Photoactivated Adenylyl Cyclase Controls Phototaxis in the Flagellate Euglena gracilis

Euglena gracilis, a unicellular freshwater protist exhibits different photomovement responses, such as phototaxis (oriented movement toward or away from the light source) and photophobic (abrupt turn in response to a rapid increase [step-up] or decrease [step-down] in the light fluence rate) responses. Photoactivated adenylyl cyclase (PAC) has been isolated from whole-cell preparations and identified by RNA interference (RNA) to be the photoreceptor for step-up photophobic responses but not for step-down photophobic responses (M. Iseki, S, Matsunaga, A. Murakami, K. Ohno, K. Shiga, C. Yoshida, M. Sugai, T. Takahashi, T. Hori, M. Watanabe [2002] Nature 415: 1047-1051). The present study shows that knockdown of PAC by RNAi also effectively suppresses both positive and negative phototaxis, indicating for the first time that PAC or a PAC homolog is also the photoreceptor for photoorientation of wild-type E. gracilis. Recovery from RNAi occurred earlier for step-up photophobic responses than for positive and negative phototaxis. In addition, we investigated several phototaxis mutant strains of E. gracilis with different cytological features regarding the stigma and paraxonemal body (PAB; believed to be the location for the phototaxis photoreceptor) as well as Astasia longa, a close relative of E. gracilis. All of the E. gracilis mutant strains had PAC mRNAs, whereas in A. longa, a different but similar mRNA was found and designated AlPAC. Consistently, all of these strains showed no photo taxis but performed step-up photophobic responses, which were suppressed by RNAi of the PAC mRNA. The fact that some of these strains possess a cytologically altered or no PAB demonstrates that at least in these strains, the PAC photoreceptor responsible for the step-up photophobic responses is not located in the PAB

Towards mainstreaming of biodiversity data publishing: recommendations of the GBIF Data Publishing Framework Task Group

<p>Abstract</p> <p>Background</p> <p>Data are the evidentiary basis for scientific hypotheses, analyses and publication, for policy formation and for decision-making. They are essential to the evaluation and testing of results by peer scientists both present and future. There is broad consensus in the scientific and conservation communities that data should be freely, openly available in a sustained, persistent and secure way, and thus standards for 'free' and 'open' access to data have become well developed in recent years. The question of effective access to data remains highly problematic.</p> <p>Discussion</p> <p>Specifically with respect to scientific publishing, the ability to critically evaluate a published scientific hypothesis or scientific report is contingent on the examination, analysis, evaluation - and if feasible - on the re-generation of data on which conclusions are based. It is not coincidental that in the recent 'climategate' controversies, the quality and integrity of data and their analytical treatment were central to the debate. There is recent evidence that even when scientific data are requested for evaluation they may not be available. The history of dissemination of scientific results has been marked by paradigm shifts driven by the emergence of new technologies. In recent decades, the advance of computer-based technology linked to global communications networks has created the potential for broader and more consistent dissemination of scientific information and data. Yet, in this digital era, scientists and conservationists, organizations and institutions have often been slow to make data available. Community studies suggest that the withholding of data can be attributed to a lack of awareness, to a lack of technical capacity, to concerns that data should be withheld for reasons of perceived personal or organizational self interest, or to lack of adequate mechanisms for attribution.</p> <p>Conclusions</p> <p>There is a clear need for institutionalization of a 'data publishing framework' that can address sociocultural, technical-infrastructural, policy, political and legal constraints, as well as addressing issues of sustainability and financial support. To address these aspects of a data publishing framework - a systematic, standard approach to the formal definition and public disclosure of data - in the context of biodiversity data, the Global Biodiversity Information Facility (GBIF, the single inter-governmental body most clearly mandated to undertake such an effort) convened a Data Publishing Framework Task Group. We conceive this data publishing framework as an environment conducive to ensure free and open access to world's biodiversity data. Here, we present the recommendations of that Task Group, which are intended to encourage free and open access to the worlds' biodiversity data.</p

H/V ratio: a tool for site effects evaluation. Results from 1-D noise simulations

Ambient vibration techniques such as the H/V method may have the potential to significantly contribute to site effect evaluation, particularly in urban areas. Previous studies interpret the so-called Nakamura's technique in relation to the ellipticity ratio of Rayleigh waves, which, for a high enough impedance contrast, exhibits a pronounced peak close to the fundamental S-wave resonance frequency. Within the European SESAME project (Site EffectS assessment using AMbient Excitations) this interpretation has been tested through noise numerical simulation under well-controlled conditions in terms of source type and distribution and propagation structure. We will present simulations for a simple realistic site (one sedimentary layer over bedrock) characterized by a rather high impedance contrast and low quality factor. Careful H/V and array analysis on these noise synthetics allow an in-depth investigation of the link between H/V ratio peaks and the noise wavefield composition for the soil model considered here: (1) when sources are near (4 to 50 times the layer thickness) and surficial, H/V curves exhibit one single peak, while the array analysis shows that the wavefield is dominated by Rayleigh waves; (2) when sources are distant (more than 50 times the layer thickness) and located inside the sedimentary layer, two peaks show up on the H/V curve, while the array analysis indicates both Rayleigh waves and strong S head waves; the first peak is due to both fundamental Rayleigh waves and resonance of head S waves, the second is only due to the resonance of head S waves; (3) when sources are deep (located inside the bedrock), whatever their distance, H/V ratio exhibit peaks at the fundamental and harmonic resonance frequencies, while array analyses indicate only non-dispersive body waves; the H/V is thus simply due to multiple reflections of S waves within the layer. Therefore, considering that experimental H/V ratio (i.e. derived from actual noise measured in the field) exhibit in most cases only one peak, we conclude that H/V ratio is (1) mainly controlled by local surface sources, (2) mainly due to the ellipticity of the fundamental Rayleigh waves. Then the amplitude of H/V peak is not able to give a good estimate of site amplification facto

ISS RADIATION ENVIRONMENT AS OBSERVED BY LIULIN TYPE-R3DR2 INSTRUMENT IN OCTOBER-NOVEMBER 2014

Space radiation was monitored using the R3DR2 spectrometer-dosimeter during the flight outside the Russian “Zvezda” module of ISS in October-November 2014. The instrument was mounted on the ESA EXPOSE-R2 platform. The R3DR2 instrument was first developed and used during the flight of ESA EXPOSE-R platform in 2009-2010 (Dachev et al, 2015a). It is a low mass, small dimension automated device that measures solar visible and ultraviolet (UV) radiation in four channels and ionizing radiation in 256 channels of a Liulin-type energy deposition spectrometer (Dachev et al, 2002). Ionizing radiation was measured and separated in 256 deposited energy spectra, which were further used for determination of the absorbed dose rate and flux. The main results obtained by the R3DR2 instrument are: (1) three different radiation sources were detected and quantified - galactic cosmic rays (GCR), energetic protons from the inner radiation belt (IRB) in the region of the South Atlantic anomaly and energetic electrons from the outer radiation belt (ORB); (2) for the first time in the history of using of the Liulin-type energy deposition spectrometers (Dachev et al, 2015b) an observable flux from solar energetic particles (SEP) was detected in the period 1-4 November 2014; (3) the obtained SEP energy deposition spectra were compared with other spectra to confirm their shape

The earthquake of 250 a.d. in Augusta Raurica, A real event with a 3D site-effect?

The Roman city Augusta Raurica is located East of Basel, Switzerland. One important topic of the city's history concerns the hypothesis of an earthquake striking the city in the middle of the third century a.d. This idea had been formulated according to archaeological features and findings, but had not been tested so far. A selection of the archaeological features were reviewed and dated in order to test the hypothesis of a single event. However, archaeological investigations do not draw a conclusive picture; it could not be proven that all features of possible destruction date to the same event. Detailed seismological investigations were performed. These included geological and geotechnical mapping of the unconsolidated sediments. Important parameters such as the thickness and composition of the unconsolidated sediments, the terrain topography and the topography of the bedrock surface were mapped. Ambient vibration H/V measurements provided the fundamental frequency of resonance for the unconsolidated sediments. The velocity of shear waves traveling through sediments is the controlling parameter for amplification of seismic waves. This material property is estimated using the relation between the ellipticity of the fundamental mode Rayleigh wave and the H/V curve. From all information we compiled a three-dimensional model of the surface geology. This model is used to simulate earthquake ground motion and amplification effects in the city, and to map the variability of the amplification. In the part of the city where possible earthquake damage was recognized, amplification occurs in the frequency band of building resonance (2-8Hz). In the other part of the city amplification occurs much above the building's resonance. From 1D modelling we estimate a difference in spectral amplification of about a factor of 2.5 to 3 between the two parts of the city. This corresponds approximately to a difference in macroseismic intensity of one unit. 3D modelling showed a large variability of ground motion within very close distance in the part of the city where possible earthquake damage was recognized. The maximum amplification reaches values up to a factor of nine, which is due to 3D effects and the choice of using vertically incident waves. Finally, all paleoseismological findings in the area of Basel were reviewed in order to find indications of a large event in the time-period of interest. Paleoseismological findings provide no hints to a large earthquake in the third century. If we assume that an earthquake caused at least part of the identified damage in Augusta Raurica, we have to assign to this event a magnitude Mw of about 6.0 or even lower, that is much smaller than the value of 6.9 that is actually in the Swiss earthquake catalogue. The earthquake source of this event must then be very close to the site of Augusta Raurica and a strong site-effect occurred in one part of the cit

A time-splitting spectral scheme for the Maxwell-Dirac system

We present a time-splitting spectral scheme for the Maxwell-Dirac system and similar time-splitting methods for the corresponding asymptotic problems in the semi-classical and the non-relativistic regimes. The scheme for the Maxwell-Dirac system conserves the Lorentz gauge condition, is unconditionally stable and highly efficient as our numerical examples show. In particular we focus in our examples on the creation of positronic modes in the semi-classical regime and on the electron-positron interaction in the non-relativistic regime. Furthermore, in the non-relativistic regime, our numerical method exhibits uniform convergence in the small parameter \dt, which is the ratio of the characteristic speed and the speed of light.Comment: 29 pages, 119 figure

Long-Term Effects of Forest Plantation Species on Chemical Soil Properties in Southern Rwanda

peer reviewedUnderstanding the long-term effects of tree species on soil properties is crucial for the development of forest restoration policies in relation to the choice of species that meet both environmental and local livelihood needs. This study was performed in the Arboretum of Ruhande, Southern Rwanda, where monocultures of 148 deciduous and 56 conifer species have been established in 0.25 ha replicated plots from 1933 onwards. We investigated the effects of six exotic and two native tree species planted in monoculture plots and native species mixed within one self-regenerated plot on soil properties in two layers (0–5 cm and 5–10 cm depth). We measured general soil properties (pH, SOM, exchangeable base cations) and water-soluble C and N as a proxy for soil functioning. Changes in soil properties were observed in the upper soil layer for all tree species. Planting Eucalyptus species caused soil acidification, whereas soil exchangeable cations and pH were higher under native species (Entandrophragma excelsum and Polyschias fulva) and mixed native species. The effects of tree species were more pronounced for hot water-extractable C and N than for other soil properties. Their analyses could be used for detecting changes in soil functioning linked to vegetation types

Effects of forest restoration tree species on soil properties in Southern Rwanda

Abstract Effects of forest restoration tree species on soil properties in Southern Rwanda 1,2 Peter Rwibasira*, 2Francois Xavier Naramabuye, 2Donat Nsabimana, and 1Monique Carnol 1University of Liège, Belgium – Plant and Microbial Ecology; 2University of Rwanda, Rwanda. *Corresponding Author: [email protected] Understanding the effects of tree species on soil properties is primordial for the development of forest restoration policies regarding the choice of species that will meet both environmental and local livelihood needs. We investigated the effects of exotic and native tree species, planted in 27 plots (31-82 years old), on selected soil properties (pH, SOM, water-extractable C and N) and soil exchangeable base cations (EBC) at two soil layers (0-5 cm and 5-10 cm) in the arboretum of Ruhande, Southern Rwanda. Given that trees were planted on one site with similar land-use history, climatic conditions, parent material, and soil type, we expect current differences in soil characteristics to reflect the influence of the tree species. The effects of tree species were most apparent in the upper thin layer (0-5 cm) and the values of parameters were higher in this layer compared to the lower soil layer. The influence of tree species at 5-10 cm depth, was less marked and the values were lower for all measured parameters except for Al3+ and Fe2+ concentration. Eucalyptus species stands had the lowest soil pH (3.7) and mixed native species had the highest soil pH (5.8) as well as the highest exchangeable base cations (EBC) at both 0-5 cm depth (63±1.4 cmol (+)/kg) and 5-10 cm depth (9.3±0.2 cmol (+)/kg). Water extractable C and N fractions were higher at the upper soil layer compared to the lower layer. At 0-5cm, hot and cold water-extractable C and N fractions were positively correlated to soil organic matter (SOM) and negatively correlated to pH, but no significant correlation was observed at 5-10 cm. Our results showed that: (i) the two soil layers (0-5 cm and 5-10 cm depths) which were visibly undistinguishable under most of the species significantly differed in soil properties. This highlights the importance of the upper thin layer (0-5 cm depth) in tropical soils, which are generally poor and rely heavily on internal nutrient cycling through rapid decomposition of above-and belowground litter from vegetation (ii) Eucalyptus had negative consequences on soil pH and EBC, whereas soil under mixed natives had higher pH and EBC (iii) The sensitivity of water-extractable C and N fractions to detect tree species effects and their correlation with SOM indicates that these fractions could be used as substitutes to SOM analysis. Keywords: Eucalyptus; organic matter; water-extractable C and N; exotic tree species; soil nutrients; soil quality; Ruhande ArboretumARES - Rwanda (Result1