung einzelner FA-Patienten bzw. Komplementationsgruppen mit ein. Dazu zählen die seltenen Untergruppen FA-T und FA-Q, für die jeweils ein neuer Patient identifiziert werden konnte. Durch die funktionelle Charakterisierung der dritten jemals beschriebenen FA-Q-Patientin konnten Einblicke in das Zusammenspiel der Reparatur von DNA-Quervernetzungen und der Nukleotidexzisionsreparatur gewonnen und die phänotypische Variabilität von FA durch die subjektive als auch zelluläre UV-Sensitivität der Patientin ergänzt werden. Darüber hinaus konnte das Mutationsspektrum in FA-I sowie FA-D2 erweitert werden. Eine genauere Untersuchung der Pseudogenregionen von FANCD2 ermöglichte dabei die gezielte Mutationsanalyse des Gens.
Insgesamt konnten die Ergebnisse dieser Arbeit dazu beitragen, das Mutationsspektrum in FA zu erweitern und durch die Identifizierung und Charakterisierung einzelner Patienten neue Einblicke in verschiedene Komponenten des FA/BRCA-Signalweges zu erhalten. Es zeigte sich, dass neue DNA-Sequenzierungsstrategien in der FA-Diagnostik eingesetzt werden können, um eine effiziente Mutationsanalyse zu gewährleisten und klassische Methoden in Teilbereichen zu ersetzen.
Multiple myeloma (MM) is a disease of terminally differentiated B-cells which accumulate in the bone marrow leading to bone lesions, hematopoietic insufficiency and hypercalcemia. Genetically, MM is characterized by a great heterogeneity. A recent next-generation sequencing approach resulted in the identification of a signaling network with an accumulation of mutations in receptor-tyrosine kinases (RTKs), adhesion molecules and downstream effectors. A deep-sequencing amplicon approach of the coding DNA sequence of the six RTKs EPHA2, EGFR, ERBB3, IGF1R, NTRK1 and NTRK2 was conducted in a patient cohort (75 MM samples and 68 corresponding normal samples) of the “Deutsche Studiengruppe Multiples Myelom (DSMM)” to further elucidate the role of RTKs in MM. As an initial approach the detected mutations were correlated with cytogenetic abnormalities and clinical data in the course of this thesis. RTK mutations were present in 13% of MM patients of the DSMM XI trial and accumulated in the ligand-binding and tyrosine-kinase domain. The newly identified mutations were associated with an adverse patient survival, but not with any cytogenetic abnormality common in MM. Especially rare patient-specific SNPs (single nucleotide polymorphism) had a negative impact on patient survival. For a more comprehensive understanding of the role of rare RTK SNPs in MM, a second amplicon sequencing approach was performed in a patient cohort of the DSMM XII trial that included 75 tumor and 184 normal samples. This approach identified a total of 23 different mutations in the six RTKs EPHA2, EGFR, ERBB3, IGF1R, NTRK1 and NTRK2 affecting 24 patients. These mutations could furthermore be divided into 20 rare SNPs and 3 SNVs (single nucleotide variant). In contrast to the first study, the rare SNPs were significantly associated with the adverse prognostic factor del17p.
IGF1R was among the most commonly mutated RTKs in the first amplicon sequencing approach and is known to play an important role in diverse cellular processes such as cell proliferation and survival. To study the role of IGF1R mutations in the hard-to-transfect MM cells, stable IGF1R-knockdown MM cell lines were established. One of the knockdown cell lines (L363-C/C9) as well as a IGF1R-WT MM cell line (AMO1) were subsequently used for the stable overexpression of WT IGF1R and mutant IGF1R (N1129S, D1146N). Overall, an impact on the MAPK and PI3K/AKT signaling pathways was observed upon the IGF1R knockdown as well as upon WT and mutant IGF1R overexpression. The resulting signaling pattern, however, differed between different MM cell lines used in this thesis as well as in a parallel performed master thesis which further demonstrates the great heterogeneity described in MM.
Taken together, the conducted sequencing and functional studies illustrate the importance of RTKs and especially of IGF1R and its mutants in the pathogenesis of MM. Moreover, the results support the potential role of IGF1R as a therapeutic target for a subset of MM patients with mutated IGF1R and/or IGF1R overexpression.
The eukaryotic parasite Trypanosoma brucei has evolved sophisticated strategies to persist within its mammalian host. Trypanosomes evade the hosts' immune system by antigenic variation of their surface coat, consisting of variant surface glycoproteins (VSGs). Out of a repertoire of thousands of VSG genes, only one is expressed at any given time from one of the 15 telomeric expression sites (ES). The VSG is stochastically exchanged either by a transcriptional switch of the active ES (in situ switch) or by a recombinational exchange of the VSG within the active ES. However, for infections to persist, the parasite burden has to be limited. The slender (sl) bloodstream form secretes the stumpy induction factor (SIF), which accumulates with rising parasitemia. SIF induces the irreversible developmental transition from the proliferative sl to the cell cycle-arrested but fly-infective stumpy (st) stage once a concentration threshold is reached. Thus, antigenic variation and st development ensure persistent infections and transmissibility. A previous study in monomorphic cells indicated that the attenuation of the active ES could be relevant for the development of trypanosomes. The present thesis investigated this hypothesis using the inducible overexpression of an ectopic VSG in pleomorphic trypanosomes, which possess full developmental competence. These studies revealed a surprising phenotypic plasticity: while the endogenous VSG was always down-regulated upon induction, the ESactivity determined whether the VSG overexpressors arrested in growth or kept proliferating. Full ES-attenuation induced the differentiation of bona fide st parasites independent of the cell density and thus represents the sole natural SIF-independent differentiation trigger to date. A milder decrease of the ES-activity did not induce phenotypic changes, but appeared to prime the parasites for SIF-induced differentiation. These results demonstrate that antigenic variation and development are linked and indicated that the ES and the VSG are independently regulated. Therefore, I investigated in the second part of my thesis how ES-attenuation and VSG-silencing can be mediated. Integration of reporters with a functional or defective VSG 3'UTR into different genomic loci showed that the maintenance of the active state of the ES depends on a conserved motif within the VSG 3'UTR. In situ switching was only triggered when the telomere-proximal motif was partially deleted, suggesting that it serves as a DNA-binding motif for a telomere-associated protein. The VSG levels seem to be additionally regulated in trans based on the VSG 3'UTR independent of the genomic context, which was reinforced by the regulation of a constitutively expressed reporter with VSG 3' UTR upon ectopic VSG overexpression.
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.
Humans tend to believe in what they can see with their own eyes. Hence, visualization methods like microscopy have always been extremely popular since their invention in the 17th century. With the advent of super-resolution microscopy, the diffraction limit of ~200 - 250 nm could be overcome to enable more detailed insights into biological samples. Especially the single molecule localization microscopy method dSTORM offers the possibility of quantitative bioimaging. Hereby, the repetitive photoswitching of organic dyes in the presence of thiols is exploited to enable a lateral resolution of 20 nm. Another, recently introduced super-resolution method is expansion microscopy (ExM) which physically expands the sample to increase the resolution by the expansion factor from four to even twenty. To enable this, the sample is embedded into a hydrogel, homogenized using an unspecific proteinase and expanded in distilled water. Within this thesis, both methods were used to shed light on plasma membrane receptor distributions and different bacterial and fungal pathogens. In the first part of this thesis dSTORM was used to elucidate the “Receptome”, the entirety of all membrane receptors, of the cell line Jurkat T-cells and primary T-cells. Within this project we could successfully visualize and quantify the distribution of the plasma membrane receptors CD2, CD3, CD4, CD5, CD7, CD11a, CD20, CD28, CD45, CD69 and CD105 with receptor densities ranging from 0.8 cluster/µm² in case of CD20 and 81.4 cluster/µm² for the highly abundant CD45 in activated primary T-cells at the basal membrane. Hereby, we could also demonstrate a homogeneous distribution of most receptors, while only few were clustered. In the case of CD3-clusters were detected in Jurkat T-cells and in primary activated T-cells, but not in naïve ones, demonstrating the activation of this receptor. This was followed by the application of dSTORM to three different clinical projects involving the receptors CD38, BCMA and CD20 which are immunotherapeutic targets by monoclonal antibodies and CAR T-cells. In the first two projects dSTORM was applied to determine the receptor upregulation upon exposure of various drugs to MM1.S cells or primary multiple myeloma patient cells. This increase in membrane receptor expression can subsequently enhance the efficacy of therapies directed against these receptors. Within the CD20-project, the superior sensitivity of dSTORM compared to flow cytometry could be demonstrated. Hereby, a substantially higher fraction of CD20-positive patient cells was detected by dSTORM than by flow cytometry. In addition, we could show that by dSTORM CD20-positive evaluated cells were eradicated by immunotherapeutic CAR T-cell treatment. These studies were followed by whole cell super-resolution imaging using both LLS-3D dSTORM and 10x ExM to exclude any artifacts caused by interactions with the glass surface. In 10x ExM signal amplification via biotinylated primary antibodies and streptavidin ATTO 643 was essential to detect even single antibodies directed against the heterodimer CD11a with standard confocal microscopes. Albeit probably not quantitative due to the process of gelation, digestion and expansion during the ExM protocol, even some putative dimers of the receptor CD2 could be visualized using 10x ExM-SIM, similar to dSTORM experiments. Within the second part of this thesis, expansion microscopy was established in bacterial and fungal pathogens. ExM enabled not only an isotropic fourfold expansion of Chlamydia trachomatis, but also allowed the discrimination between the two developmental forms by the chlamydial size after expansion into reticulate and elementary bodies. Hereafter, a new α-NH2-ω-N3-C6-ceramide was introduced enabling an efficient fixation and for the first time the use of lipids in both, 4x and 10x ExM, termed sphingolipid ExM. This compound was used to investigate the ceramide uptake and incorporation into the cell membrane of Chlamydia trachomatis and Simkania negevensis. For Chlamydia trachomatis the combined resolution power of 10x ExM and SIM even allowed the visualization of both bacterial membranes within a distance of ~30 nm. Finally, ExM was applied to the three different fungi Ustilago maydis, Fusarium oxysporum and Aspergillus fumigatus after enzymatic removal of the fungal cell wall. In case of Ustilago maydis sporidia this digestion could be applied to both, living cells resulting in protoplasts and to fixed cells, preserving the fungal morphology. This new protocol could be demonstrated for immunostainings and fluorescent proteins of the three different fungi.
Die Entwicklung hochauflösender Fluoreszenzmikroskopiemethoden hat die Lichtmikroskopie revolutioniert. Einerseits ermöglicht die höhere erzielte räumliche Auflösung die Abbildung von Strukturen, die deutlich unterhalb der beugungsbedingten Auflösungsgrenze liegen. Andererseits erhält man durch Einzelmoleküllokalisationsmikroskopiemethoden
wie dSTORM (Direct Stochastic Optical Reconstruction Microscopy) Informationen, welche man für quantitative Analysen heranziehen kann. Aufgrund der sich dadurch bietenden neuen Möglichkeiten, hat sich die hochauflösende Fluoreszenzmikroskopie rasant entwickelt und kommt mittlerweile zur Untersuchung einer Vielzahl biologischer und medizinischer Fragestellungen zum Einsatz. Trotz dieses Erfolgs ist jedoch nicht zu verleugnen, dass auch diese neuen Methoden ihre Nachteile haben. Dazu zählt die Notwendigkeit relativ hoher Laserleistungen, welche Voraussetzung für hohe Auflösung ist und bei lebenden Proben zur Photoschädigung führen kann.
Diese Arbeit widmet sich sowohl dem Thema der Photoschädigung durch Einzelmoleküllokalisationsmikroskopie,
als auch der Anwendung von dSTORM und SIM (Structured Illumination Microscopy) zur Untersuchung neurobiologischer Fragestellungen auf Proteinebene.
Zur Ermittlung der Photoschädigung wurden lebende Zellen unter typischen Bedingungen bestrahlt und anschließend für 20−24 h beobachtet. Als quantitatives Maß für den Grad der Photoschädigung wurde der Anteil sterbender Zellen bestimmt. Neben der zu erwartenden Intensitäts- und Wellenlängenabhängigkeit, zeigte sich, dass die Schwere der Photoschädigung auch von vielen weiteren Faktoren abhängt und dass sich Einzelmoleküllokalisationsmikroskopie bei Berücksichtigung der gewonnenen Erkenntnisse durchaus mit Lebendzellexperimenten vereinbaren lässt.
Ein weiteres Projekt diente der Untersuchung der A- und B-Typ-Glutamatrezeptoren an der neuromuskulären Synapse von Drosophila melanogaster mittels dSTORM. Dabei konnte eine veränderte Anordnung beider Rezeptortypen infolge synaptischer Plastizität beobachtet, sowie eine absolute Quantifizierung des A-Typ-Rezeptors durchgeführt werden.
Im Mittelpunkt eines dritten Projekts standen Cadherin-13 (CDH13) sowie der Glucosetransporter Typ 3 (GluT3), welche beide mit der Aufmerksamkeitsdefizit-Hyperaktivitätsstörung in Verbindung gebracht werden. CDH13 konnte mittels SIM in serotonergen Neuronen, sowie radiären Gliazellen der dorsalen Raphekerne des embryonalen Mausgehirns nachgewiesen werden. Die Rolle von GluT3 wurde in aus induzierten pluripotenten Stammzellen differenzierten Neuronen analysiert, welche verschiedene Kopienzahlvariation des für GluT3-codierenden SLC2A3-Gens aufwiesen. Die Proteine GluT3, Bassoon und Homer wurden mittels dSTORM relativ quantifiziert. Während die Deletion des Gens zu einer erwartenden Verminderung von GluT3 auf Proteinebene führte, hatte die Duplikation keinen Effekt auf die GluT3-Menge. Für Bassoon und Homer zeigte sich weder durch die Deletion noch die Duplikation eine signifikante Veränderung.
Charakterisierung von angeborenen Hörstörungen mit Hilfe von Hochdurchsatz-Sequenziermethoden
(2020)
Fast 500 Millionen Menschen weltweit sind von einer Hörstörung betroffen. Es wird sogar angenommen, dass diese Anzahl laut der Weltgesundheitsorganisation (WHO) noch steigen und 2050 jeder zehnte Mensch eine Hörstörung aufweisen wird. Mindestens in 50% aller Fälle ist die Hörstörung genetisch bedingt. Durch die jüngsten Fortschritte der Sequenzierungstechnologien hat die genetische Analyse von Hörstörungen an Bedeutung gewonnen, vor allem hinsichtlich Familienplanung, geeigneter Therapien und zukünftiger möglichen Therapieansätzen, um das Hörvermögen wiederherzustellen. Die folgende Arbeit stellt 155 familiäre Fälle vor, die genetisch untersucht wurden. Diese Fälle konnten in zwei Kohorten unterteilt werden. Eine Kohorte (n = 74) umfasste Patienten mit kaukasischem Hintergrund, während die andere Kohorte (n = 81) Patienten beinhaltete, die aus dem Iran rekrutiert wurden. Für die Untersuchung wurde zum einen eine Panel-Analyse mit dem TruSight One Panel (Illumina, San Diego, USA) und zum anderen eine Exom-Sequenzierung durchgeführt. Anschließend wurden die Daten mit Analyse-Programmen wie GensearchNGS (PhenoSystems, Wallonia, Belgien) ausgewertet. Insgesamt konnte für 55% aller Fälle eine pathogene oder wahrscheinlich pathogene Variante durch Next Generation Sequencing diagnostiziert werden. Die meisten der gelösten Fälle (ca. 73%) stammten aus der iranischen Kohorte, was durch elterliche Blutsverwandtschaft und erhöhte Inzidenz von Hörstörungen im Iran zu erklären ist. 27% der gelösten Fälle gehörten der zweiten Kohorte an. Mutationen in den Genen MYO15A, LHFPL5, TECTA und SLC26A4 konnten überwiegend bei iranischen Patienten identifiziert werden. Varianten im Gen TECTA als auch im Gen SLC26A4 wurden ebenfalls in der kaukasischen Kohorte identifiziert. Beide Ethnien wiesen jeweils ein eigenes Mutationsspektrum auf. Jedoch wurden in beiden Gruppen Überschneidungen im klinischen Bild durch pathogene Varianten in einer Vielzahl von Hörstörungsgenen, sowie unterschiedliche klinische Phänotypen, deren Ursache pathogene Varianten im gleichen Hörstörungsgen zugrunde liegen, und familiäre Locus-Heterogenität beobachtet.. In dieser Arbeit konnte eine De Novo Mutation im CEACAM16-Gen (DFNA4B) bestätigt und der Effekt von einer wiederholt betroffenen Aminosäure im S1PR2-Gen (DFNB68) beschrieben werden. Darüber hinaus wurden mehrere Patienten mit X-chromosomalem Hörverlust aufgrund von Defekten im POU3F4-Gen (DFNX2) und Deletionen im SMPX-Gen (DFNX4) diagnostiziert. Zusätzlich konnte mit Hilfe einer Exom-basierten Copy Number Variation-Analyse eine Deletion im OTOA-Gen (DFNB22) gefunden werden, welche sich bis in die Tandempseudogenregion erstreckte.
Diese Untersuchung zeigt die enormen Möglichkeiten zur Detektion von Mutationen bei heterogenen Erkrankungen durch Anwendung von Next Generation Sequencing. Weiterhin konnte eine intragenische Deletion im Gen COL9A1 identifiziert werden, die im Zusammenhang mit einer scheinbar isolierten Hörstörung steht und durch den komplexen Umlagerungsmechanismus FoSTeS/MMBIR (Fork Stalling und Template Switching/Microhomology-mediated Break-induced Replication) entstand, der so bei Hörstörungen noch nicht beschrieben wurde. Auf der Suche nach Genen, die bisher noch nicht mit Hörstörungen assoziiert werden konnten, wurden acht Familien in eine Kandidatengenuntersuchung miteinbezogen und eine Exom-weite Analyse durchgeführt. Bei fünf Familien konnte noch keine ursächliche Variante identifiziert werden. Jedoch wurde bei drei Familien mit einer autosomal dominanten Schwerhörigkeit eine genetische Ursache identifiziert und TECTB, ATP11A und THBS2 konnten als Kandidatengene ermittelt werden. Diese Arbeit zeigt, wie wichtig es ist, die kausale Variante bei Hörstörungspatienten zu detektieren. Eine genetische Diagnostik ermöglicht eine endgültige Diagnose eines Syndroms, ist für die Klassifizierung der Hörstörung notwendig und trägt zu einer zukünftigen Therapie der Patienten bei.
Cuticular hydrocarbons (CHC) abound on the surface of arthropods. In spite of their simple structure (molecules of carbon and hydrogen atoms), they provide pivotal functions in insects: their hydrophobic properties confer the insects a means to regulate water balance and avoid desiccation, whereas their diversity has enhanced their use as signals and cues in a wide range of communication and recognition processes. Although the study of CHC in insects over the past two decades has provided great insight into the wide range of functions they play, there is still a gap in understanding how they diversify and evolve. In this thesis, I have used members of the family Chrysididae to explore patterns of diversification of CHC. Most of the species of cuckoo wasps in this study are specialized parasitoids or kleptoparasites of mainly solitary hymenopteran hosts. Other hosts of the family include butterflies or stick insects. Cuckoo wasps are a particular interesting model to study the evolution of cuticular hydrocarbons because of their chemical adaptations that allow them to remain unrecognized by their hosts. Chemical insignificance (the reduction of the total amount of CHC on the cuticle) and chemical mimicry (the de novo production of CHC profiles resembling those of their female host) have been described in some representatives of the family and unpublished evidence suggests chemical deception is widespread in Chrysididae (Chapter 2). Nonetheless, to trace the evolution of any trait of interest, a reliable phylogenetic reconstruction of the family is required. Therefore, the first study of this thesis constitutes the largest and to-date most reliable phylogenetic reconstruction of the family Chrysididae, which includes representatives of 186 species of cuckoo wasps. While the results of this phylogenetic reconstruction are consistent with previous ideas on the relationships of subfamilies and tribes, it shows the existence of several non-monophyletic genera (Chapter 3). CHC are involved in intraspecific recognition, often acting as contact sex pheromones. Nevertheless, it is not yet understood to what extent CHC profiles differ between the two sexes and whether some compound classes are more prevalent in one or the other sex. So far, no comparison of CHC profiles of males and females has been done for more than a dozen of related species. In Chapter 4, I describe and compare CHC profiles of females and males of 58 species of cuckoo wasps in order to evaluate whether and to what extent CHC profiles of these species differ between the sexes. I demonstrated that CHC profiles of cuckoo wasps are frequently (more than 90% of the species analyzed) and strongly dimorphic (both sexes of a given species tend to produce very different CHC compounds). Methyl-branched compounds tend to be more prevalent in males (especially dimethyl-branched compounds) and unsaturated compounds prevail in females. Moreover, a sex-specific pattern in the distribution of the double bond position of alkenes was evident: internal double bond positions (> 11) occur predominantly in males, whereas alkenes with the doublé bond at position 9 were more abundant and frequent in females (Chapter4). In Chapter5, I investigated how CHC profiles of cuckoo wasps differ across species. Are CHC profiles of cuckoo wasps species-specific, enabling their use as cues for species recognition? How do CHC profiles resemble phylogenetic relatedness? In Chapter 5, I try to answer these questions by comparing CHC profiles of 59 species of cuckoo wasps. CHC profiles of cuckoo wasps are shown to be species (and sex-) specific. I show that CHC profiles are useful as a complementary tool to help delimiting taxonomically difficult sibling species. Moreover, the evaluation of CHC profiles of five commonly occurring species within a genus, showed little or no geographical variation. However, CHC profiles of closely related species may differ strongly among each other, not being useful to track the evolutionary history of species (Chapter 5). Sexual selection is generally credited for generating striking sexual dimorphism by causing changes in male traits. Most often, sexual selection has a stronger effect on males, who compete for access to and may be selected by females, thus male traits may rapidly evolve. Nevertheless, in cuckoo wasps, it appears that it is the female sex the one evolving faster changes, with females of very closely related species showing extremely divergent profiles. One plausible reason for this disparity is that natural selection acting on female’s CHC profiles may be stronger than sexual selection on males (Chapter 6). Since females of cuckoo wasps are most probably engaged in an evolutionary arms race with their female hosts, CHC profiles of female cuckoo wasps are likely rapidly evolving, thus explaining part of the strong observed sexual dimorphism of CHC (Chapter 6). In fact, Chapter 7 shows evidence of a possible ongoing evolutionary arms race between five cuckoo wasps of the genus Hedychrum and their hosts. Hedychrum species parasitize either Coleoptera-hunting or Hymenoptera-hunting digger wasps. Since the coleopteran prey of the former digger wasps is naturally better protected against fungus infestation, these wasps do not embalm their prey with alkene-enriched secretions as do the Hymenoptera-hunting digger wasps. Thus, Coleoptera-hunting digger wasps can apparently diversify their profiles to escape chemical mimicry. Interestingly, only female cuckoo wasps of these hosts have started producing the same compound classes and even the same CHC compounds as those of their hosts. Male cuckoo wasps, however retain an alkene-enriched CHC profile that reflects the molecular phylogeny of the genus (Chapter 7). Whereas, a larger number of parasite-host comparisons may be needed to further conclude that an arms race between cuckoo wasps and their hosts is capable of generating sexual dimorphism of cuckoo wasps, this thesis constitutes the first effort towards this, providing a starting point for further studies. Finally, I provide some methodological tools that may help in speeding up the sometimes cumbersome process of analyzing and identifying CHC profiles. One of the most time-demanding steps in the processing of CHC data is the alignment of CHC chromatograms. This process is often done manually, because alignment programs are mostly designed for metabolomics or are just recently being developed. I analyzed CHC profiles using a combined approach with two freely available programs. I used AMDIS (Automated Mass Spectral Deconvolution and Identification System, http://chemdata.nist.gov/mass-spc/amdis/) to deconvolute and automatically identify all CHC of interest present in a chromatogram. I then developed a series of R scripts to correct for potential, unavoidable errors while processing CHC chromatograms with AMDIS. Chapter 8 explains this procedure. In the next chapter, I developed a program that helps in the identification of one commonly occurring class of hydrocarbons. The limited number of linear alkanes (only one per carbon atom) and their characteristic diagnostic ion allows a rapid and unambigous identification of these substances. In opposition, unsaturated and methyl-branched compounds are more difficult to identify, as a result of the much larger diversity of existing compounds. To identify unsaturated compounds a derivatization is necessary to determine the position of the double bond. Methyl-branched alkanes, however can be identified from the original chromatogram if their diagnostic ions are known. Nonetheless, polymethyl-branched alkanes (e.g., compounds with two or more methyl groups along the chain) are often difficult to identify, because they may appear in mixes (e.g., 3,7 diMeC27 and 3,9 diMeC27), and tables containing the diagnostic ions are not easily available. Therefore, I developed a program that creates a table with all possiblemethyl-branched compounds containing up to 4 methyl groups, and that provides their diagnostic ions and a calculated retention index. This may allow a much faster identification of the methyl-branched compound a researcher is dealing with, without having to lose time in the tedious calculations by hand. The program is able to correctly identify, or at least, greatly reduce the number of possible options for the identification of an unknown methyl-branched compound. Thus, using this tool, most methyl-branched compounds can be readily identified (Chapter 9). This thesis ends with a general discussion (Chapter 10). Overall, this work provides a comprehensive overview of the diversity of cuticular hydrocarbons of cuckoo wasps. The analyses presented here shed light on the emergence and evolution of interspecific diversity and intraspecific sexual dimorphism of CHC profiles. In addition, two technical methods have been developed that could greatly facilitate the CHC analysis of insects.
Mit fortschreitender chronischer Niereninsuffizienz kommt es zur Akkumulation von Urämietoxinen und im Endstadium unbehandelt zum Tod im sogenannten Urämischen Syndrom. Die Blutreinigung erfolgt bei der am häufigsten verwendeten Form der Nierenersatztherapie, der Hämodialyse, nur unzureichend. Die Folge ist eine erhöhte Morbidität und Mortalität der betroffenen Patienten. Bei der Hämodialyse werden nur Urämietoxine bis zu einer Größe von 20 kDa über die im Dialysator eingesetzten Hohlfaserdialysemembranen diffusiv und konvektiv semiselektiv nach Größenausschluss entfernt. Proteingebundene Urämietoxine, deren effektive Größe durch die Bindung an Transportproteine wie beispielsweise Albumin die Trennschärfe der Dialysemembranen übersteigt, werden retiniert. In-vivo werden proteingebundene Urämietoxine im proximalen Tubulus, einem Teil des tubulären Systems des Nephrons, sekretorisch eliminiert.
Im Rahmen der vorliegenden Promotionsarbeit wurden die ersten Entwicklungsschritte auf dem Weg zu einem sogenannten bio-artifiziellen Tubulus evaluiert. Der angedachte biohybride Filter sollte aus einer Ko-Kultur funktionaler humaner proximaler Tubuluszellen und humaner Endothelzellen (HUVEC) auf synthetischen Hohlfasermembranen bestehen und könnte während der Hämodialyse als zusätzlicher Reinigungsschritt angewendet werden, um unter anderem proteingebundene Urämietoxine effektiv durch aktiven Transport aus dem Blut der Patienten zu entfernen. Die Differenzierung der proximalen Tubuluszellen erfolgte dabei aus adulten adipozytären mesenchymalen Stammzellen (ASC), deren Herkunft eine spätere autologe Behandlung ermöglicht. Die Ko-Kultur mit Endothelzellen wurde zur potentiellen Steigerung der Sekretion proteingebundener Urämietoxine verwendet.
In der vorliegenden Arbeit konnten ASCs durch eine Kombination der löslichen Differenzierungsfaktoren All-Trans-Retinoinsäure (ATRA), Aktivin A und BMP-7 erfolgreich in Zytokeratin 18-exprimierende Zellen differenziert werden, wodurch die erwünschte epitheliale Differenzierung bestätigt wurde. Die Expression funktionaler Proteine, wie das für den Wassertransport relevante Aquaporin 1 oder auch der Na+-/K+-ATPase, konnte in dieser Arbeit bereits vor der Differenzierung nachgewiesen werden. Im nächsten Schritt wurde erfolgreich gezeigt, dass eine simultane, qualitativ hochwertige Ko-Kultur von ASCs und HUVECs auf der mit dem extrazellulären Matrixprotein Fibronektin modifizierten Innen- bzw. Außenseite von synthetischen Hohlfasermembranen aus Polypropylen bzw. Polyethersulfon möglich ist. Die Viabilität beider Zelltypen wurde dabei durch die Verwendung eines für die Ko-Kultur entwickelten Nährmediums erreicht, in welchem die Proliferation von ASCs bei gleichzeitiger Aufrechterhaltung ihrer Stammzelleigenschaften deutlich erhöht war.
Die in dieser Arbeit erzielten Ergebnisse stellen eine aussichtsreiche Basis für einen bio-artifiziellen renalen Tubulus dar. Weitere Entwicklungsschritte, wie die Differenzierung der ASCs zu proximalen Tubuluszellen im 3D-Bioreaktor einschließlich ihrer funktionalen Charakterisierung anhand Tubulusepithel-spezifischer Transporter, sind erforderlich, be-vor erste funktionale Experimente vor dem „Upscaling“ auf klinisch verwendbare Module möglich sind.
Eine veränderte Expression des Transkriptionsfaktors MYC wird als entscheidender Faktor für Tumorentstehung und -progress im kolorektalen Karzinom gesehen. Somit ist die Hemmung dessen Expression und Funktion ein zentraler Ansatz bei der zielgerichteten Tumortherapie.
Als geeignete Strategie, sowohl die Halbwertszeit als auch die Translation von MYC zu verringern, erschien eine duale PI3K-/mTOR-Hemmung durch den small molecule-Inhibitor BEZ235. Gegenteilig ist jedoch unter Behandlung mit BEZ235 eine verstärkte MYC-Expression in verschiedenen Kolonkarzinom-Zelllinien zu beobachten. Neben verstärkter Transkription, konnte eine verstärkte IRES-abhängige Translation von MYC nach Hemmung der mTOR-/5´Cap-abhängigen Translation durch BEZ235, als Ursache der MYC-Induktion nachgewiesen werden.
Es konnte gezeigt werden, dass die Induktion von MYC nach PI3K-/mTOR-Hemmung durch eine kompensatorische Aktivierung des MAPK-Signalwegs in Folge einer FOXO-abhängigen Induktion von Rezeptortyrosinkinasen, stattfindet.
Eine mögliche Strategie, diese Feedback-Mechanismen zu umgehen, ist die direkte Hemmung der Translationsinitiation. Hierfür wurden Rocaglamid und dessen Derivat Silvestrol als small molecule-Inhibitoren der eIF4A-Helikase verwendet. Im Gegensatz zur PI3K/mTOR-Hemmung, ist durch eIF4A-Inhibition eine Reduktion der MYC-Proteinexpression in verschiedenen Kolonkarzinom-Zelllinien zu erreichen – ohne einhergehende MAPK-Aktivierung.
Anhand der Ergebnisse kann postuliert werden, dass Silvestrol das Potential besitzt, sowohl die Cap-/eIF4F-abhängie als auch die somit eIF4A-abhängige IRES-vermittelte Translation von MYC zu hemmen.
Weiterhin kann eine proliferationshemmende Wirkung durch Silvestrol auf Kolonkarzinom-Zellen in vitro, via Zellzyklusarrest und Induktion von Apoptose, gezeigt werden. Dies stellt die Voraussetzung für eine potentielle Eignung als tumorhemmender Wirkstoff in der Therapie des kolorektalen Karzinoms dar.
Die Schistosomiasis ist nach wie vor eine der häufigsten parasitären Erkrankungen der Welt und verursacht erhebliche gesundheitliche und wirtschaftliche Folgen, insbesondere in ärmeren, ländlichen Regionen. Durch Immunreaktionen auf die im Wirt abgelegten Eier des Parasiten können sich chronische Verlaufsformen manifestieren. Dabei kann es zu irreversiblen Schäden kommen. Um dies zu verhindern sind eine frühe und sichere Diagnose sowie eine Behandlung mit Praziquantel (PZQ) unabdingbar. Zudem spielt der zuverlässige Nachweis der Schistosomiasis eine Schlüsselrolle bei der Überwachung, Prävention und Kontrolle der Erkrankung. In epidemiologischen Studien findet am häufigsten die mikroskopische Kato-Katz (KK)-Methode zum Nachweis von Schistosoma mansoni Eiern im Stuhl Anwendung. Dieses Verfahren ist äußerst spezifisch und bietet die Möglichkeit der Quantifizierung, wodurch die Intensität der vorliegenden Infektion bestimmt werden kann. Die Sensitivität der Testmethode ist jedoch nur moderat, insbesondere bei einer niedrigen Infektionsintensität. Zudem kann eine Infektion erst nach der Präpatenzzeit nachgewiesen werden. Der ebenfalls häufig eingesetzte urinbasierte Point-of-Care Circulating Cathodic Antigen (POC-CCA)-Test weist zwar eine höhere Sensitivität aber geringere Spezifität als das KK-Verfahren auf. Als hochsensitive und sehr spezifische Methode zur Diagnose der Schistosomiasis hat sich der Nachweis von Schistosoma-spezifischer DNA mittels Real-Time PCR herausgestellt. Allerdings wird für die Durchführung dieser Technik ein gut ausgestattetes Labor benötigt, das sich in der Regel nicht in unmittelbarer Nähe zum Patienten im Feld befindet. Daher ist es besonders wichtig, über praktikable und schnelle Konservierungsmethoden zu verfügen, die bevor die Extraktion und Amplifikation der DNA stattfindet, einen einfachen Transport und eine einfache Lagerung des Probenmaterials ermöglichen.
Das Ziel des ersten Teils der vorliegenden Arbeit war, die Sensitivität und Spezifität der klassischerweise verwendeten KK-Methode und des POC-CCA-Tests mit der
Real-Time PCR- Methode unter Verwendung von Stuhlproben, Urinproben, Serumproben sowie auf Filterpapier getrocknete Blutproben (dried blood spots – DBSs) zu vergleichen. Zudem wurde die Anwendbarkeit der Real-Time PCR aus Serum- und Urinproben zur Therapiekontrolle überprüft. Die dazu notwendigen Studien wurden alle in der Region Mwanza in Tansania durchgeführt, welche als hochendemisch für S. mansoni gilt. Für die Untersuchungen zur stuhlbasierten Real-Time PCR wurden als Studienteilnehmer Schulkinder gewählt. Aufgrund der erforderlichen Blutabnahme wurden die anderen Teilstudien nur mit erwachsenen Probanden durchgeführt. Unter Verwendung der KK-Methode als Goldstandard erzielten die Real-Time PCR aus Stuhlproben und der POC-CCA-Test sehr hohe Sensitivitäten von 99,5% bzw. 89,7%, jedoch nur geringe Spezifitäten von 29,55% und 22,73%. Die KK-Methode weist bekanntermaßen nur eine geringe bis moderate Sensitivität auf und ist daher nicht gut als Referenz geeignet. Deshalb wurde zusätzlich eine latente Klassenanalyse angewandt, um die tatsächlich Erkrankten zu ermitteln und anhand dieser die diagnostische Güte der verwendeten Tests zu bestimmen. Hier zeigte der POC-CCA-Test die höchste Sensitivität (99,5%) sowie eine Spezifität von 63,4%. Der Real-Time PCR-Test hatte eine Sensitivität von 98,7% und die höchste Spezifität (81,2%). Die Spezifität der KK-Technik betrug 72,8%, die Sensitivität war signifikant niedriger (89,7%) als bei den anderen beiden Methoden. Diese Ergebnisse verdeutlichen, dass der POC-CCA-Schnelltest empfindlicher ist als die KK-Methode und zum Screening von S. mansoni-Infektionen eingesetzt werden kann. Die Stuhl-PCR war zwar ebenfalls hochsensitiv und zeigte unter den drei getesteten Diagnoseverfahren die höchste Spezifität, aber aufgrund der höheren Kosten und der komplizierten Anwendung sollte für epidemiologische Untersuchungen in Hochprävalenzregionen der POC-CCA-Test bevorzugt werden. Bei unklaren Diagnosen kann die Real-Time PCR-Methode als Bestätigungstest Anwendung finden.
In der Teilstudie zur serum- und urinbasierten Real-Time PCR in einer endemischen Region vor und nach der Behandlung mit PZQ wurden folgende Ergebnisse erzielt: Unter Verwendung einer kombinierten Referenz aus den Ergebnissen des parasitologischen KK-Tests und / oder der serumbasierten PCR konnte zu Studienbeginn eine Prävalenz von S. mansoni von 77,1% ermittelt werden. In Bezug auf die Sensitivität zeigte der DNA-Nachweis aus Serum (96,3%) und der POC-CCA-Assay (77,8%) die höchsten Ergebnisse. Die urinbasierte Real-Time PCR zeigte die geringste Empfindlichkeit (33,3%). Durch die Behandlung mit Praziquantel wurde eine signifikante Reduktion der S. mansoni Prävalenz erreicht. Zwanzig Wochen nach Therapie konnte durch die KK-Methode keine, mit dem POC-CCA-Test 33,3% und mit der serumbasierten Real-Time PCR 58,3% Infektionen festgestellt werden. Die Analyse der mittels der serumbasierten PCR bestimmten mittleren Ct-Werte im zeitlichen Verlauf zeigte, dass dieser eine Woche nach der Behandlung signifikant abnahm (von 30,3 auf 28) und 20 Wochen später über den Basiswert (34,9) anstieg. Der Ct-Wert ist umgekehrt proportional zur DNA-Ausgangsmenge, die in die PCR eingesetzt wurde. Dies deutet darauf hin, dass kurz nach der Therapie ein DNA-Anstieg zu verzeichnen war und 20 Wochen später weniger DNA als zu Beginn der Studie nachweisbar war. Dieser DNA-Verlauf lässt verschiedene Interpretationsmöglichkeiten zu. Die Daten zeigen jedoch, dass die serumbasierte Real-Time PCR eine ausgezeichnete diagnostische Genauigkeit aufweist. Da die nachgewiesene DNA jedoch keine Rückschlüsse auf das Parasitenstadium zulässt und es sich hierbei auch um DNA aus im Gewebe verbliebenen Eiern oder Reinfektionen handeln könnte, ist diese Methode in Hochprävalenz- Regionen nicht zur Therapiekontrolle geeignet. Die Verwendung von Urin zum DNA-Nachweis erzielte keine vielversprechenden Ergebnisse. Die Sensitivität der Real-Time PCR aus DBSs war ebenfalls sehr gering (45,4%) und kann ohne weitere ausführliche Testung hinsichtlich Lagertemperatur, Lagerdauer, verschiedener Filterpapierarten und Extraktionsmethoden nicht empfohlen werden.
Zusammenfassend zeigten die Ergebnisse dieser Studien, dass sowohl die stuhl- als auch die serumbasierte Real-Time PCR bei der Erkennung und Bewertung der Infektionsprävalenz, einem wichtigen Aspekt epidemiologischer Studien, deutlich empfindlicher ist als das mikroskopische KK-Verfahren. Aufgrund des hohen Kosten- und Personalaufwandes und der Notwendigkeit eines gut ausgestatteten Labors wird sich diese Methode aber nicht zum Screening in hochendemischen Ländern durchsetzen. Sie kann jedoch einen Mehrwert bei der Diagnose der Schistosomiasis bieten, vor allem bei frühen oder leichten Infektionen. Zudem kann diese hochsensitive und spezifische Methode als Bestätigungstest bei unklaren Diagnosen herangezogen werden.
Im zweiten Teil dieser Arbeit wurden malakologische Untersuchungen zur Identifizierung potenzieller Übertragungsorte für die Schistosomiasis rund um die im Viktoriasee gelegene Insel Ijinga durchgeführt. Diese Analysen fanden innerhalb eines Pilotprojektes zur Eliminierung der Erkrankung auf der Insel Ijinga statt, wobei ein intensiviertes Behandlungsprotokoll, welches die gesamte Inselbevölkerung einschloss, Anwendung fand. Die Kontrolle der Praziquanteleffektivität nach mehreren Behandlungsrunden bringt eine Reihe diagnostischer Herausforderungen mit sich. Hier könnte die Beurteilung der Schistosoma-Infektion in den Zwischenwirtschnecken vor und nach der Therapie als Indikator für den Erfolg der Maßnahme dienen. Zu diesem Zweck erfolgte zunächst eine Baseline-Untersuchung, bei der Schnecken an Uferregionen gesammelt wurden, an denen die Inselbewohner häufigen Wasserkontakt hatten. Die Schnecken wurden anhand morphologischer Merkmale identifiziert und mithilfe der Real-Time PCR-Methode auf Infektionen mit S. mansoni untersucht. Insgesamt wurden 35,4% (279/788) S. mansoni- positive Zwischenwirtschnecken (Biomphalaria) detektiert. Dies verdeutlicht, dass an den meisten Wasserkontaktstellen um die Insel Ijinga ein potentielles Risiko für die Übertragung der Schistosomiasis besteht. Die mithilfe der KK-Methode ermittelte Gesamtprävalenz von S. mansoni in der humanen Bevölkerung betrug 68,9%. Nachdem die Bewohner der Insel viermal mit PZQ behandelt wurden, zeigte sich in der kontinuierlich überwachten Sentinelgruppe eine Reduktion der Prävalenz auf 28,7%. Zu diesem Zeitpunkt wurde ebenfalls die Analyse der Schnecken wiederholt und es konnten 16,8% (57/350) Schnecken mit einer S. mansoni Infektion nachgewiesen werden. Die Reduktion der Infektionshäufigkeit in den Schnecken vor und nach der viermaligen Behandlung der Bevölkerung war signifikant (χ² = 74.335, p < 0,001). Dies deutet darauf hin, dass die intermediären Wirtsschnecken zur Überwachung von Kontrollmaßnahmen verwendet werden können.
Dispersal is a life-history trait affecting dynamics and persistence of populations; it evolves under various known selective pressures. Theoretical studies on dispersal typically assume 'natal dispersal', where individuals emigrate right after birth. But emigration may also occur during a later moment within a reproductive season ('breeding dispersal'). For example, some female butterflies first deposit eggs in their natal patch before migrating to other site(s) to continue egg-laying there. How breeding compared to natal dispersal influences the evolution of dispersal has not been explored. To close this gap we used an individual-based simulation approach to analyze (i) the evolution of timing of breeding dispersal in annual organisms, (ii) its influence on dispersal (compared to natal dispersal). Furthermore, we tested (iii) its performance in direct evolutionary contest with individuals following a natal dispersal strategy. Our results show that evolution should typically result in lower dispersal under breeding dispersal, especially when costs of dispersal are low and population size is small. By distributing offspring evenly across two patches, breeding dispersal allows reducing direct sibling competition in the next generation whereas natal dispersal can only reduce trans-generational kin competition by producing highly dispersive offspring in each generation. The added benefit of breeding dispersal is most prominent in patches with small population sizes. Finally, the evolutionary contests show that a breeding dispersal strategy would universally out-compete natal dispersal.
Das zentrale Paradigma der Systembiologie zielt auf ein möglichst umfassendes Ver-ständnis der komplexen Zusammenhänge biologischer Systeme. Die in dieser Arbeit angewandten Methoden folgen diesem Grundsatz.
Am Beispiel von drei auf Basis von Datenbanken und aktueller Literatur rekonstruier-ten Netzwerkmodellen konnte in der hier vorliegenden Arbeit die Gültigkeit analyti-scher und prädiktiver Algorithmen nachgewiesen werden, die in Form der Analy-sesoftware Jimena angewandt wurden. Die daraus resultierenden Ergebnisse sowohl für die Berechnung von stabilen Systemzuständen, der dynamischen Simulation, als auch der Identifikation zentraler Kontrollknoten konnten experimentell validiert wer-den. Die Ergebnisse wurden in einem iterativen Prozess verwendet werden um das entsprechende Netzwerkmodell zu optimieren.
Beim Vergleich des Verhaltens des semiquantitativ ausgewerteten regulatorischen Netzwerks zur Kontrolle der Differenzierung humaner mesenchymaler Stammzellen in Chondrozyten (Knorpelbildung), Osteoblasten (Knochenbildung) und Adipozyten (Fett-zellbildung) konnten 12 wichtige Faktoren (darunter: RUNX2, OSX/SP7, SOX9, TP53) mit Hilfe der Berechnung der Bedeutung (Kontrollzentralität der Netzwerkknoten identifi-ziert werden). Der Abgleich des simulierten Verhaltens dieses Netzwerkes ergab eine Übereinstimmung mit experimentellen Daten von 47,2%, bei einem widersprüchlichen Verhalten von ca. 25%, dass unter anderem durch die temporäre Natur experimentel-ler Messungen im Vergleich zu den terminalen Bedingungen des Berechnung der stabilen Systemzustände erklärt werden kann.
Bei der Analyse des Netzwerkmodells der menschlichen Immunantwort auf eine Infek-tion durch A. fumigatus konnten vier Hauptregulatoren identifiziert werden (A. fumi-gatus, Blutplättchen, hier Platelets genannt, und TNF), die im Zusammenspiel mit wei-teren Faktoren mit hohen Zentralitätswerten (CCL5, IL1, IL6, Dectin-1, TLR2 und TLR4) fähig sind das gesamte Netzwerkverhalten zu beeinflussen. Es konnte gezeigt werden, dass sich das Aktivitätsverhalten von IL6 in Reaktion auf A. fumigatus und die regulato-rische Wirkung von Blutplättchen mit den entsprechenden experimentellen Resultaten deckt.
Die Simulation, sowie die Berechnung der stabilen Systemzustände der Immunantwort von A. thaliana auf eine Infektion durch Pseudomonas syringae konnte zeigen, dass die in silico Ergebnisse mit den experimentellen Ergebnissen übereinstimmen. Zusätzlich konnten mit Hilfe der Analyse der Zentralitätswerte des Netzwerkmodells fünf Master-regulatoren identifiziert werden: TGA Transkriptionsfaktor, Jasmonsäure, Ent-Kaurenoate-Oxidase, Ent-kaurene-Synthase und Aspartat-Semialdehyd-Dehydrogenase.
Während die ersteren beiden bereits lange als wichtige Regulatoren für die Gib-berellin-Synthese bekannt sind, ist die immunregulatorische Funktion von Aspartat-Semialdehyd-Dehydrogenase bisher weitgehend unbekannt.
Erstellung eines genregulatorischen Netzwerkes zur Simulation der Entstehung von Zahnhartsubstanz
(2020)
In dieser Dissertation beschreibt der Autor die Erstellung eines grundlegenden bioinformatischen Modelles der menschlichen Zahnschmelzreifung. Mithilfe der KEGG Pathway-Datenbank wurde ein genregulatorisches Netzwerk (GRN) erstellt, welches maßgeblich auf den Signaltransduktionswegen Apoptose, Zellzyklus, Hedgehog-Signalweg, MAP-Kinase-Weg, mTOR-Signalweg Notch-Signalweg Signalweg, TGF-β-Signalweg und Wnt-Signalweg basiert. Im Weiteren wurde dieses Netzwerk durch zahlreiche verifizierte Wechselwirkungen erweitert und die zahnspezifischen Gene AMELX, AMELY, AMBN, ENAM und DSPP implementiert. In der anschließenden Simulation des Netzwerks mit dem Simulations-Tool Jimena konnten sechs stabile Zustände identifiziert werden. Diese wurden genauer untersucht und den Erkenntnissen eines GEO-Datensatzes gegenübergestellt. Langfristiges Ziel ist es, durch konsequente Optimierung des bioinformatischen Netzwerks Rückschlüsse auf die Odontogenese des Menschen zu ziehen.