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Non–Small-Cell Lung Cancer (NSCLC) is the most frequent human lung cancer and a major cause of death due to its high rate of metastasis1. These facts emphasize the urgent need for the investigation of new targets for anti-metastatic therapy. Up to now a number of genes and gene products have been identified that positively or negatively affect the probability of established human tumor cell lines to metastasize2. Previously, together with the group of Professor Ulf Rapp, we have described the first conditional mouse model for metastasis of NSCLC and identified a gene, c-MYC, that is able to orchestrate all steps of this process. We could identify potential markers for detection of metastasis and highlighted GATA4, which is exclusively expressed during lung development, as a target for future therapeutic intervention2. However, the mechanism underlying this metastatic conversion remained to be identified, and was therefore the focus of the present work. Here, GATA4 is identified as a MYC target in the development of metastasis and epigenetic alterations at the GATA4 promoter level are shown after MYC expression in NSCLC in vivo and in vitro. Such alterations include site-specific demethylation that accompanies the displacement of the MYC-associated zinc finger protein (MAZ) from the GATA4 promoter, which leads to GATA4 expression. Histone modification analysis of the GATA4 promoter revealed a switch from repressive histone marks to active histone marks after MYC binding, which corresponds to active GATA4 expression. This work identifies a novel epigenetic mechanism by which MYC activates GATA4 leading to metastasis in NSCLC, suggesting novel potential targets for the development of anti-metastatic therapy.
In the fast-evolving landscape of biomedical research, the emergence of big data has presented researchers with extraordinary opportunities to explore biological complexities. In biomedical research, big data imply also a big responsibility. This is not only due to genomics data being sensitive information but also due to genomics data being shared and re-analysed among the scientific community. This saves valuable resources and can even help to find new insights in silico. To fully use these opportunities, detailed and correct metadata are imperative. This includes not only the availability of metadata but also their correctness. Metadata integrity serves as a fundamental determinant of research credibility, supporting the reliability and reproducibility of data-driven findings. Ensuring metadata availability, curation, and accuracy are therefore essential for bioinformatic research. Not only must metadata be readily available, but they must also be meticulously curated and ideally error-free. Motivated by an accidental discovery of a critical metadata error in patient data published in two high-impact journals, we aim to raise awareness for the need of correct, complete, and curated metadata. We describe how the metadata error was found, addressed, and present examples for metadata-related challenges in omics research, along with supporting measures, including tools for checking metadata and software to facilitate various steps from data analysis to published research.
Highlights
• Data awareness and data integrity underpins the trustworthiness of results and subsequent further analysis.
• Big data and bioinformatics enable efficient resource use by repurposing publicly available RNA-Sequencing data.
• Manual checks of data quality and integrity are insufficient due to the overwhelming volume and rapidly growing data.
• Automation and artificial intelligence provide cost-effective and efficient solutions for data integrity and quality checks.
• FAIR data management, various software solutions and analysis tools assist metadata maintenance.
Since ancient times aging has also been regarded as a disease, and humankind has always strived to extend the natural lifespan. Analyzing the genes involved in aging and disease allows for finding important indicators and biological markers for pathologies and possible therapeutic targets. An example of the use of omics technologies is the research regarding aging and the rare and fatal premature aging syndrome progeria (Hutchinson-Gilford progeria syndrome, HGPS). In our study, we focused on the in silico analysis of differentially expressed genes (DEGs) in progeria and aging, using a publicly available RNA-Seq dataset (GEO dataset GSE113957) and a variety of bioinformatics tools. Despite the GSE113957 RNA-Seq dataset being well-known and frequently analyzed, the RNA-Seq data shared by Fleischer et al. is far from exhausted and reusing and repurposing the data still reveals new insights. By analyzing the literature citing the use of the dataset and subsequently conducting a comparative analysis comparing the RNA-Seq data analyses of different subsets of the dataset (healthy children, nonagenarians and progeria patients), we identified several genes involved in both natural aging and progeria (KRT8, KRT18, ACKR4, CCL2, UCP2, ADAMTS15, ACTN4P1, WNT16, IGFBP2). Further analyzing these genes and the pathways involved indicated their possible roles in aging, suggesting the need for further in vitro and in vivo research. In this paper, we (1) compare “normal aging” (nonagenarians vs. healthy children) and progeria (HGPS patients vs. healthy children), (2) enlist genes possibly involved in both the natural aging process and progeria, including the first mention of IGFBP2 in progeria, (3) predict miRNAs and interactomes for WNT16 (hsa-mir-181a-5p), UCP2 (hsa-mir-26a-5p and hsa-mir-124-3p), and IGFBP2 (hsa-mir-124-3p, hsa-mir-126-3p, and hsa-mir-27b-3p), (4) demonstrate the compatibility of well-established R packages for RNA-Seq analysis for researchers interested but not yet familiar with this kind of analysis, and (5) present comparative proteomics analyses to show an association between our RNA-Seq data analyses and corresponding changes in protein expression.
Machine learning techniques are excellent to analyze expression data from single cells. These techniques impact all fields ranging from cell annotation and clustering to signature identification. The presented framework evaluates gene selection sets how far they optimally separate defined phenotypes or cell groups. This innovation overcomes the present limitation to objectively and correctly identify a small gene set of high information content regarding separating phenotypes for which corresponding code scripts are provided. The small but meaningful subset of the original genes (or feature space) facilitates human interpretability of the differences of the phenotypes including those found by machine learning results and may even turn correlations between genes and phenotypes into a causal explanation. For the feature selection task, the principal feature analysis is utilized which reduces redundant information while selecting genes that carry the information for separating the phenotypes. In this context, the presented framework shows explainability of unsupervised learning as it reveals cell-type specific signatures. Apart from a Seurat preprocessing tool and the PFA script, the pipeline uses mutual information to balance accuracy and size of the gene set if desired. A validation part to evaluate the gene selection for their information content regarding the separation of the phenotypes is provided as well, binary and multiclass classification of 3 or 4 groups are studied. Results from different single-cell data are presented. In each, only about ten out of more than 30000 genes are identified as carrying the relevant information. The code is provided in a GitHub repository at https://github.com/AC-PHD/Seurat_PFA_pipeline.
Summary
Chapters I & II: General Introduction & General Methods
Agriculture is confronted with a rampant loss of biodiversity potentially eroding ecosystem service potentials and adding up to other stressors like climate change or the consequences of land-use change and intensive management. To counter this ‘biodiversity crisis’, agri-environment schemes (AES) have been introduced as part of ecological intensification efforts. These AES combine special management regimes with the establishment of tailored habitats to create refuges for biodiversity in agricultural landscapes and thus ensure biodiversity mediated ecosystem services such as pest control. However, little is known about how well different AES habitats fulfil this purpose and whether they benefit ecosystem services in adjacent crop fields. Here I investigated how effective different AES habitats are for restoring biodiversity in different agricultural landscapes (Chapter V) and whether they benefit natural pest control in adjacent oilseed rape (Chapter VI) and winter cereal fields (Chapter VII). I recorded biodiversity and pest control potentials using a variety of different methods (Chapters II, V, VI & VII). Moreover, I validated the methodology I used to assess predator assemblages and predation rates (Chapters III & IV).
Chapter III: How to record ground dwelling predators?
Testing methodology is critical as it ensures scientific standards and trustworthy results. Pitfall traps are widely used to record ground dwelling predators, but little is known about how different trap types affect catches. I compared different types of pitfall traps that had been used in previous studies in respect to resulting carabid beetle assemblages. While barrier traps collected more species and deliver more complete species inventories, conventional simple pitfall traps provide reliable results with comparatively little handling effort. Placing several simple pitfall traps in the field can compensate the difference while still saving handling effort.
Chapter IV: How to record predation rates?
A plethora of methods has been proposed and used for recording predation rates, but these have rarely been validated before use. I assessed whether a novel approach to record predation, the use of sentinel prey cards with glued on aphids, delivers realistic results. I compared different sampling efforts and showed that obtained predation rates were similar and could be linked to predator (carabid beetle) densities and body-sizes (a proxy often used for food intake rates). Thus, the method delivers reliable and meaningful predation rates.
Chapter V: Do AES habitats benefit multi-taxa biodiversity?
The main goal of AES is the conservation of biodiversity in agricultural landscapes. I investigated how effectively AES habitats with different temporal continuity fulfil this goal in differently structured landscapes. The different AES habitats investigated had variable effects on local biodiversity. Temporal continuity of AES habitats was the most important predictor with older, more temporally continuous habitats harbouring higher overall biodiversity and different species assemblages in most taxonomic groups than younger AES habitats. Results however varied among taxonomic groups and natural enemies were equally supported by younger habitats. Semi-natural habitats in the surrounding landscape and AES habitat size were of minor importance for local biodiversity and had limited effects. This stresses that newly established AES habitats alone cannot restore farmland biodiversity. Both AES habitats as well as more continuous semi-natural habitats synergistically increase overall biodiversity in agricultural landscapes.
Chapter VI: The effects of AES habitats on predators in adjacent oilseed rape fields
Apart from biodiversity conservation, ensuring ecosystem service delivery in agricultural landscapes is a crucial goal of AES. I therefore investigated the effects of adjacent AES habitats on ground dwelling predator assemblages in oilseed rape fields. I found clear distance decay effects from the field edges into the field centres on both richness and densities of ground dwelling predators. Direct effects of adjacent AES habitats on assemblages in oilseed rape fields however were limited and only visible in functional traits of carabid beetle assemblages. Adjacent AES habitats doubled the proportion of predatory carabid beetles indicating a beneficial role for pest control. My results show that pest control potentials are largest close to the field edges and beneficial effects are comparably short ranged.
Chapter VII: The effects of AES habitats on pest control in adjacent cereal fields
Whether distance functions and potential effects of AES habitats are universal across crops is unknown. Therefore, I assessed distance functions of predators, pests, predation rates and yields after crop rotation in winter cereals using the same study design as in the previous year. Resulting distance functions were not uniform and differed from those found in oilseed rape in the previous year, indicating that the interactions between certain adjacent habitats vary with habitat and crop types. Distance functions of cereal-leaf beetles (important cereal pests) and parasitoid wasps were moreover modulated by semi-natural habitat proportion in the surrounding landscapes. Field edges buffered assemblage changes in carabid beetle assemblages over crop rotation confirming their important function as refuges for natural enemies. My results emphasize the beneficial role of field edges for pest control potentials. These findings back the calls for smaller field sizes and more diverse, more heterogeneously structured agricultural landscapes.
Chapter VIII: General Discussion
Countering biodiversity loss and ensuring ecosystem service provision in agricultural landscapes is intricate and requires strategic planning and restructuring of these landscapes. I showed that agricultural landscapes could benefit maximally from (i) a mixture of AES habitats and semi-natural habitats to support high levels of overall biodiversity and from (ii) smaller continuously managed agricultural areas (i.e. smaller field sizes or the insertion of AES elements within large fields) to maximize natural pest control potentials in crop fields. I propose a mosaic of younger AES habitats and semi-natural habitats to support ecosystem service providers and increase edge density for ecosystem service spillover into adjacent crops. The optimal extent and density of this network as well as the location in which AES and semi-natural habitats interact most beneficially with adjacent crops need further investigation. My results provide a further step towards more sustainable agricultural landscapes that simultaneously allow biodiversity to persist and maintain agricultural production under the framework of ecological intensification.
By promoting ceramide release at the cytosolic membrane leaflet, the neutral sphingomyelinase 2 (NSM) is capable of organizing receptor and signalosome segregation. Its role in T cell receptor (TCR) signaling remained so far unknown. We now show that TCR-driven NSM activation is dispensable for TCR clustering and initial phosphorylation, but of crucial importance for further signal amplification. In particular, at low doses of TCR stimulatory antibodies, NSM is required for Ca\(^{2+}\) mobilization and T cell proliferation. NSM-deficient T cells lack sustained CD3ζ and ZAP-70 phosphorylation and are unable to polarize and stabilize their microtubular system. We identified PKCζ as the key NSM downstream effector in this second wave of TCR signaling supporting dynamics of microtubule-organizing center (MTOC). Ceramide supplementation rescued PKCζ membrane recruitment and MTOC translocation in NSM-deficient cells. These findings identify the NSM as essential in TCR signaling when dynamic cytoskeletal reorganization promotes continued lateral and vertical supply of TCR signaling components: CD3ζ, Zap70, and PKCζ, and functional immune synapses are organized and stabilized via MTOC polarization.
Die Gelbbauchunke Bombina variegata gilt als eine typische Pionierart, die bevorzugt vegetationslose, ephemere Gewässer mit hohem Austrocknungsrisiko als Laichgewässer nutzt. Kleinstgewässer dieser Art zeichnen sich durch hohe Fluktuationen abiotischer (Temperatur, Ionenkonzentration, Wasserstand), aber auch biotischer Faktoren (Dichte, Räuberdruck) aus. In Anpassung an das zeitlich und räumlich unvorhersehbare Auftreten dieser Gewässer hat die Gelbbauchunke eine für eine temperate Art außergewöhnlich lange Fortpflanzungsperiode (April - August). Die Weibchen zeigten während der Saison eine kontinuierliche Eientwicklung, die es ihnen erlaubt, opportunistisch mehrfach abzulaichen und damit eine zeitliche Risikostreuung der Gelege zu betreiben. Darüber hinaus nutzt Bombina variegata alle Möglichkeiten der räumlichen Risikostreuung, indem sie ihre Gelege in kleinen Portionen innerhalb von Pfützen, aber auch auf verschiedene Pfützen verteilt. Die hohe Variabilität in den produzierten Eigrößen, besonders zwischen den Gelegen verschiedener Weibchen, ließ auf den ersten Blick eine weitere Strategie zur Risikostreuung vermuten; allerdings war die Eigröße von der Kondition der Weibchen abhängig: während gut konditionierte Weibchen in der Lage waren, sowohl größere Eier als auch größere Gelege zu produzieren, gingen schlechter konditionierte Weibchen einen „trade-off“ zugunsten einer möglichst hohen Fekundität ein. Unter günstigen Bedingungen greift diese Strategie, während die Produktion überdurchschnittlich großer Eier unter Austrocknungsbedingungen von Vorteil ist: Kaulquappen großer Eier hatten eine entsprechend größere Schlupfgröße und zeigten gegenüber Quappen kleinerer Eier eine beschleunigte Entwicklung. Auch bei den Labor- und Freilanduntersuchungen, die sich mit der Frage be-schäftigten, wie Bombina variegata auf kritische Veränderungen des Wasservo-lumens reagiert, war eine enorme Variabilität in den Wachstums- und Entwicklungsverläufen der Kaulquappen der verschiedenen Ansätze zu beobachten, die sich nur bedingt auf abweichende Versuchsbedingungen zurückführen ließ; vielmehr dürfte die qualitative Ausstattung der Quappen eine wesentliche Rolle gespielt haben. Dabei kristallisierten sich in den verschiedenen Versuchen zwei unterschiedliche Entwicklungsstrategien heraus: Kaulquappen, die eine insgesamt relativ lange Entwicklungszeit benötigten, zeigten eine hohe phänotypische Plastizität und reagierten adaptiv auf abnehmende Wasserstände, indem sie ihre Entwicklung auf Kosten ihres Wachstums beschleunigten. Bei Quappen, die im Durchschnitt eine wesentlich schnellere Entwicklungszeit besaßen, war diese per se günstige hohe Entwicklungsrate dagegen fixiert, unabhängig davon, während welcher Entwicklungsphase die Quappen auf veränderte Bedingungen umgestellt wurden. Unter verschlechterten Bedingungen zeigten sie lediglich Wachstumseinbußen. Ähnlich reagierten Kaulquappen auf zunehmende Ionenkonzentrationen bzw. sinkende Wasserstände. Dagegen wirkte sich Ammoniak, Exkretionsprodukt von Amphibienlarven, in erhöhten Konzentrationen stark negativ aus und beeinträchtigte sowohl das Wachstum als auch die Entwicklung der Quappen. Auf Räuber, die im Vergleich zum Austrocknungsrisiko temporärer Gewässer eine eher untergeordnete Rolle spielen, reagierten Bombina variegata-Quappen nur bedingt. Erst nach Fütterung der Libellenlarven mit Unkenquappen schränkten sie vorübergehend ihre Aktivität ein und mieden den räubernahen Bereich, ohne dass dadurch die Entwicklungsgeschwindigkeit oder das Wachstum der Quappen beeinträchtigt wurde; allerdings war eine erhöhte Mortalität zu beobachten.
Chlamydia are Gram-negative obligate intracellular bacteria responsible for a wide spectrum of relevant diseases. Due to their biphasic developmental cycle Chlamydia depend on an intact host cell for replication and establishment of an acute infection. Chlamydia have therefore evolved sophisticated strategies to inhibit programmed cell death (PCD) induced by a variety of stimuli and to subvert the host immune system. This work aimed at elucidating whether an infection with C. trachomatis can influence the cellular response to double-stranded RNA (dsRNA). The synthesis of dsRNA is a prominent feature of viral replication inside infected cells that can induce both PCD and the activation of a cellular innate immune response. In order to mimic chlamydial and viral co-infections, Chlamydia-infected cells were transfected with polyinosinic:polycytidylic acid (polyI:C), a synthetic dsRNA. In the first part of this work it was investigated whether C. trachomatis-infected host cells could resist apoptosis induced by polyI:C. A significant reduction in apoptosis, determined by PARP cleavage and DNA fragmentation, could be observed in infected cells. It could be shown that processing of the initiator caspase-8 was inhibited in infected host cells. This process was dependent on early bacterial protein synthesis and was specific for dsRNA because apoptosis induced by TNFalpha was not blocked at the level of caspase-8. Interestingly, the activation of cellular factors involved in apoptosis induction by dsRNA, most importantly PKR and RNase L, was not abrogated in infected cells. Instead, RNA interference experiments revealed the crucial role of cFlip, a cellular caspase-8 inhibitor, for chlamydial inhibition of dsRNA-induced apoptosis. First data acquired by co-immunoprecipitation experiments pointed to an infection-induced concentration of cFlip in the dsRNA-induced death complex of caspase-8 and FADD. In the second part of this work, the chlamydial influence on the first line of defense against viral infections, involving expression of interferons and interleukins, was examined. Activation of the interferon regulatory factor 3 (IRF-3) and the NF-kappaB transcription factor family member p65, both central regulators of the innate immune response to dsRNA, was altered in Chlamydia-infected epithelial cells. polyI:C-induced degradation of IkappaB-alpha, the inhibitor of NF-kappaB, was accelerated in infected cells which was accompanied by a change in nuclear translocation of the transcription factor. Translocation of IRF-3, in contrast, was significantly blocked upon infection. Together the data presented here demonstrate that infection with C. trachomatis can drastically alter the cellular response to dsRNA and imply an impact of chlamydial infections on the outcome of viral super-infections.
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.
Die Evolution der Primaten zeigt eine Verbindung zwischen der zunehmenden Komplexität des sozialen Verhaltens und der Vergrößerung des humanen Gehirns, insbesondere des präfrontalen Cortex. Deshalb stellt der präfrontale Cortex bezüglich der Evolution des Menschen eine der interessantesten Strukturen im humanen Gehirn dar. Es wird angenommen, dass nicht allein die Größe, sondern auch die Funktion, vor allem das Zusammenspiel von Neuronen und nicht-neuronalen Zellen, wie z.B. Gliazellen, zur Differenzierung des menschlichen Gehirns von dem rezenter Primaten geführt hat. Daraus lässt sich schließen, dass die Gehirnfunktionen über eine ausgeglichene und gut aufeinander abgestimmte transkriptionelle Landschaft kontrolliert werden, die durch ein zugrundeliegendes genetisches und epigentisches Rückgrat organisiert ist. In dieser Studie wurden das Methylierungsprofil neuronaler und nicht-neuronaler Zellen des präfrontalen Cortex (Brodmann-Areal 10) von drei Menschen und drei Schimpansen miteinander verglichen. Die intra- und interspezifischen differenziell methylierten Regionen (DMRs) waren in bestimmten genomischen Regionen angereichert. Intraspezifische Methylierungsunterschiede zwischen neuronalen und nicht-neuronalen Zellen konnten dreimal häufiger beobachtet werden als interspezifische Unterschiede in den einzelnen Zelltypen. Rund 90% der humanen intraspezifischen DMRs wiesen eine Hypomethylierung in den neuronalen Zellen im Vergleich zu den nicht-neuronalen Zellen auf. In den intraspezifischen DMRs (Mensch und Schimpanse) waren Gene angereichert, die mit verschiedenen neuropsychiatrischen Erkrankungen assoziiert sind. Der Vergleich zwischen Menschen und Schimpanse in den neuronalen und nicht-neuronalen Zelltypen zeigte eine Anreicherung von Genen mit human-spezifischer Histonsignatur. In den nicht-neuronalen Zellen konnten mehr interspezifische DMRs (n=666) detektiert werden als in den neuronalen Zellen (n=96). Ungefähr 95% der nicht-neuronalen interspezifischen DMRs waren im Menschen, im Vergleich zum Schimpansen, hypermethyliert. Daraus ergibt sich der Eindruck, dass mehrere hundert der nicht-neuronalen Gene während der humanen Gehirnevolution einer Methylierungswelle unterlagen. Dies führt zu der Annahme, dass der Einfluss dieser Veränderungen in den nicht-neuronalen Zellen auf die Vergößerung des menschlichen Gehirns bisher stark unterschätzt wurde.
Die bekannteste genetische Ursache für erblichen Brust- und Eierstockkrebs sind Mutationen in den Tumorsuppressorgenen (TSG) BRCA1 und BRCA2. Dennoch können nur rund 20-25% der familiären Brustkrebserkrankungen über Keimbahnmutationen in BRCA1/BRCA2 erklärt werden, besonders bei Frauen, deren Erkrankung vor dem vierzigsten Lebensjahr auftritt. Epigenetische Veränderungen, die zu einer aberranten Genexpression führen, spielen ebenfalls eine wichtige Rolle bei der Karzinogenese und der Entwicklung einer Brustkrebserkrankung. Es ist bekannt, dass TSG nicht nur durch den Verlust der Heterozygotie (engl. loss of heterozygosity, LOH) oder homozygote Deletionen, sondern auch durch transkriptionelle Stilllegung via DNA-Methylierung inaktiviert werden können. Im Rahmen dieser Arbeit wurde überprüft, welchen Einfluss aberrante Methylierungsmuster im Promotorbereich von TSG auf die Brustkrebskarzinogenese und die Expression der Gene haben. Für die Quantifizierung der Epimutationen wurden die Promotorbereiche von acht TSG (BRCA1, BRCA2, RAD51C, ATM, PTEN, TP53, MLH1, RB1) und des estrogene receptor (ESR1) Gens, welches eine Rolle in der Tumorprogression spielt, mittels Deep Bisulfite Amplicon Sequencing (DBAS) analysiert. Es wurden Blutproben von zwei unabhängigen BRCA1/BRCA2-mutationsnegativen Brustkrebs (BC)-Patientenkohorten, sowie von zwei unabhängigen alters-gematchten, gesunden Kontrollkohorten untersucht. BC-Kohorte 1 beinhaltet early-onset (EO) BC-Patientinnen. Kohorte 2 enthält BC-Patientinnen mit einem Risiko von >95% eine heterozygote Mutation in BRCA1/BRCA2 (high-risk, HR) zu tragen. Allele mit >50% methylierten CpGs werden als funktionell relevante Epimutationen erachtet, da bekannt ist, dass TSG über eine Methylierung im Promotorbereich transkriptionell stillgelegt werden. Im Vergleich zu ESR1 (Ø Methylierung, 3%), welches die Methylierungslevel eines durchschnittlichen Promotors wiederspiegelt, zeigten die TSG sehr geringe durchschnittliche Methylierungswerte von weniger als 1%. Zudem waren die durchschnittlichen Epimutationsraten (EMR; <0,0001-0,1%) der TSG sehr gering. Mit der Ausnahme von BRCA1, welches eine erhöhte EMR in der BC-Kohorte verglichen zu den Kontrollen (0,31% gegen 0,06%) zeigte, gab es keine signifikanten Gruppenunterschiede zwischen BC-Patientinnen und Kontrollen. Eine von 36 HR BC-Patientinnen zeigte im Vergleich zu den restlichen Proben eine stark erhöhte EMR von 14,7% in BRCA1. Rund ein Drittel (15/44) der EO BC-Patientinnen wiesen eine erhöhte Rate an Einzel-CpG Fehlern in mehreren TSG auf. Die nachfolgenden Expressionsanalysen ergaben eine erniedrigte Expression vieler TSG je analysierter Patientin. Diese Ergebnisse führen zu der Annahme, dass epigenetische Veränderungen in normalen Körperzellen als ein möglicher Indikator für einen gestörten Mechanismus, der für die Aufrechterhaltung des unmethylierten Status und der daraus resultierenden normalen Genexpression zuständig ist, angesehen werden können. Dies kann mit einem erhöhten BC-Risiko assoziiert werden.
Although macroecology is a well‐established field, much remains to be learned about the large‐scale variation of fungal traits. We conducted a global analysis of mean fruit body size of 59 geographical regions worldwide, comprising 5340 fungal species exploring the response of fruit body size to latitude, resource availability and temperature. The results showed a hump‐shaped relationship between mean fruit body size and distance to the equator. Areas with large fruit bodies were characterised by a high seasonality and an intermediate mean temperature. The responses of mutualistic species and saprotrophs were similar. These findings support the resource availability hypothesis, predicting large fruit bodies due to a seasonal resource surplus, and the thermoregulation hypothesis, according to which small fruit bodies offer a strategy to avoid heat and cold stress and therefore occur at temperature extremes. Fruit body size may thus be an adaptive trait driving the large‐scale distribution of fungal species.
DNA microarrays have become a standard technique to assess the mRNA levels for complete genomes. To identify significantly regulated genes from these large amounts of data a wealth of methods has been developed. Despite this, the functional interpretation (i.e. deducing biological hypothesis from the data) still remains a major bottleneck in microarray data analysis. Most available methods display the set of significant genes in long lists, from which common functional properties have to be extracted. This is not only a tedious and time-consuming task, which becomes less and less feasible with increasing numbers of experimental conditions, but is also prone to errors, since it is commonly done by eye. In the course of this work methods have been developed and tested, that allow for a computerbased analysis of functional properties being relevant in the given experimental setting. To this end the Gene Ontology was chosen as an appropriate source of annotation data, because it combines human-readability with computer-accessibility of the annotations term and thus allows for a statistical analysis of functional properties. Here the gene-annotations are integrated in a Correspondence Analysis which allows to visualize genes, hybridizations and functional categories in a single plot. Due to the increasing amounts of available annotations and the fact that in most settings only few functional processes are differentially regulated, several filter criteria have been developed to reduce the number of displayed annotations to a set being relevant in the given experimental setting. The applicability of the presented visualization and filtering have both been validated on datasets of varying complexity. Starting from the well studied glucose-pathway in S. cerevisiae up to the comparison of different tumor types in human. In both settings the method generated well interpretable plots, which allowed for an immediate identification of the major functional differences between the experimental conditions [90]. While the integration of annotation data like GO facilitates functional interpretation, it lacks the capability to identify key regulatory elements. To facilitate such an analysis, the occurrence of transcription factor binding sites in upstream regions of genes has been integrated to the analysis as well. Again this methodology was biologically validated on S. cerevisiae as well human cancer data sets. In both settings TFs known to exhibit central roles for the observed transcriptional changes were plotted in marked positions and thus could be immediately identified [206]. In essence, integration of supplementary information in Correspondence Analysis visualizes genes, hybridizations and annotation data in a single, well interpretable plot. This allows for an intuitive identification of relevant annotations even in complex experimental settings. The presented approach is not limited to the shown types of data, but is generalizable to account for the majority of the available annotation data.
Morphologie und Organisation individueller oktopaminerger Neurone im Gehirn von Drosophila m.
(2009)
Das biogene Amin Oktopamin moduliert verschiedene Verhaltensweisen in Invertebraten. In verschiedenen Insektenspezies, wie Heuschrecken, Grillen oder Schaben, ist die Funktion und die Architektur des peripheren oktopaminergen Systems auf Einzelzellebene bekannt. Um die zelluläre Grundlage für die verschiedenen Funktionen von Oktopamin im Zentralnervensystem zu verstehen, ist eine detaillierte Analyse der Architektur des zentralen oktopaminergen Systems notwendig. Innerhalb meiner Doktorarbeit fertigte eine anatomische Karte individueller oktopaminerger Neurone des adulten Hirns von Drosophila an. Ich nutzte die Flp-out Technik, um einzelne oktopaminerge Neurone anzufärben. Anhand ihrer Projektionsmuster konnte ich 28 verschiedene Zelltypen in vier Oktopamin-immunoreaktiven Zellclustern identifizieren. Ihre Morphologie sowie die Verteilung genetischer Marker zeigte, dass die meisten Zelltypen mehrere Neuropile innervieren und dabei eine klare Trennung von Prä- und Postsynaptischen Regionen aufweisen. Die Mehrheit der Zelltypen bildet dendritische Verzweigungen in einer bestimmten Region, der posterioren Slope. Jedoch innerviert jeder Zelltyp stereotyp eine bestimmte Kombination von Zielregionen im Gehirn. Das deutet stark darauf hin, dass oktopaminerge Neurone kombinatorisch organisiert sind: Jedes individuelle Neuron scheint Komponente eines spezifischen neuronalen Schaltkreises zu sein. Dabei könnte jeder Zelltyp eine Art “Modul” darstellen, das selektiv bestimmte Funktionen in den jeweiligen Zielregionen moduliert. Das oktopaminerge Mittelliniencluster des Subösophagealen Ganglions zeigt eine besondere zelluläre Organisation. Es besteht aus gepaarten und ungepaarten Neuronen, die des Zentralgehirn mit extensiven Verzweigungen versorgen. Um die Ordnung hinter dieser komplexen Organisation zu verstehen, wurden die segmentale Organistion der Mittellinienneurone auf Einzelzellebene analysiert und ihre embryonalen Anlagen verglichen. Letzteres ermöglichte die morphologische Analyse von einzelnen oktopaminergen Mittellinienklonen. OA-VPM und OA-VUM Neurone bilden zusammen drei Subcluster im Subösophagealen Ganglion, die wahrscheinlich die drei gnathalen Neuromere repräsentieren. Alle OA-VUM Neurone stammen von der embryonalen Mittellinie ab. In den mandibularen und maxillaren Neuromeren formen sie morphologisch identische Zelltypen, mit stereotypen Innervationsmustern. OA-VPM Neurone gehen nicht aus der embryonalen Mittellinie hervor und sind nicht segmental dupliziert. Diese Arbeit vermittelt nicht nur einen Eindruck über die Architektur individueller oktopaminerger Neurone, sondern auch über die Organisation des oktopaminergen Systems auf Einzelzellebene.
Peritonitis is a common disease in man, frequently caused by fungi, such as Candida albicans; however, in seldom cases opportunistic infections with Saccharomyces cerevisiae are described. Resident peritoneal macrophages (prMΦ) are the major group of phagocytic cells in the peritoneum. They express a broad range of surface pattern recognition receptors (PRR) to recognize invaders. Yeast infections are primarily detected by the Dectin-1 receptor, which triggers activation of NFAT and NF-κB pathways.
The transcription of the Nfatc1 gene is directed by the two alternative promoters, inducible P1 and relatively constitutive P2 promoter. While the role of P1-directed NFATc1α-isoforms to promote survival and proliferation of activated lymphocytes is well-established, the relevance of constitutively generated NFATc1β-isoforms, mainly expressed in resting lymphocytes, myeloid and non-lymphoid cells, remains unclear. Moreover, former work at our department indicated different roles for NFATc1α- and NFATc1β-proteins in lymphocytes.
Our data revealed the functional role of NFATc1 in peritoneal resident macrophages. We demonstrated that the expression of NFATc1β is required for a proper immune response of prMΦ during fungal infection-induced acute peritonitis. We identified Ccl2, a major chemokine produced in response to fungal infections by prMΦ, as a novel NFATc1 target gene which is cooperatively regulated through the NFAT- and canonical NF-κB pathways. Consequently, we showed that NFATc1β deficiency in prMΦ results in a decreased infiltration of inflammatory monocytes, leading to a delayed clearance of peritoneal fungal infection.
We could further show that the expression of NFATc1β-isoforms is irrelevant for homeostasis of myeloid and adaptive immune system cells and that NFATc1α- (but not β-) isoforms are required for a normal development of peritoneal B1a cells. In contrast to the situation in myeloid cells, NFATc1β deficiency is compensated by increased expression of NFATc1α-isoforms in lymphoid cells. As a consequence, NFATc1ß is dispensable for activation of the adaptive immune system.
Taken together our results illustrate the redundancy and indispensability of NFATc1-isoforms in the adaptive and innate immune system, indicating a complex regulatory system for Nfatc1 gene expression in different compartments of the immune system and likely beyond that.
Methoden der Fluoreszenz-Lokalisationsmikroskopie (engl. single-molecule localization microscopy, SMLM) ermöglichen es Moleküle zu quantifizieren und deren Verteilung zu analysieren. Im Rahmen dieser Arbeit wurden verschiedene Membranmoleküle auf unterschiedlichen eukaryotischen Zellen, aber auch auf Prokaryoten mit dSTORM (engl. direct stochastic optical reconstruction microscopy) oder PALM (engl.: photoactivated localization microscopy) aufgenommen und quantifiziert. Bevor jedoch diese hochauflösende fluoreszenzbasierte Technik für biologische Fragestellungen angewendet werden konnten, mussten zunächst potentielle Artefakt-auslösende Quellen identifiziert und Strategien gefunden werden, um diese zu eliminieren.
Eine mögliche Artefakt-Quelle ist eine zu niedrige Photonenzahl, die von Fluorophoren emittiert wird. Werden zu wenige Photonen detektiert, kann die Lokalisation eines Fluorophors weniger präzise bestimmt werden. Dies kann zu einer falschen Abbildung von Strukturen führen oder zu falschen Rückschlüssen über die Verteilung von Molekülen. Eine Möglichkeit die Anzahl der emittierten Photonen zu erhöhen, ist chemische Additive als Triplettlöscher einzusetzen. Sie bewirken, dass die Fluorophore wieder in den Grundzustand relaxieren und somit wieder angeregt werden können. Es wurden verschiedene Additive, die in der Literatur als Triplettlöscher beschrieben sind, getestet. Dazu wurden zunächst ihre Auswirkungen auf den Triplettzustand verschiedener Fluorophore (Alexa Fluor (Al) 488, 532 und 647 und Atto655) mit Hilfe von Fluoreszenzkorrelationsspektroskopie (FCS) untersucht. Cyclooctatetraen (COT) bewirkte dabei eine Abnahme der Triplettausbeute von Al488, Al532 und Al647 um ~ 40-60%, bei Atto655 veränderte sie sich nicht. Obwohl die Ergebnisse der FCS-Messungen darauf hindeuten, dass COT in einer erhöhten Anzahl an emittierten Photonen resultiert, konnte dies bei dSTORM-Messungen nicht bestätigt werden. Hier hatte COT nur einen größeren positiven Effekt auf das Fluorophor Al647 (Zunahme um ~ 60%). Eine Erklärung für diese Widersprüchlichkeit zu den Ergebnissen aus den FCS-Messungen, könnte das Vorhandensein des Schaltpuffers bei dSTORM-Messungen sein. Dieser bewirkt den Übergang der Fluorophore in den Aus-Zustand bzw. entzieht dem Puffer Sauerstoff.
Bei der Zugabe von 5 mM Kaliumiodid (KI) nahm die Triplettamplitude bei FCS-Messungen nur bei Al488 ab (um ~ 80%). Eine geringe Steigerung (um ~ 10%) der Intensität von Al488 mit KI konnte bei dSTORM-Messungen mit niedrigen Konzentrationen (~ 0,5 mM) erzielt werden. Bei einer Konzentration von 5 mM sank die Intensität jedoch wieder um 40%.
Deuteriumoxid (D2O) soll, anders als die Triplettlöscher, eine Verbesserung der Photonenausbeute dadurch bewirken, dass strahlungslose Relaxationsprozesse minimiert werden. Mit dSTORM-Messungen konnte gezeigt werden, dass Atto655 und Al647 in D2O zwar pro An-Zustand mehr Photonen emittieren als in Schaltpuffer ohne D2O, da die Fluorophore hier jedoch schneller bleichen, letztendlich die gleiche Anzahl an Photonen detektiert werden.
Um die Anzahl an emittierten Photonen zu erhöhen, eignet sich also nur COT bei dSTORM-Messungen mit AL647 und KI in sehr geringen Konzentrationen bei Al488. D2O kann eingesetzt werden, wenn eine Probe schnell vermessen werden muss, wie zum Beispiel bei Lebendzellmessungen.
Nicht nur eine zu niedrige Photonenzahl, auch eine zu geringe Photoschaltrate kann Artefakte bei dSTORM-Messungen erzeugen. Dies wurde anhand von verschiedenen biologischen Strukturen, die mit unterschiedlichen Anregungsintensitäten aufgenommen wurden, deutlich gemacht. Besonders die Aufnahmen von Plasmamembranen sind anfällig für die Generierung von Artefakten. Sie weisen viele inhomogene und lokal dichte Regionen auf. Wenn nun mehr als ein Emitter pro µm² gleichzeitig an ist, erzeugt das Auswertungsprogramm große artifizielle Cluster. Die hier durchgeführten Messungen machen deutlich, wie wichtig es ist, dSTORM-Bilder immer auf mögliche Artefakte hin zu untersuchen, besonders wenn Moleküle quantifiziert werden sollen. Dafür müssen die unbearbeiteten Rohdaten sorgfältig gesichtet werden und notfalls die Messungen mit einer höheren Laserleistung wiederholt werden. Da dSTORM mittlerweile immer mehr zur Quantifizierung eingesetzt wird und Clusteranalysen durchgeführt werden, wäre es sinnvoll bei Veröffentlichungen die Rohdaten von entscheidenden Aufnahmen der Öffentlichkeit zur Verfügung zu stellen.
Die Färbemethode ist ein weiterer Punkt, durch den Artefakte bei der Abbildung von Molekülen mittels SMLM entstehen können. Häufig werden Antikörper zum Markieren verwendet. Dabei sollte darauf geachtet werden, dass möglichst kleine Antikörper oder Antikörperfragmente verwendet werden, besonders wenn Clusteranalysen durchgeführt werden sollen. Anderenfalls leidet die Auflösung darunter, bzw. erhöht sich die Gefahr der Kreuzvernetzung von Molekülen.
Im zweiten Teil der vorliegenden Arbeit, wurden Plasmamembran-Ceramide untersucht. Ceramide gehören zu den Sphingolipiden und regulieren diverse zelluläre Prozesse. Verschiedene Stimuli bewirken eine Aktivierung von Sphingomyelinasen (SMasen), die Ceramide in der Plasmamembran synthetisieren. Steigt die Konzentration von Ceramiden in der Plasmamembran an, kondensieren diese zu Ceramid-reichen Plattformen (CRPs). Bisher ist noch wenig über die Verteilung der Ceramide und die Größe der CRPs bekannt. Sie wurden hier über IgG-Antikörper in der Plasmamembran von Jurkat-, U2OS-, HBME- und primären T-Zellen angefärbt und erstmals mit dSTORM hochaufgelöst, um sie dann zu quantifizieren. Unabhängig von der Zelllinie befanden sich 50% aller Ceramidmoleküle in ~ 75 nm großen CRPs. Im Mittel bestanden die CRPs aus ~ 20 Ceramiden. Mit Hilfe einer Titrationsreihe konnte ausgeschlossen werden, dass diese Cluster nur durch die Antikörper-Färbung artifiziell erzeugt wurden. Bei Inkubation der Zellen mit Bacillus cereus Sphingomyelinase (bSMase) stieg die Gesamtkonzentration der Ceramide in der Plasmamembran an, ebenso wie die Ceramidanzahl innerhalb der CRPs, außerdem die Anzahl und Größe der CRPs. Dies könnte zu einer Veränderung der Löslichkeit von Membrankomponenten führen, was wiederum eine Akkumulation bestimmter Rezeptoren oder eine Kompartimentierung bestimmter Proteine erleichtern könnte. Die Anhäufung der Ceramide in den CRPs könnte ebenfalls die lokale Interaktion mit anderen Membranmolekülen erleichtern und dadurch möglicherweise die Reaktivität von Rezeptoren verändern.
Mittels Azid-modifizierten Ceramidanaloga und kupferfreier Click-Chemie wurden Plasmamembran-Ceramide auch in lebenden Jurkat-Zellen mit Hilfe konfokaler Laser-Raster-Mikroskopie (CLSM, engl. confocal laser scanning microscopy) und Strukturierter Beleuchtungsmikroskopie (SIM, engl. structured illumination microscopy) untersucht. Dabei konnte gezeigt werden, dass die Fettsäure-Kettenlänge und die Position des Azids bei den Ceramidanaloga eine entscheidende Rolle spielt, wie hoch das detektierte Signal in der Plasmamembran letztendlich ist. Die Versuche machen auch deutlich, dass die klickbaren Ceramidanaloga lebendzellkompatibel sind, sodass sie eine hervorragende Möglichkeit darstellen, zelluläre Reaktionen zu verfolgen.
Es wurden hier nicht nur Ceramide in eukaryotischen Zellen analysiert, sondern auch in Bakterien. Neisseria meningitidis (N. meningitidis) sind gramnegative Bakterien, die im Menschen eine Sepsis oder eine Meningitis auslösen können. Es wurde mittels immunhistochemischen Färbungen mit dem anti-Ceramid IgG-Antikörper, aber auch mit den klickbaren Ceramidanaloga, ein Signal in der Membran erhalten, was mit dSTORM hochaufgelöst wurde. In anderen Bakterien wurden ebenfalls schon Sphingolipide nachgewiesen. Studien zu Ceramiden in N. meningitidis wurden bisher jedoch noch nicht veröffentlicht. Im Rahmen dieser Arbeit konnten erstmals Ergebnisse erhalten werden, die darauf hinweisen, dass N. meningitidis ebenfalls Ceramide besitzen könnten.
In einem dritten Projekt wurde die Interaktion zwischen NK-Zellen und Aspergillus fumigatus untersucht. Der Schimmelpilz kann eine Invasive Aspergillose in immunsupprimierten Menschen auslösen, was zum Tod führen kann. Verschiedene Studien konnten schon zeigen, dass NK-Zellen eine wichtige Rolle bei der Bekämpfung des Pilzes spielen. Der genaue Mechanismus ist jedoch noch unbekannt. Im Rahmen dieser Arbeit konnte nachgewiesen werden, dass der NK-Zell-Marker CD56 entscheidend für die Pilzerkennung ist. Mit immunhistochemischen Färbungen und LSM-, aber auch dSTORM-Messungen, konnte gezeigt werden, dass die normalerweise homogen verteilten CD56-Rezeptoren auf der Plasmamembran von NK-Zellen aktiv an die Interaktionsstelle zu A. fumigatus transportiert werden. Mit der Zeit akkumulieren hier immer mehr CD56-Proteine, während das Signal in der restlichen Membran immer weiter abnimmt. Es konnte erstmals CD56 als wichtiger Erkennungsrezeptor für A. fumigatus identifiziert werden.
In dem letzten bearbeiteten Projekt, wurde die Bindung von Anti-N-Methyl-D-Aspartat (NMDA)-Rezeptor Enzephalitis Autoantikörper an Neuronen untersucht. Bei einer Anti-NMDA-Rezeptor Enzephalitis bilden die Patienten Autoantikörper gegen die NR1-Untereinheit ihrer eigenen postsynaptischen NMDA-Rezeptoren. Da die Krankheit oft sehr spät erkannt wird und die Behandlungsmöglichkeiten noch sehr eingeschränkt sind, führt sie noch oft zum Tod. Sie wurde erst vor wenigen Jahren beschrieben, sodass der genaue Mechanismus noch unbekannt ist. Im Rahmen dieser Arbeit, konnten erste Färbungen mit aufgereinigten Antikörper aus Anti-NMDA-Rezeptor Enzephalitis Patienten an NMDA-Rezeptor-transfizierte HEK-Zellen und hippocampalen Maus-Neuronen durchgeführt und mit dSTORM hochaufgelöst werden. Mit den Messungen der HEK-Zellen konnte bestätigt werden, dass die Autoantikörper an die NR1-Untereinheit der Rezeptoren binden. Es konnten erstmals auch die Bindung der Antikörper an Neuronen hochaufgelöst werden. Dabei wurde sichtbar, dass die Antikörper zum einen dicht gepackt in den Synapsen vorliegen, aber auch dünner verteilt in den extrasynaptischen Regionen. Basierend auf der Ripley’s H-Funktion konnten in den Synapsen große Cluster von ~ 90 nm Durchmesser und im Mittel ~ 500 Lokalisationen und extrasynaptisch kleinere Cluster mit einem durchschnittlichen Durchmesser von ~ 70 nm und ~ 100 Lokalisationen ausgemacht werden. Diese ersten Ergebnisse legen den Grundstein für weitere Messungen, mit denen der Mechanismus der Krankheit untersucht werden kann.
Honigbienen (Apis mellifera carnica) regulieren die Temperatur ihrer Brut in einem sehr engen Temperaturfenster, da vor allem die gedeckelte Brut sehr temperaturempfindlich reagiert (Groh et al. 2004). Die Thermoregulation ist nicht – wie lange angenommen – Beiprodukt von alltäglichen Arbeiten der Bienen im Brutbereich, sondern eine aktive und Energie- und Zeitaufwändige eigene Tätigkeit. Arbeiterinnen ziehen sich mit ihren Beinen an die Brutoberfläche, drücken ihren warmen Thorax auf die Brutdeckel und verharren so für einige Minuten um mit der eigenen Körperwärme die Brut zu temperieren (Bujok et al. 2002). Wie erwartet korrelierte die Thoraxtemperatur einer Arbeiterin mit der Frequenz der abdominalen Atembewegungen, bei sehr hohen Thoraxtemperaturen (über 40°C) erreichten die Bienen Atemfrequenzen von über 8Hz. Eine weitere Methode die Brut effektiv zu wärmen übten Bienen aus, die leere Zellen im gedeckelten Brutbereich besuchen (Kleinhenz et al. 2003). Arbeiterinnen gingen dabei bevorzugt in Zellen, die von möglichst vielen gedeckelten Zellen umgeben waren. Sowohl die Dauer der Zellbesuche, als auch die mittlere Thoraxtemperatur bei Ein- und Austritt der Zelle korrelierten mit der Anzahl der benachbarten Brutzellen – je mehr Brutzellen eine leere Zelle in ihrer direkten Nachbarschaft hatte umso länger dauerte der Besuch einer Biene und umso höher ist die Ein- bzw. Austrittstemperatur der Biene. Mindestes 48 Stunden alte Bienen unterschieden sich signifikant in ihrem Wärmeverhalten von jüngeren Bienen. Tote gedeckelte Brut wurde in manchen Fällen über viele Tage (durchgehend bis 10 Tage) gewärmt, sie unterschied sich in ihrer Temperatur nicht von unbehandelter gedeckelter Brut. In weiteren Versuchen lag die Bruttemperatur von toter Brut zwar unter der eines Kontrollbereiches, die Temperatur lag aber weiterhin im optimalen Bereich von 33,5 bis 35°C (Groh et al. 2004). In diesen Versuchen wurde die tote Brut vor dem Einsetzen in den Beobachtungsstock wieder auf 35°C erwärmt. Wachskegel in gedeckelten Zellen wurden erkannt und ausgeräumt. Aktive Signale, die von der Brut ausgehen scheinen also nicht notwendig für die effektive Bruttemperaturregulierung zu sein. Untersuchungen mittels Laser-Doppler-Vibrometrie zeigten auch keine Hinweise auf eine mechanische Kommunikation zwischen den Puppen und den Arbeiterinnen. Das Brutwärmen scheint eine Aktion zu sein, die von den Bienen nur in Gemeinschaft sinnvoll durchgeführt werden kann. In einigen Fällen kam es während der Puppenphase zu unerklärlichen Abfällen in der Bruttemperatur, die nur durch einen positiven Rückkopplungseffekt seitens der Arbeiterinnen erklärt werden kann. Beim Brutwärmen spielen die Antennen der Arbeiterinnen wahrscheinlich eine wichtige Rolle. Während sich die Bienen beim aktiven Brutwärmen den Brutdeckel annähern sind die Antennenspitzen immer auf die Brutdeckel gerichtet. Fehlen den Arbeiterinnen die Antennen, dann ist die Thermoregulation eingeschränkt oder unzureichend. Die Bruttemperatur korreliert mit der Anzahl der abgetrennten Antennensegmente, je mehr Antennensegmente fehlen, desto weniger gut wird die Temperatur im Brutbereich hoch und konstant gehalten. Zusätzlich scheint es eine Lateralität in der Antennenfunktion zu geben, wurde die rechte Antenne gekürzt wärmten die Bienen die Brut signifikant schlechter, als beim Kürzen der linken Antenne. Durch das Kürzen der Antennen änderte sich auch das Verhalten der Tiere: Kontrollbienen verharrten ruhig im Brutbereich, während Bienen mit gekürzten Antennen teilweise ähnlich warm waren, aber nicht mehr das oben beschriebene aktive Brutwärmeverhalten zeigten.
Background: Because most human stroke victims are elderly, studies of experimental stroke in the aged rather than the young rat model may be optimal for identifying clinically relevant cellular responses, as well for pinpointing beneficial interventions.
Methodology/Principal Findings: We employed the Affymetrix platform to analyze the whole-gene transcriptome following temporary ligation of the middle cerebral artery in aged and young rats. The correspondence, heat map, and dendrogram analyses independently suggest a differential, age-group-specific behaviour of major gene clusters after stroke. Overall, the pattern of gene expression strongly suggests that the response of the aged rat brain is qualitatively rather than quantitatively different from the young, i.e. the total number of regulated genes is comparable in the two age groups, but the aged rats had great difficulty in mounting a timely response to stroke. Our study indicates that four genes related to neuropathic syndrome, stress, anxiety disorders and depression (Acvr1c, Cort, Htr2b and Pnoc) may have impaired response to stroke in aged rats. New therapeutic options in aged rats may also include Calcrl, Cyp11b1, Prcp, Cebpa, Cfd, Gpnmb, Fcgr2b, Fcgr3a, Tnfrsf26, Adam 17 and Mmp14. An unexpected target is the enzyme 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 in aged rats, a key enzyme in the cholesterol synthesis pathway. Post-stroke axonal growth was compromised in both age groups.
Conclusion/Significance: We suggest that a multi-stage, multimodal treatment in aged animals may be more likely to produce positive results. Such a therapeutic approach should be focused on tissue restoration but should also address other aspects of patient post-stroke therapy such as neuropathic syndrome, stress, anxiety disorders, depression, neurotransmission and blood pressure.
Background
Cuticular hydrocarbons (CHC) have been documented to play crucial roles as species- and sex-specific cues in the chemical communication systems of a wide variety of insects. However, whether they are sufficient by themselves as the sole cue triggering sexual behavior as well as preference of con- over heterospecific mating partners is rarely assessed. We conducted behavioral assays in three representative species of parasitoid wasps (Hymenoptera: Pteromalidae) to determine their reliance on CHC as species-specific sexual signaling cues.
Results
We found a surprising degree of either unspecific or insufficient sexual signaling when CHC are singled out as recognition cues. Most strikingly, the cosmopolitan species Nasonia vitripennis, expected to experience enhanced selection pressure to discriminate against other co-occurring parasitoids, did not discriminate against CHC of a partially sympatric species from another genus, Trichomalopsis sarcophagae. Focusing on the latter species, in turn, it became apparent that CHC are even insufficient as the sole cue triggering conspecific sexual behavior, hinting at the requirement of additional, synergistic sexual cues particularly important in this species. Finally, in the phylogenetically and chemically most divergent species Muscidifurax uniraptor, we intriguingly found both CHC-based sexual signaling as well as species discrimination behavior intact although this species is naturally parthenogenetic with sexual reproduction only occurring under laboratory conditions.
Conclusions
Our findings implicate a discrepancy in the reliance on and specificity of CHC as sexual cues in our tested parasitioid wasps. CHC profiles were not sufficient for unambiguous discrimination and preference behavior, as demonstrated by clear cross-attraction between some of our tested wasp genera. Moreover, we could show that only in T. sarcophagae, additional behavioral cues need to be present for triggering natural mating behavior, hinting at an interesting shift in signaling hierarchy in this particular species. This demonstrates the importance of integrating multiple, potentially complementary signaling modalities in future studies for a better understanding of their individual contributions to natural sexual communication behavior.
1. Protection against desiccation and chemical communication are two fundamental functions of cuticular hydrocarbons (CHCs) in insects. In the parasitoid jewel wasp Nasonia vitripennis (Walker), characterised by a cosmopolitan distribution through largely different environments, CHCs function as universally recognised female sex pheromones. However, CHC uniformity as basis for sexual recognition may conflict with the desiccation protection function, expected to display considerable flexibility through adaptation to different environmental conditions.
2. We compared male and female CHC profiles of N. vitripennis across a wide latitudinal gradient in Europe and correlated their CHC variation with climatic factors associated with desiccation. Additionally, we tested male mate discrimination behaviour between populations to detect potential variations in female sexual attractiveness.
3. Results did not conform to the general expectation that longer, straight‐chain CHCs occur in higher proportions in warmer and drier climates. Instead, unexpected environmental correlations of intermediate chain‐length CHCs (C31) were found exclusively in females, potentially reflecting the different life histories of the sexes in N. vitripennis.
4. Furthermore, we found no indication of population‐specific male mate preference, confirming the stability of female sexual attractiveness, likely conveyed through their CHC profiles. C31 mono‐ and C33 di‐methyl‐branched alkanes were consistently and most strongly associated with sexual dimorphism, suggesting their potential role in encoding the female‐specific sexual signalling function.
5. Our study sheds light on how both adaptive flexibility and conserved sexual attractiveness can potentially be integrated and encoded in CHC profiles of N. vitripennis females across a wide distribution range in Europe.
Glioblastoma multiforme (GBM) represents the most aggressive form of malignant brain tumors and remains a therapeutically challenge. Intense research in the field has lead to the testing of oncolytic viruses to improve tumor control. Currently, a variety of different oncolytic viruses are being evaluated for their ability to be used in anti-cancer therapy and a few have entered clinical trials. Vaccinia virus, is one of the viruses being studied. GLV-1h68, an oncolytic vaccinia virus engineered by Genelux Corporation, was constructed by insertion of three gene cassettes, RUC-GFP fusion, β-galactosidase and β- glucuronidase into the genome of the LIVP strain. Since focal tumor radiotherapy is a mainstay for cancer treatment, including glioma therapy, it is of clinical relevance to assess how systemically administered oncolytic vaccinia virus could be combined with targeted ionizing radiation for therapeutic gain. In this work we show how focal ionizing radiation (IR) can be combined with multiple systemically delivered oncolytic vaccinia virus strains in murine models of human U-87 glioma. After initial experiments which confirmed that ionizing radiation does not damage viral DNA or alter viral tropism, animal studies were carried out to analyze the interaction of vaccinia virus and ionizing radiation in the in vivo setting. We found that irradiation of the tumor target, prior to systemic administration of oncolytic vaccinia virus GLV-1h68, increased viral replication within the U-87 xenografts as measured by viral reporter gene expression and viral titers. Importantly, while GLV-1h68 alone had minimal effect on U-87 tumor growth delay, IR enhanced GLV-1h68 replication, which translated to increased tumor growth delay and mouse survival in subcutaneous and orthotopic U-87 glioma murine models compared to monotherapy with IR or GLV-1h68. The ability of IR to enhance vaccinia replication was not restricted to the multi-mutated GLV-1h68, but was also seen with the less attenuated oncolytic vaccinia, LIVP 1.1.1. We have demonstrated that in animals treated with combination of ionizing radiation and LIVP 1.1.1 a strong pro-inflammatory tissue response was induced. When IR was given in a more clinically relevant fractionated scheme, we found oncolytic vaccinia virus replication also increased. This indicates that vaccinia virus could be incorporated into either larger hypo-fraction or more conventionally fractionated radiotherapy schemes. The ability of focal IR to mediate selective replication of systemically injected oncolytic vaccinia was demonstrated in a bilateral glioma model. In mice with bilateral U-87 tumors in both hindlimbs, systemically administered oncolytic vaccinia replicated preferentially in the focally irradiated tumor compared to the shielded non- irradiated tumor in the same mouse We demonstrated that tumor control could be further improved when fractionated focal ionizing radiation was combined with a vaccinia virus caring an anti-angiogenic payload targeting vascular endothelial growth factor (VEGF). Our studies showed that following ionizing radiation expression of VEGF is upregulated in U-87 glioma cells in culture. We further showed a concentration dependent increase in radioresistance of human endothelial cells in presence of VEGF. Interestingly, we found effects of vascular endothelial growth factor on endothelial cells were reversible by adding purified GLAF-1 to the cells. GLAF-1 is a single- chain antibody targeting human and murine VEGF and is expressed by oncolytic vaccinia virus GLV-109. In U-87 glioma xenograft murine models the combination of fractionated ionizing radiation with GLV-1h164, a vaccinia virus also targeting VEGF, resulted in the best volumetric tumor response and a drastic decrease in vascular endothelial growth factor. Histological analysis of embedded tumor sections 14 days after viral administration confirmed that blocking VEGF translated into a decrease in vessel number to 30% of vessel number found in control tumors in animals treated with GLV-164 and fractionated IR which was lower than for all other treatment groups. Our experiments with GLV-1h164 and fractionated radiotherapy have shown that in addition to ionizing radiation and viral induced tumor cell destruction we were able to effectively target the tumor vasculature. This was achieved by enhanced viral replication translating in increased levels of GLAF-2 disrupting tumor vessels as well as the radiosensitization of tumor vasculature to IR by blocking VEGF. Our preclinical results have important clinical implications of how focal radiotherapy can be combined with systemic oncolytic viral administration for highly aggressive, locally advanced tumors with the potential, by using a vaccinia virus targeting human vascular endothelial growth factor, to further increase tumor radiation sensitivity by engaging the vascular component in addition to cancer cells.
Several novel synaptic proteins have been identified by monoclonal antibodies (mAbs) of the Würzburg hybridoma library generated against homogenized Drosophila brains, e.g. cysteine string protein, synapse-associated protein of 47 kDa, and Bruchpilot. However, at present no routine technique exists to identify the antigens of mAbs of our library that label only a small number of cells in the brain. Yet these antibodies can be used to reproducibly label and thereby identify these cells by immunohistochemical staining. Here we describe the staining patterns in the Drosophila brain for ten mAbs of the Würzburg hybridoma library. Besides revealing the neuroanatomical structure and distribution of ten different sets of cells we compare the staining patterns with those of antibodies against known antigens and GFP expression patterns driven by selected Gal4 lines employing regulatory sequences of neuronal genes. We present examples where our antibodies apparently stain the same cells in different Gal4 lines suggesting that the corresponding regulatory sequences can be exploited by the split-Gal4 technique for transgene expression exclusively in these cells. The detection of Gal4 expression in cells labeled by mAbs may also help in the identification of the antigens recognized by the antibodies which then in addition to their value for neuroanatomy will represent important tools for the characterization of the antigens. Implications and future strategies for the identification of the antigens are discussed.
Background:
Chloroplast-encoded genes (matK and rbcL) have been formally proposed for use in DNA barcoding efforts targeting embryophytes. Extending such a protocol to chlorophytan green algae, though, is fraught with problems including non homology (matK) and heterogeneity that prevents the creation of a universal PCR toolkit (rbcL). Some have advocated the use of the nuclear-encoded, internal transcribed spacer two (ITS2) as an alternative to the traditional chloroplast markers. However, the ITS2 is broadly perceived to be insufficiently conserved or to be confounded by introgression or biparental inheritance patterns, precluding its broad use in phylogenetic reconstruction or as a DNA barcode. A growing body of evidence has shown that simultaneous analysis of nucleotide data with secondary structure information can overcome at least some of the limitations of ITS2. The goal of this investigation was to assess the feasibility of an automated, sequence-structure approach for analysis of IT2 data from a large sampling of phylum Chlorophyta.
Methodology/Principal Findings:
Sequences and secondary structures from 591 chlorophycean, 741 trebouxiophycean and 938 ulvophycean algae, all obtained from the ITS2 Database, were aligned using a sequence structure-specific scoring matrix. Phylogenetic relationships were reconstructed by Profile Neighbor-Joining coupled with a sequence structure-specific, general time reversible substitution model. Results from analyses of the ITS2 data were robust at multiple nodes and showed considerable congruence with results from published phylogenetic analyses.
Conclusions/Significance:
Our observations on the power of automated, sequence-structure analyses of ITS2 to reconstruct phylum-level phylogenies of the green algae validate this approach to assessing diversity for large sets of chlorophytan taxa. Moreover, our results indicate that objections to the use of ITS2 for DNA barcoding should be weighed against the utility of an automated, data analysis approach with demonstrated power to reconstruct evolutionary patterns for highly divergent lineages.
Chronic Obstructive Pulmonary Disease (COPD) exacerbations are a considerable reason for increased morbidity and mortality in patients. Infections with influenza virus (H1N1), respiratory syncytial virus (RSV) or nontypeable Haemophilus influenzae (NTHi) are important triggers of exacerbations. To date, no treatments are available which can stop the progression of COPD. Novel approaches are urgently needed. Pre-clinical models of the disease are crucial for the development of novel therapeutic options.
In order to establish pre-clinical models which mimic aspects of human COPD exacerbations, mice were exposed to cigarette smoke (CS) and additionally infected with H1N1, RSV and/or NTHi. Clinically relevant treatments such as the corticosteroids Fluticasone propionate and Dexamethasone, the phosphodiesterase-4 (PDE-4) inhibitor Roflumilast and the long-acting muscarinic receptor antagonist Tiotropium were tested in the established models. Furthermore, a novel treatment approach using antibodies (Abs) directed against IL-1α, IL-1β or IL-1R1 was examined in the established CS/H1N1 model. Levels of IFN-γ, IL-1β, IL-2, IL-6, KC, TNF-α, RANTES, IL-17, MCP-1, MIP 1α and MIP-1β were measured in lung homogenate. Numbers of total cells, neutrophils and macrophages were assessed in bronchoalveolar lavage (BAL) fluid. Hematoxylin- and eosin- (H&E-) stained lung slices were analyzed to detect pathological changes. Quantitative polymerase-chain-reaction (qPCR) was used to investigate gene expression of ICAM-1 and MUC5 A/C. The viral/bacterial load was investigated in lung homogenate or BAL fluid. In addition to the in vivo studies, the effects of the above mentioned treatments were investigated in vitro in H1N1, RSV or NTHi-infected (primary) human bronchial epithelial cells using submerged or air-liquid-interface (ALI) cell culture systems.
Four pre-clinical models (CS/H1N1, CS/RSV, CS/NTHi, CS/H1N1/NTHi) were established depicting clinically relevant aspects of COPD exacerbations such as increased inflammatory cells and cytokines in the airways and impaired lung function.
In the CS/H1N1 model, Tiotropium improved lung function and was superior in reducing inflammation in comparison to Fluticasone or Roflumilast. Moreover, Fluticasone increased the loss of body-weight, levels of IL-6, KC and TNF-α and worsened lung function. In CS/RSV-exposed mice Tiotropium but not Fluticasone or Roflumilast treatment reduced neutrophil numbers and IL-6 and TNF α levels in the lung. The viral load of H1N1 and RSV was significantly elevated in CS/virus-exposed mice and NCI-H292 cells after Fluticasone and Dexamethasone treatment. The results from these studies demonstrate that Tiotropium has anti-inflammatory effects on CS/virus-induced inflammation and might help to explain the observed reduction of exacerbation rates in Tiotropium-treated COPD patients. Furthermore, the findings from this work indicate that treatment with Fluticasone or Dexamethasone might not be beneficial to reduce inflammation in the airways of COPD patients and supports clinical studies that link treatment with corticosteroids to an increased risk for pneumonia.
Testing of anti-IL-1α, anti-IL-1β or anti-IL-1R1 Abs in the CS/H1N1 model suggests that, in line with clinical data, antagonization of IL-1β is not sufficient to reduce pulmonary inflammation and indicates a predominant role of IL-1α in CS/virus-induced airway inflammation. In line with the in vivo findings, anti-IL-1α but not anti-IL-1β Abs reduced levels of TNF-α and IL-6 in H1N1-infected primary human bronchial epithelial ALI cell culture. Blocking the IL-1R1 provided significant inhibitory effects on inflammatory cells in vivo but was inferior compared to inhibiting both its soluble ligands IL-1α and IL-1β. Concomitant usage of Abs against IL-1α/IL-1β revealed strong effects and reduced total cells, neutrophils and macrophages. Additionally, levels of KC, IL-6, TNF-α, MCP-1, MIP-1α and MIP-1β were significantly reduced and ICAM-1 mRNA expression was attenuated. These results suggest that combined inhibition of IL-1α/IL-1β might be beneficial to reduce inflammation and exacerbations in COPD patients. Moreover, combined targeting of both IL-1α/IL-1β might be more efficient compared to inhibition of the IL-1R1.
As in the CS/virus models, corticosteroid treatment failed to reduce inflammatory cells in the CS/NTHi and CS/H1N1/NTHi models, increased the loss of body-weight and the bacterial load. Furthermore, Roflumilast administration had no significant effects on cell counts or cytokines. However, it improved compliance in the CS/NTHi model. Treatment with Azithromycin reduced the bacterial load in the CS/NTHi model and reduced numbers of total cells, neutrophils, macrophages and levels of KC and TNF-α in the CS/H1N1/NTHi model.
In conclusion, the established CS/H1N1, CS/RSV, CS/NTHi, CS/H1N1/NTHi models depict clinically relevant aspects of human COPD exacerbations in mice and provide the opportunity to investigate underlying disease mechanisms and to test novel therapies.
In this thesis, synaptic transmission was studied electrophysiologically at an invertebrate model synapse, the neuromuscular junction of the Drosophila 3rd instar wandering larvae. In the first part, synaptic function is characterized at the neuromuscular junction in fly lines which are null mutants for the synaptic proteins “the synapse associated protein of 47 kDa” (Sap-47156), Synapsin (Syn97), the corresponding double mutant (Sap-47156, Syn97), a null mutant for an as yet uncharacterized Drosophila SR protein kinase, the Serine-Arginine protein kinase 3 (SRPK3), and the Löchrig (Loe) mutant which shows a strong neurodegenerative phenotype. Intracellular voltage recordings from larval body wall muscles 6 and 7 were performed to measure amplitude and frequency of spontaneous single vesicle fusion events (miniature excitatory junction potentials or mEJPs). Evoked excitatory junction potentials (eEJPs) at different frequencies and calcium concentrations were also measured to see if synaptic transmission was altered in mutants which lacked these synaptic proteins. In addition, structure and morphology of presynaptic boutons at the larval neuromuscular junction were examined immunohistochemically using monoclonal antibodies against different synaptic vesicle proteins (SAP-47, CSP, and Synapsin) as well as the active zone protein Bruchpilot. Synaptic physiology and morphology was found to be similar in all null mutant lines. However, Löchrig mutants displayed an elongated bouton morphology, a significant shift towards larger events in mEJP amplitude frequency histograms, and increased synaptic facilitation during a 10 Hz tetanus. These deficits suggest that Loe mutants may have a defect in some aspect of synaptic vesicle recycling. The second part of this thesis involved the electrophysiological characterization of heterologously expressed light activated proteins at the Drosophila neuromuscular junction. Channelrhodopsin-2 (ChR2), a light gated ion channel, and a photoactivated adenylate cyclase (PAC) were expressed in larval motor neurons using the UAS-Gal4 system. Single EJPs could be recorded from muscles 15, 16, and 17 when larva expressing ChR2 were illuminated with short (100 ms) light pulses, whereas long light pulses (10 seconds) resulted in trains of EJPs with a frequency of around 25 Hz. Larva expressing PAC in preparations where motor neurons were cut from the ventral ganglion displayed a significant increase in mEJP frequency after a 1 minute exposure to blue light. Evoked responses in low (.2 mM) calcium were also significantly increased when PAC was stimulated with blue light. When motor nerves were left intact, PAC stimulation resulted in light evoked EJPs in muscles 6 and 7 in a manner consistent with RP3 motor neuron activity. ChR2 and PAC are therefore useful and reliable tools for manipulating neuronal activity in vivo.
Biomechanik des Wachslaufens bei Crematogaster (Decacrema)-Partnerameisen von Macaranga-Bäumen
(2006)
Durch die vorliegende Arbeit konnte die große Bedeutung biomechanischer Faktoren für die Ökologie und Evolution von Insekten-Pflanzen-Interaktionen, am Beispiel des Ameisenpflanzen-Mutualismus’ Crematogaster (Decacrema)-Macaranga aufgezeigt werden. Viele Macaranga-Ameisenpflanzen besitzen Sproßachsen mit einem Überzug epikutikulärer Wachskristalle. Nur die Ameisenpartner wachsbereifter Pflanzen können sich problemlos auf den Oberflächen ihrer Wirtspflanzen fortbewegen. Durch die rutschigen, wachsbereiften Sproßachsen werden generalistische Ameisenarten ferngehalten und damit die wachslaufenden Ameisenpartner vor Fraßfeinden und Konkurrenz geschützt. Die Wachsbarrieren fördern zudem die Wirtsspezifität innerhalb dieser Ameisen-Pflanzen-Symbiose und funktionieren so als ökologischer Isolationsmechanismus. Die mechanische Barrierefunktion der Wachsbereifung birgt eine Vielzahl ökologischer Konsequenzen für beide Mutualismuspartner. Ziel dieser Arbeit war es, die proximaten Einzelmechanismen dieser ökologisch wichtigen Barriere aufzuklären, d. h. die Ursache der Rutschigkeit wachsbereifter Macaranga-Oberflächen und den Mechanismus der Wachslauffähigkeit der spezialangepaßten Crematogaster (Decacrema)-Ameisen. Im Rahmen dieser Arbeit konnten mehrere Mechanismen der Rutschigkeit wachsbereifter Macaranga-Sproßoberflächen für Insekten aufgezeigt werden. Durch die Fortbewegung von Insekten auf epikutikulären Wachskristallen werden Kristalle aus ihrem Verbund herausgebrochen und kontaminieren die Insektentarsen. Auf der Oberfläche der Haftorgane (Arolien) werden die Wachskristalle durch die Haftflüssigkeit partiell angelöst. Hierdurch entsteht ein amorpher Schmierfilm, der wahrscheinlich zu einer Verschlechterung der Haftleistung führt. In dieser Arbeit wurde gezeigt, daß unabhängig vom Abbrechen der Kristalle und der Kontamination der Tarsen auch die Mikrorauhigkeit der Macaranga-Oberflächen zu einer Rutschigkeit der Sproßachse führen kann. Sie besitzt einen entscheidenden Einfluß auf die Haft- und Lokomotionsfähigkeit von Insekten. Die Rauhigkeit von Oberflächen führt zu einer Reduzierung der effektiven Kontaktfläche des Aroliums und verringert dadurch die Haftkräfte von Insekten. Die genannten Mechanismen der Rutschigkeit schließen sich nicht gegenseitig aus, sondern können einen synergistischen, bzw. additiven Effekt haben. Bei der Untersuchung der Wachslauffähigkeit der spezialisierten Macaranga-Partnerameisen zeigte sich, daß der unterschiedliche Lauferfolg verschiedener Crematogaster (Decacrema)-Morphospezies nicht auf einer größeren Haftung beruht, sondern vor allem auf einer günstigeren Laufkinematik der Wachsläufer. Durch morphometrische Untersuchungen an acht Crematogaster (Decacrema)-Arten konnte im Rahmen dieser Arbeit gezeigt werden, daß Wachsläufer längere Beine haben als Nichtwachsläufer. Diese längeren Beine können zu einem mechanischen Vorteil beim Klettern auf senkrechten Oberflächen führen, da sie zum einen ein weiteres Herumgreifen um den Ast ermöglichen und zum anderen aufgrund des längeren Hebelarms die auf die Vorderbeine wirkenden Zugkräfte reduzieren. Amputationsexperimente zeigten eindeutig, daß die prätarsalen Krallen entscheidend für das Laufen auf wachsbereiften Macaranga-Oberflächen sind, die prätarsalen Haftorgane (Arolien) hingegen nicht. Es ist zu vermuten, daß die Krallen durch das Eintauchen der Krallenspitzen in die Wachskristallschicht Halt finden, wodurch sie theoretisch auf senkrechten Oberflächen jeden Durchmessers Halt finden können. Obwohl quantitative Unterschiede in der Krallenmorphologie (Höhe, Länge und Krümmungsdurchmesser) zwischen Crematogaster (Decacrema)-Wachsläufern und -Nichtwachsläufern nachgewiesen werden konnten, bleibt unklar, ob diese überhaupt eine Rolle für die unterschiedliche Wachslauffähigkeit spielen oder ob eher das Bewegungsmuster während des Einsatzes der Krallen entscheidend ist. Auch bei Crematogaster (Decacrema)-Wachsläufern kommt es zu einem Abbrechen von Wachskristallen und einer Kontamination der Tarsen. Crematogaster (Decacrema)-Wachsläufer zeigen im Vergleich zu -Nichtwachsläufern ein bisher nicht in der Literatur beschriebenes, Putzverhalten der Vorderbeine. Dieses Putzverhalten ist zeitsparend und effektiv in die Lokomotion der Tiere eingebunden und schließt selektiv nur die Reinigung der laufoberflächenkontaktierenden Tarsussegmente ein. Die hier beschriebenen Unterschiede in Morphologie, Kinematik und Verhalten zwischen Crematogaster (Decacrema)-Wachsläufern und -Nichtwachsläufern bringen funktionelle Vorteile der Wachsläufer auf den von ihnen besiedelten, wachsbereiften Macaranga-Pflanzenoberflächen mit sich. Die epikutikuläre Wachsbereifung kann als biomechanischer Schlüsselmechanismus angesehen werden, der im Rahmen der Evolution zu diesen vielschichtigen Veränderungen geführt hat. Die vorliegende Arbeit konnte zugrundeliegende biomechanische Faktoren, die auf beiden Seiten des Mutualismus’ eine Rolle spielen, aufklären.
Nowadays, more than half of the biotherapeutics are produced in mammalian cell lines as a result of correct protein folding and assembly as well as their faculty to bring about a variety of post-translational modifications. The widespread progression of biosimilars has moved the focus in mammalian cell-culture process development. Thereby, the modulation of quality attributes of recombinant therapeutic proteins has increasingly gained importance from early process development stages. Protein quality directly shapes the clinical efficacy and safety in vivo, and therefore, the control of the complex post-translational modifications, such as glycosylation (e.g. high mannose, fucosylation, galactosylation and sialylation), charge variants, aggregates and low-molecular-weight species formation, is pivotal for efficient receptor binding and for triggering the desired immune responses in patients. In the frame of biosimilar development, product quality modulation methods using the potential of the host cell line are particularly sought after to match the quality profile of the targeted reference medicinal product (RMP) as closely as possible. The environment the cell is dwelling in directly influences its metabolism and the resulting quality profile of the expressed protein. Thereby the cell culture medium plays a central role in upstream manufacturing. In this work, concentration adjustment of selected media components and supplementation with a variety of compounds was performed to alter various metabolic pathways, enzyme activities and in some cases the gene expression levels of Chinese Hamster Ovary (CHO) cells in culture. The supplementation of cell culture medium with the trisaccharide raffinose in fed-batch cultures entailed an increase of the abundance of high mannose glycans in two different CHO cell lines. Raffinose especially favored mannose 5 glycans. At the same time, it impaired cell culture performance, induced changes on the intracellular nucleotide levels and even varied the expression levels of glycosylation-related genes. Supplementation with a number of galactosyltransferase inhibiting compounds, in particular fluorinated galactose analogs (alpha- and beta-2F-peracetyl-galactose), consistently decreased the production of galactosylated monoclonal antibodies (mAb). By means of targeted addition during the culture rather than at the beginning, the inhibition was further increased, while limiting detrimental effects on both growth and productivity. High-throughput screening in 96-deepwell plates showed that spermine and L-ornithine also reduced the level of galactosylation. On the other hand, exploratory screening of a variety of potentially disulfide-bridge-reducing agents highlighted that the inherent low-molecular-species level of the proprietary platform cell culture process was likely due to favored reduction. This hypothesis was reinforced by the observation that supplementation of cysteine and N-acetylcysteine promoted fragmentation. Additionally, fragmentation decreased with higher protein expression.
At that point, aiming to improve the efficiency in process development, a rational experimental design method was developed to identify and to define the optimal concentration range of quality modulating compounds by calling on a combination of high throughput fed-batch testing and multivariate data analysis. Seventeen medium supplements were tested in five parallel 96-deepwell plate experiments. The selection process of promising modulators for the follow-up experiment in shake tubes consisted in a three-step procedure, including principal component analysis, quantitative evaluation of their performance with respect to the specifications for biosimilarity and selection following a hierarchical order of decisions using a decision tree. The method resulted in a substantial improvement of the targeted glycosylation profile in only two experimental rounds. Subsequent development stages, namely validation and transfer to industrial-scale facilities require tight control of product quality. Accordingly, further mechanistic understanding of the underlying processes was acquired by non-targeted metabolomic profiling of a CHO cell line expressing a mAb cultured in four distinct process formats. Univariate analysis of intra- and extracellular metabolite and temporal glycosylation profiles provided insights in various pathways. The numerous of parameters were the main driver to carry out principal component analysis, and then, using the methodology of partial-least-square (PLS) projection on latent structures, a multivariate model was built to correlate the extracellular data with the distinct glycosylation profiles. The PLS observation model proved to be reliable and showed its great benefit for glycan pattern control in routine manufacturing, especially at large scale. Rather than relying on post-production interpretation of glycosylation results, glycosylation can be predicted in real-time based on the extracellular metabolite levels in the bioreactor.
Finally, for the bioactivity assessment of the glycan differences between the biosimilar and the reference medicinal product (RMP), the health agencies may ask for in the drug registration process, extended ranges of glycan variants need to be generated so that the in vitro assays pick up the changes. The developed glycosylation modulator library enabled the generation of extreme glycosylation variants, including high mannose, afucosylated, galactosylated as well as sialic acid species of both a mAb and an antibody fusion molecule with three N-glycosylation sites. Moreover, to create increased variety, enzymatic glycoengineering was explored for galactosylation and sialylation. The glyco variants induced significant responses in the respective in vitro biological activity assays. The data of this work highlight the immense potential of cell culture medium optimization to adjust product quality. Medium and feed supplementation of a variety of compounds resulted in reproducible and important changes of the product quality profile of both mAbs and a fusion antibody. In addition to the intermediate modulation ranges that largely met the requirements for new-biological-entity and biosimilar development, medium supplementation even enabled quick and straightforward generation of extreme glycan variants suitable for biological activity testing.
Large parts of the tropical lowland rain forests of Sabah (Malaysia) were transformed into secondary forests due to heavy logging. Additionally the remaining forest remnants are isolated from each other by large scale oil palm plantations. Biodiversity patterns and responses of the community of leaf litter ants were studied in anthropogenically disturbed habitats and primary forests of different size. In logged over forests, only 70 per cent of the species of a primary forest were present even 25 years after timber extraction. The ant communities were thinned and could be described by a lower species density producing lower species numbers and a different community composition. The similarity in species number and community composition between logged over forests of different degrees of disturbance was explained by source-sink dynamics within a heterogeneous forest matrix. Rain forest fragments displayed even higher reductions in species density, numbers and diversity due to a more pronounced thinning effect. Even forest isolates exceeding 4 000 ha in size did not support more than 50 per cent of the species of the leaf litter ant community of a contiguous primary rain forest. Additionally, an increase in tramp species was recorded with decreasing size of the forest fragments, leading to a very different community composition. Regarding the leaf litter ant community, the remaining rain forest fragments of Sabah are effectively isolated by a barrier of oil palm plantation, now stretching all over the lowlands of the east coast. Only 13 species, which belonged to the forest ant community in highly disturbed areas were collected in these plantations. Some of the 10 other species of the highly reduced ground-dwelling ant community in the plantations are known as invasive tramp species, forming large exclusive territories. Correlative evidence and a field experiment implied, that leaf litter humidity, volume and temperature affect the distribution and community composition of forest leaf litter ant species. The smaller primary forests and the most disturbed logged over forests in this study revealed higher temperatures and lower humidity levels and a reduction in leaf litter volume compared to a large primary forest or forests affected by a lower impact of timber harvesting. If the pattern for leaf litter ants is confirmed for other taxa, the implications for any efficient management design aiming to preserve the majority of the biodiversity of the country are tremendous and current concepts need rethinking.
Die Entstehung maligner Zellen durch irreversible genetische Veränderungen ist ein allgegenwärtiger Prozess im menschlichen Organismus. Allein die spontane Mutationsrate genügt um in einem Organismus permanent transformierte Zellen entstehen zu lassen, welche den Körper in kürzester Zeit überschwemmen würden. Auch wenn bestimmte genetische Schäden frühzeitig durch Reparaturmechanismen beseitigt werden und sich nicht jede transformierte Zelle in einem Tumor manifestiert, so ist die eigentliche Frage nicht, warum Krebs entsteht, sondern warum er bei der hohen Mutationsrate so selten auftritt. Verantwortlich für die frühe Erkennung und Beseitigung transformierter Zellen ist das körpereigene Immunsystem, das in der Lage ist die meisten aberranten Zellen zu entfernen, sodass der manifeste Tumor die Ausnahme und nicht die Regel ist. Der menschliche Organismus verfügt über ein angeborenes und ein erworbenes Immunsystem. Bis heute ist nicht eindeutig geklärt, ob maligne Zellen mit ihren veränderten Oberflächenstrukturen erst eine Immunantwort induzieren müssen oder ob, wie bei der Abwehr infektiöser Partikel, die angeborene Immunität für die Beseitigung von Tumorzellen verantwortlich ist. Die in dieser Arbeit verwendete humane Hybridoma Technologie (Immortalisierung menschlicher Lymphozyten und Isolierung monoklonaler Antikörper) bietet die einzigartige Möglichkeit, sowohl aus an Krebs erkrankten Patienten als auch aus gesunden Probanden tumorspezifische Antikörper zu isolieren und durch deren genauere Charakterisierung Einblicke in die humorale Immunität gegen maligne Zellen zu erhalten. In der vorliegenden Arbeit werden fünf humane monoklonale Antikörper beschrieben, die aus verschiedenen Tumorpatienten gewonnen wurden, sowie zwei Antikörper, die aus gesunden Probanden isoliert werden konnten. In allen Fällen erwiesen sich die Antikörper als tumorspezifisch, d.h. sie reagieren nicht mit gesundem Gewebe und sind demnach keine Autoantikörper. Es handelt sich weiterhin in allen Fällen um Antikörper des IgM-Isotyps; es konnten keinen Antikörper anderer Ig-Klassen isoliert werden. Genetische Analysen ergaben, dass alle isolierten Antikörper gering oder gar nicht mutiert waren, was bedeutet, dass sie nicht durch Stimulation affinitätsgereift sind. Zudem konnte demonstriert werden, dass alle Antikörper Apoptose von Tumorzellen induzieren und dass sie an eine Zuckerkette ihrer Antigene binden oder solche Carbohydrate zumindest entscheidend in die Bindung involviert sind. Die Eigenschaften der in dieser Arbeit beschriebenen Antikörper wurden mit anderen bereits etablierten IgM-Antikörpern verglichen. Hierbei stellte sich heraus, dass alle Antikörper, welche sich als tumorspezifisch erwiesen, ähnliche Eigenschaften zeigen. Interessant ist zudem die Beobachtung, dass die Keuzreaktion der Antikörper, also ihre Reaktion mit anderen Tumorgeweben, reziprok mit dem Mutations-grad korreliert ist. Je mehr Mutationen ein Antikörper aufweist, desto eingeschränkter und spezifischer sind demnach seine Reaktionen mit anderen Tumoren. Dies deutet darauf hin, dass auch innerhalb der Keimbahn-kodierten Antikörper durch vereinzelte Mutationen eine höhere Variabilität erzeugt werden kann. Ähnlich wie bei der Affinitätsreifung der erworbenen Immunität scheint sich auch hier die Spezifität mit der Anzahl der Mutationen zu erhöhen. Zusammenfassend weisen die erhaltenen Ergebnisse darauf hin, dass zumindest die humorale Immunität gegen maligne Zellen das Resultat der angeborenen Immunität ist und nicht von Tumorzellen induziert wird. Dies bedeutet zudem, dass Moleküle wie natürliche Antikörper in der Immunität eine viel größere Rolle spielen als bisher angenommen. Ähnliche Ergebnisse wurden bereits bei der Untersuchung der Immunität gegen bakterielle Antigene erzielt, sodass hier vermutet werden kann, dass die gleichen Mechanismen zugrunde liegen wie bei der Abwehr transformierter Zellen. Darüber hinaus wird die Frage beantwortet, warum ein manifester Tumor eine Ausnahme bleibt. Die angeborene, primäre Immunität verfügt über ein existierendes Repertoire an Rezeptoren, welche eine ausreichende Variabilität aufweisen, und muss daher nicht erst über ein komplexes System von Erkennung und Stimulation, wie die adaptierte Immunität, induziert werden. Dieser logistische Vorsprung der natürlichen Immunität garantiert eine permanente Überwachung und eine schnelle Reaktion gegenüber veränderten Zellen und fremden Partikeln.
Abstract
Background
HLA-G is a non-classical MHC class I molecule which exerts strong immunosuppressive effects on various immune cells. Several membrane-bound and soluble isoforms are known. Physiologically, HLA-G is predominantly expressed in the placenta, where it contributes to protecting the semi-allogeneic embryo from rejection by the maternal immune system. However, HLA-G is also often upregulated during tumourigenesis, such as in ovarian cancer. The aim of this thesis is to investigate how soluble HLA-G may contribute to local immunosuppression in ovarian carcinomas, and to characterize HLA-G expression in different ovarian carcinoma subtypes and metastases.
Results
As reported by others, physiological HLA-G expression is restricted to few tissues, such as placenta and testes. Here, HLA-G was also detected in the medulla of the adrenal gland. In contrast, HLA-G expression was frequently detected in tumours of all assessed subtypes of ovarian carcinomas (serous, mucinous, endometrioid and clear cell). Highest expression levels were detected in high-grade serous carcinomas. In primary tumours, expression of HLA-G correlated with expression of classical MHC class I molecules HLA-A, -B and -C. Surprisingly, high levels of HLA-G were also detected on dendritic cells in local lymph nodes. As no expression of HLA-G was inducible in monocytes or dendritic cells from healthy donors in response to IL-10 or IL-4, we speculated that tumour-derived soluble HLA-G might be transferred to dendritic cells via the lymphatic system. Accordingly, high levels of tumour-derived soluble HLA-G were detected in ovarian cancer ascites samples. In vitro, dendritic cells expanded in the presence of IL-4, IL-10 and GM-CSF (DC-10) were particularly prone to binding high amounts of soluble HLA-G via ILT receptors. Furthermore, HLA-G loaded DC-10 cells inhibited the proliferation of CD8 effector cells and induced regulatory T cells, even when the DC-10 cells had been fixed with paraformaldehyde.
Conclusion
The immunosuppressive molecule HLA-G is overexpressed in high-grade serous ovarian carcinomas, which account for the majority of ovarian cancers. In particular tumours with a high mutational burden and intact expression of classical, immunogenic MHC class Ia molecules may use HLA-G to escape from immunosurveillance. Additionally, tumour-derived soluble HLA-G may inhibit adaptive immune responses by binding to dendritic cells in local lymph nodes. Dendritic cells usually play a decisive role in the initiation of adaptive anti-tumour immune responses by presenting tumour antigens to cytotoxic T cells. In contrast, dendritic cells loaded with soluble HLA-G inhibit the proliferation of effector T cells and promote the induction of regulatory T cells. Thus, soluble HLA-G that is transferred to dendritic cells via lymphatic vessels may enable ovarian carcinomas to remotely suppress anti-tumour immune responses in local lymph nodes. This novel immune-escape mechanism may also exist in other solid tumours that express HLA-G.
HyphaTracker: An ImageJ toolbox for time-resolved analysis of spore germination in filamentous fungi
(2018)
The dynamics of early fungal development and its interference with physiological signals and environmental factors is yet poorly understood. Especially computational analysis tools for the evaluation of the process of early spore germination and germ tube formation are still lacking. For the time-resolved analysis of conidia germination of the filamentous ascomycete Fusarium fujikuroi we developed a straightforward toolbox implemented in ImageJ. It allows for processing of microscopic acquisitions (movies) of conidial germination starting with drift correction and data reduction prior to germling analysis. From the image time series germling related region of interests (ROIs) are extracted, which are analysed for their area, circularity, and timing. ROIs originating from germlings crossing other hyphae or the image boundaries are omitted during analysis. Each conidium/hypha is identified and related to its origin, thus allowing subsequent categorization. The efficiency of HyphaTracker was proofed and the accuracy was tested on simulated germlings at different signal-to-noise ratios. Bright-field microscopic images of conidial germination of rhodopsin-deficient F. fujikuroi mutants and their respective control strains were analysed with HyphaTracker. Consistent with our observation in earlier studies the CarO deficient mutant germinated earlier and grew faster than other, CarO expressing strains.
Whole Genome Duplications Shaped the Receptor Tyrosine Kinase Repertoire of Jawed Vertebrates
(2016)
The receptor tyrosine kinase (RTK) gene family, involved primarily in cell growth and differentiation, comprises proteins with a common enzymatic tyrosine kinase intracellular domain adjacent to a transmembrane region. The amino-terminal portion of RTKs is extracellular and made of different domains, the combination of which characterizes each of the 20 RTK subfamilies among mammals. We analyzed a total of 7,376 RTK sequences among 143 vertebrate species to provide here the first comprehensive census of the jawed vertebrate repertoire. We ascertained the 58 genes previously described in the human and mouse genomes and established their phylogenetic relationships. We also identified five additional RTKs amounting to a total of 63 genes in jawed vertebrates. We found that the vertebrate RTK gene family has been shaped by the two successive rounds of whole genome duplications (WGD) called 1R and 2R (1R/2R) that occurred at the base of the vertebrates. In addition, the Vegfr and Ephrin receptor subfamilies were expanded by single gene duplications. In teleost fish, 23 additional RTK genes have been retained after another expansion through the fish-specific third round (3R) of WGD. Several lineage-specific gene losses were observed. For instance, birds have lost three RTKs, and different genes are missing in several fish sublineages. The RTK gene family presents an unusual high gene retention rate from the vertebrate WGDs (58.75% after 1R/2R, 64.4% after 3R), resulting in an expansion that might be correlated with the evolution of complexity of vertebrate cellular communication and intracellular signaling.
Millionen Menschen weltweit leiden an den verschiedensten Autoimmunerkrankungen. Diese Krankheiten entstehen, wenn das Immunsystem gesundes körpereigenes Gewebe angreift und zerstört. An der Pathogenese sind sowohl Komponenten des angeborenen Immunsystems als auch Bestandteile des adaptiven Immunsystems, wie Lymphozyten und Antikörper, beteiligt. Da die Ursachen und molekularen Mechanismen der Pathogenese dieser Erkrankungen bis heute weitgehend unbekannt sind, wurden in dieser Arbeit autoaggressive Lymphozyten bei den humanen Autoimmunerkrankungen Polymyositis und Multiple Sklerose näher untersucht. Die Polymyositis ist eine chronisch entzündliche Erkrankung der Skelettmuskulatur. Die Muskelfasern werden dabei von zytotoxischen CD8+ gd-T-Lymphozyten infiltriert, attackiert und schließlich zerstört. In einem seltenen Fall der Polymyositis wurden die Muskelzellen hingegen in ähnlicher Weise von CD8- gd-T-Lymphozyten angegriffen. Die gd-T-Lymphozyten waren monoklonal expandiert und ihr Rezeptor, im Folgenden als M88 bezeichnet, wurde als Vg1.3+Vd2+ identifiziert. Frühere Untersuchungen der Antigenspezifität dieser Zellen zeigten, dass M88 mehrere funktionell und strukturell verschiedene Proteine aus unterschiedlichen Spezies erkennt. Die Bindung erfolgt spezifisch durch die Antigenerkennungsregionen beider Rezeptorketten von M88. In dieser Arbeit wurden verschiedene bakterielle und humane Proteine des Translationsapparates als Antigene von M88 identifiziert. Weitere ausführliche Untersuchungen eines paradigmatischen bakteriellen Antigens, dem Translationsinitiationsfaktor EcIF1, zeigten, dass M88 an Oberflächen-exponierte Konformationsepitope von Proteinen bindet. Interessanterweise erkennt M88 mehrere humane Aminoacyl-tRNA-Synthetasen, Antigene, die in anderen Formen der Myositis von Autoantikörpern angegriffen werden. Diese Beobachtung ergibt eine bemerkenswerte Verbindung zwischen T-Zell- und Antikörper-vermittelten B-Zell-Antworten bei der autoimmunen Myositis. Bei der Multiplen Sklerose ist das zentrale Nervensystem betroffen. Autoaggressive Lymphozyten greifen die Myelinschicht der Nervenzellen im Gehirn und Rückenmark an und zerstören sie. Im Liquor cerebrospinalis von Patienten lassen sich klonal expandierte und affinitätsgereifte B-Zellen sowie „oligoklonale Banden“ (OKB) Antikörper nachweisen. Obwohl diese Merkmale auf eine Antigen-induzierte Immunantwort hindeuten, sind die zugrundeliegenden Antigene und die Rolle der OKB bei der Pathogenese bis heute unbekannt. In dieser Arbeit wurde die Antigenspezifität von fünf IgG OKB-Antikörpern aus drei Patienten untersucht. Durch verschiedene proteinbiochemische Methoden konnten intrazelluläre Kandidatenantigene identifiziert werden. Interessanterweise sind darunter mehrere nukleäre Proteine, die an der Transkriptionsregulation oder der RNA-Prozessierung beteiligt sind. Reaktivitäten gegen intrazelluläre Antigene treten auch bei anderen Autoimmunerkrankungen, wie beispielsweise dem systemischen Lupus erythematodes, auf. Diese Ergebnisse könnten auf einen allgemeinen Mechanismus der Entstehung und Funktion von Autoantikörpern bei diesen humanen Autoimmunerkrankungen hindeuten.
Background: In most trypanosomes, endo and exocytosis only occur at a unique organelle called the flagellar pocket (FP) and the flagellum exits the cell via the FP. Investigations of essential cytoskeleton-associated structures located at this site have revealed a number of essential proteins. The protein TbBILBO1 is located at the neck of the FP in a structure called the flagellar pocket collar (FPC) and is essential for biogenesis of the FPC and parasite survival. TbMORN1 is a protein that is present on a closely linked structure called the hook complex (HC) and is located anterior to and overlapping the collar. TbMORN1 is essential in the bloodstream form of T. brucei. We now describe the location and function of BHALIN, an essential, new FPC-HC protein. Methodology/Principal Findings: Here, we show that a newly characterised protein, BHALIN (BILBO1 Hook Associated LINker protein), is localised to both the FPC and HC and has a TbBILBO1 binding domain, which was confirmed in vitro. Knockdown of BHALIN by RNAi in the bloodstream form parasites led to cell death, indicating an essential role in cell viability. Conclusions/Significance: Our results demonstrate the essential role of a newly characterised hook complex protein, BHALIN, that influences flagellar pocket organisation and function in bloodstream form T. brucei parasites.
(1) Background: The recurrence of glioblastoma multiforme (GBM) is mainly due to invasion of the surrounding brain tissue, where organic solutes, including glucose and inositol, are abundant. Invasive cell migration has been linked to the aberrant expression of transmembrane solute-linked carriers (SLC). Here, we explore the role of glucose (SLC5A1) and inositol transporters (SLC5A3) in GBM cell migration. (2) Methods: Using immunofluorescence microscopy, we visualized the subcellular localization of SLC5A1 and SLC5A3 in two highly motile human GBM cell lines. We also employed wound-healing assays to examine the effect of SLC inhibition on GBM cell migration and examined the chemotactic potential of inositol. (3) Results: While GBM cell migration was significantly increased by extracellular inositol and glucose, it was strongly impaired by SLC transporter inhibition. In the GBM cell monolayers, both SLCs were exclusively detected in the migrating cells at the monolayer edge. In single GBM cells, both transporters were primarily localized at the leading edge of the lamellipodium. Interestingly, in GBM cells migrating via blebbing, SLC5A1 and SLC5A3 were predominantly detected in nascent and mature blebs, respectively. (4) Conclusion: We provide several lines of evidence for the involvement of SLC5A1 and SLC5A3 in GBM cell migration, thereby complementing the migration-associated transportome. Our findings suggest that SLC inhibition is a promising approach to GBM treatment.
Im Neuroblastom ist die Amplifikation des MYCN-Gens, das für den Transkriptionsfaktor N-Myc kodiert, der klinisch bedeutendste Faktor für eine schlechte Prognose. Als Mitglied der onkogenen Myc-Familie induziert N-Myc die Expression von Genen, die in vielen biologischen Prozessen wie Metabolismus, Zellzyklusprogression, Zellwachstum und Apoptose eine wichtige Rolle spielen. Die Deregulation der MYCN-Expression führt zu einem charakteristischen Genexpressionsprofil und einem aggressiven Phenotyp in den Tumorzellen.
In normalen neuronalen Vorläuferzellen wird N-Myc gewöhnlich sehr schnell proteasomal abgebaut. Während der Mitose wird N-Myc an Serin 62 phosphoryliert. Diese Phosphorylierung dient als Erkennungssignal für die Kinase GSK3β, die die Phosphorylierung an Threonin 58 katalysiert. Das Phosphodegron wird von Fbxw7, einer Komponente des E3-Ubiquitinligase-Komplex SCFFbxw7, erkannt. Die anschließende Ubiquitinierung induziert den proteasomalen Abbau des Proteins. Die Reduktion der N-Myc–Proteinlevel ermöglicht den neuronalen Vorläuferzellen den Austritt aus dem Zellzyklus und führt zu einer terminalen Differenzierung.
In einem shRNA Screen konnte AURKA als essentielles Gen für die Proliferation MYCN-amplifizierter Neuroblastomzellen identifiziert werden. Eine Aurora-A–Depletion hatte jedoch keinen Einfluss auf das Wachstum nicht-amplifizierter Zellen.
Während dieser Doktorarbeit konnte gezeigt werden, dass Aurora-A speziell den Fbxw7-vermittelten Abbau verhindert und dadurch N-Myc stabilisiert. Für die Stabilisierung ist zwar die Interaktion der beiden Proteine von entscheidender Bedeutung, überraschenderweise spielt die Kinaseaktivität von Aurora-A jedoch keine Rolle.
Zwei spezifische Aurora-A–Inhibitoren, MLN8054 und MLN8237, sind allerdings in der Lage, nicht nur die Kinaseaktivität zu hemmen, sondern auch die N-Myc-Proteinlevel zu reduzieren. Beide Moleküle induzieren eine Konformationsänderung in der Kinasedomäne von Aurora-A. Diese ungewöhnliche strukturelle Veränderung hat zur Folge, dass der N-Myc/Aurora-A–Komplex dissoziiert und N-Myc mit Hilfe von Fbxw7 proteasomal abgebaut werden kann. In MYCN-amplifizierten Zellen führt diese Reduktion an N-Myc zu einem Zellzyklusarrest in der G1-Phase. Die in vitro Daten konnten in einem transgenen Maus-Modell für das MYCN-amplifizierte Neuroblastom bestätigt werden. Die Behandlung mit MLN8054 und MLN8237 führte in den Tumoren ebenfalls zu einer N-Myc-Reduktion. Darüber hinaus konnte ein prozentualer Anstieg an differenzierten Zellen, die vollständige Tumorregression in der Mehrzahl der Neuroblastome und eine gesteigerte Lebenserwartung beobachtet werden.
Insgesamt zeigen die in vitro und in vivo Daten, dass die spezifischen Aurora-A–Inhibitoren ein hohes therapeutisches Potential gegen das MYCN-amplifizierte Neuroblastom besitzen.
Background: High mobility group A (HMGA) proteins regulate gene transcription through architectural modulation of chromatin and the formation of multi-protein complexes on promoter/enhancer regions. Differential expression of HMGA variants has been found to be important for distinct differentiation processes and deregulated expression was linked to several disorders. Here we used mouse C2C12 myoblasts and C2C12 cells stably over-expressing HMGA1a-eGFP to study the impact of deregulated HMGA1 expression levels on cellular differentiation. Results: We found that induction of the myogenic or osteogenic program of C2C12 cells caused an immediate down-regulation of HMGA1. In contrast to wild type C2C12 cells, an engineered cell line with stable overexpression of HMGA1a-eGFP failed to differentiate into myotubes. Immunolocalization studies demonstrated that sustained HMGA1a-eGFP expression prevented myotube formation and chromatin reorganization that normally accompanies differentiation. Western Blot analyses showed that elevated HMGA1a-eGFP levels affected chromatin composition through either down-regulation of histone H1 or premature expression of MeCP2. RT-PCR analyses further revealed that sustained HMGA1a expression also affected myogenic gene expression and caused either down-regulation of genes such as MyoD, myogenin, Igf1, Igf2, Igfbp1-3 or up-regulation of the transcriptional repressor Msx1. Interestingly, siRNA experiments demonstrated that knock-down of HMGA1a was required and sufficient to reactivate the myogenic program in induced HMGA1a over-expressing cells. Conclusions: Our data demonstrate that HMGA1 down-regulation after induction is required to initiate the myogenic program in C2C12 cells. Sustained HMGA1a expression after induction prevents expression of key myogenic factors. This may be due to specific gene regulation and/or global effects on chromatin. Our data further corroborate that altered HMGA1 levels influence the expression of other chromatin proteins. Thus, HMGA1 is able to establish a specific chromatin composition. This work contributes to the understanding of how differential HMGA1 expression is involved in chromatin organization during cellular differentiation processes and it may help to comprehend effects of HMGA1 over-expression occurring in malign or benign tumours.
HMG-Proteine sind nach den Histonen die zweithäufigste Superfamilie nukleärer Proteine. Sie binden an DNA und Nukleosomen und induzieren strukturelle Veränderungen im Chromatin. Sie spielen eine wichtige Rolle in der Dynamik des Chromatins und beeinflussen dadurch DNA-abhängige Prozesse, wie Transkription und Replikation. Proteine der HMGA-Familie sind charakterisiert durch konservierte DNA-Bindungsmotive, den AT-Hooks, welche eine Bindung an AT-reiche DNA-Sequenzen vermitteln und durch einen sauren C-Terminus. HMGA-Proteine sind verstärkt im Heterochromatin konzentriert und stehen in Verbindung mit der Expressionsregulation spezifischer Gene aufgrund der Stabilisierung von Nukleoproteinkomplexen, so genannten Enhanceosomen. HMGA-Proteine spielen des Weiteren eine entscheidende Rolle in verschiedenen Entwicklungsprozessen und bei der Tumorprogression . Um den Einfluss von HMGA1 auf die zelluläre Differenzierung und die Chromatinmodulation zu untersuchen, wurden C2C12 Maus-Myoblastenzellen verwendet. Die Induktion der Myogenese in diesen Zellen geht mit der Herunterregulierung von HMGA1 einher. Durch die Etablierung einer C2C12-Zelllinie, welche ein EGFP-markiertes HMGA1a stabil exprimierte, konnte gezeigt werden, dass eine anhaltende HMGA1-Expression spezifisch die Myogeneseprozess inhibierte, während die Osteogenese davon unbeeinflusst zu bleiben schien. Dieser hemmende Effekt kann durch die HMGA1-abhängige Fehlexpression verschiedener Gene, welche für eine einwandfreie Muskeldifferenzierung nötig sind und in die Zellzyklusregulation eingreifen, erklärt werden. Unter der Verwendung von RNAi konnte gezeigt werden, dass die Herunterregulierung von HMGA1-Proteinen für eine korrekte Genexpression und den Muskeldifferenzierungsprozess notwendig ist. Während der terminalen Differenzierung wird die Umorganisation des Chromatins durch die Fusion der Chromozentren offensichtlich. Fotobleichtechniken, wie „fluorescence recovery after photobleaching“ (FRAP) zeigten, dass HMGA1-Proteine mit dem Methyl-CpG-bindenden Protein 2 (MeCP2), welches eine wichtige Rolle in der Chromozentrenfusion spielt, um DNA-Bindungsstellen konkurriert und dieses vom Chromatin verdrängt. Diese dynamische Konkurrenz zwischen einem anhaltend exprimierten HMGA1 und MeCP2 trägt somit zur Inhibition der differenzierungsabhängigen Modulation des Chromatins während der späten Myogenese bei. Die Untersuchungen in C2A1a-Zellen lieferten weitere Hinweise dafür, dass der wesentlichste Umbau des Chromatins in einem Zeitfenster um den dritten Tag nach Induktion der Myogenese stattfindet, an welchem HMGA1 natürlicherweise nahezu vollständig herunterreguliert sind. In diesem Zeitraum kommt es zur Dissoziation der Chromozentren, zu veränderten Expressionsmustern in bestimmten Genen, zu Modulationen in Histonmodifikationen (H3K4me2, H3K4me3, H3K27me3), zur Replikations-unabhängigen Akkumulation von Histon H3 in den Chromozentren über ungefähr einen Zellzyklus hinweg und zu eine signifikanten Erhöhung der HP1-Dynamik. Durch den Einsatz von Bimolekularer Fluoreszenzkomplementierung (BiFC), die es erlaubt Protein-Protein-Interaktionen in vivo zu visualisieren, konnte gezeigt werden, dass der saure C-Terminus des HMGA mit der Chromodomäne (CD) des HP1 interagiert. Zusätzlich ist für diese Interaktion die korrekte DNA-Bindung des HMGA nötig. FRAP-Messungen mit HP1-EGFP-Fusionsproteinen in Zellen die wildtypisches oder ein mutiertes HMGA koexprimierten, bestätigten diese Daten und wiesen darauf hin, dass die HP1-Verweildauer im Heterochromatin maßgeblich von der Gegenwart eines funktionellen HMGA1 abhängig ist. Des Weiteren zeigten C2C12-Myoblasten, die HMGA1 natürlicherweise exprimieren, eine hohe HP1-Verweildauer, die nach HMGA1-knock down drastisch verringert ist. Umgekehrt ist die HP1-Verweildauer nach einer Herunterregulierung von HMGA1 an Tag 3 der Myogenese gering und steigt durch die Koexpression von HMGA1 auf das in Myoblasten gemessene Niveau an. Zusammengenommen zeigen diese Daten, dass die differenzielle Expression von HMGA1 und ihre Fähigkeit mit HP1 zu interagieren, sowie ihre Konkurrenz mit MeCP2 um DNA-Bindungsstellen einen entscheidende Rolle in der Regulation der Aufrechterhaltung und Plastizität des Heterochromatins während der Differenzierung spielen. Daher ist eine zeitlich festgelegte Herunterregulierung von HMGA1 notwendig, um die Modulation des Chromatins und dadurch den Differenzierungsprozess zu ermöglichen
At the end of the first larval stage, the nematode Caenorhabditis elegans developing in harsh environmental conditions is able to choose an alternative developmental path called the dauer diapause. Dauer larvae exhibit different physiology and behaviors from non-dauer larvae. Using focused ion beam-scanning electron microscopy (FIB-SEM), we volumetrically reconstructed the anterior sensory apparatus of C. elegans dauer larvae with unprecedented precision. We provide a detailed description of some neurons, focusing on structural details that were unknown or unresolved by previously published studies. They include the following: (1) dauer-specific branches of the IL2 sensory neurons project into the periphery of anterior sensilla and motor or putative sensory neurons at the sub-lateral cords; (2) ciliated endings of URX sensory neurons are supported by both ILso and AMso socket cells near the amphid openings; (3) variability in amphid sensory dendrites among dauers; and (4) somatic RIP interneurons maintain their projection into the pharyngeal nervous system. Our results support the notion that dauer larvae structurally expand their sensory system to facilitate searching for more favorable environments.
To rapidly process biologically relevant stimuli, sensory systems have developed a broad variety of coding mechanisms like parallel processing and coincidence detection. Parallel processing (e.g., in the visual system), increases both computational capacity and processing speed by simultaneously coding different aspects of the same stimulus. Coincidence detection is an efficient way to integrate information from different sources. Coincidence has been shown to promote associative learning and memory or stimulus feature detection (e.g., in auditory delay lines). Within the dual olfactory pathway of the honeybee both of these mechanisms might be implemented by uniglomerular projection neurons (PNs) that transfer information from the primary olfactory centers, the antennal lobe (AL), to a multimodal integration center, the mushroom body (MB). PNs from anatomically distinct tracts respond to the same stimulus space, but have different physiological properties, characteristics that are prerequisites for parallel processing of different stimulus aspects. However, the PN pathways also display mirror-imaged like anatomical trajectories that resemble neuronal coincidence detectors as known from auditory delay lines. To investigate temporal processing of olfactory information, we recorded PN odor responses simultaneously from both tracts and measured coincident activity of PNs within and between tracts. Our results show that coincidence levels are different within each of the two tracts. Coincidence also occurs between tracts, but to a minor extent compared to coincidence within tracts. Taken together our findings support the relevance of spike timing in coding of olfactory information (temporal code).
Highlights
• The GLA variant S126G is not associated with Fabry symptoms in the presented case
• S126G has no effect on α-GAL A activity or Gb3 levels in this patient
• S126G sensory neurons show no electrophysiological abnormalities
Abstract
Fabry disease (FD) is a life-limiting disorder characterized by intracellular globotriaosylceramide (Gb3) accumulations. The underlying α-galactosidase A (α-GAL A) deficiency is caused by variants in the gene GLA. Variants of unknown significance (VUS) are frequently found in GLA and challenge clinical management. Here, we investigated a 49-year old man with cryptogenic lacunar cerebral stroke and the chance finding of the VUS S126G, who was sent to our center for diagnosis and initiation of a costly and life-long FD-specific treatment. We combined clinical examination with in vitro investigations of dermal fibroblasts (HDF), induced pluripotent stem cells (iPSC), and iPSC-derived sensory neurons. We analyzed α-GAL A activity in iPSC, Gb3 accumulation in all three cell types, and action potential firing in sensory neurons. Neurological examination and small nerve fiber assessment was normal except for reduced distal skin innervation. S126G iPSC showed normal α-GAL A activity compared to controls and no Gb3 deposits were found in all three cell types. Baseline electrophysiological characteristics of S126G neurons showed no difference compared to healthy controls as investigated by patch-clamp recordings. We pioneer multi-level cellular characterization of the VUS S126G using three cell types derived from a patient and provide further evidence for the benign nature of S126G in GLA, which is of great importance in the management of such cases in clinical practice.
Climate and land-use changes cause increasing stress to pollinators but the molecular pathways underlying stress responses are poorly understood. Here, we analyzed the transcriptomic response of Bombus lucorum workers to temperature and livestock grazing. Bumblebees sampled along an elevational gradient, and from differently managed grassland sites (livestock grazing vs unmanaged) in the German Alps did not differ in the expression of genes known for thermal stress responses. Instead, metabolic energy production pathways were upregulated in bumblebees sampled in mid- or high elevations or during cool temperatures. Extensive grazing pressure led to an upregulation of genetic pathways involved in immunoregulation and DNA-repair. We conclude that widespread bumblebees are tolerant toward temperature fluctuations in temperate mountain environments. Moderate temperature increases may even release bumblebees from metabolic stress. However, transcriptome responses to even moderate management regimes highlight the completely underestimated complexity of human influence on natural pollinators.
We steered the soil microbiome via applications of organic residues (mix of cover crop residues, sewage sludge + compost, and digestate + compost) to enhance multiple ecosystem services in line with climate-smart agriculture. Our result highlights the potential to reduce greenhouse gases (GHG) emissions from agricultural soils by the application of specific organic amendments (especially digestate + compost). Unexpectedly, also the addition of mineral fertilizer in our mesocosms led to similar combined GHG emissions than one of the specific organic amendments. However, the application of organic amendments has the potential to increase soil C, which is not the case when using mineral fertilizer. While GHG emissions from cover crop residues were significantly higher compared to mineral fertilizer and the other organic amendments, crop growth was promoted. Furthermore, all organic amendments induced a shift in the diversity and abundances of key microbial groups. We show that organic amendments have the potential to not only lower GHG emissions by modifying the microbial community abundance and composition, but also favour crop growth-promoting microorganisms. This modulation of the microbial community by organic amendments bears the potential to turn soils into more climate-smart soils in comparison to the more conventional use of mineral fertilizers.
Recently, we have shown that C6-ceramides efficiently suppress viral replication by trapping the virus in lysosomes. Here, we use antiviral assays to evaluate a synthetic ceramide derivative α-NH2-ω-N3-C6-ceramide (AKS461) and to confirm the biological activity of C6-ceramides inhibiting SARS-CoV-2. Click-labeling with a fluorophore demonstrated that AKS461 accumulates in lysosomes. Previously, it has been shown that suppression of SARS-CoV-2 replication can be cell-type specific. Thus, AKS461 inhibited SARS-CoV-2 replication in Huh-7, Vero, and Calu-3 cells up to 2.5 orders of magnitude. The results were confirmed by CoronaFISH, indicating that AKS461 acts comparable to the unmodified C6-ceramide. Thus, AKS461 serves as a tool to study ceramide-associated cellular and viral pathways, such as SARS-CoV-2 infections, and it helped to identify lysosomes as the central organelle of C6-ceramides to inhibit viral replication.
Most natural learning situations are of a complex nature and consist of a tight conjunction of the animal's behavior (B) with the perceived stimuli. According to the behavior of the animal in response to these stimuli, they are classified as being either biologically neutral (conditioned stimuli, CS) or important (unconditioned stimuli, US or reinforcer). A typical learning situation is thus identified by a three term contingency of B, CS and US. A functional characterization of the single associations during conditioning in such a three term contingency has so far hardly been possible. Therefore, the operational distinction between classical conditioning as a behavior-independent learning process (CS-US associations) and operant conditioning as essentially behavior-dependent learning (B-US associations) has proven very valuable. However, most learning experiments described so far have not been successful in fully separating operant from classical conditioning into single-association tasks. The Drosophila flight simulator in which the relevant behavior is a single motor variable (yaw torque), allows for the first time to completely separate the operant (B-US, B-CS) and the classical (CS-US) components of a complex learning situation and to examine their interactions. In this thesis the contributions of the single associations (CS-US, B-US and B-CS) to memory formation are studied. Moreover, for the first time a particularly prominent single association (CS-US) is characterized extensively in a three term contingency. A yoked control shows that classical (CS-US) pattern learning requires more training than operant pattern learning. Additionally, it can be demonstrated that an operantly trained stimulus can be successfully transferred from the behavior used during training to a new behavior in a subsequent test phase. This result shows unambiguously that during operant conditioning classical (CS-US) associations can be formed. In an extension to this insight, it emerges that such a classical association blocks the formation of an operant association, which would have been formed without the operant control of the learned stimuli. Instead the operant component seems to develop less markedly and is probably merged into a complex three-way association. This three-way association could either be implemented as a sequential B-CS-US or as a hierarchical (B-CS)-US association. The comparison of a simple classical (CS-US) with a composite operant (B, CS and US) learning situation and of a simple operant (B-US) with another composite operant (B, CS and US) learning situation, suggests a hierarchy of predictors of reinforcement. Operant behavior occurring during composite operant conditioning is hardly conditioned at all. The associability of classical stimuli that bear no relation to the behavior of the animal is of an intermediate value, as is operant behavior alone. Stimuli that are controlled by operant behavior accrue associative strength most easily. If several stimuli are available as potential predictors, again the question arises which CS-US associations are formed? A number of different studies in vertebrates yielded amazingly congruent results. These results inspired to examine and compare the properties of the CS-US association in a complex learning situation at the flight simulator with these vertebrate results. It is shown for the first time that Drosophila can learn compound stimuli and recall the individual components independently and in similar proportions. The attempt to obtain second-order conditioning with these stimuli, yielded a relatively small effect. In comparison with vertebrate data, blocking and sensory preconditioning experiments produced conforming as well as dissenting results. While no blocking could be found, a sound sensory preconditioning effect was obtained. Possible reasons for the failure to find blocking are discussed and further experiments are suggested. The sensory preconditioning effect found in this study is revealed using simultaneous stimulus presentation and depends on the amount of preconditioning. It is argued that this effect is a case of 'incidental learning', where two stimuli are associated without the need of reinforcement. Finally, the implications of the results obtained in this study for the general understanding of memory formation in complex learning situations are discussed.
Mathematical optimization framework allows the identification of certain nodes within a signaling network. In this work, we analyzed the complex extracellular-signal-regulated kinase 1 and 2 (ERK1/2) cascade in cardiomyocytes using the framework to find efficient adjustment screws for this cascade that is important for cardiomyocyte survival and maladaptive heart muscle growth. We modeled optimal pharmacological intervention points that are beneficial for the heart, but avoid the occurrence of a maladaptive ERK1/2 modification, the autophosphorylation of ERK at threonine 188 (ERK\(^{Thr188}\) phosphorylation), which causes cardiac hypertrophy. For this purpose, a network of a cardiomyocyte that was fitted to experimental data was equipped with external stimuli that model the pharmacological intervention points. Specifically, two situations were considered. In the first one, the cardiomyocyte was driven to a desired expression level with different treatment strategies. These strategies were quantified with respect to beneficial effects and maleficent side effects and then which one is the best treatment strategy was evaluated. In the second situation, it was shown how to model constitutively activated pathways and how to identify drug targets to obtain a desired activity level that is associated with a healthy state and in contrast to the maleficent expression pattern caused by the constitutively activated pathway. An implementation of the algorithms used for the calculations is also presented in this paper, which simplifies the application of the presented framework for drug targeting, optimal drug combinations and the systematic and automatic search for pharmacological intervention points. The codes were designed such that they can be combined with any mathematical model given by ordinary differential equations.
Circadian endogenous clocks of eukaryotic organisms are an established and rapidly developing research field. To investigate and simulate in an effective model the effect of external stimuli on such clocks and their components we developed a software framework for download and simulation. The application is useful to understand the different involved effects in a mathematical simple and effective model. This concerns the effects of Zeitgebers, feedback loops and further modifying components. We start from a known mathematical oscillator model, which is based on experimental molecular findings. This is extended with an effective framework that includes the impact of external stimuli on the circadian oscillations including high dose pharmacological treatment. In particular, the external stimuli framework defines a systematic procedure by input-output-interfaces to couple different oscillators. The framework is validated by providing phase response curves and ranges of entrainment. Furthermore, Aschoffs rule is computationally investigated. It is shown how the external stimuli framework can be used to study biological effects like points of singularity or oscillators integrating different signals at once. The mathematical framework and formalism is generic and allows to study in general the effect of external stimuli on oscillators and other biological processes. For an easy replication of each numerical experiment presented in this work and an easy implementation of the framework the corresponding Mathematica files are fully made available. They can be downloaded at the following link: https://www.biozentrum.uni-wuerzburg.de/bioinfo/computing/circadian/.
In this work models for molecular networks consisting of ordinary differential equations are extended by terms that include the interaction of the corresponding molecular network with the environment that the molecular network is embedded in. These terms model the effects of the external stimuli on the molecular network. The usability of this extension is demonstrated with a model of a circadian clock that is extended with certain terms and reproduces data from several experiments at the same time.
Once the model including external stimuli is set up, a framework is developed in order to calculate external stimuli that have a predefined desired effect on the molecular network. For this purpose the task of finding appropriate external stimuli is formulated as a mathematical optimal control problem for which in order to solve it a lot of mathematical methods are available. Several methods are discussed and worked out in order to calculate a solution for the corresponding optimal control problem. The application of the framework to find pharmacological intervention points or effective drug combinations is pointed out and discussed. Furthermore the framework is related to existing network analysis tools and their combination for network analysis in order to find dedicated external stimuli is discussed.
The total framework is verified with biological examples by comparing the calculated results with data from literature. For this purpose platelet aggregation is investigated based on a corresponding gene regulatory network and associated receptors are detected. Furthermore a transition from one to another type of T-helper cell is analyzed in a tumor setting where missing agents are calculated to induce the corresponding switch in vitro. Next a gene regulatory network of a myocardiocyte is investigated where it is shown how the presented framework can be used to compare different treatment strategies with respect to their beneficial effects and side effects quantitatively. Moreover a constitutively activated signaling pathway, which thus causes maleficent effects, is modeled and intervention points with corresponding treatment strategies are determined that steer the gene regulatory network from a pathological expression pattern to physiological one again.
The unique stem cell system of the immortal larva of the human parasite Echinococcus multilocularis
(2014)
Background
It is believed that in tapeworms a separate population of undifferentiated cells, the germinative cells, is the only source of cell proliferation throughout the life cycle (similar to the neoblasts of free living flatworms). In Echinococcus multilocularis, the metacestode larval stage has a unique development, growing continuously like a mass of vesicles that infiltrate the tissues of the intermediate host, generating multiple protoscoleces by asexual budding. This unique proliferation potential indicates the existence of stem cells that are totipotent and have the ability for extensive self-renewal.
Results
We show that only the germinative cells proliferate in the larval vesicles and in primary cell cultures that undergo complete vesicle regeneration, by using a combination of morphological criteria and by developing molecular markers of differentiated cell types. The germinative cells are homogeneous in morphology but heterogeneous at the molecular level, since only sub-populations express homologs of the post-transcriptional regulators nanos and argonaute. Important differences are observed between the expression patterns of selected neoblast marker genes of other flatworms and the E. multilocularis germinative cells, including widespread expression in E. multilocularis of some genes that are neoblast-specific in planarians. Hydroxyurea treatment results in the depletion of germinative cells in larval vesicles, and after recovery following hydroxyurea treatment, surviving proliferating cells grow as patches that suggest extensive self-renewal potential for individual germinative cells.
Conclusions
In E. multilocularis metacestodes, the germinative cells are the only proliferating cells, presumably driving the continuous growth of the larval vesicles. However, the existence of sub-populations of the germinative cells is strongly supported by our data. Although the germinative cells are very similar to the neoblasts of other flatworms in function and in undifferentiated morphology, their unique gene expression pattern and the evolutionary loss of conserved stem cells regulators suggest that important differences in their physiology exist, which could be related to the unique biology of E. multilocularis larvae.
Background
The metacestode larva of Echinococcus multilocularis (Cestoda: Taeniidae) develops in the liver of intermediate hosts (typically rodents, or accidentally in humans) as a labyrinth of interconnected cysts that infiltrate the host tissue, causing the disease alveolar echinococcosis. Within the cysts, protoscoleces (the infective stage for the definitive canid host) arise by asexual multiplication. These consist of a scolex similar to that of the adult, invaginated within a small posterior body. Despite the importance of alveolar echinococcosis for human health, relatively little is known about the basic biology, anatomy and development of E. multilocularis larvae, particularly with regard to their nervous system.
Results
We describe the existence of a subtegumental nerve net in the metacestode cysts, which is immunoreactive for acetylated tubulin-α and contains small populations of nerve cells that are labeled by antibodies raised against several invertebrate neuropeptides. However, no evidence was found for the existence of cholinergic or serotoninergic elements in the cyst wall. Muscle fibers occur without any specific arrangement in the subtegumental layer, and accumulate during the invaginations of the cyst wall that form brood capsules, where protoscoleces develop. The nervous system of the protoscolex develops independently of that of the metacestode cyst, with an antero-posterior developmental gradient. The combination of antibodies against several nervous system markers resulted in a detailed description of the protoscolex nervous system, which is remarkably complex and already similar to that of the adult worm.
Conclusions
We provide evidence for the first time of the existence of a nervous system in the metacestode cyst wall, which is remarkable given the lack of motility of this larval stage, and the lack of serotoninergic and cholinergic elements. We propose that it could function as a neuroendocrine system, derived from the nervous system present in the bladder tissue of other taeniids. The detailed description of the development and anatomy of the protoscolex neuromuscular system is a necessary first step toward the understanding of the developmental mechanisms operating in these peculiar larval stages.
Background
The metacestode of the tapeworm Echinococcus multilocularis is the causative agent of alveolar echinococcosis, a lethal zoonosis. Infections are initiated through establishment of parasite larvae within the intermediate host’s liver, where high concentrations of insulin are present, followed by tumour-like growth of the metacestode in host organs. The molecular mechanisms determining the organ tropism of E. multilocularis or the influences of host hormones on parasite proliferation are poorly understood.
Results
Using in vitro cultivation systems for parasite larvae we show that physiological concentrations (10 nM) of human insulin significantly stimulate the formation of metacestode larvae from parasite stem cells and promote asexual growth of the metacestode. Addition of human insulin to parasite larvae led to increased glucose uptake and enhanced phosphorylation of Echinococcus insulin signalling components, including an insulin receptor-like kinase, EmIR1, for which we demonstrate predominant expression in the parasite’s glycogen storage cells. We also characterized a second insulin receptor family member, EmIR2, and demonstrated interaction of its ligand binding domain with human insulin in the yeast two-hybrid system. Addition of an insulin receptor inhibitor resulted in metacestode killing, prevented metacestode development from parasite stem cells, and impaired the activation of insulin signalling pathways through host insulin.
Conclusions
Our data indicate that host insulin acts as a stimulant for parasite development within the host liver and that E. multilocularis senses the host hormone through an evolutionarily conserved insulin signalling pathway. Hormonal host-parasite cross-communication, facilitated by the relatively close phylogenetic relationship between E. multilocularis and its mammalian hosts, thus appears to be important in the pathology of alveolar echinococcosis. This contributes to a closer understanding of organ tropism and parasite persistence in larval cestode infections. Furthermore, our data show that Echinococcus insulin signalling pathways are promising targets for the development of novel drugs.
A gene (Imsod) encoding superoxide dismutase (SOD; EC 1.15.1.1) of the facultative intracellular pathogen, Listeria monocytogenes, was cloned by functional complementation of an SOD-deficient Escherichia coli mutant. The nucleotide sequence was determined and the deduced amino acid (aa) sequence (202 aa) showed close similarity to manganese-containing SOD's from other organisms. Subunits of the recombinant L. monocytogenes SOD (re-SOD) and of both E. coli SODs formed enzymatically active hybrid enzymes in vivo. DNA/DNA-hybridization experiments showed that this type of recombinant re-sod gene is conserved within the genus Listeria.
Die Popeye domain containing (Popdc)-Gene bilden eine evolutionär stark konservierte Genfamilie mit präferenzieller Expression im Herzen und in der Skelettmuskulatur. In dieser Arbeit konnte gezeigt werden, dass Popdc1 in kardialen Myozyten in Glanzstreifen, lateralen Membranen und im T-Tubuli-System exprimiert wird und mit Ionenkanälen und anderen myozytären Membranproteinen wie Cav1.2, Caveolin 3 und NCX1 kolokalisiert ist. Im ventrikulären Reizleitungssystem ist die Expression von Popdc1 gegenüber dem ventrikulären Arbeitsmyokard erhöht, während Atrium und Sinusknoten nahezu äquivalente Expressionsdomänen aufweisen. Mithilfe von elektrophysiologischen Untersuchungen konnte bei den Popdc1-Nullmutanten eine stressinduzierte Sinusbradykardie festgestellt werden, die altersabhängig auftritt und auf Sinuspausen zurückzuführen ist. Histologische Untersuchungen, unter Zuhilfenahme des Sinusknotenmarkers HCN4, zeigten einen Zellverlust im inferioren Teil des Sinusknotens. Popdc1 ist ein Transmembranprotein, das eine 150 Aminosäure umfassende, stark konservierte Popeye-Domäne aufweist. Für diese Domäne konnte auf struktureller Ebene eine Homologie zu zyklischen Nukleotid-Bindungsdomänen vorhergesagt und eine Bindung an cAMP und cGMP experimentell demonstriert werden. Es handelt sich bei den Popdc-Proteinen um einen neuen Zweig der Bindungsproteine für zyklische Nukleotidmonophosphate (cNMP). Die Bindungssequenz weist signifikante Unterschiede zu anderen bereits identifizierten cNMP-Bindungsproteinen auf. Weiterhin wurde die Interaktion von Popdc1 mit TREK1, einem Mitglied der Tandemporenkanäle untersucht. Es zeigte sich, dass Popdc1 nach Koexpression in Froschoozyten, den TREK1-Strom erhöht und dass die β-adrenerge Inhibition des TREK1 Kanals durch Popdc1 verstärkt wird. Im Arbeitsmyokard, im kardialen Reizleitungssystem und in kotransfizierten Cos7-Zellen werden beide Proteine überlappend exprimiert. Diese Daten zeigen, dass Popdc1 eine wichtige Funktion bei der Regulation der Schrittmacheraktivität, der Aufrechterhaltung der Sinusknotenmorphologie und der Modulation von Ionenkanälen aufweist. Interessanterweise wurden von unserer Arbeitsgruppe bereits die gleichen Phänotypen für die Popdc2 Maus beschrieben, sodass die Popdc Genfamilie überlappende und redundante Funktionen aufweist.
Agricultural Policies Exacerbate Honeybee Pollination Service Supply-Demand Mismatches Across Europe
(2014)
Declines in insect pollinators across Europe have raised concerns about the supply of pollination services to agriculture. Simultaneously, EU agricultural and biofuel policies have encouraged substantial growth in the cultivated area of insect pollinated crops across the continent. Using data from 41 European countries, this study demonstrates that the recommended number of honeybees required to provide crop pollination across Europe has risen 4.9 times as fast as honeybee stocks between 2005 and 2010. Consequently, honeybee stocks were insufficient to supply >90% of demands in 22 countries studied. These findings raise concerns about the capacity of many countries to cope with major losses of wild pollinators and highlight numerous critical gaps in current understanding of pollination service supplies and demands, pointing to a pressing need for further research into this issue.
Background: Successful cooperation depends on reliable identification of friends and foes. Social insects discriminate colony members (nestmates/friends) from foreign workers (non-nestmates/foes) by colony-specific, multi-component colony odors. Traditionally, complex processing in the brain has been regarded as crucial for colony recognition. Odor information is represented as spatial patterns of activity and processed in the primary olfactory neuropile, the antennal lobe (AL) of insects, which is analogous to the vertebrate olfactory bulb. Correlative evidence indicates that the spatial activity patterns reflect odor-quality, i.e., how an odor is perceived. For colony odors, alternatively, a sensory filter in the peripheral nervous system was suggested, causing specific anosmia to nestmate colony odors. Here, we investigate neuronal correlates of colony odors in the brain of a social insect to directly test whether they are anosmic to nestmate colony odors and whether spatial activity patterns in the AL can predict how odor qualities like ‘‘friend’’ and ‘‘foe’’ are attributed to colony odors. Methodology/Principal Findings: Using ant dummies that mimic natural conditions, we presented colony odors and investigated their neuronal representation in the ant Camponotus floridanus. Nestmate and non-nestmate colony odors elicited neuronal activity: In the periphery, we recorded sensory responses of olfactory receptor neurons (electroantennography), and in the brain, we measured colony odor specific spatial activity patterns in the AL (calcium imaging). Surprisingly, upon repeated stimulation with the same colony odor, spatial activity patterns were variable, and as variable as activity patterns elicited by different colony odors. Conclusions: Ants are not anosmic to nestmate colony odors. However, spatial activity patterns in the AL alone do not provide sufficient information for colony odor discrimination and this finding challenges the current notion of how odor quality is coded. Our result illustrates the enormous challenge for the nervous system to classify multi-component odors and indicates that other neuronal parameters, e.g., precise timing of neuronal activity, are likely necessary for attribution of odor quality to multi-component odors.
Cooperation is beneficial for social groups and is exemplified in its most sophisticated form in social insects. In particular, eusocial Hymenoptera, like ants and honey bees, exhibit a level of cooperation only rarely matched by other animals. To assure effective defense of group members, foes need to be recognized reliably. Ants use low-volatile, colony-specific profiles of cuticular hydrocarbons (colony odor) to discriminate colony members (nestmates) from foreign workers (non-nestmates). For colony recognition, it is assumed that multi-component colony odors are compared to a neuronal template, located in a so far unidentified part of the nervous system, where a mismatch results in aggression. Alternatively, a sensory filter in the periphery of the nervous system has been suggested to act as a template, causing specific anosmia to nestmate colony odor due to sensory adaptation and effectively blocking perception of nestmates. Colony odors are not stable, but change over time due to environmental influences. To adjust for this, the recognition system has to be constantly updated (template reformation). In this thesis, I provide evidence that template reformation can be induced artificially, by modifying the sensory experience of carpenter ants (Camponotus floridanus; Chapter 1). The results of the experiments showed that template reformation is a relatively slow process taking several hours and this contradicts the adaptation-based sensory filter hypothesis. This finding is supported by first in-vivo measurements describing the neuronal processes underlying template reformation (Chapter 5). Neurophysiological measurements were impeded at the beginning of this study by the lack of adequate technical means to present colony odors. In a behavioral assay, I showed that tactile interaction is not necessary for colony recognition, although colony odors are of very low volatility (Chapter 2). I developed a novel stimulation technique (dummy-delivered stimulation) and tested its suitability for neurophysiological experiments (Chapter 3). My experiments showed that dummy-delivered stimulation is especially advantageous for presentation of low-volatile odors. Colony odor concentration in headspace was further increased by moderately heating the dummies, and this allowed me to measure neuronal correlates of colony odors in the peripheral and the central nervous system using electroantennography and calcium imaging, respectively (Chapter 4). Nestmate and non-nestmate colony odor elicited strong neuronal responses in olfactory receptor neurons of the antenna and in the functional units of the first olfactory neuropile of the ant brain, the glomeruli of the antennal lobe (AL). My results show that ants are not anosmic to nestmate colony odor and this clearly invalidates the previously suggested sensory filter hypothesis. Advanced two-photon microscopy allowed me to investigate the neuronal representation of colony odors in different neuroanatomical compartments of the AL (Chapter 5). Although neuronal activity was distributed inhomogeneously, I did not find exclusive representation restricted to a single AL compartment. This result indicates that information about colony odors is processed in parallel, using the computational power of the whole AL network. In the AL, the patterns of glomerular activity (spatial activity patterns) were variable, even in response to repeated stimulation with the same colony odor (Chapter 4&5). This finding is surprising, as earlier studies indicated that spatial activity patterns in the AL reflect how an odor is perceived by an animal (odor quality). Under natural conditions, multi-component odors constitute varying and fluctuating stimuli, and most probably animals are generally faced with the problem that these elicit variable neuronal responses. Two-photon microscopy revealed that variability was higher in response to nestmate than to non-nestmate colony odor (Chapter 5), possibly reflecting plasticity of the AL network, which allows template reformation. Due to their high variability, spatial activity patterns in response to different colony odors were not sufficiently distinct to allow attribution of odor qualities like ‘friend’ or ‘foe’. This finding challenges our current notion of how odor quality of complex, multi-component odors is coded. Additional neuronal parameters, e.g. precise timing of neuronal activity, are most likely necessary to allow discrimination. The lower variability of activity patterns elicited by non-nestmate compared to nestmate colony odor might facilitate recognition of non-nestmates at the next level of the olfactory pathway. My research efforts made the colony recognition system accessible for direct neurophysiological investigations. My results show that ants can perceive their own nestmates. The neuronal representation of colony odors is distributed across AL compartments, indicating parallel processing. Surprisingly, the spatial activity patterns in response to colony are highly variable, raising the question how odor quality is coded in this system. The experimental advance presented in this thesis will be useful to gain further insights into how social insects discriminate friends and foes. Furthermore, my work will be beneficial for the research field of insect olfaction as colony recognition in social insects is an excellent model system to study the coding of odor quality and long-term memory mechanisms underlying recognition of complex, multi-component odors.
Cysteines play important roles in the biochemistry of many proteins. The high reactivity, redox properties, and ability of the free thiol group to coordinate metal ions designate cysteines as the amino acids of choice to form key catalytic components of many enzymes. Also, cysteines readily react with reactive oxygen and nitrogen species to form reversible oxidative thiol modifications. Over the last few years, an increasing number of proteins have been identified that use redox-mediated thiol modifications to modulate their function, activity, or localization. These redox-regulated proteins are central players in numerous important cellular processes. First aim of this study was to discover nitric oxide (NO) sensitive proteins in E. coli, whose redox-mediated functional changes might explain the physiological alterations observed in E. coli cells suffering from NO-stress. To identify E. coli proteins that undergo reversible thiol modifications upon NO-treatment in vivo, I applied a differential thiol trapping technique combined with two-dimensional gel analysis. 10 proteins were found to contain thiol groups sensitive to NO-treatment. Subsequent genetic studies revealed that the oxidative modifications of AceF & IlvC are, in part, responsible for the observed NO-induced growth inhibition. Noteworthy, the majority of identified protein targets turned out to be specifically sensitive towards reactive nitrogen species. This oxidant specificity was tested on one NO-sensitive protein, the small subunit of glutamate synthase. In vivo and in vitro activity studies demonstrated that glutamate synthase rapidly inactivates upon nitric oxide treatment but is resistant towards other oxidative stressors. These results imply that reactive oxygen and nitrogen species affect distinct physiological processes in bacteria. The second aim of my study was to identify redox-sensitive proteins in S. cerevisiae and to use their redox state as in vivo read-out to assess the role of oxidative stress during the eukaryotic aging process. I first determined the precise in vivo thiol status of almost 300 yeast proteins located in the cytosol and sub-cellular compartments of yeast cells using a highly quantitative mass spectrometry based thiol trapping technique, called OxICAT. The identified proteins can be clustered in four groups: 1) proteins, whose cysteine residues are oxidation resistant; 2) proteins with structurally or functionally important cysteine modifications 3) proteins with highly oxidation-sensitive active site cysteines, which are partially oxidized in exponentially growing yeast cells due to their exquisite sensitivity towards low amounts of ROS; 4) proteins that are reduced in exponentially growing cells but harbor redox-sensitive cysteine(s) that affect the catalytic function of the protein during oxidative stress. These oxidative stress sensitive proteins were identified by exposure of yeast cells to sublethal concentrations of H2O2 or superoxide. It was shown that the major targets of peroxide- and superoxide-mediated stress in the cell are proteins involved in translation, glycolysis, TCA cycle and amino acid biosynthesis. These targets indicate that cells rapidly redirect the metabolic flux and energy towards the pentose phosphate pathway in an attempt to ensure the production of the reducing equivalent NADPH to counterattack oxidative stress. These results reveal that the quantitative assessment of a protein’s oxidation state is a valuable tool to identify catalytically active and redox-sensitive cysteine residues. The OxICAT technology was then used to precisely determine extent and onset of oxidative stress in chronologically aging S. cerevisiae cells by utilizing the redox status of proteins as physiological read-out. I found that chronological aging yeast cells undergo a global collapse of the cellular redox homeostasis, which precedes cell death. The onset of this collapse appears to correlate with the yeast life span, as caloric restriction increases the life span and delays the redox collapse. These results suggest that maintenance of the redox balance might contribute to the life expanding benefits of regulating the caloric intake of yeast. Clustering analysis of all oxidatively modified proteins in chronological aging yeast revealed a subset of proteins whose oxidative thiol modifications significantly precede the general redox collapse. Oxidation of these early target proteins, which most likely results in a loss of their activity, might contribute to or even cause the observed loss of redox homeostasis (i.e., thioredoxin reductase) in chronologically aging yeast. These studies in aging yeast expand our understanding how changes in redox homeostasis affect the life span of yeast cells and confirm the importance of oxidative thiol modifications as key posttranslational modifications in pro- and eukaryotic organisms.
Untersuchungen der Transkriptionsebene individueller präimplantatorischer Embryonalstadien können wertvolle Informationen über den physiologischen Status der betrachteten Embryonen, die z.B. zur Verbesserung der Systeme zur In vitro-Produktion von Embryonen genutzt werden können, liefern. Bisher fehlte es jedoch an einer geeigneten Technologie, um eine große Anzahl von Transkripten in einzelnen Embryonen zu erfassen. Zielsetzung der vorliegenden Arbeit war es, ein Verfahren zur globalen Amplifikation embryonaler mRNA-Präparationen zu entwickeln, das die Analyse der Transkriptionsebene einzelner präimplantatorischer Embryonalstadien über die cDNA-Array-Technologie ermöglicht. Dazu wurde die Strategie gewählt, zwei bereits etablierte Amplifikationsverfahren, Polymerasekettenreaktion und In vitro-Transkription, zu kombinieren, um so synergistische Effekte beider Verfahren zu nutzen. Die Evaluierung des entwickelten Verfahrens zeigte eine hohe Reproduzierbarkeit der erhaltenen Genexpressionsdaten und belegte, dass die relativen Mengenverhältnisse einzelner mRNA-Spezies zueinander während der globalen mRNA-Amplifikation nur unwesentlich verändert wurden. Die entwickelte Methodik ist somit geeignet, komplexe Genexpressionsprofile einzelner Blastozysten zu erstellen und Unterschiede in der Expressionsstärke einzelner Transkripte zu detektieren. Es konnte weiterhin gezeigt werden, dass es möglich ist, über heterologe Hybridisierung Genexpressionsprofile boviner Blastozysten mit cDNA-Arrays, die murine Probensequenzen enthalten, reproduzierbar darzustellen. Neben der Detektion individueller Unterschiede in den Genexpressionsprofilen diverser muriner Embryonalstadien und boviner Blastozysten lag ein Schwerpunkt dieser Arbeit in der Untersuchung der Auswirkungen verschiedener in vitro-Produktionssysteme auf die embryonale Genexpression. Die erhaltenen cDNA-Array Expressionsdaten muriner Oozyten, Zweizeller und Blastozysten befanden sich dabei in Übereinstimmung mit Daten früherer Publikationen anderer Arbeitsgruppen. Genexpressionsprofile in vitro fertilisierter boviner Blastozysten ließen eine Beurteilung der Auswirkungen unterschiedlicher Proteinsupplemente des Kulturmediums auf die embryonale Genexpression zu. Im Rahmen dieser Arbeit wurden zum ersten Mal Genexpressionsprofile einzelner präimplantatorischer Säugerembryonen über cDNA-Array-Analyse erstellt. Die entwickelte Technologie ermöglicht es -bei Verwendung entsprechender cDNA-Array-Systeme-, eine theoretisch unbegrenzte Zahl von Transkripten in individuellen Säugerembryonen semiquantitativ zu erfassen. Dies ist ein wichtiger Schritt hin zu einem besseren Verständnis komplexer Regulationsabläufe während der frühen Embryonalentwicklung und einer besseren Beurteilung der Lebensfähigkeit und Entwicklungskompetenz in vitro produzierter Embryonen, was für die Verbesserung von In vitro-Produktionssystemen für Embryonen sowohl bei Tieren als auch beim Menschen unerlässlich ist.
Gene and genome duplications are major mechanisms of eukaryotic genome evolution. Three rounds of genome duplication have occurred in the vertebrate lineage, two rounds (1R, 2R) during early vertebrate evolution and a third round, the fish-specific genome duplication (FSGD), in ray-finned fishes at the base of the teleost lineage. Whole genome duplications (WGDs) are considered to facilitate speciation processes and to provide the genetic raw material for major evolutionary transitions and increases in morphological complexity. In the present study, I have used comparative genomic approaches combining molecular phylogenetic reconstructions, synteny analyses as well as gene function studies (expression analyses and knockdown experiments) to investigate the evolutionary consequences and significance of the three vertebrate WGDs. First, the evolutionary history of the endothelin signaling system consisting of endothelin ligands and receptors was reconstructed. The endothelin system is a key component for the development of a major vertebrate innovation, the neural crest. This analysis shows that the endothelin system emerged in an ancestor of the vertebrate lineage and that its members in extant vertebrate genomes are derived from the vertebrate WGDs. Each round of WGD was followed by co-evolution of the expanding endothelin ligand and receptor repertoires. This supports the importance of genome duplications for the origin and diversification of the neural crest, but also underlines a major role for the co-option of new genes into the neural crest regulatory network. Next, I have studied the impact of the FSGD on the evolution of teleost pigment cell development and differentiation. The investigation of 128 genes showed that pigmentation genes have been preferentially retained in duplicate after the FSGD so that extant teleost genomes contain around 30% more putative pigmentation genes than tetrapods. Large parts of pigment cell regulatory pathways are present in duplicate being potentially involved in teleost pigmentary innovations. There are also important differences in the retention of duplicated pigmentation genes among divergent teleost lineages. Functional studies of pigment synthesis enzymes in zebrafish and medaka, particularly of the tyrosinase family, revealed lineage-specific functional evolution of duplicated pigmentation genes in teleosts, but also pointed to anciently conserved gene functions in vertebrates. These results suggest that the FSGD has facilitated the evolution of the teleost pigmentary system, which is the most complex and diverse among vertebrates. In conclusion, the present study supports a major role of WGDs for phenotypic evolution and biodiversity in vertebrates, particularly in fish.
Recent development of proteomic approaches and generation of large-scale proteomic datasets calls for new methods for biological interpretation of the obtained results. Systems biological approaches such as integrated network analysis and functional module search have become an essential part of proteomic investigation. Proteomics is especially applied in anucleate cells such as platelets. The underlying molecular mechanisms of platelet activation and their pharmacological modulation are of immense importance for clinical research. Advances in platelet proteomics have provided a large amount of proteomic data, which has not yet been comprehensively investigated in a systems biological perspective. To this end, I assembled platelet specific data from proteomic and transcriptomic studies by detailed manual curation and worked on the generation of a comprehensive human platelet repository for systems biological analysis of platelets in the functional context of integrated networks (PlateletWeb) (http:/PlateletWeb.bioapps.biozentrum.uni-wuerzburg.de). I also added platelet-specific experimentally validated phosphorylation data and generated kinase predictions for 80% of the newly identified platelet phosphosites. The combination of drug, disease and pathway information with phosphorylation and interaction data makes this database the first integrative platelet platform available for platelet research. PlateletWeb contains more than 5000 platelet proteins, which can also be analyzed and visualized in a network context, allowing identification of all major signaling modules involved in platelet activation and inhibition. Using the wealth of integrated data I performed a series of platelet-specific analyses regarding the platelet proteome, pathways, drug targets and novel platelet phosphorylation events involved in crucial signaling events. I analyzed the statistical enrichment of known pathways for platelet proteins and identified endocytosis as a highly represented pathway in platelets. Further results revealed that highly connected platelet proteins are more often targeted by drugs. Using integrated network analysis offered by PlateletWeb, I analyzed the crucial activation signaling pathway of adenosine diphosphate (ADP), visualizing how the signal flow from receptors to effectors is maintained. My work on integrin inside-out signaling was also based on the integrated network approach and examined new platelet-specific phosphorylation sites and their regulation using kinase predictions. I generated hypothesis on integrin signaling, by investigating the regulation of Ser269 phosphorylation site on the docking protein 1 (DOK1). This phosphorylation site may influence the inhibiting effect of DOK1 on integrin a2bb3. Extending the integrated network approach to further cell lines, I used the assembled human interactome information for the analysis of functional modules in cellular networks. The investigation was performed with a previously developed module detection algorithm, which finds maximum-scoring subgraphs in transcriptomic datasets by using assigned values to the network nodes. We extended the algorithm to qualitative proteomic datasets and enhanced the module search by adding functional information to the network edges to concentrate the solution onto modules with high functional similarity. I performed a series of analyses to validate its performance in small-sized (virus-infected gastric cells) and medium-sized networks (human lymphocytes). In both cases the algorithm extracted characteristic modules of sample proteins with high functional similarity. The functional module search is especially useful in site-specific phosphoproteomic datasets, where kinase regulation of the detected sites is often sparse or lacking. Therefore, I used the module detection algorithm in quantitative phosphoproteomic datasets. In a platelet phosphorylation dataset, I presented a pipeline for network analysis of detected phosphorylation sites. In a second approach, the functional module detecting algorithm was used on a phosphoproteome network of human embryonic stem cells, in which nodes represented the maximally changing phosphorylation sites in the experiment. Additional kinases from the human phosphoproteome in PlateletWeb were included to the network to investigate the regulation of the signal flow. Results indicated important phosphorylation sites and their upstream kinases and explained changes observed in embryonic stem cells during differentiation. This work presents novel approaches for integrated network analysis in cells and introduces for the first time a systematic biological investigation of the human platelet proteome based on the platelet-specific knowledge base PlateletWeb. The extended methods for optimized functional module detection offer an invaluable tool for exploring proteomic datasets and covering gaps in complex large-scale data analysis. By combining exact module detection approaches with functional information data between interacting proteins, characteristic functional modules with high functional resemblance can be extracted from complex datasets, thereby focusing on important changes in the observed networks.
Mapping human pressures on biodiversity across the planet uncovers anthropogenic threat complexes
(2020)
Climate change and other anthropogenic drivers of biodiversity change are unequally distributed across the world. Overlap in the distributions of different drivers have important implications for biodiversity change attribution and the potential for interactive effects. However, the spatial relationships among different drivers and whether they differ between the terrestrial and marine realm has yet to be examined.
We compiled global gridded datasets on climate change, land‐use, resource exploitation, pollution, alien species potential and human population density. We used multivariate statistics to examine the spatial relationships among the drivers and to characterize the typical combinations of drivers experienced by different regions of the world.
We found stronger positive correlations among drivers in the terrestrial than in the marine realm, leading to areas with high intensities of multiple drivers on land. Climate change tended to be negatively correlated with other drivers in the terrestrial realm (e.g. in the tundra and boreal forest with high climate change but low human use and pollution), whereas the opposite was true in the marine realm (e.g. in the Indo‐Pacific with high climate change and high fishing).
We show that different regions of the world can be defined by Anthropogenic Threat Complexes (ATCs), distinguished by different sets of drivers with varying intensities. We identify 11 ATCs that can be used to test hypotheses about patterns of biodiversity and ecosystem change, especially about the joint effects of multiple drivers.
Our global analysis highlights the broad conservation priorities needed to mitigate the impacts of anthropogenic change, with different priorities emerging on land and in the ocean, and in different parts of the world.
Head and neck squamous cell carcinoma (HNSCC) is known to overexpress a variety of receptor tyrosine kinases, such as the HGF receptor Met. Like other malignancies, HNSCC involves a mutual interaction between the tumor cells and surrounding tissues and cells. We hypothesized that activation of HGF/Met signaling in HNSCC influences glucose metabolism and therefore substantially changes the tumor microenvironment. To determine the effect of HGF, we submitted three established HNSCC cell lines to mRNA sequencing. Dynamic changes in glucose metabolism were measured in real time by an extracellular flux analyzer. As expected, the cell lines exhibited different levels of Met and responded differently to HGF stimulation. As confirmed by mRNA sequencing, the level of Met expression was associated with the number of upregulated HGF-dependent genes. Overall, Met stimulation by HGF leads to increased glycolysis, presumably mediated by higher expression of three key enzymes of glycolysis. These effects appear to be stronger in Met\(^{high}\)-expressing HNSCC cells. Collectively, our data support the hypothesized role of HGF/Met signaling in metabolic reprogramming of HNSCC.
Neoplasms of the skin represent the most frequent tumors worldwide; fortunately, most of them are benign or semi-malignant and well treatable. However, the two most aggressive and deadly forms of malignant skin-neoplasms are melanoma and Merkel cell carcinoma (MCC), being responsible for more than 90% of skin-cancer related deaths. The last decade has yielded enormous progress in melanoma therapy with the advent of targeted therapies, like BRAF or MEK inhibitors, and immune-stimulating therapies, using checkpoint antibodies targeting CTLA- 4, PD-1 or PD-L1. Very recent studies suggest that also MCC patients benefit from a treatment with checkpoint antibodies. Nevertheless, in an advanced metastatic stage, a cure for both of these aggressive malignancies is still hard to achieve: while only a subset of patients experience durable benefit from the immune-based therapies, the widely applicable targeted therapies struggle with development of resistances that inevitably occur in most patients, and finally lead to their death. The four articles included in this thesis addressed current questions concerning therapy and carcinogenesis of melanoma and MCC. Moreover, they are discussed in the light of the up-to-date research regarding targeted and immune-based therapies. In article I we demonstrated that besides apoptosis, MAPK pathway inhibition in BRAF-mutated melanoma cells also induces senescence, a permanent cell cycle arrest. These cells may provide a source for relapse, as even permanently arrested cancer cells can contribute to a pro-tumorigenic milieu. To identify molecular factors determining the differential response, we established M14 melanoma cell line derived single cell clones that either undergo cell death or arrest when treated with BRAF/MEK inhibitors. Using these single cell clones, we demonstrated in article IV that downregulation of the pro-apoptotic BH3-only protein BIK via epigenetic silencing is involved in apoptosis deficiency, which can be overcome by HDAC inhibitors. These observations provide a possible explanation for the lack of a complete and durable response to MAPK inhibitor treatment in melanoma patients, and suggest the application of HDAC inhibitors as a complimentary therapy to MAPK pathway inhibition. Concerning MCC, we scrutinized the interactions between the Merkel cell polyomavirus’ (MCV) T antigens (TA) and the tumor suppressors p53 and Rb in article II and III, respectively. In article III, we demonstrated that the cell cycle master regulator Rb is the crucial target of MCV large T (LT), while it - in contrast to other polyomavirus LTs - exhibits much lower affinity to the related proteins p107 and p130. Knockdown of MCV LT led to proliferation arrest in MCC cells, which can be rescued by knockdown of Rb, but not by knockdown of p107 and p130. Contrary to Rb, restriction of p53 in MCC seems to be independent of the MCV TAs, as we demonstrated in article II. In conclusion, the presented thesis has revealed new molecular details, regarding the response of melanoma cells towards an important treatment modality and the mechanisms of viral carcinogenesis in MCC.
The Glycosylphosphatidylinositol Anchor: A Linchpin for Cell Surface Versatility of Trypanosomatids
(2021)
The use of glycosylphosphatidylinositol (GPI) to anchor proteins to the cell surface is widespread among eukaryotes. The GPI-anchor is covalently attached to the C-terminus of a protein and mediates the protein’s attachment to the outer leaflet of the lipid bilayer. GPI-anchored proteins have a wide range of functions, including acting as receptors, transporters, and adhesion molecules. In unicellular eukaryotic parasites, abundantly expressed GPI-anchored proteins are major virulence factors, which support infection and survival within distinct host environments. While, for example, the variant surface glycoprotein (VSG) is the major component of the cell surface of the bloodstream form of African trypanosomes, procyclin is the most abundant protein of the procyclic form which is found in the invertebrate host, the tsetse fly vector. Trypanosoma cruzi, on the other hand, expresses a variety of GPI-anchored molecules on their cell surface, such as mucins, that interact with their hosts. The latter is also true for Leishmania, which use GPI anchors to display, amongst others, lipophosphoglycans on their surface. Clearly, GPI-anchoring is a common feature in trypanosomatids and the fact that it has been maintained throughout eukaryote evolution indicates its adaptive value. Here, we explore and discuss GPI anchors as universal evolutionary building blocks that support the great variety of surface molecules of trypanosomatids.
Abstract: Understanding the causes and consequences of dispersal is a prerequisite for the effective management of natural populations. Rather than treating dispersal as a fixed trait, it should be considered a plastic process that responds to both genetic and environmental conditions. Here, we consider how the ambient temperature experienced by juvenile Erigone atra, a spider inhabiting crop habitat, influences adult dispersal. This species exhibits 2 distinct forms of dispersal, ballooning (long distance) and rappelling (short distance). Using a half-sib design we raised individuals under 4 different temperature regimes and quantified the spiders' propensity to balloon and to rappel. Additionally, as an indicator of investment in settlement, we determined the size of the webs build by the spiders following dispersal. The optimal temperature regimes for reproduction and overall dispersal investment were 20 °C and 25 °C. Propensity to perform short-distance movements was lowest at 15 °C, whereas for long-distance dispersal it was lowest at 30 °C. Plasticity in dispersal was in the direction predicted on the basis of the risks associated with seasonal changes in habitat availability; long-distance ballooning occurred more frequently under cooler, spring-like conditions and short-distance rappelling under warmer, summer-like conditions. Based on these findings, we conclude that thermal conditions during development provide juvenile spiders with information about the environmental conditions they are likely to encounter as adults and that this information influences the spider's dispersal strategy. Climate change may result in suboptimal adult dispersal behavior, with potentially deleterious population level consequences.
Abstract: From a conservation point of view, species- tolerances towards disturbance are often generalised and lack reference to spatial scales and underlying processes. In order to investigate how average typical species react to habitat fragmentation and disturbance, we adopted a multi-species approach to address occupancy patterns of five specialised dune arthropods (butterflies Hipparchia semele, Issoria lathonia; grasshopper Oedipoda caerulescens; spiders Alopecosa fabrilis, Xysticus sabulosus) in recently fragmented coastal dune habitats which are subjected to varying levels and modes of local disturbance, i.e. trampling by cattle or people. Occupancy patterns were assessed during two successive years in 133 grey dune fragments of the Flemish coastal dunes (Belgium, France). By treating species as a random factor in our models, emphasis was placed on generalisations rather than documenting species-specific patterns. Our study demonstrates that deteriorating effects of local disturbance on arthropod incidence cannot be interpreted independent of its landscape context, and appear to be more severe when patch area and connectivity decrease. When controlled for patch area and trampling intensity, the probability of species occupancy in poorly connected patches is higher under cattle trampling than under recreation. Incidences additionally decrease with increasing intensity of cattle trampling, but increases with trampling by tourists. This study provides evidence of mode- and landscape-dependent effects of local disturbance on species occupancy patterns. Most importantly, it demonstrates that trampling of sensitive dune fragments will lead to local and metapopulation extinction in landscapes where trampling occurs in a spatially autocorrelated way, but that the outcome (spatial patterns) varies in relation to disturbance mode, indicating that effects of disturbance cannot be generalised.
Abstract: Intensification of land-use in agricultural landscapes is responsible for a decline of biodiversity which provide important ecosystem services like pest-control. Changes in landscape composition may also induce behavioural changes of predators in response to variation in the biotic or abiotic environment. By controlling for environmentally confounding factors, we here demonstrate that the orb web spider Araneus diadematus alters its web building behaviour in response to changes in the composition of agricultural landscapes. Thereby, the species increases its foraging efficiency (i.e. investments in silk and web asymmetry) with an increase of agricultural land-use at intermediate spatial scales. This intensification is also related to a decrease in the abundance of larger prey. A negative effect of landscape properties at similar spatial scales on spider fitness was recorded when controlling for relative investments in capture thread length. This study consequently documents the web building flexibility in response to changes in landscape composition, possibly due to changes in prey availability.
Background: Male killing endosymbionts manipulate their arthropod host reproduction by only allowing female embryos to develop into infected females and killing all male offspring. Because of the reproductive manipulation, we expect them to have an effect on the evolution of host dispersal rates. In addition, male killing endosymbionts are expected to approach fixation when fitness of infected individuals is larger than that of uninfected ones and when transmission from mother to offspring is nearly perfect. They then vanish as the host population crashes. High observed infection rates and among-population variation in natural systems can consequently not be explained if defense mechanisms are absent and when transmission efficiency is perfect. Results: By simulating the host-endosymbiont dynamics in an individual-based metapopulation model we show that male killing endosymbionts increase host dispersal rates. No fitness compensations were built into the model for male killing endosymbionts, but they spread as a group beneficial trait. Host and parasite populations face extinction under panmictic conditions, i.e. conditions that favor the evolution of high dispersal in hosts. On the other hand, deterministic 'curing' (only parasite goes extinct) can occur under conditions of low dispersal, e.g. under low environmental stochasticity and high dispersal mortality. However, high and stable infection rates can be maintained in metapopulations over a considerable spectrum of conditions favoring intermediate levels of dispersal in the host. Conclusion: Male killing endosymbionts without explicit fitness compensation spread as a group selected trait into a metapopulation. Emergent feedbacks through increased evolutionary stable dispersal rates provide an alternative explanation for both, the high male-killing endosymbiont infection rates and the high among-population variation in local infection rates reported for some natural systems.
Many organisms show polymorphism in dispersal distance strategies. This variation is particularly ecological relevant if it encompasses a functional separation of short- (SDD) and long-distance dispersal (LDD). It remains, however, an open question whether both parts of the dispersal kernel are similarly affected by landscape related selection pressures. We implemented an individual-based model to analyze the evolution of dispersal traits in fractal landscapes that vary in the proportion of habitat and its spatial configuration. Individuals are parthenogenetic with dispersal distance determined by two alleles on each individual‘s genome: one allele coding for the probability of global dispersal and one allele coding for the variance of a Gaussian local dispersal with mean value zero. Simulations show that mean distances of local dispersal and the probability of global dispersal, increase with increasing habitat availability, but that changes in the habitat's spatial autocorrelation impose opposing selective pressure: local dispersal distances decrease and global dispersal probabilities increase with decreasing spatial autocorrelation of the available habitat. Local adaptation of local dispersal distance emerges in landscapes with less than 70% of clumped habitat. These results demonstrate that long and short distance dispersal evolve separately according to different properties of the landscape. The landscape structure may consequently largely affect the evolution of dispersal distance strategies and the level of dispersal polymorphism.
Background: Male killing endosymbionts manipulate their arthropod host reproduction by only allowing female embryos to develop into infected females and killing all male offspring. Because the resulting change in sex ratio is expected to affect the evolution of sex-specific dispersal, we investigated under which environmental conditions strong sex-biased dispersal would emerge, and how this would affect host and endosymbiont metapopulation persistence. Results: We simulated host-endosymbiont metapopulation dynamics in an individual-based model, in which dispersal rates are allowed to evolve independently for the two sexes. Prominent male-biased dispersal emerges under conditions of low environmental stochasticity and high dispersal mortality. By applying a reshuffling algorithm, we show that kin-competition is a major driver of this evolutionary pattern because of the high within-population relatedness of males compared to those of females. Moreover, the evolution of sex-specific dispersal rescues metapopulations from extinction by (i) reducing endosymbiont fixation rates and (ii) by enhancing the extinction of endosymbionts within metapopulations that are characterized by low environmental stochasticity. Conclusion: Male killing endosymbionts induce the evolution of sex-specific dispersal, with prominent male-biased dispersal under conditions of low environmental stochasticity and high dispersal mortality. This male-biased dispersal emerges from stronger kin-competition in males compared to females and induces an evolutionary rescue mechanism.
Abstract: 1. The response of dispersal towards evolution largely depends on its heritability for which upper limits are determined by the trait's repeatability. 2. In the Linyphiid spider E. atra, we were able to separate long- and short-distance dispersal behaviours (respectively ballooning and rappelling) under laboratory conditions. By performing repeated behavioural trials for females, we show that average dispersal trait values decrease with increasing testing days. By comparing mated and unmated individuals during two periods (before and after mating for the mated group, and the same two periods for the unmated group), we show that mating has no effect on the mean displayed dispersal behaviour or its within-individual variation. Repeatabilities were high and consistent for ballooning motivation, but not for rappelling. 3. Ballooning motivation can be regarded as highly individual-specific behaviour, while general pre-dispersal and rappelling behaviours showed more individual variation. Such difference in repeatability between long-and short-distance dispersal suggests that short-and long-distance dispersal events are triggered by different ecological and evolutionary mechanisms.
Antibodies directed against RNA polymerase II (B) from Drosophila melanogaster were obtained from rabbit sera and, as monoclonal immunoglobulins, from mouse hybridomas and shown to cross-react with the amphibian enzyme protein. Localization by indirect immunofluorescence microscopy revealed the association of this enzyme with chromatin of interphase nuclei of amphibian cells and its absence in nucleoli. Purified immunoglobulins were microinjected in to nuclei ofliving vitellogenic oocytes of Ple1lrodeles waltlii and X enopus laevis and their effects on transcriptional processes were monitored by biochemical and light and electron microscopic stud ies. RNA polymerase II antibodies from rabbit sera caused a rapid and almost complete release of nascent transcripts from the chromatin axis of the loops of lampbrush chromosomes, followed by collapse of the loops and their retraction on the main chromosome axis. Monoclonal murine antibodies to the Iarge RNA polymerase II subunits also inhibited transcription in chromosome Ioops but appeared to inhibit initiation rather than elongation events. Activities of class land III RNA polymerases were not significantly affected by injection of antibodies to polymerase II, indicating immunological differences between the three RNA polymerases. The potential value of the in vitro test system described , as a very sensitive assay for detecting proteins involved in transcription in living cells, is discussed. 1
For determination of structures and structural dynamics of proteins organic fluorophores are a standard instrument. Intra- and intermolecular contact of biomolecular structures are determined in time-resolved and stationary fluorescence microscopy experiments by quenching of organic fluorophores due to Photoinduced Electron Transfer (PET) and dimerization interactions. Using PET we show in this work that end-to-end contact dynamics of serine-glycine peptides are slowed down by glycosylation. This slow down is due to a change in reaction enthalpy for end-to-end contact and is partly compensated by entropic effects. In a second step we test how dimerization of MR121 fluorophore pairs reports on end-to-end contact dynamics. We show that in aqueous solutions containing strong denaturants MR121 dimerization reports advantageously on contact dynamics for glycine-serine oligopeptides compared to the previously used MR121/tryptophane PET reporters. Then we analyze dimer interactions and quenching properties of different commercially available fluorophores being standards in Förster Resonance Energy Transfer (FRET) measurements. Distances in biomolecules are determinable using FRET, but for very flexible biomolecules the analysis of masurement data can be distorted if contact of the two FRET fluorophores is likely. We quantify how strong the quenching of fluorophore pairs with two different or two identical fluorophores is. Dimer spectra and association constants are quantified to estimate if fluophores are applicable in various applications, e.g. in FRET measurements with unstructured peptides and proteins.
This work was aimed at experimentally studying whether climatic variables act as environmental cues for workers’ building behaviour in leaf-cutting ants of the genus Acromyrmex, and to what extent building responses account for the maintenance of nest climate in a proper range for the inhabiting colony. Specifically, this work presents independent analysis in different Acromyrmex species with disparate ecology and nesting habits, aimed at understanding to what extent: i) temperature and humidity act as cues for workers’ building behaviour, ii) inter- and intraspecific differences in the nesting habits observed in South American Acromyrmex are based on distinct building behaviours and on the variation in regional climate across continent, iii) differences in nest architecture account for the maintenance of nest climate in a proper range for colony members and, iv) climatic variables trigger building responses aimed at controlling short-term changes in nest climate. It is first experimentally shown that soil temperature acts as a cue for workers’ digging behaviour. Acromyrmex lundi workers were observed to respond to both soil temperature as well as its changes, and to decide accordingly where to start or whether to stop digging. The soil temperature range preferred by workers to dig, between 20°C and maximally 30.6°C, matches the range at which colony growth is expected to be maximized. Temperature-sensitive digging might therefore lead to the establishment of the fungus chambers in soil layers with a proper range of temperatures for colony growth. Based on that, it was hypothesized that nest depth in Acromyrmex largely depends on the depth at which this temperature range is located across the soil profile, i.e., the higher the temperature in the superficial soil layers, the deeper the nest location, since soil temperature decreases with increasing depth. A bibliographic survey on nesting habits of 21 South American Acromyrmex species confirmed that the warmer the soil temperature at 50 cm depth throughout the South American continent, the higher the number of species presenting subterranean nests, compared with those inhabiting superficial nests. Temperature-sensitive digging in Acromyrmex would therefore explain the geographical distribution of nesting habits observed for this genus in the South American continent, i.e., subterranean in the northern tropical regions, and superficial in the southern temperate ones. In addition, results showed that Acromyrmex colonies from temperate regions indeed achieve thermoregulatory benefits through the determination of nest depth based on thermoregulatory needs. In sympatrically-occurring colonies of the grass-cutting ant A. heyeri, temperature inside superficial thatched nests was higher, and more suitable for colony growth, than that inside subterranean nests. This temperature surplus was even higher in spring, at the time of production of sexual brood, than in winter or summer. It was demonstrated that such temperature surplus was brought about by the low thermal diffusivity of the nest thatch, which prevents diurnal nest overheating by the incoming solar radiation, and avoids losses of the accumulated daily heat into the cold air during night, thus leading to high average nest temperatures. Although highly advantageous for colonies in terms of nest temperature, the determination of nest depth based on thermoregulatory needs may differentially affect nest ventilation and humidity depending on how nest exposition influences the exchange of nest air with the outside air. For instance, colonies with a superficial nesting habit might benefit from improved nest ventilation, but be at risk of desiccation due to their exposition and the consequent humidity losses into the dry outside air. Results demonstrated that in two Acromyrmex species, short-term regulatory building responses triggered and spatially organized by climatic variables occur, and may counteract undesired changes in internal nest humidity. Workers of the thatching grass-cutting ant A. heyeri, for instance, closed a number of nest-thatch openings as a response to desiccation of the outside air, even at a nest temperature that otherwise triggered the response of opening them so as to reduce nest temperature. In the leaf-cutting ant A. ambiguus, the direction of the airflow inside nest tunnels was shown to act as a cue for spatially guiding the building behaviour of plugging nest entrances. However, workers only responded if the humidity content of the circulating air was low, trading therefore nest ventilation for humidity maintenance.
The construction of mound-shaped nests by ants is considered as a behavioral adaptation to low environmental temperatures, i.e., colonies achieve higher and more stables temperatures than those of the environment. Besides the well-known nests of boreal Formica wood-ants, several species of South American leaf-cutting ants of the genus Acromyrmex construct thatched nests. Acromyrmex workers import plant fragments as building material, and arrange them so as to form a thatch covering a central chamber, where the fungus garden is located. Thus, the degree of thermoregulation attained by the fungus garden inside the thatched nest largely depends on how the thatch affects the thermal relations between the fungus and the environment. This work was aimed at studying the thermoregulatory function of the thatched nests built by the grass-cutting ant Acromyrmex heyeri Forel (Hymenoptera: Formicidae: Myrmicinae). Nest and environmental temperatures were measured as a function of solar radiation on the long-term. The thermal diffusivity of the nest thatch was measured and compared to that of the surrounding soil, in order to assess the influence of the building material on the nest’s thermoregulatory ability. The results showed that the average core temperature of thatched nests was higher than that of the environment, but remained below values harmful for the fungus. This thermoregulation was brought about by the low thermal diffusivity of the nest thatch built by workers with plant fragments, instead of the readily-available soil particles that have a higher thermal diffusivity. The thatch prevented diurnal nest overheating by the incoming solar radiation, and avoided losses of the accumulated daily heat into the cold air during the night. The adaptive value of thatching behavior in Acromyrmex leaf-cutting ants occurring in the southernmost distribution range is discussed.
Background: Acquisition of information about food sources is essential for animals that forage collectively like social insects. Foragers deliver two commodities to the nest, food and information, and they may favor the delivery of one at the expenses of the other. We predict that information needs should be particularly high at the beginning of foraging: the decision to return faster to the nest will motivate a grass-cutting ant worker to reduce its loading time, and so to leave the source with a partial load. Principal Findings: Field results showed that at the initial foraging phase, most grass-cutting ant foragers (Acromyrmex heyeri) returned unladen to the nest, and experienced head-on encounters with outgoing workers. Ant encounters were not simply collisions in a probabilistic sense: outgoing workers contacted in average 70% of the returning foragers at the initial foraging phase, and only 20% at the established phase. At the initial foraging phase, workers cut fragments that were shorter, narrower, lighter and tenderer than those harvested at the established one. Foragers walked at the initial phase significantly faster than expected for the observed temperatures, yet not at the established phase. Moreover, when controlling for differences in the fragment-size carried, workers still walked faster at the initial phase. Despite the higher speed, their individual transport rate of vegetable tissue was lower than that of similarly-sized workers foraging later at the same patch. Conclusions/Significance: At the initial foraging phase, workers compromised their individual transport rates of material in order to return faster to the colony. We suggest that the observed flexible cutting rules and the selection of partial loads at the beginning of foraging are driven by the need of information transfer, crucial for the establishment and maintenance of a foraging process to monopolize a discovered resource.
The aim of this study was to investigate if the biomarkers myelin basic protein (MBP) and neurofilament-H (NF-H) yielded informative value in forensic diagnostics when examining cadaveric cerebrospinal fluid (CSF) biochemically via an enzyme-linked immunosorbent assay (ELISA) and comparing the corresponding brain tissue in fatal traumatic brain injury (TBI) autopsy cases by immunocytochemistry versus immunohistochemistry. In 21 trauma and 19 control cases, CSF was collected semi-sterile after suboccipital puncture and brain specimens after preparation. The CSF MBP (p = 0.006) and NF-H (p = 0.0002) levels after TBI were significantly higher than those in cardiovascular controls. Immunohistochemical staining against MBP and against NF-H was performed on cortical and subcortical samples from also biochemically investigated cases (5 TBI cases/5 controls). Compared to the controls, the TBI cases showed a visually reduced staining reaction against MBP or repeatedly ruptured neurofilaments against NF-H. Immunocytochemical tests showed MBP-positive phagocytizing macrophages in CSF with a survival time of > 24 h. In addition, numerous TMEM119-positive microglia could be detected with different degrees of staining intensity in the CSF of trauma cases. As a result, we were able to document that elevated levels of MBP and NF-H in the CSF should be considered as useful neuroinjury biomarkers of traumatic brain injury.
In the last few years, quantitative analysis of metabolites in body fluids using LC/MS has become an established method in laboratory medicine and toxicology. By preparing metabolite profiles in biological specimens, we are able to understand pathophysiological mechanisms at the biochemical and thus the functional level. An innovative investigative method, which has not yet been used widely in the forensic context, is to use the clinical application of metabolomics. In a metabolomic analysis of 41 samples of postmortem cerebrospinal fluid (CSF) samples divided into cohorts of four different causes of death, namely, cardiovascular fatalities, isoIated torso trauma, traumatic brain injury, and multi-organ failure, we were able to identify relevant differences in the metabolite profile between these individual groups. According to this preliminary assessment, we assume that information on biochemical processes is not gained by differences in the concentration of individual metabolites in CSF, but by a combination of differently distributed metabolites forming the perspective of a new generation of biomarkers for diagnosing (fatal) TBI and associated neuropathological changes in the CNS using CSF samples.
Interaktionen zwischen Insekten und Pflanzen können auf chemischen oder mechanischen Faktoren beruhen. Mechanische Faktoren spielen eine besonders wichtige Rolle bei den Fallen karnivorer Pflanzen. Ziel dieser Arbeit war es, die Rolle mechanischer Faktoren in der Interaktion zwischen der Kannenpflanze Nepenthes bicalcarata und der Ameise Camponotus schmitzi aufzuklären, bei der Ameisen Gegenanpassungen zu spezialisierten pflanzlichen Fangstrukturen entwickelt haben. Im Rahmen meiner Arbeit habe ich mich mit den Fragen beschäftigt, 1) welche Kannenstrukturen und welche Mechanismen für den Fang von Arthropoden wichtig sind und 2) welche speziellen Anpassungen C. schmitzi-Ameisen für das Leben auf ihrer karnivoren Wirtspflanze besitzen. Bisher wurde angenommen, dass Nepenthes-Kannen Tiere mit Hilfe von rutschigen Wachskristallschichten fangen. Ich konnte zeigen, dass ein weiterer, bisher unbekannter Fangmechanismus existiert, welcher auf speziellen Oberflächeneigenschaften des Kannenrandes (Peristom) und "Insekten-Aquaplaning" basiert. Das Peristom besitzt eine regelmäßige Mikrostruktur, welche dafür sorgt, dass die Oberfläche vollständig mit Wasser benetzbar ist, so dass sie bei feuchter Witterung von homogenen Flüssigkeitsfilmen überzogen ist. Auf dem trockenen Peristom können Ameisen ohne Schwierigkeiten laufen und Nektar von den am inneren Peristomrand gelegenen Nektarien ernten. Wird die Oberfläche aber beispielsweise durch Regen nass, rutschen die meisten Tiere ab und stürzen in die Kanne. Messungen der Reibungskräfte von Weberameisen (Oecophylla smaragdina) auf dem Peristom von N. bicalcarata zeigten, dass Flüssigkeitsfilme auf der Oberfläche die Anhaftung der Haftorgane (Arolien) verhindern, und dass die Mikrostruktur des Peristoms auch den Einsatz der Krallen unterbindet. Versuche an Nepenthes alata zeigten darüber hinaus, dass dieser Fangmechanismus des Peristoms auch für Nepenthes-Arten mit wachsbereifter Kanneninnenwand essentiell, und die Wachsschicht eher für die Retention gefangener Tiere wichtig ist. Zur Analyse der ökologischen Auswirkungen des "Aquaplaning"-Fangmechanismus habe ich die Peristomfeuchte von Nepenthes rafflesiana var. typica-Kannen zeitgleich mit meteorologischen Daten im Feld kontinuierlich aufgezeichnet und mit Experimenten zur Beurteilung der Fangeffizienz der Kannen kombiniert. Die Ergebnisse dieser Versuche zeigen, dass die Kannen abhängig vom Befeuchtungsgrad des Peristoms zeitweise sehr effiziente Fallen mit Fangraten von 80% sein können, während sie zu anderen Zeiten vollkommen ineffizient sind. Die Variation der Peristomfeuchte wird durch Regen, Kondensation und von den Peristomnektarien sezerniertem Nektar verursacht. Es ist zu vermuten, dass die nur zeitweise und unvorhersehbare Aktivierung der Nepenthes-Kannenfallen durch Nässe der Evolution von Vermeidungsstrategien bei Beutetieren entgegenwirkt. Im Rahmen der Untersuchungen, welche mechanischen Anpassungen C. schmitzi-Ameisen für das Leben auf N. bicalcarata besitzen habe ich mich auf die Fragen konzentriert, wie es den Ameisen gelingt den Peristom-Fangmechanismus zu umgehen und welche Anpassungen sie besitzen um in der Kannenflüssigkeit tauchend und schwimmend nach Nahrung zu suchen. Im Gegensatz zu generalistischen Arten stürzen C. schmitzi-Ameisen auf dem nassen Peristom nicht ab. Durch selektive Manipulation der tarsalen Haftstrukturen konnte ich demonstrieren, dass die Arolien für die Peristomlauffähigkeit der C. schmitzi-Ameisen eine wesentliche Rolle spielen. Für das Furagieren in der Kannenflüssigkeit verfügen C. schmitzi-Ameisen über ein sich wiederholendes, stereotypes Verhaltensmuster, welches aus einer Unterwasserlauf- und einer Oberflächenschwimmphase besteht. Meine Untersuchungen dieses Verhaltensmusters zeigten, dass die Ameisen am Ende der Unterwasserlaufphase mit Hilfe ihres stets vorhandenen Auftriebs zur Flüssigkeitsoberfläche aufsteigen. Dabei taucht ein Teil ihres Hinterleibs aus der Kannenflüssigkeit auf, was den Ameisen die Sauerstoffaufnahme aus der Luft ermöglicht. Nach dem Auftauchen schwimmen C. schmitzi-Ameisen mittels schneller Beinbewegungen an der Oberfläche der Kannenflüssigkeit. Dabei ähnelt die Bewegungskoordination ihrer Beine dem bei Ameisen für die Fortbewegung an Land typischen Dreifußgang. Ein Vergleich der Kinematik von schwimmenden und laufenden C. schmitzi-Ameisen hat gezeigt, dass schwimmende Ameisen ihre Beine in der Schlagphase mit einer höheren Winkelgeschwindigkeit als in der Rückholphase bewegen, während dies bei den laufenden Tieren genau umgekehrt ist. Ferner strecken schwimmende Ameisen ihre Beine während der Schlagphase weiter aus als in der Rückholphase, wohingegen laufende Ameisen in beiden Bewegungsphasen vergleichbare Beinradien aufweisen. Dies lässt den Schluss zu, dass die Schwimmkinematik der C. schmitzi-Ameisen eine abgewandelte Form ihrer Laufkinematik darstellt, welche für die Erzeugung von Vortrieb im Wasser optimiert wurde.
Members of the Diaphanous (Dia) protein family are key regulators of fundamental actin driven cellular processes, which are conserved from yeast to humans. Researchers have uncovered diverse physiological roles in cell morphology, cell motility, cell polarity, and cell division, which are involved in shaping cells into tissues and organs. The identification of numerous binding partners led to substantial progress in our understanding of the differential functions of Dia proteins. Genetic approaches and new microscopy techniques allow important new insights into their localization, activity, and molecular principles of regulation.
Plants may use different strategies to attract pollinators in long distance (e.g. floral display) and in short distance (e.g. ratio between differentially colored flowers) scales. The Verbenaceae Lantana canescens Kunth is a wide spread species in open sites of the Brazilian Pantanal wetland. Individuals of this generalist species can produce a variable number of open inflorescences with yellow and white flowers that are organized in whorls. In this study we tested the hypothesis that increased floral display (long distance attraction) and the ratio between yellow and white flowers (short distance attraction) enhances the number of pollinator species and individuals. We observed flower visitors and calculated floral parameters in 38 plots of 1 m2 each, that contained a varying number of flowering L. canescens individuals. Non-metric multidimensional scaling and Bray-Curtis distances were used to account for flower visitor composition and the relative visitation rate, respectively. We used a structural equation model to test the power of each predictor variable on the visitation rate and a covariance analysis to disentangle the effect of each independent variable on the frequency of plant-pollinator interactions. We found that the number of flower visitors and the visitation rate increased with increasing number of inflorescences. Disentangling long and short distance attraction indicated that the number of inflorescences (per plot) and the number of yellow flowers (yellowing effect) contributed most to flower visitation at long and short distance, respectively.
1. The oil‐collecting bee Centris analis (Fabricius, 1804) is an important pollinator for the Neotropical region. The species can be attracted to nest in human‐made cavities. Such trap nests or insect hotels offer the opportunity to study the behaviour of populations in semifield conditions.
2. We studied a newly established trap nest aggregation of C. analis in Mato Grosso do Sul, Brazil and tested the effect that differentially painted nesting options have on the rate of nest foundation, and on the ability of relocating the nest when returning from a foraging trip (homing behaviour). Moreover, we tested if the duration of foraging trips decreased with time.
3. We found that females preferred to nest in painted nests compared to unpainted nests, with blue nests being the most occupied ones, followed by purple, yellow, white, and green. Furthermore, bees improved their homing behaviour with time, however, nest colour did not seem to have an effect on this process. Moreover, we found that bees reduce the duration of their foraging trips with time. This could be an indicator of improved foraging efficiency through learning.
4. These findings could inform a new and fruitful line of research on the behaviour and ecology of trap nesting solitary bees.
Increasing natural pest control in agricultural fields is an important aim of ecological intensification. Combined effects of landscape context and local placement of agri‐environmental schemes (AES) on natural pest control and within‐field distance functions of natural pest control agents have rarely been addressed but might affect the distribution of biocontrol providers. Importantly, it is currently unknown whether ecosystem services provided by adjacent AES are consistent for different crop types during crop rotation.
In this study, we assessed whether crop rotation from oilseed rape to cereals altered within‐field distance functions of ground‐dwelling predators from adjacent agri‐environmental fields along a gradient in landscape context. Additionally, we recorded crop pests, predation rates, parasitoids as well as crop yields on a total of 30 study sites.
Distance functions varied between trophic levels: Carabid richness decreased while densities of carabid beetles, staphylinid beetles as well as crop yields increased towards the field centres. Distance functions of parasitoids and pests were modulated by the amount of semi‐natural habitat in the surrounding landscape, while the effects of adjacent AES were limited.
Distance decay functions found for ground‐dwelling predators in oilseed rape in the previous year were not always present in cereals. Increasing distance to the field edge also increased effects of crop rotation on carabid beetle assemblages, indicating a source habitat function of field edges.
Synthesis and applications. Distance functions of natural pest control are not universal and the effects of agri‐environmental schemes (AES) in different adjacent crops during crop rotation vary and depend on ecological contrasts. A network of semi‐natural habitats and spatially optimized AES habitats can benefit pest control in agricultural landscapes, but constraints as a result of crop type need to be addressed by annually targeted, spatially shifting agri‐environment schemes for different crops.
It’s a matter of design - how pitfall trap design affects trap samples and possible predictions
(2018)
Background:
Pitfall traps are commonly used to assess ground dwelling arthropod communities. The effects of different pitfall trap designs on the trapping outcome are poorly investigated however they might affect conclusions drawn from pitfall trap data greatly.
Methods:
We tested four pitfall trap types which have been used in previous studies for their effectiveness: a simple type, a faster exchangeable type with an extended plastic rim plate and two types with guidance barriers (V- and X-shaped). About 20 traps were active for 10 weeks and emptied biweekly resulting in 100 trap samples.
Results:
Pitfall traps with guidance barriers were up to five times more effective than simple pitfall traps and trap samples resulted in more similar assemblage approximations. Pitfall traps with extended plastic rim plates did not only perform poorly but also resulted in distinct carabid assemblages with less individuals of small species and a larger variation.
Discussion:
Due to the obvious trait filtering and resulting altered assemblages, we suggest not to use pitfall traps with extended plastic rim plates. In comprehensive biodiversity inventories, a smaller number of pitfall traps with guidance barriers and a larger number of spatial replicates is of advantage, while due to comparability reasons, the use of simple pitfall traps will be recommended in most other cases.
Predation on pest organisms is an essential ecosystem function supporting yields in modern agriculture. However, assessing predation rates is intricate, and they can rarely be linked directly to predator densities or functions. We tested whether sentinel prey aphid cards are useful tools to assess predation rates in the field. Therefore, we looked at aphid cards of different sizes on the ground level as well as within the vegetation. Additionally, by trapping ground‐dwelling predators, we examined whether obtained predation rates could be linked to predator densities and traits. Predation rates recorded with aphid cards were independent of aphid card size. However, predation rates on the ground level were three times higher than within the vegetation. We found both predatory carabid activity densities as well as community weighted mean body size to be good predictors for predation rates. Predation rates obtained from aphid cards are stable over card type and related to predator assemblages. Aphid cards, therefore, are a useful, efficient method for rapidly assessing the ecosystem function predation. Their use might especially be recommended for assessments on the ground level and when time and resource limitations rule out more elaborate sentinel prey methods using exclosures with living prey animals.
3. Zusammenfassung Ein noch immer unvollständig verstandenes Problem sind die exakten Mechanismen der Arbeitsteilung und Koordination innerhalb von Bienenvölkern Apis mellifera. Auf der einen Seite muss die sensorische und neuronale Ausstattung jedes Individuums das Potential zur Kommunikation und Aufgabenbewältigung enthalten, zum anderen müssen jedem Bienenvolk Mechanismen zur Steuerung zur Verfügung stehen, die auch so weit in die Zukunft reichenden Notwendigkeiten wie Wintervorbereitungen zuverlässig durchführen. Die vorliegende Arbeit beleuchtet daraus ausgewählte Aspekte. Zum einen werden Aspekte der kognitiven Fähigkeiten der Einzelbienen untersucht, die im Hinblick auf ihre Rolle als sammelnde Arbeiterinnen eine wichtige Rolle spielen. Das Erkennen und Verarbeiten von Mustern spielt eine wichtige Rolle beim Auffinden von potentiellen Nahrungsquellen. Hier konnte mittels des DMTS – Paradigma ein hoher Abstraktionsgrad der Musterverarbeitung sowie eine Speicherung auch komplexer Muster gezeigt werden. Zum anderen wird die Bruttemperatur als ein Einfluss auf die Puppenentwicklung und dessen mögliche Folgen auf kognitive Fähigkeiten und Lebenshistorie untersucht. Variation der Bruttemperatur wurde in verschiedenen Zusammenhängen als starker Einfluss auf unterschiedliche Aspekte der Entwicklung gezeigt. In der vorliegenden Arbeit kann diese Bruttemperatur als möglicher Faktor der nachfolgend unterschiedlichen Ausprägung von Verhaltensmustern gezeigt werden. Dabei wird ebenso auf die Unterschiede im Verhaltensmuster von täglichen Stocktätigkeiten wie auf die resultierenden Unterschiede in der Lebensgeschichte und –spanne eingegangen, die aus unterschiedlichen Brutaufzuchtstemperaturen resultieren können. Als Aufzuchtstemperaturen werden dabei 32°C, 35°C sowie 36°C verwendet, um eine Vari ation zwischen der an anderer Stelle berichteten mittleren, der niedrigsten und der höchsten Temperatur für morphologisch vollständig entwickelte Bienen zu erreichen und die daraus resultierenden Arbeiterinnen zu untersuchen. Sowohl die Ergebnisse der Verhaltensuntersuchungen von Stockbienen wie auch der Vergleich von Lebensaktivität und –spanne zeigen dabei signifikante Unterschiede zwischen den bei unterschiedlichen Temperaturen aufgezogenen Arbeiterinnen in deren analysiertem Verhalten.
Community-acquired (CA) Staphylococcus aureus cause various diseases even in healthy individuals. Enhanced virulence of CA-strains is partly attributed to increased production of toxins such as phenol-soluble modulins (PSM). The pathogen is internalized efficiently by mammalian host cells and intracellular S. aureus has recently been shown to contribute to disease. Upon internalization, cytotoxic S. aureus strains can disrupt phagosomal membranes and kill host cells in a PSM-dependent manner. However, PSM are not sufficient for these processes. Here we screened for factors required for intracellular S. aureus virulence. We infected escape reporter host cells with strains from an established transposon mutant library and detected phagosomal escape rates using automated microscopy. We thereby, among other factors, identified a non-ribosomal peptide synthetase (NRPS) to be required for efficient phagosomal escape and intracellular survival of S. aureus as well as induction of host cell death. By genetic complementation as well as supplementation with the synthetic NRPS product, the cyclic dipeptide phevalin, wild-type phenotypes were restored. We further demonstrate that the NRPS is contributing to virulence in a mouse pneumonia model. Together, our data illustrate a hitherto unrecognized function of the S. aureus NRPS and its dipeptide product during S. aureus infection.
Staphylococcus aureus is a prevalent commensal bacterium which represents one of the leading causes in health care-associated bacterial infections worldwide and can cause a variety of different diseases ranging from simple abscesses to severe and life threatening infections including pneumonia, osteomyelitis and sepsis.
In recent times multi-resistant strains have emerged, causing severe problems in nosocomial as well as community-acquired (CA) infection settings, especially in the United States (USA). Therefore S. aureus has been termed as a superbug by the WHO, underlining the severe health risk originating from it. Today, infections in the USA are dominated by S. aureus genotypes which are classified as USA300 and USA400, respectively. Strains of genotype USA300 are responsible for about 70% of the CA infections.
The molecular mechanisms which render S. aureus such an effective pathogen are still not understood in its entirety. For decades S. aureus was thought to be a strictly extracellular pathogen relying on pore-forming toxins like α-hemolysin to damage human cells and tissue. Only recently it has been shown that S. aureus can enter non-professional phagocytes, using adhesins like the fibronectin-binding proteins which mediate an endocytotic uptake into the host cells. The bacteria are consequently localized to endosomes, where the degradation of enclosed bacterial cells through phagosome maturation would eventually occur.
S. aureus can avoid degradation, and translocate to the cellular cytoplasm, where it can replicate. The ability to cause this so-called phagosomal escape has mainly been attributed to a family of amphiphilic peptides called phenol soluble modulins (PSMs), but as studies have shown, they are not sufficient.
In this work I used a transposon mutant library in combination with automated fluorescence microscopy to screen for genes involved in the phagosomal escape process and intracellular survival of S. aureus. I thereby identified a number of genes, including a non-ribosomal peptide synthetase (NRPS). The NRPS, encoded by the genes ausA and ausB, produces two types of small peptides, phevalin and tyrvalin. Mutations in the ausAB genes lead to a drastic decrease in phagosomal escape rates in epithelial cells, which were readily restored by genetic complementation in trans as well as by supplementation of synthetic phevalin. In leukocytes, phevalin interferes with calcium fluxes and activation of neutrophils and promotes cytotoxicity of intracellular bacteria in both, macrophages and neutrophils. Further ausAB is involved in survival and virulence of the bacterium during mouse lung pneumoniae.
The here presented data demonstrates the contribution of the bacterial cyclic dipeptide phevalin to S. aureus virulence and suggests, that phevalin directly acts on a host cell target to promote cytotoxicity of intracellular bacteria.
Members of the enabled/vasodilator-stimulated phosphoprotein (Ena/VASP) family are important regulators of the actin cytoskeleton dynamics. VASP functions as well as its interactions with other proteins are regulated by phosphorylation at three sites - serine157 (S157), serine239 (S239), and threonine278 (T278) in humans. cAMP- and cGMP- dependent protein kinases phosphorylate S157 and S239, respectively. In contrast, the kinase responsible for T278 was as yet unknown and identified in the first part of this thesis. In a screen for T278 phosphorylating kinases using a phospho-specific antibody against phosphorylated T278 AMP-activated protein kinase (AMPK) was identified in endothelial cells. Mutants of AMPK with altered kinase-activity modulate T278-phosphorylation levels in cells. AMPK-driven T278-phosphorylation impaired stress fiber formation and changed cell morphology in living cells. AMPK is a fundamental sensor of cellular and whole body energy homeostasis. Zucker Diabetic Fatty (ZDF) rats, which are an animal model for type II diabetes mellitus, were used to analyze the impact of phosphorylated T278 in vivo. AMPK-activity and T278-phosphorylation were substantially reduced in arterial vessel walls of ZDF rats in comparison to control animals. These findings demonstrate that VASP is a new AMPK substrate, that VASP phosphorylation mediates the effects of metabolic regulation on actin cytoskeleton rearrangements, and that this signaling system becomes down-regulated in diabetic vessel disorders in rats. In the second part of this thesis, a functional analysis of differential VASP phosphorylations was performed. To systematically address VASP phosphorylation patterns, a set of VASP phosphomimetic mutants was cloned. These mutants enable the mimicking of defined phosphorylation patterns and the specific analysis of single kinase-mediated phosphorylations. VASP localization to the cell periphery was increased by S157- phosphorylation and modulated by phosphorylation at S239 and T278. Latter phosphorylations synergistically reduced actin polymerization. In contrast, S157- phosphorylation had no effect on actin-dynamics. Taken together, the results of the second part show that phosphorylation of VASP serves as a fine regulator of localization and actin polymerization activity. In summary, this study revealed the functions of VASP phosphorylations and established novel links between signaling pathways and actin cytoskeleton rearrangement.
Background: The frequency of the most observed cancer, Non Hodgkin Lymphoma (NHL), is further rising. Diffuse large B-cell lymphoma (DLBCL) is the most common of the NHLs. There are two subgroups of DLBCL with different gene expression patterns: ABC (“Activated B-like DLBCL”) and GCB (“Germinal Center B-like DLBCL”). Without therapy the patients often die within a few months, the ABC type exhibits the more aggressive behaviour. A further B-cell lymphoma is the Mantle cell lymphoma (MCL). It is rare and shows very poor prognosis. There is no cure yet. Methods: In this project these B-cell lymphomas were examined with methods from bioinformatics, to find new characteristics or undiscovered events on the molecular level. This would improve understanding and therapy of lymphomas. For this purpose we used survival, gene expression and comparative genomic hybridization (CGH) data. In some clinical studies, you get large data sets, from which one can reveal yet unknown trends. Results (MCL): The published proliferation signature correlates directly with survival. Exploratory analyses of gene expression and CGH data of MCL samples (n=71) revealed a valid grouping according to the median of the proliferation signature values. The second axis of correspondence analysis distinguishes between good and bad prognosis. Statistical testing (moderate t-test, Wilcoxon rank-sum test) showed differences in the cell cycle and delivered a network of kinases, which are responsible for the difference between good and bad prognosis. A set of seven genes (CENPE, CDC20, HPRT1, CDC2, BIRC5, ASPM, IGF2BP3) predicted, similarly well, survival patterns as proliferation signature with 20 genes. Furthermore, some bands could be associated with prognosis in the explorative analysis (chromosome 9: 9p24, 9p23, 9p22, 9p21, 9q33 and 9q34). Results (DLBCL): New normalization of gene expression data of DLBCL patients revealed better separation of risk groups by the 2002 published signature based predictor. We could achieve, similarly well, a separation with six genes. Exploratory analysis of gene expression data could confirm the subgroups ABC and GCB. We recognized a clear difference in early and late cell cycle stages of cell cycle genes, which can separate ABC and GCB. Classical lymphoma and best separating genes form a network, which can classify and explain the ABC and GCB groups. Together with gene sets which identify ABC and GCB we get a network, which can classify and explain the ABC and GCB groups (ASB13, BCL2, BCL6, BCL7A, CCND2, COL3A1, CTGF, FN1, FOXP1, IGHM, IRF4, LMO2, LRMP, MAPK10, MME, MYBL1, NEIL1 and SH3BP5; Altogether these findings are useful for diagnosis, prognosis and therapy (cytostatic drugs).
The proventriculus regulates the food passage from crop to midgut. As the haemolymph provides a constantly updated indication of an insect’s nutritional state, it is assumed that the factor controlling the proventri-culus activity is to be found in the haemolymph. The purpose of this doctoral thesis was to investigate how output (metabolic rate), input (food quality and food quantity) and internal state variables (haemolymph osmolarity and haemolymph sugar titer) affect each other and which of these factors controls the activity of the proventriculus in the honeybee. Therefore free-flying foragers were trained to collect con-trolled amounts of different sugar solutions. Immediately after feeding, metabolic rates were measured over different periods of time, then crop-emptying rates and haemolymph sugar titers were measured for the same individual bees. Under all investigated conditions, both the sugar transport rates through the proventriculus and the haemolyph sugar titers depended mainly on the metabolism. For bees collecting controlled amounts of 15 per cent, 30 per cent or 50 per cent sucrose solution haemolymph trehalose, glucose and fructose titers were constant for metabolic rates from 0 to 4.5 mlCO2/h. At higher metabolic rates, trehalose concentration decreased while that of glucose and fructose increased with the exception of bees fed 15 per cent sucrose solution. As the supply of sugar from the crop via the proventriculus was sufficient to support even the highest metabolic rates, the observed pattern must result from an upper limit in the capacity of the fat body to synthesise trehalose. The maximal rate of conversion of glucose to trehalose in the fat body was therefore calculated to average 92.4 µg glucose/min. However, for bees fed 15 per cent sucrose solution both the rate of conversion of glucose to trehalose and the rate of sugar transport from the crop to the midgut were limited, causing an overall decrease in total haemolymph sugar titers for metabolic rates higher than 5 mlCO2/h. Haemolymph sucrose titers were generally low but increased with increasing metabolic rates, even though sucrose was not always detected in bees with high metabolic rates. Though foragers were able to adjust their sugar transport rates precisely to their metabolic rates, a fixed surplus of sugars was transported through the proventriculus under specific feed-ing conditions. This fixed amount of sugars increased with increasing concentration and in-creasing quantity of fed sugar solution, but decreased with progressing time after feeding. This fixed amount of sugars was independent of the metabolic rates of the bees and of the molarity and viscosity of the fed sugar solution. As long as the bees did not exhaust their crop content, the haemolymph sugar titers were unaffected by the sugar surplus, by the time after feeding, by the concentration and by the viscosity of fed sugar solution. When bees were fed pure glucose (or fructose) solutions, un-usually little fructose (or glucose) was found in the haemolymph, leading to lower total haemolymph sugar titers, while the trehalose titer remained unaffected. In order to investigate the mechanisms underlying the regulation of the honeybee proven-triculus, foraging bees were injected either with metabolisable (glucose, fructose, trehalose), or non-metabolisable sugars (sorbose). Bees reacted to injections of metabolisable sugars with reduced crop-emptying rates, but injection of non-metabolisable sugars had no influence on crop emptying. Therefore it is concluded that the proventriculus regulation is controlled by the concentration of metabolisable compounds in the haemolymph, and not by the haemo-lymph osmolarity. A period of 10min was enough to observe reduced crop emptying rates after injections. It is suggested that glucose and fructose have an effect on the proventriculus activity only via their transformation to trehalose. However, when the bees were already in-jected 5min after feeding, no response was detectable. In addition it was investigated whether the overregulation is the result of feed-forward regulation for the imminent take-off and flight. In a first experiment, we investigated whether the bees release an extra amount of sugar solution very shortly before leaving for the hive. In a second experiment, it was tested whether the distance covered by the bees might have an influence on the surplus amount released prior to the take-off. In a third experiment, it was investigated if walking bees fail to release this extra amount of sugars, as they do not have to fly. Though we were not able to demonstrate that the overregulation is the result of feed-forward regulation for the imminent take-off and flight, it is conceivable that this phenome-non is a fixed reaction in foragers that can not be modulated. To investigate whether regulated haemolymph sugar titers are also observed in honeybee foragers returning from natural food sources, their crop contents and haemolymph sugar titers were investigated. While the quantity of the collected nectar was without influence on the haemolymph sugar titers, foragers showed increasing haemolymph sugar titers of glucose, fructose and sucrose with increasing sugar concentration of the carried nectar. In contrast no relationship between crop nectar concentrations and haemolymph trehalose titers was observed. We are sure that the regulation of food passage from crop to midgut is controlled by the trehalose titer. However, under some conditions the balance between consumption and income is not numerically exact. This imprecision depends on the factors which have an impact on the foraging energetics of the bees but are independent of those without influence on the foraging energetics. Therefore we would assume that the proventriculus activity is modulated by the motivational state of the bees.
Heritabilities and repeatabilities are presented for various behavioural attributes affecting foraging performance and fitness in Aquarius (Gerris) remigis (Heteroptera: Gerridae) females. These behavioural attributes were patch choice, foraging success, capture accuracy, and measures of mobility, activity, skittishness and aggressiveness. Most heritabilities were not significantly different from zero, which may be related to the low sampIe size. Conclusions as to the potential of direct selection on behaviour in this species were consequently limited. In contrast, with a few exceptions (capture accuracy, foraging success), most repeatabilities were significant and at times high (range=O'22-O'79), indicating consistent, stereotypical individual behaviour. Tbe Iife history or reproductive state of the daughter generation individuals signifieantly affected the magnitude of the repeatabilities as weil as the mean values of many of the variables (notably mobility and aggressiveness), the latter in a manner consistent with field observations. This indicates that the state of the organism affects the general environmental variance, thus contributing to the discrepancies between the repeatabilities and the heritabilities obtained. It is suggested that common physiological proeesses (e.g. hormones) may underlie several of the behavioural attributes examined, resulting in possible pleiotropie effects and eonstraints on selection in a heterogeneous environment. It is further suggested that field studies of selection on behavioural attributes may be a more fruitful approach in this species, whose suitability for genetic analysis is limited.
Lungfish and coelacanths are the only living sarcopterygian fish. The phylogenetic relationship of lungfish to the last common ancestor of tetrapods and their close morphological similarity to their fossil ancestors make this species uniquely interesting. However their genome size, the largest among vertebrates, is hampering the generation of a whole genome sequence. To provide a partial solution to the problem, a high-coverage lungfish reference transcriptome was generated and assembled. The present findings indicate that lungfish, not coelacanths, are the closest relatives to land-adapted vertebrates. Whereas protein-coding genes evolve at a very slow rate, possibly reflecting a “living fossil” status, transposable elements appear to be active and show high diversity, suggesting a role for them in the remarkable expansion of the lungfish genome. Analyses of single genes and gene families documented changes connected to the water to land transition and demonstrated the value of the lungfish reference transcriptome for comparative studies of vertebrate evolution.
Amphibians evolved in the Devonian period about 400 Mya and represent a transition step in tetrapod evolution. Among amphibians, high-throughput sequencing data are very limited for Caudata, due to their largest genome sizes among terrestrial vertebrates. In this paper we present the transcriptome from the fire bellied newt Cynops orientalis. Data here presented display a high level of completeness, comparable to the fully sequenced genomes available from other amphibians. Moreover, this work focused on genes involved in gametogenesis and sexual development. Surprisingly, the gsdf gene was identified for the first time in a tetrapod species, so far known only from bony fish and basal sarcopterygians. Our analysis failed to isolate fgf24 and foxl3, supporting the possible loss of both genes in the common ancestor of Rhipidistians. In Cynops, the expression analysis of genes described to be sex-related in vertebrates singled out an expected functional role for some genes, while others displayed an unforeseen behavior, confirming the high variability of the sex-related pathway in vertebrates.
A comparative view on sex differentiation and gametogenesis genes in lungfish and coelacanths
(2018)
Gonadal sex differentiation and reproduction are the keys to the perpetuation of favorable gene combinations and positively selected traits. In vertebrates, several gonad development features that differentiate tetrapods and fishes are likely to be, at least in part, related to the water-to-land transition. The collection of information from basal sarcopterygians, coelacanths, and lungfishes, is crucial to improve our understanding of the molecular evolution of pathways involved in reproductive functions, since these organisms are generally regarded as “living fossils” and as the direct ancestors of tetrapods. Here, we report for the first time the characterization of >50 genes related to sex differentiation and gametogenesis in Latimeria menadoensis and Protopterus annectens. Although the expression profiles of most genes is consistent with the intermediate position of basal sarcopterygians between actinopterygian fish and tetrapods, their phylogenetic placement and presence/absence patterns often reveal a closer affinity to the tetrapod orthologs. On the other hand, particular genes, for example, the male gonad factor gsdf (Gonadal Soma-Derived Factor), provide examples of ancestral traits shared with actinopterygians, which disappeared in the tetrapod lineage.
Polyploid genomes present a challenge for cytogenetic and genomic studies, due to the high number of similar size chromosomes and the simultaneous presence of hardly distinguishable paralogous elements. The karyotype of the Siberian sturgeon (Acipenser baerii) contains around 250 chromosomes and is remarkable for the presence of paralogs from two rounds of whole-genome duplications (WGD). In this study, we applied the sterlet-derived acipenserid satDNA-based whole chromosome-specific probes to analyze the Siberian sturgeon karyotype. We demonstrate that the last genome duplication event in the Siberian sturgeon was accompanied by the simultaneous expansion of several repetitive DNA families. Some of the repetitive probes serve as good cytogenetic markers distinguishing paralogous chromosomes and detecting ancestral syntenic regions, which underwent fusions and fissions. The tendency of minisatellite specificity for chromosome size groups previously observed in the sterlet genome is also visible in the Siberian sturgeon. We provide an initial physical chromosome map of the Siberian sturgeon genome supported by molecular markers. The application of these data will facilitate genomic studies in other recent polyploid sturgeon species.
Background
Neisseria meningitidis is a naturally transformable, facultative pathogen colonizing the human nasopharynx. Here, we analyze on a genome-wide level the impact of recombination on gene-complement diversity and virulence evolution in N. meningitidis. We combined comparative genome hybridization using microarrays (mCGH) and multilocus sequence typing (MLST) of 29 meningococcal isolates with computational comparison of a subset of seven meningococcal genome sequences.
Principal Findings
We found that lateral gene transfer of minimal mobile elements as well as prophages are major forces shaping meningococcal population structure. Extensive gene content comparison revealed novel associations of virulence with genetic elements besides the recently discovered meningococcal disease associated (MDA) island. In particular, we identified an association of virulence with a recently described canonical genomic island termed IHT-E and a differential distribution of genes encoding RTX toxin- and two-partner secretion systems among hyperinvasive and non-hyperinvasive lineages. By computationally screening also the core genome for signs of recombination, we provided evidence that about 40% of the meningococcal core genes are affected by recombination primarily within metabolic genes as well as genes involved in DNA replication and repair. By comparison with the results of previous mCGH studies, our data indicated that genetic structuring as revealed by mCGH is stable over time and highly similar for isolates from different geographic origins.
Conclusions
Recombination comprising lateral transfer of entire genes as well as homologous intragenic recombination has a profound impact on meningococcal population structure and genome composition. Our data support the hypothesis that meningococcal virulence is polygenic in nature and that differences in metabolism might contribute to virulence.
Cooperative Breeding in the Ambrosia Beetle Xyleborus affinis and Management of Its Fungal Symbionts
(2020)
Fungus-farming is known from attine ants, macrotermites, and ambrosia beetles (Scolytinae, Platypodinae). Farming ant and termite societies are superorganismal and grow fungal cultivars in monocultures. Social organization of ambrosia beetle groups and their farming systems are poorly studied, because of their enigmatic life within tunnel systems inside of wood. Ambrosia beetle-fungus symbioses evolved many times independently in both the beetles and their fungal cultivars. Observations suggest that there is evolutionary convergence between these lineages, but also a high variation in the degree of sociality and the modes of fungiculture. Using a laboratory observation technique, I here tried to give insights into the social system and fungus symbiosis of the sugar-cane borer, Xyleborus affinis Eichhoff (Scolytinae: Curculionidae), a currently poorly studied ambrosia beetle. The study revealed a cooperatively breeding system characterized by delayed dispersal of adult daughters, alloparental brood care by larvae and adults, and about half of the totipotent adult daughters laying eggs within the natal nest. Most interesting, there was a tendency of egg-laying females to engage more commonly in mutually beneficial behaviors than non-egg-layers. Fungus gardens covering gallery walls composed of five different filamentous fungi. A Raffaelea isolate was predominant and together with an unidentified fungus likely served as the main food for adults and larvae. Three isolates, a Mucor, a Fusarium and a Phaeoacremonium isolate were most abundant in the oldest gallery part close to the entrance; Mucor, Fusarium and the Raffaelea isolate in diseased individuals. Additionally, there was correlative evidence for some fungal isoaltes influencing beetle feeding and hygienic behaviors. Overall, X. affinis is now the second ambrosia beetle that can be classified as a cooperative breeder with division of labor among and between adults and larvae.
Bedeutung der NO-sensitiven Guanylyl Cyclase bei der Angiogenese und der Arteriogenese in der Maus
(2014)
Stickstoffmonoxid (NO) spielt eine wichtige Rolle bei Gefäßremodelling-Prozessen wie Angiogenese und Arteriogenese. Die NO-Synthese im Gefäßsystem wird hauptsächlich durch die endotheliale NO-Synthase (eNOS) gewährleistet. Sie kann durch verschiedene Faktoren wie Scherkräfte und Zytokine wie der vaskuläre endotheliale Wachstumsfaktor (VEGF) reguliert werden. VEGF ist ein wichtiger Stimulator der Angiogenese und wird während dieses Prozesses hochreguliert. Die meisten physiologischen Effekte von NO werden durch die NO-sensitive Guanylyl-Cyclase (NO-GC) vermittelt. Als Hauptrezeptor für NO produziert die NO-GC den sekundären Botenstoff cyklisches Guanosinmonophosphat (cGMP) und führt dadurch zur Stimulation der verschiedenen Effektoren wie z.B. der PKG. Ob die Wirkung von NO in Angiogenese und Arteriogenese ebenfalls durch NO-GC vermittelt wird, war bis zum Beginn dieser Arbeit noch unklar.
Die NO-GC besteht aus zwei Untereinheiten (α und ß). Die Deletion der ß1-Untereinheit in Mäusen resultiert in einer vollständigen Knockout Maus (GCKO). Mithilfe des Cre-LoxP-Systems wurden zusätzlich zellspezifische Knockout-Mäuse für glatte Muskelzellen (SMC-GCKO) und Endothelzellen (EC-GCKO) generiert. Um die Rolle der NO-GC in der Angiogenese und Arteriogenese zu untersuchen, wurden drei gut etablierte Methoden benutzt.
Im ersten Teil des Projekts sollte die Expression der NO-GC in Endothelzellen untersucht werden. Zu diesem Zweck wurde die reverse Transkriptase-Polymerase-Kettenreaktion (RT-PCR) benutzt. Die Ergebnisse zeigen, dass die NO-GC in Endothelzellen der Lunge nur äußerst gering wenig exprimiert ist. Durch den Aortenring-Assay wurde eine Rolle der NO-GC bei der VEGF-vermittelten Angiogenese festgestellt. Dabei zeigte sich eine stärkere Angiogeneserate bei globaler Abwesenheit der NO-GC. Bei Fehlen der NO-GC ausschließlich in Endothelzellen zeigte sich kein Unterschied in den aussprossenden Aorten im Vergleich zu den Kontroll-Tieren. Dies zeigt, dass die NO-GC in Endothelzellen sehr wahrscheinlich keine Rolle bei der VEGF-vermittelten Angiogenese spielt.
Im zweiten Teil wurde die Rolle der NO-GC bei der Angiogenese in einem in vivo-Modell untersucht. In dem Modell der Sauerstoff-induzierten-Retinopathie zeigten die GCKO-Mäuse eine verringerte Vaso-Obliteration, eine verlangsamte Angiogenese und eine erhöhte Tuft-Bildung. Ähnliche Ergebnisse wurden bei den SMC-GCKO-Tieren beobachtet. EC-GCKO-Mäuse zeigten eine gegenüber den Kontroll-Tieren unveränderte Vaso-Obliteration, Angiogeneserate und Tuft-Bildung. Diese Ergebnisse lassen darauf schließen, dass die NO-GC in Endothelzellen keine Rolle spielt. Immunfluoreszenz-Aufnahmen zeigten die Expression von NO-GC in Perizyten der Gefäßkapillaren der Mausretina. Daher könnte die NO-GC in diesem Zelltyp letztendlich für die Effekte bei den GCKO- und SMC-GCKO-Tieren verantwortlich sein.
Im letzten Teil dieser Arbeit wurde eine Versuchsreihe unter Anwendung des Hinterlauf-Ischämie-Modells durchgeführt. Hierbei entwickelten die Pfoten aller GCKO- und teilweise der SMC-GCKO-Tiere nach der Ligation der Femoralarterie eine Nekrose. Die Regeneration der Hinterläufe der EC-GCKO-Tiere nach der Operation verlief normal. Diese Ergebnisse schließen eine bedeutende Rolle der NO-GC in Endothelzellen aus, zeigen allerdings, dass die NO-GC in den glatten Muskelzellen essentiell für den Arteriogenese-Prozess ist.
Zusammengefasst führt die Deletion der NO-GC in glatten Muskelzellen und wahrscheinlich auch in Perizyten zur einer verlangsamten Angiogenese und Inhibierung der Arteriogenese.