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Bacteriophage P22 recognizes O-antigen polysaccharides of Salmonella enterica subsp. enterica (S.) with its tailspike protein (TSP). In the serovars S. Typhimurium, S. Enteritidis, and S. Paratyphi A, the tetrasaccharide repeat units of the respective O-antigens consist of an identical main chain trisaccharide but different 3,6-dideoxyhexose substituents. Here, the epimers abequose, tyvelose and paratose determine the specific serotype. P22 TSP recognizes O-antigen octasaccharides in an extended binding site with a single 3,6-dideoxyhexose binding pocket. We have isolated S. Paratyphi A octasaccharides which were not available previously and determined the crystal structure of their complex with P22 TSP. We discuss our data together with crystal structures of complexes with S. Typhimurium and S. Enteritidis octasaccharides determined earlier. Isothermal titration calorimetry showed that S. Paratyphi A octasaccharide binds P22 TSP less tightly, with a difference in binding free energy of similar to 7 kJ mol(-1) at 20 degrees C compared with S. Typhimurium and S. Enteritidis octasaccharides. Individual protein-carbohydrate contacts were probed by amino acid replacements showing that the dideoxyhexose pocket contributes to binding of all three serotypes. However, S. Paratyphi A octasaccharides bind in a conformation with an energetically unfavorable phi/epsilon glycosidic bond angle combination. In contrast, octasaccharides from the other serotypes bind as solution-like conformers. Two water molecules are conserved in all P22 TSP complexes with octasaccharides of different serotypes. They line the dideoxyhexose binding pocket and force the S. Paratyphi A octasaccharides to bind as nonsolution conformers. This emphasizes the role of solvent as part of carbohydrate binding sites.
In this study, we evaluated the potential of the hydrogen isotopic composition of algal lipid biomarkers as a proxy for past hydroclimatic variability in hypersaline Isabel Lake, Mexico (Eastern Pacific). We compared rainfall variability recorded in the region over the last 65 years with changes in delta D values of the most abundant compounds preserved in the uppermost 16 cm of lake sediment. Changes in delta D values of the 1,15-C-32 diol (delta D-diol), a specific biomarker of algal populations, were related to rainfall variability; specifically, n-alkyl diols were more deuterium-enriched (depleted) during wetter (drier) periods. Strikingly, neither the magnitude of lipid biomarker isotopic changes over interannual timescales (of up to 70-80 parts per thousand) nor the direction of that variability can be explained by changes in delta D values of the water source or salinity fluctuations (approximately 30 on the practical salinity scale) controlled by seasonal rainfall. However, changes in sedimentary biomarker composition, higher total organic carbon content and less negative delta C-13 values of the 1,15-C-32 diol indicate enhanced algal growth during wetter periods. We find that these conditions result in less negative delta D values of n-alkyl diols. We hypothesize that due to higher lipid demand during enhanced algal growth, an increasing proportion of hydrogen for lipid synthesis is derived from the cytosol via oxidation of polysaccharides, which may cause a deuterium enrichment of the acetogenic compounds. This study has significant implications for paleohydrological reconstructions using algal lipid delta D values, particularly in highly seasonal environments such as Isabel Lake. In such environments, delta D values of specific algal lipid biomarkers may not record the full seasonal cycle in source water delta D but appear to be mainly controlled by the physiological state of algal populations. Our data provide the first evidence that changes in D/H fractionation due to algal growth conditions can be recorded in sediments. For paleoclimate reconstructions in such environments, algal growth conditions should be constrained with additional proxy data (delta C-13 values of the same biomarkers), as the net D/H fractionation between water and lipids may not have been constant over time.
In both animal and plant kingdoms, body size is a fundamental but still poorly understood attribute of biological systems. Here we report that the Arabidopsis NAC transcription factor Regulator of Proteasomal Gene Expression' (RPX) controls leaf size by positively modulating proteasome activity. We further show that the cis-element recognized by RPX is evolutionarily conserved between higher plant species. Upon over-expression of RPX, plants exhibit reduced growth, which may be reversed by a low concentration of the pharmacological proteasome inhibitor MG132. These data suggest that the rate of protein turnover during growth is a critical parameter for determining final organ size.
Development of apical membrane organization and V-ATPase regulation in blowfly salivary glands
(2013)
Secretory cells in blowfly salivary gland are specialized via morphological and physiological attributes in order to serve their main function, i.e. the transport of solutes at a high rate in response to a hormonal stimulus, namely serotonin (5-HT). This study examines the way that 5-HT-insensitive precursor cells differentiate into morphologically complex 5-HT-responsive secretory cells. By means of immunofluorescence microscopy, immunoblotting and measurements of the transepithelial potential changes, we show the following. (1) The apical membrane of the secretory cells becomes organized into an elaborate system of canaliculi and is folded into pleats during the last pupal day and the first day of adulthood. (2) The structural reorganization of the apical membrane is accompanied by an enrichment of actin filaments and phosphorylated ERM protein (phospho-moesin) at this membrane domain and by the deployment of the membrane-integral part of vacuolar-type H+-ATPase (V-ATPase). These findings suggest a role for phospho-moesin, a linker between actin filaments and membrane components, in apical membrane morphogenesis. (3) The assembly and activation of V-ATPase can be induced immediately after eclosion by way of 8-CPT-cAMP, a membrane-permeant cAMP analogue. (4) 5-HT, however, produces the assembly and activation of V-ATPase only in flies aged for at least 2 h after eclosion, indicating that, at eclosion, the 5-HT receptor/adenylyl cyclase/cAMP signalling pathway is inoperative upstream of cAMP. (5) 5-HT activates both the Ca2+ signalling pathway and the cAMP signalling cascade in fully differentiated secretory cells. However, the functionality of these signalling cascades does not seem to be established in a tightly coordinated manner during cell differentation.
Individual-based models (IBMs) predict how dynamics at higher levels of biological organization emerge from individual-level processes. This makes them a particularly useful tool for ecotoxicology, where the effects of toxicants are measured at the individual level but protection goals are often aimed at the population level or higher. However, one drawback of IBMs is that they require significant effort and data to design for each species. A solution would be to develop IBMs for chemical risk assessment that are based on generic individual-level models and theory. Here we show how one generic theory, Dynamic Energy Budget (DEB) theory, can be used to extrapolate the effect of toxicants measured at the individual level to effects on population dynamics. DEB is based on first principles in bioenergetics and uses a common model structure to model all species. Parameterization for a certain species is done at the individual level and allows to predict population-level effects of toxicants for a wide range of environmental conditions and toxicant concentrations. We present the general approach, which in principle can be used for all animal species, and give an example using Daphnia magna exposed to 3,4-dichloroaniline. We conclude that our generic approach holds great potential for standardized ecological risk assessment based on ecological models. Currently, available data from standard tests can directly be used for parameterization under certain circumstances, but with limited extra effort standard tests at the individual would deliver data that could considerably improve the applicability and precision of extrapolation to the population level. Specifically, the measurement of a toxicant's effect on growth in addition to reproduction, and presenting data over time as opposed to reporting a single EC50 or dose response curve at one time point.
The M-type kinesin isoform, Kif9, has recently been implicated in maintaining a physical connection between the centrosome and nucleus in Dictyostelium discoideum. However, the mechanism by which Kif9 functions to link these two organelles remains obscure. Here we demonstrate that the Kif9 protein is localized to the nuclear envelope and is concentrated in the region underlying the centrosome point of attachment. Nuclear anchorage appears mediated through a specialized transmembrane domain located in the carboxyl terminus. Kif9 interacts with microtubules in in vitro binding assays and effects an endwise depolymerization of the polymer. These results suggest a model whereby Kif9 is anchored to the nucleus and generates a pulling force that reels the centrosome up against the nucleus. This is a novel activity for a kinesin motor, one important for progression of cells into mitosis and to ensure centrosome-nuclear parity in a multinuclear environment.
In this note we analyze the incentives to merge in a mixed duopoly if firms compete in prices or quantities. Our model framework mainly follows Barcena-Ruiz and Garzon (J Econ 80:27-42, 2003) who set up the model with quantity competition. We extend their analysis by analyzing the case of competition in prices. Further we compare the incentives to merge with Bertrand and Cournot competition. Comparing quantity with price competition we can show that a merger is more likely with Cournot competition than with Bertrand competition.
ORE1 balances leaf senescence against maintenance by antagonizing G2-like-mediated transcription
(2013)
Leaf senescence is a key physiological process in all plants. Its onset is tightly controlled by transcription factors, of which NAC factor ORE1 (ANAC092) is crucial in Arabidopsis thaliana. Enhanced expression of ORE1 triggers early senescence by controlling a downstream gene network that includes various senescence-associated genes. Here, we report that unexpectedly ORE1 interacts with the G2-like transcription factors GLK1 and GLK2, which are important for chloroplast development and maintenance, and thereby for leaf maintenance. ORE1 antagonizes GLK transcriptional activity, shifting the balance from chloroplast maintenance towards deterioration. Our finding identifies a new mechanism important for the control of senescence by ORE1.
Aim To assess how habitat loss and climate change interact in affecting the range dynamics of species and to quantify how predicted range dynamics depend on demographic properties of species and the severity of environmental change. Location South African Cape Floristic Region. Methods We use data-driven demographic models to assess the impacts of past habitat loss and future climate change on range size, range filing and abundances of eight species of woody plants (Proteaceae). The species-specific models employ a hybrid approach that simulates population dynamics and long-distance dispersal on top of expected spatio-temporal dynamics of suitable habitat. Results Climate change was mainly predicted to reduce range size and range filling (because of a combination of strong habitat shifts with low migration ability). In contrast, habitat loss mostly decreased mean local abundance. For most species and response measures, the combination of habitat loss and climate change had the most severe effect. Yet, this combined effect was mostly smaller than expected from adding or multiplying effects of the individual environmental drivers. This seems to be because climate change shifts suitable habitats to regions less affected by habitat loss. Interspecific variation in range size responses depended mostly on the severity of environmental change, whereas responses in range filling and local abundance depended mostly on demographic properties of species. While most surviving populations concentrated in areas that remain climatically suitable, refugia for multiple species were overestimated by simply overlying habitat models and ignoring demography. Main conclusions Demographic models of range dynamics can simultaneously predict the response of range size, abundance and range filling to multiple drivers of environmental change. Demographic knowledge is particularly needed to predict abundance responses and to identify areas that can serve as biodiversity refugia under climate change. These findings highlight the need for data-driven, demographic assessments in conservation biogeography.
We show how the maximum magnitude within a predefined future time horizon may be estimated from an earthquake catalog within the context of Gutenberg-Richter statistics. The aim is to carry out a rigorous uncertainty assessment, and calculate precise confidence intervals based on an imposed level of confidence a. In detail, we present a model for the estimation of the maximum magnitude to occur in a time interval T-f in the future, given a complete earthquake catalog for a time period T in the past and, if available, paleoseismic events. For this goal, we solely assume that earthquakes follow a stationary Poisson process in time with unknown productivity Lambda and obey the Gutenberg-Richter law in magnitude domain with unknown b-value. The random variables. and b are estimated by means of Bayes theorem with noninformative prior distributions. Results based on synthetic catalogs and on retrospective calculations of historic catalogs from the highly active area of Japan and the low-seismicity, but high-risk region lower Rhine embayment (LRE) in Germany indicate that the estimated magnitudes are close to the true values. Finally, we discuss whether the techniques can be extended to meet the safety requirements for critical facilities such as nuclear power plants. For this aim, the maximum magnitude for all times has to be considered. In agreement with earlier work, we find that this parameter is not a useful quantity from the viewpoint of statistical inference.
Humans have substantially altered the nitrogen cycle of ecosystems through the application of agricultural fertilizer. Fertilization may not only affect plant species diversity, but also insect dynamics by altering plant nitrogen supplies. We investigated the effect of experimental fertilization on the vegetation, with the ribwort plantain as the focal plant, and on higher trophic levels on differently managed grasslands throughout Germany. Over a period of 2 years, we examined two specialist herbivores and their parasitoid on Plantago lanceolata L., and the composition and structure of the surrounding vegetation. Over 70 sites in three geographic regions, within the large-scale project "German Biodiversity Exploratories", were included in the study. The model system consisted of the host plant P. lanceolata L., the monophagous weevils Mecinus labilis Herbst and M. pascuorum Gyllenhal, and their parasitoid Mesopolobus incultus Walker. Fertilization decreased plant species richness and host plant abundance, whereas it enhanced the total vegetation growth. The increased size and heigher leaf nitrogen content did not improve herbivore performance. On the contrary, the abundance of the two herbivores was decreased by fertilization. The parasitoid depended on the abundance of one of its hosts, M. pascuorum (positively density-dependent). Reduced herbivore abundance due to fertilization might be explained by a lower abundance of the host plant, a lower stalk number, and by changed patterns of host localization within higher vegetation. Fertilization negatively affected the third trophic level by cascading up via host abundance. The relationships between fertilization, surrounding vegetation and the tritrophic system were measured throughout the three regions and over the 2-year period. Our findings present consequences of intensification for a plant-herbivore-parasitoid system, and may have significant implications for the conservation of multitrophic systems in managed grasslands.
Individual-based models (IBMs) are increasingly used to link the dynamics of individuals to higher levels of biological organization. Still, many IBMs are data hungry, species specific, and time-consuming to develop and analyze. Many of these issues would be resolved by using general theories of individual dynamics as the basis for IBMs. While such theories have frequently been examined at the individual level, few cross-level tests exist that also try to predict population dynamics. Here we performed a cross-level test of dynamic energy budget (DEB) theory by parameterizing an individual-based model using individual-level data of the water flea, Daphnia magna, and comparing the emerging population dynamics to independent data from population experiments. We found that DEB theory successfully predicted population growth rates and peak densities but failed to capture the decline phase. Further assumptions on food-dependent mortality of juveniles were needed to capture the population dynamics after the initial population peak. The resulting model then predicted, without further calibration, characteristic switches between small-and large-amplitude cycles, which have been observed for Daphnia. We conclude that cross-level tests help detect gaps in current individual-level theories and ultimately will lead to theory development and the establishment of a generic basis for individual-based models and ecology.
Irradiating a ferromagnet with a femtosecond laser pulse is known to induce an ultrafast demagnetization within a few hundred femtoseconds. Here we demonstrate that direct laser irradiation is in fact not essential for ultrafast demagnetization, and that electron cascades caused by hot electron currents accomplish it very efficiently. We optically excite a Au/Ni layered structure in which the 30 nm Au capping layer absorbs the incident laser pump pulse and subsequently use the X-ray magnetic circular dichroism technique to probe the femtosecond demagnetization of the adjacent 15 nm Ni layer. A demagnetization effect corresponding to the scenario in which the laser directly excites the Ni film is observed, but with a slight temporal delay. We explain this unexpected observation by means of the demagnetizing effect of a superdiffusive current of non-equilibrium, non-spin-polarized electrons generated in the Au layer.
Value creation in scene-based music production - the case of electronic club music in Germany
(2013)
The focus of this article is on the variability of value creation in the popular music industry. Recent trends in electronic music have been based on both the valorization of global tastes and of local specialities in performance and production. Depending on musical styles and market niches, local scenes have become important forces behind heterogeneous globalocal markets. At the same time, technological change and the virtualization of music production and distribution contribute to increasingly differentiated configurations of value creation. It is therefore necessary to reconstruct theoretically and empirically the new interplay among the local music production, digital media markets, and virtual communities that are involved. On the basis of empirical explorations in a German hot spot of electronic club-music production (the city of Berlin), the article indentifies local interaction practice and constellations of stakeholders. The findings show that value creation in these rapidly changing production scenes has moved away from the large-scale distribution of producer-induced media to audience-induced live performance and interactive soundtrack production. This change involves the rising importance of cultural embeddings such as taste building, reputation building among artists and producers, and local community building. Starting from an open theoretical problematization of value creation with regard to fluid scenes and shifting modes of production, the results of first empirical reconstructions are taken as inputs to an evolving discussion on the configurations of value creation in consumer-based strands of music production.
We assessed the automaticity of spatial-numerical and spatial-musical associations by testing their intentionality and load sensitivity in a dual-task paradigm. In separate sessions, 16 healthy adults performed magnitude and pitch comparisons on sung numbers with variable pitch. Stimuli and response alternatives were identical, but the relevant stimulus attribute (pitch or number) differed between tasks. Concomitant tasks required retention of either color or location information. Results show that spatial associations of both magnitude and pitch are load sensitive and that the spatial association for pitch is more powerful than that for magnitude. These findings argue against the automaticity of spatial mappings in either stimulus dimension.
Parafoveal semantic processing has recently been well documented in reading Chinese sentences, presumably because of language-specific features. However, because of a large variation of fixation landing positions on pretarget words, some preview words actually were located in foveal vision when readers' eyes landed close to the end of the pretarget words. None of the previous studies has completely ruled out a possibility that the semantic preview effects might mainly arise from these foveally processed preview words. This case, whether previously observed positive evidence for parafoveal semantic processing can still hold, has been called into question. Using linear mixed models, we demonstrate in this study that semantic preview benefit from word N+1 decreased if fixation on pretarget word N was close to the preview. We argue that parafoveal semantic processing is not a consequence of foveally processed preview words.
Objective: To compare lateralized cerebral activations elicited during self-initiated movement mirroring and observation of movements.
Subjects: A total of 15 right-handed healthy subjects, age range 22-56 years.
Methods: Functional imaging study comparing movement mirroring with movement observation, in both hands, in an otherwise identical setting. Imaging data were analysed using statistical parametric mapping software, with significance threshold set at p<0.01 (false discovery rate) and a minimum cluster size of 20 voxels.
Results: Movement mirroring induced additional activation in primary and higher-order visual areas strictly contralateral to the limb seen by the subject. There was no significant difference of brain activity when comparing movement observation of somebody else's right hand with left hand.
Conclusion: Lateralized cerebral activations are elicited by inversion of visual feedback (movement mirroring), but not by movement observation.
In many hydrological applications, ground-wave velocity measurements are increasingly used to map and monitor shallow soil water content. In this study, we propose an automated spectral velocity analysis method to determine the direct ground-wave (DGW) velocity from common midpoint (CMP) or multi-offset ground-penetrating radar (GPR) data. The method introduced in this paper is a variation of the well-known spectral velocity analysis for seismic and GPR reflection events where velocity spectra are computed using different coherency measures along hyperbolas following the normal moveout model. Here, the unnormalized cross-correlation is computed between waveforms across data gathers that are corrected with a linear moveout equation using a predefined range of velocities. Peaks in the resulting velocity spectra identify linear events in the GPR data gathers like DGW events and allow for estimating the corresponding velocities. In addition to obtaining a DGW velocity measurement, we propose a robust method to estimate the associated velocity uncertainties based on the width of the peak in the calculated velocity spectrum. Our proposed method is tested on synthetic data examples to evaluate the influence of subsurface velocity, surveying geometry and signal frequency on the accuracy of estimated ground-wave velocities. In addition, we investigate the influence of such velocity uncertainties on subsequent soil water content estimates using an established petrophysical relationship. Furthermore, we apply our approach to analyse field data, which were collected across a test site in Canada to monitor a wide range of seasonal soil moisture variations. A comparison between our spectral velocity estimates and results derived from manually picked ground-wave arrivals shows good agreement, which illustrates that our spectral velocity analysis is a feasible tool to analyse DGW arrivals in multi-offset GPR data gathers in an objective and more automated manner.
Beta diversity is a conceptual link between diversity at local and regional scales. Various additional methodologies of quantifying this and related phenomena have been applied. Among them, measures of pairwise (dis)similarity of sites are particularly popular. Undersampling, i.e. not recording all taxa present at a site, is a common situation in ecological data. Bias in many metrics related to beta diversity must be expected, but only few studies have explicitly investigated the properties of various measures under undersampling conditions. On the basis of an empirical data set, representing near-complete local inventories of the Lepidoptera from an isolated Pacific island, as well as simulated communities with varying properties, we mimicked different levels of undersampling. We used 14 different approaches to quantify beta diversity, among them dataset-wide multiplicative partitioning (i.e. true beta diversity') and pairwise site x site dissimilarities. We compared their values from incomplete samples to true results from the full data. We used these comparisons to quantify undersampling bias and we calculated correlations of the dissimilarity measures of undersampled data with complete data of sites. Almost all tested metrics showed bias and low correlations under moderate to severe undersampling conditions (as well as deteriorating precision, i.e. large chance effects on results). Measures that used only species incidence were very sensitive to undersampling, while abundance-based metrics with high dependency on the distribution of the most common taxa were particularly robust. Simulated data showed sensitivity of results to the abundance distribution, confirming that data sets of high evenness and/or the application of metrics that are strongly affected by rare species are particularly sensitive to undersampling. The class of beta measure to be used should depend on the research question being asked as different metrics can lead to quite different conclusions even without undersampling effects. For each class of metric, there is a trade-off between robustness to undersampling and sensitivity to rare species. In consequence, using incidence-based metrics carries a particular risk of false conclusions when undersampled data are involved. Developing bias corrections for such metrics would be desirable.