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.

Characterization of DnmA, the Dnmt2 homolog in Dictyostelium discoideum

Eukaryotic DNA m5C methyltransferases (MTases) play a major role in many epigenetic regulatory processes like genomic imprinting, X-chromosome inactivation, silencing of transposons and gene expression. Members of the two DNA m5C MTase families, Dnmt1 and Dnmt3, are relatively well studied and many details of their biological functions, biochemical properties as well as interaction partners are known. In contrast, the biological functions of the highly conserved Dnmt2 family, which appear to have non-canonical dual substrate specificity, remain enigmatic despite the efforts of many researchers. The genome of the social amoeba Dictyostelium encodes Dnmt2-homolog, the DnmA, as the only DNA m5C MTase which allowed us to study Dnmt2 function in this organism without interference by the other enzymes. The dnmA gene can be easily disrupted but the knock-out clones did not show obvious phenotypes under normal lab conditions, suggesting that the function of DnmA is not vital for the organism. It appears that the dnmA gene has a low expression profile during vegetative growth and is only 5-fold upregulated during development. Fluorescence microscopy indicated that DnmA-GFP fusions were distributed between both the nucleus and cytoplasm with some enrichment in nuclei. Interestingly, the experiments showed specific dynamics of DnmA-GFP distribution during the cell cycle. The proteins colocalized with DNA in the interphase and were mainly removed from nuclei during mitosis. DnmA functions as an active DNA m5C MTase in vivo and is responsible for weak but detectable DNA methylation of several regions in the Dictyostelium genome. Nevertheless, gel retardation assays showed only slightly higher affinity of the enzyme to dsDNA compared to ssDNA and no specificity towards various sequence contexts, although weak but detectable specificity towards AT-rich sequences was observed. This could be due to intrinsic curvature of such sequences. Furthermore, DnmA did not show denaturant-resistant covalent complexes with dsDNA in vitro, although it could form covalent adducts with ssDNA. Low binding and methyltransfer activity in vitro suggest the necessity of additional factor in DnmA function. Nevertheless, no candidates could be identified in affinity purification experiments with different tagged DnmA fusions. In this respect, it should be noted that tagged DnmA fusion preparations from Dictyostelium showed somewhat higher activity in both covalent adduct formation and methylation assays than DnmA expressed in E.coli. Thus, the presence of co-purified factors cannot be excluded. The low efficiency of complex formation by the recombinant enzyme and the failure to define interacting proteins that could be required for DNA methylation in vivo, brought up the assumption that post-translational modifications could influence target recognition and enzymatic activity. Indeed, sites of phosphorylation, methylation and acetylation were identified within the target recognition domain (TRD) of DnmA by mass spectrometry. For phosphorylation, the combination of MS data and bioinformatic analysis revealed that some of the sites could well be targets for specific kinases in vivo. Preliminary 3D modeling of DnmA protein based on homology with hDNMT2 allowed us to show that several identified phosphorylation sites located on the surface of the molecule, where they would be available for kinases. The presence of modifications almost solely within the TRD domain of DnmA could potentially modulate the mode of its interaction with the target nucleic acids. DnmA was able to form denaturant-resistant covalent intermediates with several Dictyostelium tRNAs, using as a target C38 in the anticodon loop. The formation of complexes not always correlated with the data from methylation assays, and seemed to be dependent on both sequence and structure of the tRNA substrate. The pattern, previously suggested by the Helm group for optimal methyltransferase activity of hDNMT2, appeared to contribute significantly in the formation of covalent adducts but was not the only feature of the substrate required for DnmA and hDNMT2 functions. Both enzymes required Mg2+ to form covalent complexes, which indicated that the specific structure of the target tRNA was indispensable. The dynamics of covalent adduct accumulation was different for DnmA and different tRNAs. Interestingly, the profiles of covalent adduct accumulation for different tRNAs were somewhat similar for DnmA and hDNMT2 enzymes. According to the proposed catalytic mechanism for DNA m5C MTases, the observed denaturant-resistant complexes corresponded to covalent enamine intermediates. The apparent discrepancies in the data from covalent complex formation and methylation assays may be interpreted by the possibility of alternative pathways of the catalytic mechanism, leading not to methylation but to exchange or demethylation reactions. The reversibility of enamine intermediate formation should also be considered. Curiously, native gel retardation assays showed no or little difference in binding affinities of DnmA to different RNA substrates and thus the absence of specificity in the initial enzyme binding. The meaning of the tRNA methylation as well as identification of novel RNA substrates in vivo should be the aim of further experiments.

Characterization theorem for classical orthogonal polynomials on non-uniform lattices: The functional approach

Using the functional approach, we state and prove a characterization theorem for classical orthogonal polynomials on non-uniform lattices (quadratic lattices of a discrete or a q-discrete variable) including the Askey-Wilson polynomials. This theorem proves the equivalence between seven characterization properties, namely the Pearson equation for the linear functional, the second-order divided-difference equation, the orthogonality of the derivatives, the Rodrigues formula, two types of structure relations,and the Riccati equation for the formal Stieltjes function.

Dynamic characterization of olfactory receptors in the fruit fly Drosophila melanogaster

Temporal changes in odor concentration are vitally important to many animals orienting and navigating in their environment. How are such temporal changes detected? Within the scope of the present work an accurate stimulation and analysis system was developed to examine the dynamics of physiological properties of Drosophila melanogaster olfactory receptor organs. Subsequently a new method for delivering odor stimuli was tested and used to present the first dynamic characterization of olfactory receptors at the level of single neurons. Initially, recordings of the whole antenna were conducted while stimulating with different odors. The odor delivery system allowed the dynamic characterization of the whole fly antenna, including its sensilla and receptor neurons. Based on the obtained electroantennogram data a new odor delivery method called digital sequence method was developed. In addition the degree of accuracy was enhanced, initially using electroantennograms, and later recordings of odorant receptor cells at the single sensilla level. This work shows for the first time that different odors evoked different responses within one neuron depending on the chemical structure of the odor. The present work offers new insights into the dynamic properties of olfactory transduction in Drosophila melanogaster and describes time dependent parameters underlying these properties.

Large-Size AlGaN/GaN HEMT Large-Signal Electrothermal Characterization and Modeling for Wireless Digital Communications

The rapid growth in high data rate communication systems has introduced new high spectral efficient modulation techniques and standards such as LTE-A (long term evolution-advanced) for 4G (4th generation) systems. These techniques have provided a broader bandwidth but introduced high peak-to-average power ratio (PAR) problem at the high power amplifier (HPA) level of the communication system base transceiver station (BTS). To avoid spectral spreading due to high PAR, stringent requirement on linearity is needed which brings the HPA to operate at large back-off power at the expense of power efficiency. Consequently, high power devices are fundamental in HPAs for high linearity and efficiency. Recent development in wide bandgap power devices, in particular AlGaN/GaN HEMT, has offered higher power level with superior linearity-efficiency trade-off in microwaves communication. For cost-effective HPA design to production cycle, rigorous computer aided design (CAD) AlGaN/GaN HEMT models are essential to reflect real response with increasing power level and channel temperature. Therefore, large-size AlGaN/GaN HEMT large-signal electrothermal modeling procedure is proposed. The HEMT structure analysis, characterization, data processing, model extraction and model implementation phases have been covered in this thesis including trapping and self-heating dispersion accounting for nonlinear drain current collapse. The small-signal model is extracted using the 22-element modeling procedure developed in our department. The intrinsic large-signal model is deeply investigated in conjunction with linearity prediction. The accuracy of the nonlinear drain current has been enhanced through several issues such as trapping and self-heating characterization. Also, the HEMT structure thermal profile has been investigated and corresponding thermal resistance has been extracted through thermal simulation and chuck-controlled temperature pulsed I(V) and static DC measurements. Higher-order equivalent thermal model is extracted and implemented in the HEMT large-signal model to accurately estimate instantaneous channel temperature. Moreover, trapping and self-heating transients has been characterized through transient measurements. The obtained time constants are represented by equivalent sub-circuits and integrated in the nonlinear drain current implementation to account for complex communication signals dynamic prediction. The obtained verification of this table-based large-size large-signal electrothermal model implementation has illustrated high accuracy in terms of output power, gain, efficiency and nonlinearity prediction with respect to standard large-signal test signals.

Characterization of Novel Fabry Pérot Filter Arrays for Nanospectrometers in Medical Applications

Optische Spektroskopie ist eine sehr wichtige Messtechnik mit einem hohen Potential für zahlreiche Anwendungen in der Industrie und Wissenschaft. Kostengünstige und miniaturisierte Spektrometer z.B. werden besonders für moderne Sensorsysteme “smart personal environments” benötigt, die vor allem in der Energietechnik, Messtechnik, Sicherheitstechnik (safety and security), IT und Medizintechnik verwendet werden. Unter allen miniaturisierten Spektrometern ist eines der attraktivsten Miniaturisierungsverfahren das Fabry Pérot Filter. Bei diesem Verfahren kann die Kombination von einem Fabry Pérot (FP) Filterarray und einem Detektorarray als Mikrospektrometer funktionieren. Jeder Detektor entspricht einem einzelnen Filter, um ein sehr schmales Band von Wellenlängen, die durch das Filter durchgelassen werden, zu detektieren. Ein Array von FP-Filter wird eingesetzt, bei dem jeder Filter eine unterschiedliche spektrale Filterlinie auswählt. Die spektrale Position jedes Bandes der Wellenlänge wird durch die einzelnen Kavitätshöhe des Filters definiert. Die Arrays wurden mit Filtergrößen, die nur durch die Array-Dimension der einzelnen Detektoren begrenzt werden, entwickelt. Allerdings erfordern die bestehenden Fabry Pérot Filter-Mikrospektrometer komplizierte Fertigungsschritte für die Strukturierung der 3D-Filter-Kavitäten mit unterschiedlichen Höhen, die nicht kosteneffizient für eine industrielle Fertigung sind. Um die Kosten bei Aufrechterhaltung der herausragenden Vorteile der FP-Filter-Struktur zu reduzieren, wird eine neue Methode zur Herstellung der miniaturisierten FP-Filtern mittels NanoImprint Technologie entwickelt und präsentiert. In diesem Fall werden die mehreren Kavitäten-Herstellungsschritte durch einen einzigen Schritt ersetzt, die hohe vertikale Auflösung der 3D NanoImprint Technologie verwendet. Seit dem die NanoImprint Technologie verwendet wird, wird das auf FP Filters basierende miniaturisierte Spectrometer nanospectrometer genannt. Ein statischer Nano-Spektrometer besteht aus einem statischen FP-Filterarray auf einem Detektorarray (siehe Abb. 1). Jeder FP-Filter im Array besteht aus dem unteren Distributed Bragg Reflector (DBR), einer Resonanz-Kavität und einen oberen DBR. Der obere und untere DBR sind identisch und bestehen aus periodisch abwechselnden dünnen dielektrischen Schichten von Materialien mit hohem und niedrigem Brechungsindex. Die optischen Schichten jeder dielektrischen Dünnfilmschicht, die in dem DBR enthalten sind, entsprechen einen Viertel der Design-Wellenlänge. Jeder FP-Filter wird einer definierten Fläche des Detektorarrays zugeordnet. Dieser Bereich kann aus einzelnen Detektorelementen oder deren Gruppen enthalten. Daher werden die Seitenkanal-Geometrien der Kavität aufgebaut, die dem Detektor entsprechen. Die seitlichen und vertikalen Dimensionen der Kavität werden genau durch 3D NanoImprint Technologie aufgebaut. Die Kavitäten haben Unterschiede von wenigem Nanometer in der vertikalen Richtung. Die Präzision der Kavität in der vertikalen Richtung ist ein wichtiger Faktor, der die Genauigkeit der spektralen Position und Durchlässigkeit des Filters Transmissionslinie beeinflusst.

Characterization of the molecular clockwork in the cockroach Rhyparobia maderae

Der Wechsel von Tag und Nacht erzeugt einen regelmäßigen Rhythmus von verschiedenen Umweltreizen, allen voran Licht und Temperatur. Fast jedes bis zum heutigen Tage untersuchte Lebewesen besitzt einen endogenen Mechanismus zur Zeitwahrnehmung, und diese "innere Uhr" befähigt Lebewesen dazu, sich vorausschauend an rhythmische Umwelt-Änderungen anzupassen. Circadiane Rhythmen bestehen auch ohne jegliche äußere Reize und basieren auf einem molekularen Rückkopplungs-Mechanismus, der Rhythmen in Genexpression und Proteinkonzentration von etwa 24 Stunden erzeugt. Obwohl sich die grundsätzlichen Mechanismen und Komponenten dieses molekularen Uhrwerks in allen Insekten ähneln, zeigte sich jedoch immer mehr, dass es im Detail doch wesentliche Unterschiede zwischen verschiedenen Insektengruppen gibt. Während das molekulare Uhrwerk der Fruchtfliege Drosophila melanogaster inzwischen sehr gut untersucht ist, fehlen bei den meisten Insektengruppen immernoch eingehende Untersuchungen. Fast nichts ist über die molekulare Basis von circadianen Rhythmen bei der Schabe Rhyparobia maderae bekannt, obwohl diese Art bereits seit Langem als Modellorganismus in der Chronobiologie dient. Um mit der Forschung am molekularen, circadianen System von R. maderae zu beginnen, wurde die Struktur und das Expressionsprofil der core feedback loop Gene per, tim1 und cry2 analysiert. Mittels degenerierten Primern und RACE konnte das vollständige offene Leseraster (OLR) von rmPer und rmCry2, und ein Teil des rmTim1 OLR kloniert werden. Eine phylogenetische Analyse gruppierte rmPER und rmCRY2 gemeinsam mit den Orthologa hemimetaboler Insekten. Viele bei D. melanogaster funktionell charakterisierte Domänen sind bei diesen Proteinen konserviert, was auf eine ähnliche Funktion in der inneren Uhr von R. maderae hinweist. Mittels quantitativer PCR konnte gezeigt werden, dass die mRNA von rmPer, rmTim1 und rmCry2 in verschiedenen Lichtregimen in der gleichen Phasenlage Tageszeit-abhängig schwankt. Die Phasenlage stellte sich bei unterschiedlichen Photoperioden jeweils relativ zum Beginn der Skotophase ein, mit Maxima in der ersten Hälfte der Nacht. Auch im Dauerdunkel zeigen sich Rhythmen in der rmTim1 und rmCry2 Expression. Die Amplitude der rmPer Expressionsrhythmen war jedoch so gering, dass keine signifikanten Unterschiede zwischen den einzelnen Zeitgeberzeiten (ZT) festgestellt werden konnten. Mittels Laufrad-Assays wurde untersucht wie Kurz- und Langtag Lichtregime die Verhaltensrhythmen beeinflussen. Es konnten nur Unterschiede in der Periodenlänge unter freilaufenden Bedingungen festgestellt werden, wenn höhere Lichtintensitäten (1000lx) zur Synchronisation (entrainment) genutzt wurden. Die Periode des freilaufenden Rhythmus war bei Tieren aus dem Kurztag länger. Die photoperiodische Plastizität zeigte sich also auch auf Verhaltensebene, obwohl höhere Lichtintensitäten notwendig waren um einen Effekt zu beobachten. Basierend auf den Sequenzen der zuvor klonierten OLR wurden gegen rmPER, rmTIM1 und rmCRY2 gerichtete Antikörper hergestellt. Die Antikörper gegen rmPER und rmTIM1 erkannten in western blots sehr wahrscheinlich spezifisch das jeweilige Protein. Zeitreihen von Gehirngewebe-Homogenisaten zeigten keinen offensichtlichen circadianen Rhythmus in der Proteinkonzentration, wahrscheinlich auf Grund einer Oszillation mit niedriger Amplitude. In Immunhistochemischen Färbungen konnte nur mit dem gegen rmPER gerichteten Antikörper aus Kaninchen ein Signal beobachtet werden. Beinahe jede Zelle des Zentralnervensystems war rmPER-immunreaktiv im Zellkern. Es konnten keine Unterschiede zwischen den untersuchten ZTs festgestellt werden, ähnlich wie bei den western blot Zeitreihen. In dieser Studie konnten erstmals molekulare Daten der circadianen Uhr von R. maderae erfasst und dargestellt werden. Die Uhrgene per, tim1 und cry2 werden in dieser Schabenart exprimiert und ihre Domänenstruktur sowie das circadiane Expressionsmuster ähneln dem hypothetischen ursprünglichen Insektenuhrwerk, welches der circadianen Uhr von Vertebraten nahesteht. Das molekulare Uhrwerk von R. maderae kann sich an unterschiedliche Photoperioden anpassen, und diese Anpassungen manifestieren sich im Expressionsprofil der untersuchten Uhrgene ebenso wie im Verhalten.