Identification and characterization of sRNAs in Streptomyces coelicolor

Streptomyces coelicolor ist der Modellorganismus der GC reichen, Gram+ Actinomyceten, die mehr als zwei Drittel aller bekannten Antibiotika produzieren. Phänotypisch zeichnet er sich durch die Bildung eines Substrat- und eines Luftmyzels aus, welches im Laufe der weiteren Differenzierung Sporen bildet. Streptomyceten produzieren neben Antibiotika noch eine Vielzahl biotechnologisch interessanter Metaboliten. Der komplexe Lebenszyklus und Stoffwechsel erfordern eine genaue Regulation der Genexpression. Die letzten Jahre haben gezeigt, dass neben Proteinen auch die RNA eine regulatorische Funktion hat. Verschiedene regulatorisch aktive RNA Elemente wie Riboswitche, RNA-Thermometer und kleine nicht kodierende RNAs (small noncoding RNAs – sRNAs) wurden identifiziert. sRNAs wirken meist als antisense Riboregulatoren, indem sie ihre Ziel-mRNA binden und dadurch die Translation hemmen oder fördern. In dieser Arbeit wurden verschiedene bioinformatische Methoden verwendet, um sRNAs im Genom von S. coelicolor vorherzusagen. Es wurden Terminatorstrukturen und konservierte Sekundärstrukturen in den intergenen Regionen vorhergesagt, die keinem Gen zuzuordnen waren. In einem weiteren Ansatz wurden Bindestellen des Regulatorproteins DasR vorhergesagt, um DasR kontrollierte sRNAs zu identifizieren. Zusätzlich wurde mittels 454 Sequenzierung erstmalig das Transkriptom von S. coeliocolor analysiert. Auf diese Weise konnten etwa 500 sRNAs vorhergesagt werden. Eine der beiden charakterisierten sRNAs, sc32, ist 139 nt lang. Ihr Promoter liegt im kodierenden Bereich des Gens bldC und sie wird spezifisch durch Kälteschock induziert. Die zweite charakterisierte sRNA, sc1, ist 159 nt lang und in allen sequenzierten Streptomyceten konserviert. Ihre Expression wird nur bei Stickstoffmangel in der Stationärphase reprimiert. Durch molekularbiologische Analysen konnte ein Zielgen von sc1 identifiziert werden, die extrazelluläre Agarase DagA. Es konnte gezeigt werden, dass sc1 an die dagA-mRNA bindet und dadurch die Translation inhibiert. Als zweites mögliches Ziel von sc1 konnte die Histidinkinase SCO5239 identifiziert werden. Hier wurde gezeigt, dass Koexpression von sc1 die Expression einer SCO5239 Reportergenfusion um den Faktor acht steigert. Durch Analyse des Proteoms von sc1 Mutanten, konnte die differenzierte Expression von elf weiteren Proteinen gezeigt werden. Sc1 scheint als Regulator zu agieren, indem es auf die Stickstoffversorgung der Zelle reagiert und den Sekundärmetabolismus deaktiviert.Streptomyces coelicolor is the model organism for the class of GC rich, gram+ actinomycetes that produce more than two thirds of all known antibiotics. It grows in a characteristic substrate and areal mycelium that during further development diffentiaties into spores. Next to antibiotics, Streptomycetes produce a variety of biotechnological interesting metabolites. This complex life cycle and metabolism demands a strict regulation of gene expression. The last years have shown, that next to proteins also RNA can have a regulatory function. Numerous regulatory active RNA elements like riboswitches, RNA-thermometers and small non coding RNAs (sRNAs) have been identified. In most cases sRNAs act as antisense riboregulators by binding to their target-mRNA and thereby blocking or activating its translation. In this work, several different bioinformatic methods were used to predict sRNAs in the genome of S. coelicolor. With these methods terminators and other conserved secondary structures in the intergenic regions of the genome that could not be assigned to an annotated gene were predicted. In another approach binding sites for the global regulator protein DasR were predicted to identify DasR-controlled sRNAs. Additionally for the first time the transcriptome of S. coelicolor was analyzed by 454 deep sequencing. Using this methods ~ 500 sRNAs could be predicted in the genome of S. coelicolor. One of the two characterized sRNAs – sc32 – is 139nt long. Its promoter resides in the conding region of the gene bldC and its expression is specifically induced by cold-shock conditions. The second characterized sRNA – sc1 – is 159nt long and conserved among all Streptomyces species sequenced today. Its expression is repressed by nitrogen starvation in stationary phase. By biochemical analyses a target mRNA of sc1 could be identified – the extracellular agarase dagA. It could be shown that sc1 binds to the dagA-mRNA and thereby hinders translation. As a second putative target of sc1 the histidine kinase SCO5239 could be identified. It was shown that coexpression of sc1 increases the expression of an SCO5239 reporter gene fusion eight times. Analysis of the proteome of sc1 mutants showed a differential expression of further eleven proteins. Sc1 seems to act as a regulator by sensing the nitrogen supply of the cell and in response deactivating the secondary metabolism

Early Pleistocene complex cut-and-fill sequences in the Alps

Cut-and-fill sequences are the result of climatically or tectonically induced alternating aggradation and incision phases of a fluvial system. A recently established cosmogenic nuclide chronology of the Cover Gravels (Deckenschotter in German) in the northern Alpine Foreland, which are the oldest Quaternary glaciofluvial gravels and comprise evidence of early Pleistocene glaciations, suggests a cut-and-fill build-up. This suggested cut-and-fill architecture challenges the morphostratigraphy. The Deckenschotter deposits represent a suitable archive for reconstructing drainage patterns, base level changes, and the landscape evolution of the northern Alpine Foreland during the early Pleistocene. In this study, we focused on the highest morphostratigraphic Deckenschotter sites: three at Irchel and one in the area around Lake Constance. Sediment analyses were performed to determine their provenance and depositional environments. The geochronology was established using isochron-burial dating. The results indicate that the sediments were transported from the Central and eastern Central Alps, as well as from the Molasse, to the foreland and deposited in a proximal glaciofluvial environment. Based on these findings, we propose that the Deckenschotter are cut-and-fill sequences that accumulated in three stages during the early Pleistocene at ca. 2.5 Ma, ca. 1.5 Ma, and ca. 1 Ma. The presence of a cut-and-fill system implies that the regional base level was relatively constant during the early Pleistocene. In addition, the ca. 2.5 Ma glaciofluvial gravels document the first evidence of glaciers in the northern Alpine Foreland. This timing is synchronous with the onset of Quaternary glaciation in the northern hemisphere at ca. 2.7 Ma

Age of the Most Extensive Glaciation in the Alps

Previous research suggested that the Alpine glaciers of the Northern Swiss Foreland reached their maximum extensive position during the Middle Pleistocene. Relict tills and glaciofluvial deposits, attributed to the Most Extensive Glaciation (MEG), have been found only beyond the extents of the Last Glacial Maximum (LGM). Traditionally, these sediments have been correlated to the Riss glaciation sensu Penck and Brückner and have been morphostratigraphically classified as the Higher Terrace (HT) deposits. The age of the MEG glaciation was originally proposed to be intermediate to the Brunhes/Matuyama transition (780 ka) and the Marine Isotope Stage 6 (191 ka). In this study, we focused on the glacial deposits in Möhlin (Canton of Aargau, Switzerland), in order to constrain the age of the MEG. The sediments from these deposits were analyzed to determine the provenance and depositional environments. We applied isochron-burial dating, with cosmogenic 10Be and 26Al, to the till layer in the Bünten gravel pit near Möhlin. Our results indicate that a glacier of Alpine origin reached its most extensive position during the Middle Pleistocene (500 ± 100 ka). The age of the MEG thus appears to be synchronous with the most extensive glaciations in the northern hemisphere

Nonuniform Late Pleistocene glacier fluctuations in tropical Eastern Africa

Today’s ice caps and glaciers in Africa are restricted to the highest peaks, but during the Pleistocene, several mountains on the continent were extensively glaciated. However, little is known about regional differences in the timing and extent of past glaciations and the impact of paleoclimatic changes on the afro-alpine environment and settlement history. Here, we present a glacial chronology for the Ethiopian Highlands in comparison with other East African Mountains. In the Ethiopian Highlands, glaciers reached their maximum 42 to 28 ka thousand years ago before the global Last Glacial Maximum. The local maximum was accompanied by a temperature depression of 4.4° to 6.0°C and a ~700-m downward shift of the afro-alpine vegetation belt, reshaping the human and natural habitats. The chronological comparison reveals that glaciers in Eastern Africa responded in a nonuniform way to past climatic changes, indicating a regionally varying influence of precipitation, temperature, and orography on paleoglacier dynamics

Strong lateral exchange coupling and current-induced switching in single-layer ferrimagnetic films with patterned compensation temperature

Strong, adjustable magnetic couplings are of great importance to all devices based on magnetic materials. Controlling the coupling between adjacent regions of a single magnetic layer, however, is challenging. In this work, we demonstrate strong exchange-based coupling between arbitrarily shaped regions of a single ferrimagnetic layer. This is achieved by spatially patterning the compensation temperature of the ferrimagnet by either oxidation or He+ irradiation. The coupling originates at the lateral interface between regions with different compensation temperature and scales inversely with their width. We show that this coupling generates large lateral exchange coupling fields and we demonstrate its application to control the switching of magnetically compensated dots with an electric current

Absolute Determination of the 22Na(p,g) Reaction Rate in Novae

Gamma-ray telescopes in orbit around the Earth are searching for evidence of the elusive radionuclide 22Na produced in novae. Previously published uncertainties in the dominant destructive reaction, 22Na(p,g)23Mg, indicated new measurements in the proton energy range of 150 to 300 keV were needed to constrain predictions. We have measured the resonance strengths, energies, and branches directly and absolutely by using protons from the University of Washington accelerator with a specially designed beamline, which included beam rastering and cold vacuum protection of the 22Na implanted targets. The targets, fabricated at TRIUMF-ISAC, displayed minimal degradation over a ~ 20 C bombardment as a result of protective layers. We avoided the need to know the stopping power, and hence the target composition, by extracting resonance strengths from excitation functions integrated over proton energy. Our measurements revealed that resonance strengths for E_p = 213, 288, 454, and 610 keV are stronger by factors of 2.4 to 3.2 than previously reported. Upper limits have been placed on proposed resonances at 198-, 209-, and 232-keV. We have re-evaluated the 22Na(p,g) reaction rate, and our measurements indicate the resonance at 213 keV makes the most significant contribution to 22Na destruction in novae. Hydrodynamic simulations including our rate indicate that the expected abundance of 22Na ejecta from a classical nova is reduced by factors between 1.5 and 2, depending on the mass of the white-dwarf star hosting the nova explosion.Comment: 20 pages, 18 figures; shortened paper, accepted in Phys. Rev.

Radionuclides in surface waters around the damaged Fukushima Daiichi NPP one month after the accident : Evidence of significant tritium release into the environment

Following the Fukushima nuclear accident (2011), radionuclides mostly of volatile elements (e.g., 131I, 134,137Cs, 132Te) have been investigated frequently for their presence in the atmosphere, pedosphere, biosphere, and the Pacific Ocean. Smaller releases of radionuclides with intermediate volatility, (e.g., 90Sr), have been reported for soil. However, few reports have been published which targeted the contamination of surface (fresh) waters in Japan soon after the accident. In the present study, 10 surface water samples (collected on April 10, 2011) have been screened for their radionuclide content (3H, 90Sr, 129I, 134Cs, and 137Cs), revealing partly unusually high contamination levels. Especially high tritium levels (184 ± 2 Bq·L−1; the highest levels ever reported in scientific literature after Fukushima) were found in a puddle water sample from close to the Fukushima Daiichi nuclear power plant. The ratios between paddy/puddle water from one location only a few meters apart vary around 1% for 134Cs, 12% for 129I (131I), and around 40% for both 3H and 90Sr. This illustrates the adsorption of radiocesium on natural minerals and radioiodine on organic substances (in the rice paddy), whereas the concentration differences of 3H and 90Sr between the two waters are mainly dilution driven.Peer reviewe