TY - JOUR A1 - Domahs, Ulrike A1 - Knaus, Johannes A1 - Orzechowska, Paula A1 - Wiese, Richard T1 - Stress "deafness" in a language with fixed word stress an ERR study on Polish JF - Frontiers in psychology N2 - The aim of the present contribution was to examine the factors influencing the prosodic processing in a language with predictable word stress. For Polish, a language with fixed penultimate stress but several well-defined exceptions, difficulties in the processing and representation of prosodic information have been reported (e.g., Peperkamp and Dupoux, 2002). The present study utilized event-related potentials (ERPs) to investigate the factors influencing prosodic processing in Polish. These factors are (i) the predictability of stress and (ii) the prosodic structure in terms of metrical feet. Polish native speakers were presented with correctly and incorrectly stressed Polish words and instructed to judge the correctness of the perceived stress patterns. For some stress violations, an early negativity was found which was interpreted as a reflection of an error-detection mechanism. In addition, exceptional stress patterns (=antepenultimate stress) and post-lexical (=initial) stress evoked a task-related positivity effect (P300) whose amplitude and latency is correlated with the degree of anomaly and deviation from an expectation. In contrast, violations involving the default (=penultimate stress) did not produce such an effect. This asymmetrical result is interpreted to reflect that Polish native speakers are less sensitive to the default pattern than to the exceptional or post-lexical patterns. Behavioral results are orthogonal to the electrophysiological results showing that Polish speakers had difficulties to reject any kind of stress violation. Thus, on a meta-linguistic level Polish speakers appeared to be stress-"deaf" for any kind of stress manipulation, whereas the neural reactions differentiate between the default and lexicalized patterns. KW - stress "deafness" KW - fixed stress system KW - prosodic representation KW - P300 KW - generalized error-detection mechanism Y1 - 2012 U6 - https://doi.org/10.3389/fpsyg.2012.00439 SN - 1664-1078 VL - 3 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Rocchetti, Alessandra A1 - Sharma, Tripti A1 - Wulfetange, Camilla A1 - Scholz-Starke, Joachim A1 - Grippa, Alexandra A1 - Carpaneto, Armando A1 - Dreyer, Ingo A1 - Vitale, Alessandro A1 - Czempinski, Katrin A1 - Pedrazzini, Emanuela T1 - The putative K+ channel subunit AtKCO3 forms stable dimers in arabidopsis JF - Frontiers in plant science N2 - The permeation pore of K+ channels is formed by four copies of the pore domain. AtKCO3 is the only putative voltage-independent K+ channel subunit of Arabidopsis thaliana with a single pore domain. KCO3-like proteins recently emerged in evolution and, to date, have been found only in the genus Arabidopsis (A. thaliana and A. lyrata). We show that the absence of KCO3 does not cause marked changes in growth under various conditions. Only under osmotic stress we observed reduced root growth of the kco3-1 null-allele line. This phenotype was complemented by expressing a KCO3 mutant with an inactive pore, indicating that the function of KCO3 under osmotic stress does not depend on its direct ability to transport ions. Constitutively overexpressed AtKCO3 or AtKCO3::G FP are efficiently sorted to the tonoplast indicating that the protein is approved by the endoplasmic reticulum quality control. However, vacuoles isolated from transgenic plants do not have significant alterations in current density. Consistently, both AtKCO3 and AtKCO3::GFP are detected as homodimers upon velocity gradient centrifugation, an assembly state that would not allow for activity. We conclude that if AtKCO3 ever functions as a K+ channel, active tetramers are held by particularly weak interactions, are formed only in unknown specific conditions and may require partner proteins. KW - Arabidopsis KW - membrane proteins KW - potassium channels KW - protein assembly KW - tonoplast Y1 - 2012 U6 - https://doi.org/10.3389/fpls.2012.00251 SN - 1664-462X VL - 3 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Lucia Gomez-Porras, Judith A1 - Mauricio Riano-Pachon, Diego A1 - Benito, Begona A1 - Haro, Rosario A1 - Sklodowski, Kamil A1 - Rodriguez-Navarro, Alonso A1 - Dreyer, Ingo T1 - Phylogenetic analysis of K+ transporters in bryophytes, lycophytes, and flowering plants indicates a specialization of vascular plants JF - Frontiers in plant science N2 - As heritage from early evolution, potassium (K+) is absolutely necessary for all living cells. It plays significant roles as stabilizer in metabolism and is important for enzyme activation, stabilization of protein synthesis, and neutralization of negative charges on cellular molecules as proteins and nucleic acids. Land plants even enlarged this spectrum of K+ utilization after having gone ashore, despite the fact that K+ is far less available in their new oligotrophic habitats than in sea water. Inevitably, plant cells had to improve and to develop unique transport systems for K+ accumulation and distribution. In the past two decades a manifold of K+ transporters from flowering plants has been identified at the molecular level. The recently published genome of the fern ally Selaginella moellendorffii now helps in providing a better understanding on the molecular changes involved in the colonization of land and the development of the vasculature and the seeds. In this article we present an inventory of K+ transporters of this lycophyte and pigeonhole them together with their relatives from the moss Physcomitrella patens, the monocotyledon Oryza sativa, and two dicotyledonous species, the herbaceous plant Arabidopsis thaliana, and the tree Populus trichocarpa. Interestingly, the transition of green plants from an aqueous to a dry environment coincides with a dramatic reduction in the diversity of voltage-gated potassium channels followed by a diversification on the basis of one surviving K+ channel class. The first appearance of K+ release (K-out) channels in S. moellendorffii that were shown in Arabidopsis to be involved in xylem loading and guard cell closure coincides with the specialization of vascular plants and may indicate an important adaptive step. KW - potassium KW - transport KW - channel KW - voltage-dependent KW - voltage-independent KW - high-affinity KW - Selaginella Y1 - 2012 U6 - https://doi.org/10.3389/fpls.2012.00167 SN - 1664-462X VL - 3 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Christian, Jan-Ole A1 - Braginets, Rostyslav A1 - Schulze, Waltraud X. A1 - Walther, Dirk T1 - Characterization and prediction of protein phosphorylation hotspots in Arabidopsis thaliana JF - Frontiers in plant science N2 - The regulation of protein function by modulating the surface charge status via sequence-locally enriched phosphorylation sites (P-sites) in so called phosphorylation "hotspots" has gained increased attention in recent years. We set out to identify P-hotspots in the model plant Arabidopsis thaliana. We analyzed the spacing of experimentally detected P-sites within peptide-covered regions along Arabidopsis protein sequences as available from the PhosPhAt database. Confirming earlier reports (Schweiger and Lanial, 2010), we found that, indeed, P-sites tend to cluster and that distributions between serine and threonine P-sites to their respected closest next P-site differ significantly from those for tyrosine P-sites. The ability to predict P-hotspots by applying available computational P-site prediction programs that focus on identifying single P-sites was observed to be severely compromised by the inevitable interference of nearby P-sites. We devised a new approach, named HotSPotter, for the prediction of phosphorylation hotspots. HotSPotter is based primarily on local amino acid compositional preferences rather than sequence position-specific motifs and uses support vector machines as the underlying classification engine. HotSPotter correctly identified experimentally determined phosphorylation hotspots in A. thaliana with high accuracy. Applied to the Arabidopsis proteome, HotSPotter-predicted 13,677 candidate P-hotspots in 9,599 proteins corresponding to 7,847 unique genes. Hotspot containing proteins are involved predominantly in signaling processes confirming the surmised modulating role of hotspots in signaling and interaction events. Our study provides new bioinformatics means to identify phosphorylation hotspots and lays the basis for further investigating novel candidate P-hotspots. All phosphorylation hotspot annotations and predictions have been made available as part of the PhosPhAt database at http://phosphat.mpimp-golm.mpg.de. KW - protein phosphorylation KW - hotspots KW - Arabidopsis thaliana KW - support vector machines KW - regulation Y1 - 2012 U6 - https://doi.org/10.3389/fpls.2012.00207 SN - 1664-462X VL - 3 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Balazadeh, Salma A1 - Jaspert, Nils A1 - Arif, Muhammad A1 - Müller-Röber, Bernd A1 - Maurino, Veronica G. T1 - Expression of ROS-responsive genes and transcription factors after metabolic formation of H2O2 in chloroplasts JF - Frontiers in plant science N2 - Glycolate oxidase (GO) catalyses the oxidation of glycolate to glyoxylate, thereby consuming O-2 and producing H2O2. In this work, Arabidopsis thaliana plants expressing GO in the chloroplasts (GO plants) were used to assess the expressional behavior of reactive oxygen species (ROS)-responsive genes and transcription factors (TFs) after metabolic induction of H2O2 formation in chloroplasts. In this organelle, GO uses the glycolate derived from the oxygenase activity of RubisCO. Here, to identify genes responding to an abrupt production of H2O2 in chloroplasts we used quantitative real-time PCR (qRT-PCR) to test the expression of 187 ROS-responsive genes and 1880 TFs after transferring GO and wild-type (WT) plants grown at high CO2 levels to ambient CO2 concentration. Our data revealed coordinated expression changes of genes of specific functional networks 0.5 h after metabolic induction of H2O2 production in GO plants, including the induction of indole glucosinolate and camalexin biosynthesis genes. Comparative analysis using available microarray data suggests that signals for the induction of these genes through H2O2 may originate in the chloroplast. The TF profiling indicated an up-regulation in GO plants of a group of genes involved in the regulation of proanthocyanidin and anthocyanin biosynthesis. Moreover, the upregulation of expression of IF and IF interacting proteins affecting development (e.g., cell division, stem branching, flowering time, flower development) would impact growth and reproductive capacity, resulting in altered development under conditions that promote the formation of H2O2. KW - glycolate oxidase KW - H2O2 KW - ROS-responsive genes KW - transcription factors Y1 - 2012 U6 - https://doi.org/10.3389/fpls.2012.00234 SN - 1664-462X VL - 3 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Spijkerman, Elly A1 - Wacker, Alexander A1 - Weithoff, Guntram A1 - Leya, Thomas T1 - Elemental and fatty acid composition of snow algae in Arctic habitats JF - Frontiers in microbiology N2 - Red, orange or green snow is the macroscopic phenomenon comprising different eukaryotic algae. Little is known about the ecology and nutrient regimes in these algal communities. Therefore, eight snow algal communities from five intensively tinted snow fields in western Spitsbergen were analysed for nutrient concentrations and fatty acid (FA) composition. To evaluate the importance of a shift from green to red forms on the FA-variability of the field samples, four snow algal strains were grown under nitrogen replete and moderate light (+N+ML) or N-limited and high light (-N+HL) conditions. All eight field algal communities were dominated by red and orange cysts. Dissolved nutrient concentration of the snow revealed a broad range of NH4+ (<0.005-1.2 mg NI-1) and only low PO43- (< 18 mu g P I-1) levels. The external nutrient concentration did not reflect cellular nutrient ratios as C:N and C:P ratios of the communities were highest at locations containing relatively high concentrations of NH4- and PO43-. Molar N:P ratios ranged from 11 to 21 and did not suggest clear limitation of a single nutrient. On a per carbon basis, we found a 6-fold difference in total FA content between the eight snow algal communities, ranging from 50 to 300 mg FA g C-1. In multivariate analyses total FA content opposed the cellular N:C quota and a large part of the FA variability among field locations originated from the abundant FAs C181n-9, C18 2n-6, and C183n-3. Both field samples and snow algal strains grown under -N+HL conditions had high concentrations of C181n-9. FAs possibly accumulated due to the cessation of growth. Differences in color and nutritional composition between patches of snow algal communities within one snow field were not directly related to nutrient conditions. We propose that the highly patchy distribution of snow algae within and between snow fields may also result from differences in topographical and geological parameters such as slope, melting water rivulets, and rock formation. KW - Arctic snow algal bloom KW - cellular C:N:P ratio KW - ecology KW - extremophiles KW - lipids KW - nutrients KW - psychrophilic. KW - Spitsbergen Y1 - 2012 U6 - https://doi.org/10.3389/fmicb.2012.00380 SN - 1664-302X VL - 3 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Sauer, Patrick A1 - Glombitza, Clemens A1 - Kallmeyer, Jens T1 - A system for incubations at high gas partial pressure JF - Frontiers in microbiology N2 - High-pressure is a key feature of deep subsurface environments. High partial pressure of dissolved gasses plays an important role in microbial metabolism, because thermodynamic feasibility of many reactions depends on the concentration of reactants. For gases, this is controlled by their partial pressure, which can exceed 1 MPa at in situ conditions. Therefore, high hydrostatic pressure alone is not sufficient to recreate true deep subsurface in situ conditions, but the partial pressure of dissolved gasses has to be controlled as well. We developed an incubation system that allows for incubations at hydrostatic pressure up to 60 MPa, temperatures up to 120 degrees C, and at high gas partial pressure. The composition and partial pressure of gasses can be manipulated during the experiment. To keep costs low, the system is mainly made from off-the-shelf components with only very few custommade parts. A flexible and inert PVDF (polyvinylidene fluoride) incubator sleeve, which is almost impermeable for gases, holds the sample and separates it from the pressure fluid. The flexibility of the incubator sleeve allows for sub-sampling of the medium without loss of pressure. Experiments can be run in both static and flow-through mode. The incubation system described here is usable for versatile purposes, not only the incubation of microorganisms and determination of growth rates, but also for chemical degradation or extraction experiments under high gas saturation, e.g., fluid-gas-rock-interactions in relation to carbon dioxide sequestration. As an application of the system we extracted organic compounds from sub-bituminous coal using H2O as well as a H2O-CO2 mixture at elevated temperature (90 degrees C) and pressure (5 MPa). Subsamples were taken at different time points during the incubation and analyzed by ion chromatography. Furthermore we demonstrated the applicability of the system for studies of microbial activity, using samples from the Isis mud volcano. We could detect an increase in sulfate reduction rate upon the addition of methane to the sample. KW - high-pressure incubation system KW - gas partial pressure KW - sub-sampling KW - carbon dioxide KW - low molecular weight organic acids Y1 - 2012 U6 - https://doi.org/10.3389/fmicb.2012.00025 SN - 1664-302X VL - 3 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Kaplan, Aaron A1 - Harel, Moshe A1 - Kaplan-Levy, Ruth N. A1 - Hadas, Ora A1 - Sukenik, Assaf A1 - Dittmann-Thünemann, Elke T1 - The languages spoken in the water body (or the biological role of cyanobacterial toxins) JF - Frontiers in microbiology N2 - Although intensification of toxic cyanobacterial blooms over the last decade is a matter of growing concern due to bloom impact on water quality, the biological role of most of the toxins produced is not known. In this critical review we focus primarily on the biological role of two toxins, microcystins and cylindrospermopsin, in inter- and intra-species communication and in nutrient acquisition. We examine the experimental evidence supporting some of the dogmas in the field and raise several open questions to be dealt with in future research. We do not discuss the health and environmental implications of toxin presence in the water body. KW - aoa KW - cylindrospermopsin KW - microcystin KW - cyr KW - mcy Y1 - 2012 U6 - https://doi.org/10.3389/fmicb.2012.00138 SN - 1664-302X VL - 3 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Bickel, Samantha L. A1 - Tang, Kam W. A1 - Grossart, Hans-Peter T1 - Ciliate epibionts associated with crustacean zooplankton in German lakes - distribution, motility, and bacterivory JF - Frontiers in microbiology N2 - Ciliate epibionts associated with crustacean zooplankton are widespread in aquatic systems, but their ecological roles are little known. We studied the occurrence of ciliate epibionts on crustacean zooplankton in nine German lakes with different limnological features during the summer of 2011. We also measured the detachment and re-attachment rates of the ciliates, changes in their motility, and the feeding rates of attached vs. detached ciliate epibionts. Epibionts were found in all lakes sampled except an acidic lake with large humic inputs. Epibiont prevalence was as high as 80.96% on the cladoceran Daphnia cucullata, 67.17% on the cladoceran Diaphanosoma brachyurum, and 46.67% on the calanoid copepod Eudiaptomus gracilis. Both cladoceran groups typically had less than 10 epibionts per individual, while the epibiont load on E. gracilis ranged from 1 to >30 epibionts per individual. After the death of the zooplankton host, the peritrich ciliate epibiont Epistylis sp. detached in an exponential fashion with a half-life of 5 min, and 98% detached within 30 min, leaving behind the stalks used for attachment. Immediately after detachment, the ciliates were immotile, but 62% became motile within 60 min. When a new host was present, only 27% reattached after 120 min. The average measured ingestion rate and clearance rate of Epistylis were 11,745 bacteria ciliate(-1) h(-1) and 24.33 mu l ciliate(-1) h(-1), respectively. Despite their high feeding rates, relatively low epibiont abundances were observed in the field, which suggests either diversion of energy to stalk formation, high metabolic loss by the epibionts, or high mortality among the epibiont populations. KW - ciliate epibionts KW - Epistylis KW - crustacean zooplankton KW - bacterivory KW - epibiont motility Y1 - 2012 U6 - https://doi.org/10.3389/fmicb.2012.00243 SN - 1664-302X VL - 3 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Mengel, Matthias A1 - Levermann, Anders A1 - Schleussner, Carl-Friedrich A1 - Born, Andreas T1 - Enhanced Atlantic subpolar gyre variability through baroclinic threshold in a coarse resolution model JF - Earth system dynamics N2 - Direct observations, satellite measurements and paleo records reveal strong variability in the Atlantic subpolar gyre on various time scales. Here we show that variations of comparable amplitude can only be simulated in a coupled climate model in the proximity of a dynamical threshold. The threshold and the associated dynamic response is due to a positive feedback involving increased salt transport in the subpolar gyre and enhanced deep convection in its centre. A series of sensitivity experiments is performed with a coarse resolution ocean general circulation model coupled to a statistical-dynamical atmosphere model which in itself does not produce atmospheric variability. To simulate the impact of atmospheric variability, the model system is perturbed with freshwater forcing of varying, but small amplitude and multi-decadal to centennial periodicities and observational variations in wind stress. While both freshwater and wind-stress-forcing have a small direct effect on the strength of the subpolar gyre, the magnitude of the gyre's response is strongly increased in the vicinity of the threshold. Our results indicate that baroclinic self-amplification in the North Atlantic ocean can play an important role in presently observed SPG variability and thereby North Atlantic climate variability on multi-decadal scales. Y1 - 2012 U6 - https://doi.org/10.5194/esd-3-189-2012 SN - 2190-4979 SN - 2190-4987 VL - 3 IS - 2 SP - 189 EP - 197 PB - Copernicus CY - Göttingen ER -