Investigation of cell fate decision in Schizosaccharomyces pombe by ncRNA annotation and statistical analyses

Studies in the fission yeast Schizosaccharomyces pombe (S. pombe) have done much to inform the view of heterochromatin and its control by the RNA interference (RNAi) machinery. Using cDNA synthesised from poly(A)-enriched RNA samples, numerous novel ncRNA loci were discovered, and the 50 and 30 ends of many other genes were refined in previous studies. Although some of these transcripts may encode novel proteins the function of the majority is yet to be determined. The authors have used strand-specific deep sequencing of RNA, irrespective of poly(A) status, to reveal a highly structured antisense programme that modulates gene expression to dictate cell fate decisions during sexual differentiation. They show that an extensive and elaborate array of ncRNA production accompanies sexual differentiation in the fission yeast S. pombe. Experimental manipulation suggests that these transcripts specifically regulate the function of the target genes.

delta 13C, delta 15N and delta 34S of temperate eelgrass food web in the western Baltic Sea

Simultaneous triple stable isotope analysis of carbon, nitrogen and sulphur was employed to study the temporal variation in the food web of a subtidal eelgrass (Zostera marina) bed in the western Baltic Sea. Samples of three potential food sources: eelgrass, epiphytes and seston, as well as consumer species were collected biweekly from March through September 2011. Temporal variation of stable isotope signatures was observed in primary producers and consumer species. However, variation within a species, particularly omnivores, often exceeded variation over time. The high degree of omnivory among the generalist feeders in this eelgrass community allows for generalist feeders to flexibly switch food sources, thus enhancing food web stability. As coastal systems are subject to seasonal changes, as well as alterations related to human disturbance and climate, these food webs may retain a certain resilience due to their plentiful omnivores.

Stable isotope analysis of jellyfish in Kiel Fjord, Western Baltic Sea during POLARFUCHS cruises (June - October 2011)

A temporal change in stable isotope (SI) composition of jellyfish in the Kiel Fjord, Western Baltic Sea, was documented by analyzing delta13C, delta15N and delta34S of bell tissue of Aurelia aurita and Cyanea capillata in the period between June and October 2011. A strong and significant temporal change in all SI values of A. aurita was found, including an increase of ~3permille in delta13C, a decrease of ~4permille in delta15N and sharp decline of ~7permille in delta34S. Sampling from 18 m to surface.

Age determination of sediment cores of the Golf of Lions

Siliciclastic turbidites represent huge volumes of sediments, which are of particular significance for (1) petroleum researchers, interested in their potential as oil reservoirs and (2) sedimentologists, who aim at understanding sediment transport processes from continent to deep-basins. An important challenge when studying marine turbidites has been to establish a reliable chronology for the deposits. Indeed, conventional marine proxies applied to hemipelagic sediments are often unreliable in detrital clays. In siliciclastic turbidites, those proxies can be used only in hemipelagic intervals, providing a poor constraint on their chronology. In this study, we have used sediments from the Rhône Neofan (NW Mediterranean Sea) to demonstrate that pollen grains can provide a high-resolution chronostratigraphical framework for detrital clays in turbidites. Vegetation changes occurring from the end of Marine Isotopic Stage 3 to the end of Marine Isotopic Stage 2 (from ~30 to ~18 ka cal. BP) are clearly recorded where other proxies have failed previously, mainly because the scarcity of foraminifers in these sediments prevented any continuous Sea Surface Temperature (SST) record and radiocarbon dating to be obtained. We show also that the use of palynology in turbidite deposits is able to contribute to oceanographical and sedimentological purposes: (1) Pinus pollen grains can document the timing of sea-level rise, (2) the ratio between pollen grains transported from the continent via rivers and dinoflagellate cysts (elutriating) allows us to distinguish clearly detrital sediments from pelagic clays. Finally, taken together, all these tools show evidence that the Rhône River disconnected from the canyon during the sea-level rise and thus evidence the subsequent rapid starvation of the neofan at 18.5 ka cal. BP. Younger sediments are hemipelagic: the frequency of foraminifers allowed to date sediments with radiocarbon. First results of Sea Surface Temperature obtained on foraminifers are in good agreement with the dinoflagellate cysts climatic signal. Both provide information on the end of the deglaciation and the Holocene.

Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Seawater carbonate chemistry and Mytilus edulis biological processes during experiments, 2010

CO2 emissions are leading to an acidification of the oceans. Predicting marine community vulnerability towards acidification is difficult, as adaptation processes cannot be accounted for in most experimental studies. Naturally CO2 enriched sites thus can serve as valuable proxies for future changes in community structure. Here we describe a natural analogue site in the Western Baltic Sea. Seawater pCO2 in Kiel Fjord is elevated for large parts of the year due to upwelling of CO2 rich waters. Peak pCO2 values of >230 Pa (>2300 µatm) and pHNBS values of <7.5 are encountered during summer and autumn, average pCO2 values are ~70 Pa (~700 µatm). In contrast to previously described naturally CO2 enriched sites that have suggested a progressive displacement of calcifying auto- and heterotrophic species, the macrobenthic community in Kiel Fjord is dominated by calcifying invertebrates. We show that blue mussels from Kiel Fjord can maintain control rates of somatic and shell growth at a pCO2 of 142 Pa (1400 µatm, pHNBS = 7.7). Juvenile mussel recruitment peaks during the summer months, when high water pCO2 values of ~100 Pa (~1000 µatm) prevail. Our findings indicate that calcifying keystone species may be able to cope with surface ocean pHNBS values projected for the end of this century when food supply is sufficient. However, owing to non-linear synergistic effects of future acidification and upwelling of corrosive water, peak seawater pCO2 in Kiel Fjord and many other productive estuarine habitats could increase to values >400 Pa (>4000 µatm). These changes will most likely affect calcification and recruitment, and increase external shell dissolution.

Seawater carbonate chemistry and conditions of Mytilus edulis extracellular body fluids and shell composition in a pH-treatment experiment: Acid-base status, trace elements and delta11B, 2012

Mytilus edulis were cultured for 3 months under six different seawater pCO2 levels ranging from 380 to 4000 µatm. Specimen were taken from Kiel Fjord (Western Baltic Sea, Germany) which is a habitat with high and variable seawater pCO2 and related shifts in carbonate system speciation (e.g., low pH and low CaCO3 saturation state). Hemolymph (HL) and extrapallial fluid (EPF) samples were analyzed for pH and total dissolved inorganic carbon (CT) to calculate pCO2 and [HCO3]. A second experiment was conducted for 2 months with three different pCO2 levels (380, 1400 and 4000 µatm). Boron isotopes (delta11B) were investigated by LA-MC-ICP-MS (Laser Ablation-Multicollector-Inductively Coupled Plasma-Mass Spectrometry) in shell portions precipitated during experimental treatment time. Additionally, elemental ratios (B/Ca, Mg/Ca and Sr/Ca) in the EPF of specimen from the second experiment were measured via ICP-OES (Inductively Coupled Plasma-Optical Emission Spectrometry). Extracellular pH was not significantly different in HL and EPF but systematically lower than ambient water pH. This is due to high extracellular pCO2 values, a prerequisite for metabolic CO2 excretion. No accumulation of extracellular [HCO3] was measured. Elemental ratios (B/Ca, Mg/Ca and Sr/Ca) in the EPF increased slightly with pH which is in accordance with increasing growth and calcification rates at higher seawater pH values. Boron isotope ratios were highly variable between different individuals but also within single shells. This corresponds to a high individual variability in fluid B/Ca ratios and may be due to high boron concentrations in the organic parts of the shell. The mean delta11B value shows no trend with pH but appears to represent internal pH (EPF) rather than ambient water pH.