Structural characterization and distribution of zebrafish germ plasm during interphase and mitosis

In zebrafish, germ cells are responsible for transmitting the genetic information from one generation to the next. During the first cleavages of zebrafish embryonic development, a specialized part of the cytoplasm known as germ plasm, is responsible of committing four blastomeres to become the progenitors of all germ cells in the forming embryo. Much is known about how the germ plasm is spatially distributed in early stages of primordial germ cell development, a process described to be dependant on microtubules and actin. However, little is known about how the material is inherited after it reorganizes into a perinuclear location, or how is the symmetrical distribution regulated in order to ensure proper inheritance of the material by both daughter cells. It is also not clear whether there is a controlled mechanism that regulates the number of granules inherited by the daughter cells, or whether it is a random process. We describe the distribution of germ plasm material from 4hpf to 24hpf in zebrafish primordial germ cells using Vasa protein as marker. Vasa positive material appears to be conglomerate into 3 to 4 big spherical structures at 4hpf. While development progresses, these big structures become smaller perinuclear granules that reach a total number of approximately 30 at 24hpf. We investigated how this transformation occurs and how the minus-end microtubule dependent motor protein Dynein plays a role in this process. Additionally, we describe specific colocalization of microtubules and perinuclear granules during interphase and more interestingly, during all different stages of cell division. We show that distribution of granules follow what seems to be a regulated distribution: during cells division, daughter cells inherit an equal number of granules. We propose that due to the permanent colocalization of microtubular structures with germinal granules during interphase and cell division, a coordinated mechanism between these structures may ensure proper distribution of the material among daughter cells. Furthermore, we show that exposure to the microtubule-depolymerizing drug nocodazole leads to disassembly of the germ cell nuclear lamin matrix, chromatin condensation, and fusion of granules to a big conglomerate, revealing dependence of granular distribution on microtubules and proper nuclear structure.

Nuclear organisation and epigenetic regulation of gene expression in Dictyostelium discoideum

A series of vectors for the over-expression of tagged proteins in Dictyostelium were designed, constructed and tested. These vectors allow the addition of an N- or C-terminal tag (GFP, RFP, 3xFLAG, 3xHA, 6xMYC and TAP) with an optimized polylinker sequence and no additional amino acid residues at the N or C terminus. Different selectable markers (Blasticidin and gentamicin) are available as well as an extra chromosomal version; these allow copy number and thus expression level to be controlled, as well as allowing for more options with regard to complementation, co- and super-transformation. Finally, the vectors share standardized cloning sites, allowing a gene of interest to be easily transfered between the different versions of the vectors as experimental requirements evolve. The organisation and dynamics of the Dictyostelium nucleus during the cell cycle was investigated. The centromeric histone H3 (CenH3) variant serves to target the kinetochore to the centromeres and thus ensures correct chromosome segregation during mitosis and meiosis. A number of Dictyostelium histone H3-domain containing proteins as GFP-tagged fusions were expressed and it was found that one of them functions as CenH3 in this species. Like CenH3 from some other species, Dictyostelium CenH3 has an extended N-terminal domain with no similarity to any other known proteins. The targeting domain, comprising α-helix 2 and loop 1 of the histone fold is required for targeting CenH3 to centromeres. Compared to the targeting domain of other known and putative CenH3 species, Dictyostelium CenH3 has a shorter loop 1 region. The localisation of a variety of histone modifications and histone modifying enzymes was examined. Using fluorescence in situ hybridisation (FISH) and CenH3 chromatin-immunoprecipitation (ChIP) it was shown that the six telocentric centromeres contain all of the DIRS-1 and most of the DDT-A and skipper transposons. During interphase the centromeres remain attached to the centrosome resulting in a single CenH3 cluster which also contains the putative histone H3K9 methyltransferase SuvA, H3K9me3 and HP1 (heterochromatin protein 1). Except for the centromere cluster and a number of small foci at the nuclear periphery opposite the centromeres, the rest of the nucleus is largely devoid of transposons and heterochromatin associated histone modifications. At least some of the small foci correspond to the distal telomeres, suggesting that the chromosomes are organised in a Rabl-like manner. It was found that in contrast to metazoans, loading of CenH3 onto Dictyostelium centromeres occurs in late G2 phase. Transformation of Dictyostelium with vectors carrying the G418 resistance cassette typically results in the vector integrating into the genome in one or a few tandem arrays of approximately a hundred copies. In contrast, plasmids containing a Blasticidin resistance cassette integrate as single or a few copies. The behaviour of transgenes in the nucleus was examined by FISH, and it was found that low copy transgenes show apparently random distribution within the nucleus, while transgenes with more than approximately 10 copies cluster at or immediately adjacent to the centromeres in interphase cells regardless of the actual integration site along the chromosome. During mitosis the transgenes show centromere-like behaviour, and ChIP experiments show that transgenes contain the heterochromatin marker H3K9me2 and the centromeric histone variant H3v1. This clustering, and centromere-like behaviour was not observed on extrachromosomal transgenes, nor on a line where the transgene had integrated into the extrachromosomal rDNA palindrome. This suggests that it is the repetitive nature of the transgenes that causes the centromere-like behaviour. A Dictyostelium homolog of DET1, a protein largely restricted to multicellular eukaryotes where it has a role in developmental regulation was identified. As in other species Dictyostelium DET1 is nuclear localised. In ChIP experiments DET1 was found to bind the promoters of a number of developmentally regulated loci. In contrast to other species where it is an essential protein, loss of DET1 is not lethal in Dictyostelium, although viability is greatly reduced. Loss of DET1 results in delayed and abnormal development with enlarged aggregation territories. Mutant slugs displayed apparent cell type patterning with a bias towards pre-stalk cell types.

Information Exchange and Fusion in Dynamic and Heterogeneous Distributed Environments

Context awareness, dynamic reconfiguration at runtime and heterogeneity are key characteristics of future distributed systems, particularly in ubiquitous and mobile computing scenarios. The main contributions of this dissertation are theoretical as well as architectural concepts facilitating information exchange and fusion in heterogeneous and dynamic distributed environments. Our main focus is on bridging the heterogeneity issues and, at the same time, considering uncertain, imprecise and unreliable sensor information in information fusion and reasoning approaches. A domain ontology is used to establish a common vocabulary for the exchanged information. We thereby explicitly support different representations for the same kind of information and provide Inter-Representation Operations that convert between them. Special account is taken of the conversion of associated meta-data that express uncertainty and impreciseness. The Unscented Transformation, for example, is applied to propagate Gaussian normal distributions across highly non-linear Inter-Representation Operations. Uncertain sensor information is fused using the Dempster-Shafer Theory of Evidence as it allows explicit modelling of partial and complete ignorance. We also show how to incorporate the Dempster-Shafer Theory of Evidence into probabilistic reasoning schemes such as Hidden Markov Models in order to be able to consider the uncertainty of sensor information when deriving high-level information from low-level data. For all these concepts we provide architectural support as a guideline for developers of innovative information exchange and fusion infrastructures that are particularly targeted at heterogeneous dynamic environments. Two case studies serve as proof of concept. The first case study focuses on heterogeneous autonomous robots that have to spontaneously form a cooperative team in order to achieve a common goal. The second case study is concerned with an approach for user activity recognition which serves as baseline for a context-aware adaptive application. Both case studies demonstrate the viability and strengths of the proposed solution and emphasize that the Dempster-Shafer Theory of Evidence should be preferred to pure probability theory in applications involving non-linear Inter-Representation Operations.

Untersuchungen zu Controlled Traffic Farming und satellitenbasierten Lenksystemen

Diese Arbeit behandelt Controlled Traffic Farming (CTF) Anbausysteme, bei denen für alle Arbeitsgänge satellitengesteuert immer dieselben Fahrspuren benutzt werden. Lässt sich mit CTF die Belastung des Bodens verringern und die Effizienz von Direktsaat-Anbausystemen steigern? Neben agronomischen und bodenphysikalischen Parametern wurden Auswirkungen von Lenksystemen und Umsetzungsmöglichkeiten von CTF in die Praxis untersucht. Die Analyse einer CTF-Umsetzung unter europäischen Bedingungen mit der Verwendung von Standardmaschinen zeigte, dass sich CTF-Anbausysteme mit den heute zur Verfügung stehenden Maschinen für Dauergrünland, Mähdruschfrüchte und Mais auf kleiner und grösser strukturierten Flächen relativ einfach mechanisieren lassen. Bei Zuckerrüben und Kartoffeln können Kompromisse notwendig sein. Generell erfordern CTF-Anbausysteme eine sorgfältige Planung und Umsetzung in die Praxis. Im dreijährigen Feldversuch (Winterweizen, Wintergerste, Kunstwiese mit Kleegrasmischung) auf einem Lehmboden wurde CTF-Direktsaat mit konventionell zufällig befahrenen Direktsaat- und Pflugverfahren verglichen. Unter CTF zeigte sich eine Differenzierung der nicht, gering und intensiv befahrenen Varianten. Auf dem vorliegenden kompakten Boden mit 1150 mm Jahresniederschlag waren die Unterschiede zwischen den nicht befahrenen Flächen und den mit niedrigem Kontaktflächendruck befahrenen Flächen eher gering. In den nicht befahrenen Flächen entwickelten Eindringwiderstand und Kohlendioxidgehalt der Bodenluft nach drei Jahren signifikant bessere Werte. Bodendichte und Porosität zeigten hingegen keinen eindeutig interpretierbaren Trend. Aufgrund teils suboptimaler Feldaufgänge liess sich keine generelle agronomische Tendenz ableiten. Die intensive Befahrung der Pflegefahrgassen zeigte allerdings klar negative bodenkundliche und planzenbauliche Auswirkungen. Es bietet sich daher an, vor allem für Pflegearbeiten permanent dieselben Fahrspuren zu nutzen. In der Untersuchung zu den Auswirkungen von Lenksystemen zeigten sich signifikante Vorteile von Lenksystemen in einer Verminderung der Fahrerbelastung und einer höheren Lenkgenauigkeit vor allem bei grossen Arbeitsbreiten ohne Spuranreisser. Die meisten anderen Messparameter waren mit Lenksystem leicht vorteilhafter als ohne, unterschieden sich aber nicht signifikant voneinander. Fahrer und naturräumliche Gegebenheiten wie die Schlagform hatten einen wesentlich grösseren Einfluss. Gesamthaft betrachtet erweitert CTF in Kombination mit weiteren Bodenschutzmass-nahmen die Möglichkeiten, Bodenverdichtungen zu vermeiden, den Bedarf an energieintensiver Bodenlocke-rung zu reduzieren und die Entwicklung einer stabileren Bodenstruktur mit höherer Tragfähigkeit zu fördern. Zusammen mit einer an Kultur und Anbausystem angepassten Saatbettbereitung und den in geraden Reihen einfacher durchführbaren mechanischen Pflegemassnahmen ergeben sich gute Voraussetzungen für die Gestaltung agronomisch leistungsfähiger und ökologisch nachhaltiger Anbausysteme.