On the function of the Dictyostelium Argonaute A protein (AgnA) in epigenetic gene regulation

With molecular biology methods and bioinformatics, the Argonaute proteins in Dictyostelium discoideum were characterized, and the function of the AgnA protein in RNAi and DNA methylation was investigated, as well as cellular features. Also interaction partners of the PAZ-Piwi domain of AgnA (PAZ-PiwiAgnA) were discovered. The Dictyostelium genome encodes five Argonaute proteins, termed AgnA/B/C/D/E. The expression level of Argonaute proteins was AgnB/D/E > AgnA > AgnC. All these proteins contain the characteristic conserved of PAZ and Piwi domains. Fluorescence microscopy revealed that the overexpressed C-terminal GFP-fusion of PAZ-PiwiAgnA (PPWa-GFP) localized to the cytoplasm. Overexpression of PPWa-GFP leaded to an increased gene silencing efficiency mediated by RNAi but not by antisense RNA. This indicated that PAZ-PiwiAgnA is involved in the RNAi pathway, but not in the antisense pathway. An analysis of protein-protein interactions by a yeast-two-hybrid screen on a cDNA library from vegetatively grown Dictyostelium revealed that several proteins, such as EF2, EF1-I, IfdA, SahA, SamS, RANBP1, UAE1, CapA, and GpdA could interact with PAZ-PiwiAgnA. There was no interaction between PAZ-PiwiAgnA and HP1, HelF and DnmA detected by direct yeast-two-hybrid analysis. The fluorescence microscopy images showed that the overexpressed GFP-SahA or IfdA fusion proteins localized to both cytoplasm and nuclei, while the overexpressed GFP-SamS localized to the cytoplasm. The expression of SamS in AgnA knock down mutants was strongly down regulated on cDNA and mRNA level in, while the expression of SahA was only slightly down regulated. AgnA knock down mutants displayed defects in growth and phagocytosis, which suggested that AgnA affects also cell biological features. The inhibition of DNA methylation on DIRS-1 and Skipper retroelements, as well as the endogenous mvpB and telA gene, observed for the same strains, revealed that AgnA is involved in the DNA methylation pathway. Northern blot analysis showed that Skipper and DIRS-1 were rarely expressed in Ax2, but the expression of Skipper was upregulated in AgnA knock down mutants, while the expression of DIRS-1 was not changed. A knock out of the agnA gene failed even though the homologous recombination of the disruption construct occurred at the correct site, which indicated that there was a duplication of the agnA gene in the genome. The same phenomenon was also observed in ifdA knock out experiments.

Squeezed thermal phonons precurse nonthermal melting of silicon as a function of fluence

A femtosecond-laser pulse can induce ultrafast nonthermal melting of various materials along pathways that are inaccessible under thermodynamic conditions, but it is not known whether there is any structural modification at fluences just below the melting threshold. Here, we show for silicon that in this regime the room-temperature phonons become thermally squeezed, which is a process that has not been reported before in this material. We find that the origin of this effect is the sudden femtosecond-laser-induced softening of interatomic bonds, which can also be described in terms of a modification of the potential energy surface. We further find in ab initio molecular-dynamics simulations on laser-excited potential energy surfaces that the atoms move in the same directions during the first stages of nonthermal melting and thermal phonon squeezing. Our results demonstrate how femtosecond-laser-induced coherent fluctuations precurse complete atomic disordering as a function of fluence. The common underlying bond-softening mechanism indicates that this relation between thermal squeezing and nonthermal melting is not material specific.

Evaluation of water retention capacity and flood control function of the forest catchment

This research quantitatively evaluates the water retention capacity and flood control function of the forest catchments by using hydrological data of the large flood events which happened after the serious droughts. The objective sites are the Oodo Dam and the Sameura Dam catchments in Japan. The kinematic wave model, which considers saturated and unsaturated sub-surface soil zones, is used for the rainfall-runoff analysis. The result shows that possible storage volume of the Oodo Dam catchment is 162.26 MCM in 2005, while that of Samerua is 102.83 MCM in 2005 and 102.64 MCM in 2007. Flood control function of the Oodo Dam catchment is 173 mm in water depth in 2005, while the Sameura Dam catchment 114 mm in 2005 and 126 mm in 2007. This indicates that the Oodo Dam catchment has more than twice as big water capacity as its capacity (78.4 mm), while the Sameura Dam catchment has about one-fifth of the its storage capacity (693 mm).

The function of SIFamide, PDF, and further neuropeptides in the circadian system of Rhyparobia maderae

Der täglich Wechsel von Hell- und Dunkelphasen führte während der Evolution zur Entwicklung innerer Uhren in nahezu allen Organismen. In der Schabe Rhyparobia maderae lokalisierten Läsions- und Transplantationsexperimente die innere Uhr in der akzessorischen Medulla (AME). Dieses kleine birnenförmige Neuropil am ventromedianen Rand der Medulla ist mit etwa 240 Neuronen assoziiert, die eine hohe Anzahl an zum Teil kolokalisierten Neuropeptiden und Neurotransmittern exprimieren. Diese Signalstoffe scheinen essentiell zu sein für die Synchronisation der inneren Uhr mit der Umwelt, der Kopplung der beiden bilateralen AME, der Aufrechterhaltung des circadianen Rhythmus sowie der zeitlichen Steuerung bestimmter Verhaltensweisen. Während die Funktion einiger dieser neuronalen Botenstoffe bereits gut untersucht ist, fehlt sie für andere. Zudem ist noch ungeklärt, wann einzelne Botenstoffe im circadianen Netzwerk agieren. Im Fokus dieser Studie lag daher die Erforschung der Funktion von SIFamide und Corazonin im circadianen Netzwerk sowie die weitere Untersuchung der Funktionen der Neuropeptide MIP und PDF. Es konnte gezeigt werden, dass SIFamide auch in R. maderae in vier großen neurosekretorischen Zellen in der pars intercerebralis exprimiert wird. Varikosenreiche SIFamide-immureaktive (-ir) Fasern innervieren eine Vielzahl an Neuropilen und finden sich auch in der Hüllregion der AME. Injektionsexperimente resultierten in einer monophasischen Phasen-Antwort-Kurve (PRC) mit einer Verzögerung zur frühen subjektiven Nacht. SIFamide ist also ein Eingangssignal für das circadiane Netzwerk und könnte in der Kontrolle der Schalf/Wach-Homöostase involviert sein. Auch Corazonin fungiert als Eingangssignal. Da die Injektionsexperimente in einer monophasischen PRC mit einem Phasenvorschub zur späten subjektiven Nacht resultierten, ist davon auszugehen, dass die Corazonin-ir AME-Zelle Bestandteil des Morning-Oszillator-Netzwerkes in R. maderae ist. Darüber hinaus zeigten Backfill-Experimente, dass MIP an der Kopplung beider AMAE beteiligt ist. ELISA-Quantifizierungen der PDF-Level im Tagesverlauf ergaben Schwankungen in der Konzentration, die auf eine Ausschüttung des Peptids während des Tages hindeuten – ähnlich wie es in Drosophila melanogaster der Fall ist. Dies spiegelt sich in der vervollständigten bimodalen PDF-PRC wieder. Hier führen Injektionen zu einem Phasenvorschub, bevor maximale Peptidlevel erreicht werden, sowie zu einer Phasenverzögerung, sobald die Peptidlevel wieder zu sinken beginnen. Die PRCs erlauben somit Rückschlüsse auf den Zeitpunkt der maximalen Peptidfreisetzung. PDF-ir Neuriten findet sich zudem in sämtlichen Ganglien des ventralen Strickleiternervensystems, was eine Funktion in der Kontrolle der Prozesse impliziert, die durch die Mustergeneratoren in Thorakal- und Abdominalganglien gesteuert werden.