TY - JOUR A1 - Hafer, Jörg A1 - Kiy, Alexander A1 - Lucke, Ulrike T1 - Moodle & Co. auf dem Weg zur Personal Learning Environment JF - eleed N2 - Ausgehend von der typischen IT‐Infrastruktur für E‐Learning an Hochschulen auf der einen Seite sowie vom bisherigen Stand der Forschung zu Personal Learning Environments (PLEs) auf der anderen Seite zeigt dieser Beitrag auf, wie bestehende Werkzeuge bzw. Dienste zusammengeführt und für die Anforderungen der modernen, rechnergestützten Präsenzlehre aufbereitet werden können. Für diesen interdisziplinären Entwicklungsprozess bieten sowohl klassische Softwareentwicklungsverfahren als auch bestehende PLE‐Modelle wenig Hilfestellung an. Der Beitrag beschreibt die in einem campusweiten Projekt an der Universität Potsdam verfolgten Ansätze und die damit erzielten Ergebnisse. Dafür werden zunächst typische Lehr‐/Lern‐bzw. Kommunikations‐Szenarien identifiziert, aus denen Anforderungen an eine unterstützende Plattform abgeleitet werden. Dies führt zu einer umfassenden Sammlung zu berücksichtigender Dienste und deren Funktionen, die gemäß den Spezifika ihrer Nutzung in ein Gesamtsystem zu integrieren sind. Auf dieser Basis werden grundsätzliche Integrationsansätze und technische Details dieses Mash‐Ups in einer Gesamtschau aller relevanten Dienste betrachtet und in eine integrierende Systemarchitektur überführt. Deren konkrete Realisierung mit Hilfe der Portal‐Technologie Liferay wird dargestellt, wobei die eingangs definierten Szenarien aufgegriffen und exemplarisch vorgestellt werden. Ergänzende Anpassungen im Sinne einer personalisierbaren bzw. adaptiven Lern‐(und Arbeits‐)Umgebung werden ebenfalls unterstützt und kurz aufgezeigt. Y1 - 2014 UR - https://eleed.campussource.de/archive/10/4085 SN - 1860-7470 VL - 2014 IS - 10 ER - TY - JOUR A1 - Boggio, Jose M. Chavez A1 - Bodenmueller, D. A1 - Fremberg, T. A1 - Haynes, R. A1 - Roth, Martin M. A1 - Eisermann, R. A1 - Lisker, M. A1 - Zimmermann, L. A1 - Boehm, Michael T1 - Dispersion engineered silicon nitride waveguides by geometrical and refractive-index optimization JF - Journal of the Optical Society of America : B, Optical physics N2 - Dispersion engineering in silicon nitride (SiXNY) waveguides is investigated through the optimization of the waveguide transversal dimensions and refractive indices in a multicladding arrangement. Ultraflat dispersion of -84.0 +/- 0.5 ps/nm/km between 1700 and 2440 nm and 1.5 +/- 3 ps/nm/km between 1670 and 2500 nm is numerically demonstrated. It is shown that typical refractive index fluctuations as well as dimension fluctuations during fabrication of the SiXNY waveguides are a limitation for obtaining ultraflat dispersion profiles. Single- and multicladding waveguides are fabricated and their dispersion profiles measured (over nearly 1000 nm) using a low-coherence frequency domain interferometric technique. By appropriate thickness optimization, the zero-dispersion wavelength is tuned over a large spectral range in single-and multicladding waveguides with small refractive index contrast (3%). A flat dispersion profile with +/- 3.2 ps/nm/km variation over 500 nm is obtained in a multicladding waveguide fabricated with a refractive index contrast of 37%. Finally, we generate a nearly three-octave supercontinuum in this dispersion flattened multicladding SiXNY waveguide. (C) 2014 Optical Society of America Y1 - 2014 U6 - https://doi.org/10.1364/JOSAB.31.002846 SN - 0740-3224 SN - 1520-8540 VL - 31 IS - 11 SP - 2846 EP - 2857 PB - Optical Society of America CY - Washington ER - TY - JOUR A1 - Schmaelzlin, Elmar A1 - Moralejo, Benito A1 - Rutowska, Monika A1 - Monreal-Ibero, Ana A1 - Sandin, Christer A1 - Tarcea, Nicolae A1 - Popp, Juergen A1 - Roth, Martin M. T1 - Raman imaging with a fiber-coupled multichannel spectrograph JF - Sensors N2 - Until now, spatially resolved Raman Spectroscopy has required to scan a sample under investigation in a time-consuming step-by-step procedure. Here, we present a technique that allows the capture of an entire Raman image with only one single exposure. The Raman scattering arising from the sample was collected with a fiber-coupled high-performance astronomy spectrograph. The probe head consisting of an array of 20 x 20 multimode fibers was linked to the camera port of a microscope. To demonstrate the high potential of this new concept, Raman images of reference samples were recorded. Entire chemical maps were received without the need for a scanning procedure. KW - multichannel Raman spectroscopy KW - astronomy spectrograph KW - optical fiber bundle KW - Raman imaging Y1 - 2014 U6 - https://doi.org/10.3390/s141121968 SN - 1424-8220 VL - 14 IS - 11 SP - 21968 EP - 21980 PB - MDPI CY - Basel ER - TY - JOUR A1 - Beisheim, Marianne A1 - Liese, Andrea Margit T1 - Summing up : key findings and avenues for future research Y1 - 2014 SN - 978-1-137-35925-0 ER - TY - JOUR A1 - Badalyan, Artavazd A1 - Dierich, Marlen A1 - Stiba, Konstanze A1 - Schwuchow, Viola A1 - Leimkühler, Silke A1 - Wollenberger, Ulla T1 - Electrical wiring of the aldehyde oxidoreductase PaoABC with a polymer containing osmium redox centers BT - biosensors for benzaldehyde and GABA JF - Biosensors N2 - Biosensors for the detection of benzaldehyde and g-aminobutyric acid (GABA) are reported using aldehyde oxidoreductase PaoABC from Escherichia coli immobilized in a polymer containing bound low potential osmium redox complexes. The electrically connected enzyme already electrooxidizes benzaldehyde at potentials below −0.15 V (vs. Ag|AgCl, 1 M KCl). The pH-dependence of benzaldehyde oxidation can be strongly influenced by the ionic strength. The effect is similar with the soluble osmium redox complex and therefore indicates a clear electrostatic effect on the bioelectrocatalytic efficiency of PaoABC in the osmium containing redox polymer. At lower ionic strength, the pH-optimum is high and can be switched to low pH-values at high ionic strength. This offers biosensing at high and low pH-values. A “reagentless” biosensor has been formed with enzyme wired onto a screen-printed electrode in a flow cell device. The response time to addition of benzaldehyde is 30 s, and the measuring range is between 10–150 µM and the detection limit of 5 µM (signal to noise ratio 3:1) of benzaldehyde. The relative standard deviation in a series (n = 13) for 200 µM benzaldehyde is 1.9%. For the biosensor, a response to succinic semialdehyde was also identified. Based on this response and the ability to work at high pH a biosensor for GABA is proposed by coimmobilizing GABA-aminotransferase (GABA-T) and PaoABC in the osmium containing redox polymer. KW - redox polymer KW - aldehyde oxidoreductase KW - ionic strength KW - benzaldehyde KW - GABA KW - biosensor Y1 - 2014 U6 - https://doi.org/10.3390/bios4040403 VL - 4 IS - 4 SP - 403 EP - 421 PB - MDPI CY - Basel ER - TY - JOUR A1 - Fritzsch, Claire A1 - Wang, Jing A1 - dos Santos, Luara Ferreira A1 - Mauritz, Karl-Heinz A1 - Brunetti, Maddalena A1 - Dohle, Christian T1 - Different effects of the mirror illusion on motor and somatosensory processing JF - Restorative neurology and neuroscience N2 - Purpose: Mirror therapy can improve motor and sensory functions, but effects of the mirror illusion on primary motor and somatosensory cortex could not be established consistently. Methods: Fifteen right handed healthy volunteers performed or observed a finger-thumb opposition task. Cerebral activations during normal movement (NOR), mirrored movement (MIR) and movement observation (OBS) by means of a video chain were recorded with functional magnetic resonance imaging (fMRI). Activation sizes in movement > static conditions were identified using SPM8 (p < 0.001, unc.) and attributed to predefined areas employing the Anatomy toolbox 1.8. Laterality indices for the responsive areas were calculated on the basis of the number of activated voxels. Results: Relevant bilateral BOLD responses were found in primary motor (M1) and somatosensory (S1 - BA 2, 3b and 3a) cortex, premotor and parietal areas and V5. When comparing MIR to NOR, no significant change of contralateral activation in M1 was found, but clearly at S1 with differences between hands. Conclusion: The mirror illusion does not elicit immediate changes in motor areas, yet there is a direct effect on somatosensory areas, especially for left hand movements. These results suggest different effects of mirror therapy on processing and rehabilitation of motor and sensory function. KW - Movement KW - mirror KW - laterality KW - stroke KW - sensorimotor cortex Y1 - 2014 U6 - https://doi.org/10.3233/RNN-130343 SN - 0922-6028 SN - 1878-3627 VL - 32 IS - 2 SP - 269 EP - 280 PB - IOS Press CY - Amsterdam ER - TY - JOUR A1 - Röder, Katrin T1 - Reparative reading, post-structuralist Hermeneutics and T. S. Eliot's four quartets JF - Anglia : journal of English philology N2 - This essay approaches T. S. Eliot's Four Quartets (1935-1942) from the perspectives of Eve Kosofsky Sedgwick's critical practice of reparative reading and of Paul Ricoeur's poststructuralist hermeneutics. It demonstrates that Sedgwick's and Ricoeur's approaches can be productively combined to investigate hermeneutic processes in which the textual energy of a dissemination of meaning is redirected by a reparative or integrative impulse. In Four Quartets, this impetus induces the creation of semantic innovation through a violation of semantic pertinence, that is, through novel, tensional and provisional connections between formerly separate textual elements and semantic units. Y1 - 2014 U6 - https://doi.org/10.1515/anglia-2014-0004 SN - 0340-5222 SN - 1865-8938 VL - 132 IS - 1 SP - 58 EP - 77 PB - De Gruyter CY - Berlin ER - TY - JOUR A1 - Dolgener, Nicola A1 - Freudenberger, L. A1 - Schneeweiss, N. A1 - Ibisch, P. L. A1 - Tiedemann, Ralph T1 - Projecting current and potential future distribution of the Fire-bellied toad Bombina bombina under climate change in north-eastern Germany JF - Regional environmental change N2 - Environmental change is likely to have a strong impact on biodiversity, and many species may shift their distribution in response. In this study, we aimed at projecting the availability of suitable habitat for an endangered amphibian species, the Fire-bellied toad Bombina bombina, in Brandenburg (north-eastern Germany). We modelled a potential habitat distribution map based on (1) a database with 10,581 presence records for Bombina from the years 1990 to 2009, (2) current estimates for ecogeographical variables (EGVs) and (3) the future projection of these EGVs according to the statistical regional model, respectively, the soil and water integrated model, applying the maximum entropy approach (Maxent). By comparing current and potential future distributions, we evaluated the projected change in distribution of suitable habitats and identified the environmental variables most associated with habitat suitability that turned out to be climatic variables related to the hydrological cycle. Under the applied scenario, our results indicate increasing habitat suitability in many areas and an extended range of suitable habitats. However, even if the environmental conditions in Brandenburg may change as predicted, it is questionable whether the Fire-bellied toad will truly benefit, as dispersal abilities of amphibian species are limited and strongly influenced by anthropogenic disturbances, that is, intensive agriculture, habitat destruction and fragmentation. Furthermore, agronomic pressure is likely to increase on productive areas with fertile soils and high water retention capacities, indeed those areas suitable for B. bombina. All these changes may affect temporary pond hydrology as well as the reproductive success and breeding phenology of toads. KW - Brandenburg KW - Climate change KW - Distribution modelling KW - Endangered species KW - Fire-bellied toad KW - Maxent Y1 - 2014 U6 - https://doi.org/10.1007/s10113-013-0468-9 SN - 1436-3798 SN - 1436-378X VL - 14 IS - 3 SP - 1063 EP - 1072 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Dolgener, N. A1 - Freudenberger, L. A1 - Schluck, M. A1 - Schneeweiss, N. A1 - Ibisch, P. L. A1 - Tiedemann, Ralph T1 - Environmental niche factor analysis (ENFA) relates environmental parameters to abundance and genetic diversity in an endangered amphibian, the fire-bellied-toad (Bombina bombina) JF - Conservation genetics N2 - Increasing attempts are made to understand the factors responsible for both the demographic and genetic depletion in amphibian populations. Landscape genetics aims at a spatially explicit correlation of genetic population parameters to landscape features. Using data from the endangered fire-bellied toad Bombina bombina in Brandenburg (Northeastern Germany), we performed an environmental niche factor analysis (ENFA), relating demographic (abundance) and genetic (diversity at 17 microsatellite loci and partial sequences of the mitochondrial control region in 434 individuals from 16 populations) parameters to ecological and anthropogenic variables such as temperature, precipitation, soil wetness, water runoff, vegetation density, and road/traffic impact. We found significant correlations between road disturbance and observed heterozygosity and between soil wetness and mitochondrial diversity. As the influences of the environmental variables can differ between different indicators for genetic diversity, population size and abundance data, our ENFA-based landscape genetics approach allows us to put various aspects of long- versus short term effective population size and genetic connectivity into an ecological and spatially explicit context, enabling potentially even forecast assessment under future environmental scenarios. KW - Distribution modelling KW - ENFA KW - Genetic diversity KW - Fire-bellied toad KW - Landscape genetics KW - Road disturbance Y1 - 2014 U6 - https://doi.org/10.1007/s10592-013-0517-4 SN - 1566-0621 SN - 1572-9737 VL - 15 IS - 1 SP - 11 EP - 21 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Tiedemann, Ralph A1 - Schneider, Anja R. R. A1 - Havenstein, Katja A1 - Blanck, Torsten A1 - Meier, Elmar A1 - Raffel, Martina A1 - Zwartepoorte, Henk A1 - Plath, Martin T1 - New microsatellite markers allow high-resolution taxon delimitation in critically endangered Asian box turtles, genus Cuora JF - Salamandra : German journal of herpetology N2 - We isolated and characterized 16 new di- and tetranudeotide microsatellite markers for the critically endangered Asian box turtle genus Cuora, focusing on the "Cuora trifasciata" species complex. The new markers were then used to analyse genetic variability and divergence amongst five described species within this complex, namely C. aurocapitata (n = 18), C. cyclornata (n = 31), C. pani (n = 6), C. trifasciata (n = 58), and C. zhoui (n = 7). Our results support the view that all five species represent valid taxa. Within two species (C. trifasciata and C. cyclornata), two distinct morphotypes were corroborated by microsatellite divergence. For three individuals, morphologically identified as being of hybrid origin, the hybrid status was confirmed by our genetic analysis. Our results confirm the controversial species (Cuora aurocapitata, C. cyclornata) and subspecies/morphotypes (C. cyclornata meieri, C. trifasciata cf. trifasciata) to be genetically distinct, which has critical implications for conservation strategies. KW - Testudines KW - Cuora KW - box turtles KW - captive breeding KW - conservation units KW - microsatellites Y1 - 2014 SN - 0036-3375 VL - 50 IS - 3 SP - 139 EP - 146 PB - Deutsche Gesellschaft für Herpetologie und Terrarienkunde CY - Darmstadt ER - TY - JOUR A1 - Metzler, Ralf A1 - Jeon, Jae-Hyung A1 - Cherstvy, Andrey G. A1 - Barkai, Eli T1 - Anomalous diffusion models and their properties BT - non-stationarity, non-ergodicity, and ageing at the centenary of single particle tracking JF - physical chemistry, chemical physics : PCCP N2 - Modern microscopic techniques following the stochastic motion of labelled tracer particles have uncovered significant deviations from the laws of Brownian motion in a variety of animate and inanimate systems. Such anomalous diffusion can have different physical origins, which can be identified from careful data analysis. In particular, single particle tracking provides the entire trajectory of the traced particle, which allows one to evaluate different observables to quantify the dynamics of the system under observation. We here provide an extensive overview over different popular anomalous diffusion models and their properties. We pay special attention to their ergodic properties, highlighting the fact that in several of these models the long time averaged mean squared displacement shows a distinct disparity to the regular, ensemble averaged mean squared displacement. In these cases, data obtained from time averages cannot be interpreted by the standard theoretical results for the ensemble averages. Here we therefore provide a comparison of the main properties of the time averaged mean squared displacement and its statistical behaviour in terms of the scatter of the amplitudes between the time averages obtained from different trajectories. We especially demonstrate how anomalous dynamics may be identified for systems, which, on first sight, appear to be Brownian. Moreover, we discuss the ergodicity breaking parameters for the different anomalous stochastic processes and showcase the physical origins for the various behaviours. This Perspective is intended as a guidebook for both experimentalists and theorists working on systems, which exhibit anomalous diffusion. KW - intermittent chaotic systems KW - Fokker-Planck equations KW - time random-walks KW - fluorescence photobleaching recovery KW - fluctuation-dissipation theorem KW - fractional dynamics approach KW - photon-counting statistics KW - weak ergodicity breaking KW - flight search patterns KW - levy flights Y1 - 2014 U6 - https://doi.org/10.1039/c4cp03465a SN - 1463-9076 SN - 1463-9084 VL - 2014 IS - 16 SP - 24128 EP - 24164 ER - TY - JOUR A1 - Wessig, Pablo A1 - Gerngroß, Maik A1 - Pape, Simon A1 - Bruhns, Philipp A1 - Weber, Jens T1 - Novel porous materials based on oligospiroketals (OSK) JF - RSC Advances : an international journal to further the chemical sciences N2 - New porous materials based on covalently connected monomers are presented. The key step of the synthesis is an acetalisation reaction. In previous years we used acetalisation reactions extensively to build up various molecular rods. Based on this approach, investigations towards porous polymeric materials were conducted by us. Here we wish to present the results of these studies in the synthesis of 1D polyacetals and porous 3D polyacetals. By scrambling experiments with 1D acetals we could prove that exchange reactions occur between different building blocks (evidenced by MALDI-TOF mass spectrometry). Based on these results we synthesized porous 3D polyacetals under the same mild conditions. KW - microporous organic polymers KW - molecular rods KW - construction KW - frameworks KW - membranes KW - sorption KW - models Y1 - 2014 U6 - https://doi.org/10.1039/c4ra04437a SN - 2046-2069 VL - 2014 IS - 4 SP - 31123 EP - 31129 ER - TY - JOUR A1 - Zamponi, Flavio A1 - Penfold, Thomas J. A1 - Nachtegaal, Maarten A1 - Lübcke, Andrea A1 - Rittmann, Jochen A1 - Milne, Chris J. A1 - Chergui, Majed A1 - van Bokhoven, Jeroen A. T1 - Probing the dynamics of plasmon-excited hexanethiol-capped gold nanoparticles by picosecond X-ray absorption spectroscopy JF - physical chemistry, chemical physics : PCCP N2 - Picosecond X-ray absorption spectroscopy (XAS) is used to investigate the electronic and structural dynamics initiated by plasmon excitation of 1.8 nm diameter Au nanoparticles (NPs) functionalised with 1-hexanethiol. We show that 100 ps after photoexcitation the transient XAS spectrum is consistent with an 8% expansion of the Au–Au bond length and a large increase in disorder associated with melting of the NPs. Recovery of the ground state occurs with a time constant of ∼1.8 ns, arising from thermalisation with the environment. Simulations reveal that the transient spectrum exhibits no signature of charge separation at 100 ps and allows us to estimate an upper limit for the quantum yield (QY) of this process to be <0.1. KW - TiO2 nanoparticles KW - diimine-complexes KW - electron-transfer KW - supported gold KW - visible-light KW - water KW - surface KW - reactivity KW - nanoclusters KW - excitation Y1 - 2014 U6 - https://doi.org/10.1039/c4cp03301a SN - 1463-9076 SN - 1463-9084 VL - 2014 IS - 16 SP - 23157 EP - 23163 ER - TY - JOUR A1 - Cherstvy, Andrey G. A1 - Chechkin, Aleksei V. A1 - Metzler, Ralf T1 - Particle invasion, survival, and non-ergodicity in 2D diffusion processes with space-dependent diffusivity JF - Soft matter N2 - We study the thermal Markovian diffusion of tracer particles in a 2D medium with spatially varying diffusivity D(r), mimicking recently measured, heterogeneous maps of the apparent diffusion coefficient in biological cells. For this heterogeneous diffusion process (HDP) we analyse the mean squared displacement (MSD) of the tracer particles, the time averaged MSD, the spatial probability density function, and the first passage time dynamics from the cell boundary to the nucleus. Moreover we examine the non-ergodic properties of this process which are important for the correct physical interpretation of time averages of observables obtained from single particle tracking experiments. From extensive computer simulations of the 2D stochastic Langevin equation we present an in-depth study of this HDP. In particular, we find that the MSDs along the radial and azimuthal directions in a circular domain obey anomalous and Brownian scaling, respectively. We demonstrate that the time averaged MSD stays linear as a function of the lag time and the system thus reveals a weak ergodicity breaking. Our results will enable one to rationalise the diffusive motion of larger tracer particles such as viruses or submicron beads in biological cells. KW - anomalous diffusion KW - intracellular-transport KW - adenoassociated virus KW - infection pathway KW - escherichia-coli KW - endosomal escape KW - living cells KW - trafficking KW - cytoplasm KW - models Y1 - 2014 U6 - https://doi.org/10.1039/c3sm52846d SN - 2046-2069 VL - 2014 IS - 10 SP - 1591 EP - 1601 PB - Royal Society of Chemistry ER - TY - JOUR A1 - Meyer, Sören A1 - Matissek, M. A1 - Müller, Sandra Marie A1 - Taleshi, M. S. A1 - Ebert, Franziska A1 - Francesconi, Kevin A. A1 - Schwerdtle, Tanja T1 - In vitro toxicological characterisation of three arsenic-containing hydrocarbons JF - Metallomics N2 - Arsenic-containing hydrocarbons are one group of fat-soluble organic arsenic compounds (arsenolipids) found in marine fish and other seafood. A risk assessment of arsenolipids is urgently needed, but has not been possible because of the total lack of toxicological data. In this study the cellular toxicity of three arsenic-containing hydrocarbons was investigated in cultured human bladder (UROtsa) and liver (HepG2) cells. Cytotoxicity of the arsenic-containing hydrocarbons was comparable to that of arsenite, which was applied as the toxic reference arsenical. A large cellular accumulation of arsenic, as measured by ICP-MS/MS, was observed after incubation of both cell lines with the arsenolipids. Moreover, the toxic mode of action shown by the three arsenic-containing hydrocarbons seemed to differ from that observed for arsenite. Evidence suggests that the high cytotoxic potential of the lipophilic arsenicals results from a decrease in the cellular energy level. This first in vitro based risk assessment cannot exclude a risk to human health related to the presence of arsenolipids in seafood, and indicates the urgent need for further toxicity studies in experimental animals to fully assess this possible risk. KW - cod-liver KW - human-cells KW - arsenolipids present KW - excision-repair KW - fatty-acids KW - marine oils KW - RP-HPLC KW - metabolites KW - identification KW - trivalent Y1 - 2014 U6 - https://doi.org/10.1039/c4mt00061g SN - 1756-591X SN - 1756-5901 VL - 2014 IS - 6 SP - 1023 EP - 1033 ER - TY - JOUR A1 - Unterberg, Marlies A1 - Leffers, Larissa A1 - Hübner, Florian A1 - Humpf, Hans-Ulrich A1 - Lepikhov, Konstantin A1 - Walter, Jörn A1 - Ebert, Franziska A1 - Schwerdtle, Tanja T1 - Toxicity of arsenite and thio-DMAV after long-term (21 days) incubation of human urothelial cells: cytotoxicity, genotoxicity and epigenetics JF - Toxicology Research N2 - This study aims to further mechanistically understand toxic modes of action after chronic inorganic arsenic exposure. Therefore long-term incubation studies in cultured cells were carried out, to display chronically attained changes, which cannot be observed in the generally applied in vitro short-term incubation studies. Particularly, the cytotoxic, genotoxic and epigenetic effects of an up to 21 days incubation of human urothelial (UROtsa) cells with pico- to nanomolar concentrations of iAsIII and its metabolite thio-DMAV were compared. After 21 days of incubation, cytotoxic effects were strongly enhanced in the case of iAsIII and might partly be due to glutathione depletion and genotoxic effects on the chromosomal level. These results are in strong contrast to cells exposed to thio-DMAV. Thus, cells seemed to be able to adapt to this arsenical, as indicated among others by an increase in the cellular glutathione level. Most interestingly, picomolar concentrations of both iAsIII and thio-DMAV caused global DNA hypomethylation in UROtsa cells, which was quantified in parallel by 5-medC immunostaining and a newly established, reliable, high resolution mass spectrometry (HRMS)-based test system. This is the first time that epigenetic effects are reported for thio-DMAV; iAsIII induced epigenetic effects occur in at least 8000 fold lower concentrations as reported in vitro before. The fact that both arsenicals cause DNA hypomethylation at really low, exposure-relevant concentrations in human urothelial cells suggests that this epigenetic effect might contribute to inorganic arsenic induced carcinogenicity, which for sure has to be further investigated in future studies. KW - induced malignant-transformation KW - genomic dna methylation KW - vitro toxicological characterization KW - thio-dimethylarsinic acid KW - bladder-cancer KW - methyltransferases dnmt3a KW - cytosine methylation KW - carcinogen exposure KW - mass-spectrometry KW - gene-expression Y1 - 2014 SN - 2045-4538 SN - 2045-452X VL - 3 IS - 6 SP - 456 EP - 464 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Palyulin, Vladimir V. A1 - Ala-Nissila, Tapio A1 - Metzler, Ralf ED - Metzler, Ralf T1 - Polymer translocation: the first two decades and the recent diversification JF - Soft matter N2 - Probably no other field of statistical physics at the borderline of soft matter and biological physics has caused such a flurry of papers as polymer translocation since the 1994 landmark paper by Bezrukov, Vodyanoy, and Parsegian and the study of Kasianowicz in 1996. Experiments, simulations, and theoretical approaches are still contributing novel insights to date, while no universal consensus on the statistical understanding of polymer translocation has been reached. We here collect the published results, in particular, the famous–infamous debate on the scaling exponents governing the translocation process. We put these results into perspective and discuss where the field is going. In particular, we argue that the phenomenon of polymer translocation is non-universal and highly sensitive to the exact specifications of the models and experiments used towards its analysis. KW - solid-state nanopores KW - single-stranded-dna KW - posttranslational protein translocation KW - anomalous diffusion KW - monte-carlo KW - structured polynucleotides KW - dynamics simulation KW - equation approach KW - osmotic-pressure KW - membrane channel Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-76266 SN - 1744-683X VL - 45 IS - 10 SP - 9016 EP - 9037 PB - the Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Jeon, Jae-Hyung A1 - Chechkin, Aleksei V. A1 - Metzler, Ralf T1 - Scaled Brownian motion: a paradoxical process with a time dependent diffusivity for the description of anomalous diffusion JF - Physical chemistry, chemical physics : PCCP N2 - Anomalous diffusion is frequently described by scaled Brownian motion (SBM){,} a Gaussian process with a power-law time dependent diffusion coefficient. Its mean squared displacement is ?x2(t)? [similar{,} equals] 2K(t)t with K(t) [similar{,} equals] t[small alpha]-1 for 0 < [small alpha] < 2. SBM may provide a seemingly adequate description in the case of unbounded diffusion{,} for which its probability density function coincides with that of fractional Brownian motion. Here we show that free SBM is weakly non-ergodic but does not exhibit a significant amplitude scatter of the time averaged mean squared displacement. More severely{,} we demonstrate that under confinement{,} the dynamics encoded by SBM is fundamentally different from both fractional Brownian motion and continuous time random walks. SBM is highly non-stationary and cannot provide a physical description for particles in a thermalised stationary system. Our findings have direct impact on the modelling of single particle tracking experiments{,} in particular{,} under confinement inside cellular compartments or when optical tweezers tracking methods are used. KW - single-particle tracking KW - living cells KW - random-walks KW - subdiffusion KW - dynamics KW - nonergodicity KW - coefficients KW - transport KW - membrane KW - behavior Y1 - 2014 U6 - https://doi.org/10.1039/C4CP02019G VL - 30 IS - 16 SP - 15811 EP - 15817 PB - The Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Teske, Daniel T1 - Geocoder accuracy ranking JF - Process design for natural scientists: an agile model-driven approach N2 - Finding an address on a map is sometimes tricky: the chosen map application may be unfamiliar with the enclosed region. There are several geocoders on the market, they have different databases and algorithms to compute the query. Consequently, the geocoding results differ in their quality. Fortunately the geocoders provide a rich set of metadata. The workflow described in this paper compares this metadata with the aim to find out which geocoder is offering the best-fitting coordinate for a given address. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 161 EP - 174 PB - Springer CY - Berlin ER - TY - JOUR A1 - Sens, Henriette T1 - Web-Based map generalization tools put to the test: a jABC workflow JF - Process Design for Natural Scientists: an agile model-driven approach N2 - Geometric generalization is a fundamental concept in the digital mapping process. An increasing amount of spatial data is provided on the web as well as a range of tools to process it. This jABC workflow is used for the automatic testing of web-based generalization services like mapshaper.org by executing its functionality, overlaying both datasets before and after the transformation and displaying them visually in a .tif file. Mostly Web Services and command line tools are used to build an environment where ESRI shapefiles can be uploaded, processed through a chosen generalization service and finally visualized in Irfanview. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 175 EP - 185 PB - Springer CY - Berlin ER - TY - JOUR A1 - Noack, Franziska T1 - CREADED: Colored-Relief application for digital elevation data JF - Process design for natural scientists: an agile model-driven approach N2 - In the geoinformatics field, remote sensing data is often used for analyzing the characteristics of the current investigation area. This includes DEMs, which are simple raster grids containing grey scales representing the respective elevation values. The project CREADED that is presented in this paper aims at making these monochrome raster images more significant and more intuitively interpretable. For this purpose, an executable interactive model for creating a colored and relief-shaded Digital Elevation Model (DEM) has been designed using the jABC framework. The process is based on standard jABC-SIBs and SIBs that provide specific GIS functions, which are available as Web services, command line tools and scripts. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 186 EP - 199 PB - Springer CY - Berlin ER - TY - JOUR A1 - Respondek, Tobias T1 - A workflow for computing potential areas for wind turbines JF - Process design for natural scientists: an agile model-driven approach N2 - This paper describes the implementation of a workflow model for service-oriented computing of potential areas for wind turbines in jABC. By implementing a re-executable model the manual effort of a multi-criteria site analysis can be reduced. The aim is to determine the shift of typical geoprocessing tools of geographic information systems (GIS) from the desktop to the web. The analysis is based on a vector data set and mainly uses web services of the “Center for Spatial Information Science and Systems” (CSISS). This paper discusses effort, benefits and problems associated with the use of the web services. Y1 - 2014 SN - 978-3-662-45005-5 IS - 500 SP - 200 EP - 215 PB - Springer CY - Berlin ER - TY - JOUR A1 - Scheele, Lasse T1 - Location analysis for placing artificial reefs JF - Process design for natural scientists: an agile model-driven approach N2 - Location analyses are among the most common tasks while working with spatial data and geographic information systems. Automating the most frequently used procedures is therefore an important aspect of improving their usability. In this context, this project aims to design and implement a workflow, providing some basic tools for a location analysis. For the implementation with jABC, the workflow was applied to the problem of finding a suitable location for placing an artificial reef. For this analysis three parameters (bathymetry, slope and grain size of the ground material) were taken into account, processed, and visualized with the The Generic Mapping Tools (GMT), which were integrated into the workflow as jETI-SIBs. The implemented workflow thereby showed that the approach to combine jABC with GMT resulted in an user-centric yet user-friendly tool with high-quality cartographic outputs. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 216 EP - 228 PB - Springer CY - Berlin ER - TY - JOUR A1 - Kind, Josephine T1 - Creation of topographic maps JF - Process design for natural scientists: an agile model-driven approach N2 - Location analyses are among the most common tasks while working with spatial data and geographic information systems. Automating the most frequently used procedures is therefore an important aspect of improving their usability. In this context, this project aims to design and implement a workflow, providing some basic tools for a location analysis. For the implementation with jABC, the workflow was applied to the problem of finding a suitable location for placing an artificial reef. For this analysis three parameters (bathymetry, slope and grain size of the ground material) were taken into account, processed, and visualized with the The Generic Mapping Tools (GMT), which were integrated into the workflow as jETI-SIBs. The implemented workflow thereby showed that the approach to combine jABC with GMT resulted in an user-centric yet user-friendly tool with high-quality cartographic outputs. Y1 - 2014 SN - 978-3-662-45005-5 IS - 500 SP - 229 EP - 238 PB - Springer CY - Berlin ER - TY - JOUR A1 - Holler, Robin T1 - GraffDok - a graffiti documentation application JF - Process design for natural scientists: an agile model-driven approach N2 - GraffDok is an application helping to maintain an overview over sprayed images somewhere in a city. At the time of writing it aims at vandalism rather than at beautiful photographic graffiti in an underpass. Looking at hundreds of tags and scribbles on monuments, house walls, etc. it would be interesting to not only record them in writing but even make them accessible electronically, including images. GraffDok’s workflow is simple and only requires an EXIF-GPS-tagged photograph of a graffito. It automatically determines its location by using reverse geocoding with the given GPS-coordinates and the Gisgraphy WebService. While asking the user for some more meta data, GraffDok analyses the image in parallel with this and tries to detect fore- and background – before extracting the drawing lines and make them stand alone. The command line based tool ImageMagick is used here as well as for accessing EXIF data. Any meta data is written to csv-files, which will stay easily accessible and can be integrated in TeX-files as well. The latter ones are converted to PDF at the end of the workflow, containing a table about all graffiti and a summary for each – including the generated characteristic graffiti pattern image. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 239 EP - 251 PB - Springer CY - Berlin ER - TY - JOUR A1 - Reso, Judith ED - Lambrecht, Anna-Lena ED - Margaria, Tiziana T1 - Protein Classification Workflow JF - Process Design for Natural Scientists: an agile model-driven approach N2 - The protein classification workflow described in this report enables users to get information about a novel protein sequence automatically. The information is derived by different bioinformatic analysis tools which calculate or predict features of a protein sequence. Also, databases are used to compare the novel sequence with known proteins. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 65 EP - 72 PB - Springer Verlag CY - Berlin ER - TY - JOUR A1 - Schulze, Gunnar T1 - Workflow for rapid metagenome analysis JF - Process design for natural scientists: an agile model-driven approach N2 - Analyses of metagenomes in life sciences present new opportunities as well as challenges to the scientific community and call for advanced computational methods and workflows. The large amount of data collected from samples via next-generation sequencing (NGS) technologies render manual approaches to sequence comparison and annotation unsuitable. Rather, fast and efficient computational pipelines are needed to provide comprehensive statistics and summaries and enable the researcher to choose appropriate tools for more specific analyses. The workflow presented here builds upon previous pipelines designed for automated clustering and annotation of raw sequence reads obtained from next-generation sequencing technologies such as 454 and Illumina. Employing specialized algorithms, the sequence reads are processed at three different levels. First, raw reads are clustered at high similarity cutoff to yield clusters which can be exported as multifasta files for further analyses. Independently, open reading frames (ORFs) are predicted from raw reads and clustered at two strictness levels to yield sets of non-redundant sequences and ORF families. Furthermore, single ORFs are annotated by performing searches against the Pfam database Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 88 EP - 100 PB - Springer CY - Berlin ER - TY - JOUR A1 - Vierheller, Janine ED - Lambrecht, Anna-Lena ED - Margaria, Tiziana T1 - Exploratory Data Analysis JF - Process Design for Natural Scientists: an agile model-driven approach N2 - In bioinformatics the term exploratory data analysis refers to different methods to get an overview of large biological data sets. Hence, it helps to create a framework for further analysis and hypothesis testing. The workflow facilitates this first important step of the data analysis created by high-throughput technologies. The results are different plots showing the structure of the measurements. The goal of the workflow is the automatization of the exploratory data analysis, but also the flexibility should be guaranteed. The basic tool is the free software R. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 110 EP - 126 PB - Axel Springer Verlag CY - Berlin ER - TY - JOUR A1 - Schütt, Christine T1 - Identification of differentially expressed genes JF - Process design for natural scientists: an agile model-driven approach N2 - With the jABC it is possible to realize workflows for numerous questions in different fields. The goal of this project was to create a workflow for the identification of differentially expressed genes. This is of special interest in biology, for it gives the opportunity to get a better insight in cellular changes due to exogenous stress, diseases and so on. With the knowledge that can be derived from the differentially expressed genes in diseased tissues, it becomes possible to find new targets for treatment. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 127 EP - 139 PB - Springer CY - Berlin ER - TY - JOUR A1 - Kuntzsch, Christian T1 - Visualization of data transfer paths JF - Process design for natural scientists: an agile model-driven approach N2 - A workflow for visualizing server connections using the Google Maps API was built in the jABC. It makes use of three basic services: An XML-based IP address geolocation web service, a command line tool and the Static Maps API. The result of the workflow is an URL leading to an image file of a map, showing server connections between a client and a target host. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 140 EP - 148 PB - Springer CY - Berlin ER - TY - JOUR A1 - Hibbe, Marcel ED - Lambrecht, Anna-Lena ED - Margaria, Tiziana T1 - Spotlocator - Guess Where the Photo Was Taken! JF - Process Design for Natural Scientists: an agile model-driven approach N2 - Spotlocator is a game wherein people have to guess the spots of where photos were taken. The photos of a defined area for each game are from panoramio.com. They are published at http://spotlocator. drupalgardens.com with an ID. Everyone can guess the photo spots by sending a special tweet via Twitter that contains the hashtag #spotlocator, the guessed coordinates and the ID of the photo. An evaluation is published for all tweets. The players are informed about the distance to the real photo spots and the positions are shown on a map. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 149 EP - 160 PB - Springer Verlag CY - Berlin ER - TY - JOUR A1 - Blaese, Leif T1 - Data mining for unidentified protein squences JF - Process design for natural scientists: an agile model-driven approach N2 - Through the use of next generation sequencing (NGS) technology, a lot of newly sequenced organisms are now available. Annotating those genes is one of the most challenging tasks in sequence biology. Here, we present an automated workflow to find homologue proteins, annotate sequences according to function and create a three-dimensional model. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 73 EP - 87 PB - Springer CY - Berlin ER - TY - JOUR A1 - Lis, Monika ED - Lambrecht, Anna-Lena ED - Margaria, Tiziana T1 - Constructing a Phylogenetic Tree JF - Process Design for Natural Scientists: an agile model-driven approach N2 - In this project I constructed a workflow that takes a DNA sequence as input and provides a phylogenetic tree, consisting of the input sequence and other sequences which were found during a database search. In this phylogenetic tree the sequences are arranged depending on similarities. In bioinformatics, constructing phylogenetic trees is often used to explore the evolutionary relationships of genes or organisms and to understand the mechanisms of evolution itself. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 101 EP - 109 PB - Springer Verlag CY - Berlin ER - TY - JOUR A1 - Hegyes, Péter István ED - Badó, Attila ED - Belling, Detlev W. T1 - Hungarian Rules of the Liability for Game Damage JF - Rechtsentwicklungen aus europäischer Perspektive im 21. Jahrhundert Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-74605 IS - 2 SP - 191 EP - 204 ER - TY - JOUR A1 - Nagy, Zsolt ED - Badó, Attila ED - Belling, Detlev W. T1 - The Future of Hungarian Legal Training and Profession within the European Union JF - Rechtsentwicklungen aus europäischer Perspektive im 21. Jahrhundert Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-74635 IS - 2 SP - 233 EP - 243 ER - TY - JOUR A1 - Varga, Norbert ED - Badó, Attila ED - Belling, Detlev W. T1 - The Practice of Leading Cases in the Hungarian High Court (Curia), with Special Attention to the Civil Procedure Act of 1911 JF - Rechtsentwicklungen aus europäischer Perspektive im 21. Jahrhundert Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-74661 IS - 2 SP - 281 EP - 289 ER - TY - JOUR A1 - Ghosh, Surya K. A1 - Cherstvy, Andrey G. A1 - Metzler, Ralf ED - Metzler, Ralf T1 - Non-universal tracer diffusion in crowded media of non-inert obstacles JF - Physical Chemistry Chemical Physics N2 - We study the diffusion of a tracer particle, which moves in continuum space between a lattice of excluded volume, immobile non-inert obstacles. In particular, we analyse how the strength of the tracer–obstacle interactions and the volume occupancy of the crowders alter the diffusive motion of the tracer. From the details of partitioning of the tracer diffusion modes between trapping states when bound to obstacles and bulk diffusion, we examine the degree of localisation of the tracer in the lattice of crowders. We study the properties of the tracer diffusion in terms of the ensemble and time averaged mean squared displacements, the trapping time distributions, the amplitude variation of the time averaged mean squared displacements, and the non-Gaussianity parameter of the diffusing tracer. We conclude that tracer–obstacle adsorption and binding triggers a transient anomalous diffusion. From a very narrow spread of recorded individual time averaged trajectories we exclude continuous type random walk processes as the underlying physical model of the tracer diffusion in our system. For moderate tracer–crowder attraction the motion is found to be fully ergodic, while at stronger attraction strength a transient disparity between ensemble and time averaged mean squared displacements occurs. We also put our results into perspective with findings from experimental single-particle tracking and simulations of the diffusion of tagged tracers in dense crowded suspensions. Our results have implications for the diffusion, transport, and spreading of chemical components in highly crowded environments inside living cells and other structured liquids. KW - fluorescence correlation spectroscopy KW - single-particle tracking KW - anomalous diffusion KW - living cells KW - physiological consequences KW - langevin equation KW - infection pathway KW - excluded volume KW - brownian-motion KW - random-walks Y1 - 2014 SN - 1463-9076 VL - 3 IS - 17 SP - 1847 EP - 1858 PB - The Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Shin, Jaeoh A1 - Cherstvy, Andrey G. A1 - Metzler, Ralf ED - Metzler, Ralf T1 - Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size JF - Soft Matter N2 - The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible polymer chains in the presence of different degrees of crowding. From the analysis of the looping–unlooping rates and the looping probabilities of the chain ends we show that the presence of small crowders typically slows down the chain dynamics but larger crowders may in fact facilitate the looping. We rationalise these non-trivial and often counterintuitive effects of the crowder size on the looping kinetics in terms of an effective solution viscosity and standard excluded volume. It is shown that for small crowders the effect of an increased viscosity dominates, while for big crowders we argue that confinement effects (caging) prevail. The tradeoff between both trends can thus result in the impediment or facilitation of polymer looping, depending on the crowder size. We also examine how the crowding volume fraction, chain length, and the attraction strength of the contact groups of the polymer chain affect the looping kinetics and hairpin formation dynamics. Our results are relevant for DNA looping in the absence and presence of protein mediation, DNA hairpin formation, RNA folding, and the folding of polypeptide chains under biologically relevant high-crowding conditions. KW - gene-regulation kinetics KW - physiological consequences KW - spatial-organization KW - anomalous diffusion KW - folding kinetics KW - living cells KW - dna coiling KW - in-vitro KW - dynamics KW - mixtures Y1 - 2014 SN - 1744-683X SP - 472 EP - 488 PB - The Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Dorsch, Christian A1 - Dörfler, Thomas T1 - Organized hypocrisy of the international community BT - an institutionalist explanation of the UN security council’s contradictory activity on darfur JF - Zeitschrift für Genozidforschung Y1 - 2014 U6 - https://doi.org/10.5771/1438-8332-2014-1-2-8 SN - 1438-8332 SN - 2589-1510 VL - 15 IS - 1-2 SP - 8 EP - 31 PB - Velbrück Wissenschaft CY - Weilerswist ER - TY - JOUR A1 - Richter, Rico A1 - Döllner, Jürgen Roland Friedrich T1 - Concepts and techniques for integration, analysis and visualization of massive 3D point clouds JF - Computers, environment and urban systems N2 - Remote sensing methods, such as LiDAR and image-based photogrammetry, are established approaches for capturing the physical world. Professional and low-cost scanning devices are capable of generating dense 3D point clouds. Typically, these 3D point clouds are preprocessed by GIS and are then used as input data in a variety of applications such as urban planning, environmental monitoring, disaster management, and simulation. The availability of area-wide 3D point clouds will drastically increase in the future due to the availability of novel capturing methods (e.g., driver assistance systems) and low-cost scanning devices. Applications, systems, and workflows will therefore face large collections of redundant, up-to-date 3D point clouds and have to cope with massive amounts of data. Hence, approaches are required that will efficiently integrate, update, manage, analyze, and visualize 3D point clouds. In this paper, we define requirements for a system infrastructure that enables the integration of 3D point clouds from heterogeneous capturing devices and different timestamps. Change detection and update strategies for 3D point clouds are presented that reduce storage requirements and offer new insights for analysis purposes. We also present an approach that attributes 3D point clouds with semantic information (e.g., object class category information), which enables more effective data processing, analysis, and visualization. Out-of-core real-time rendering techniques then allow for an interactive exploration of the entire 3D point cloud and the corresponding analysis results. Web-based visualization services are utilized to make 3D point clouds available to a large community. The proposed concepts and techniques are designed to establish 3D point clouds as base datasets, as well as rendering primitives for analysis and visualization tasks, which allow operations to be performed directly on the point data. Finally, we evaluate the presented system, report on its applications, and discuss further research challenges. KW - 3D point clouds KW - System architecture KW - Classification KW - Out-of-core KW - Visualization Y1 - 2014 U6 - https://doi.org/10.1016/j.compenvurbsys.2013.07.004 SN - 0198-9715 SN - 1873-7587 VL - 45 SP - 114 EP - 124 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Omosa, Leonidah K. A1 - Amugune, Beatrice A1 - Ndunda, Beth A1 - Milugo, Trizah K. A1 - Heydenreich, Matthias A1 - Yenesew, Abiy A1 - Midiwo, Jacob O. T1 - Antimicrobial flavonoids and diterpenoids from Dodonaea angustifolia JF - South African journal of botany : an international interdisciplinary journal for botanical sciences KW - Dodonaea angustifolia KW - Surface exudates KW - Flavone KW - Flavanone KW - Diterpenoid KW - Antimicrobial activities Y1 - 2014 U6 - https://doi.org/10.1016/j.sajb.2013.11.012 SN - 0254-6299 SN - 1727-9321 VL - 91 SP - 58 EP - 62 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Lamanna, Francesco A1 - Kirschbaum, Frank A1 - Tiedemann, Ralph T1 - De novo assembly and characterization of the skeletal muscle and electric organ transcriptomes of the African weakly electric fish Campylomormyrus compressirostris (Mormyridae, Teleostei) JF - Molecular ecology resources N2 - African weakly electric fishes (Mormyridae) underwent an outstanding adaptive radiation (about 200 species), putatively owing to their ability to communicate through species-specific weak electric signals. The electric organ discharge (EOD) is produced by muscle-derived electrocytes organized in piles to form an electric organ. Despite the importance of this trait as a prezygotic isolation mechanism, genomic resources remained limited. We present here a first draft of the skeletal muscle and electric organ transcriptomes from the weakly electric fish species Campylomormyrus compressirostris, obtained using the Illumina HiSeq2000 sequencing technology. Approximately 6.8 Gbp of cDNA sequence data were produced from both tissues, resulting in 57268109 raw reads for the skeletal muscle and 46934923 for the electric organ, and assembled de novo into 46143 and 89270 contigs, respectively. About 50% of both transcriptomes were annotated after protein databases search. The two transcriptomes show similar profiles in terms of Gene Ontology categories composition. We identified several candidate genes which are likely to play a central role in the production and evolution of the electric signal. For most of these genes, and for many other housekeeping genes, we were able to obtain the complete or partial coding DNA sequences (CDS), which can be used for the development of primers to be utilized in qRT-PCR experiments. We present also the complete mitochondrial genome and compare it to those available from other weakly electric fish species. Additionally, we located 1671 SSR-containing regions with their flanking sites and designed the relative primers. This study establishes a first step in the development of genomic tools aimed at understanding the role of electric communication during speciation. KW - cSSR KW - electric fish KW - electric organ KW - skeletal muscle KW - transcriptome Y1 - 2014 U6 - https://doi.org/10.1111/1755-0998.12260 SN - 1755-098X SN - 1755-0998 VL - 14 IS - 6 SP - 1222 EP - 1230 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Stief, Anna A1 - Altmann, Simone A1 - Hoffmann, Karen A1 - Pant, Bikram Datt A1 - Scheible, Wolf-Rüdiger A1 - Bäurle, Isabel T1 - Arabidopsis miR156 regulates tolerance to recurring environmental stress through SPL transcription factors JF - The plant cell N2 - Plants are sessile organisms that gauge stressful conditions to ensure survival and reproductive success. While plants in nature often encounter chronic or recurring stressful conditions, the strategies to cope with those are poorly understood. Here, we demonstrate the involvement of ARGONAUTE1 and the microRNA pathway in the adaptation to recurring heat stress (HS memory) at the physiological and molecular level. We show that miR156 isoforms are highly induced after HS and are functionally important for HS memory. miR156 promotes sustained expression of HS-responsive genes and is critical only after HS, demonstrating that the effects of modulating miR156 on HS memory do not reflect preexisting developmental alterations. miR156 targets SPL transcription factor genes that are master regulators of developmental transitions. SPL genes are posttranscriptionally downregulated by miR156 after HS, and this is critical for HS memory. Altogether, the miR156-SPL module mediates the response to recurring HS in Arabidopsis thaliana and thus may serve to integrate stress responses with development. Y1 - 2014 U6 - https://doi.org/10.1105/tpc.114.123851 SN - 1040-4651 SN - 1532-298X VL - 26 IS - 4 SP - 1792 EP - 1807 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Kabelitz, Tina A1 - Kappel, Christian A1 - Henneberger, Kirstin A1 - Benke, Eileen A1 - Noeh, Christiane A1 - Bäurle, Isabel T1 - eQTL mapping of transposon silencing reveals a position-dependent stable escape from epigenetic silencing and transposition of AtMu1 in thee arabidopsis lineage JF - The plant cell N2 - Transposons are massively abundant in all eukaryotic genomes and are suppressed by epigenetic silencing. Transposon activity contributes to the evolution of species; however, it is unclear how much transposition-induced variation exists at a smaller scale and how transposons are targeted for silencing. Here, we exploited differential silencing of the AtMu1c transposon in the Arabidopsis thaliana accessions Columbia (Col) and Landsberg erecta (Ler). The difference persisted in hybrids and recombinant inbred lines and was mapped to a single expression quantitative trait locus within a 20-kb interval. In Ler only, this interval contained a previously unidentified copy of AtMu1c, which was inserted at the 39 end of a protein-coding gene and showed features of expressed genes. By contrast, AtMu1c(Col) was intergenic and associated with heterochromatic features. Furthermore, we identified widespread natural AtMu1c transposition from the analysis of over 200 accessions, which was not evident from alignments to the reference genome. AtMu1c expression was highest for insertions within 39 untranslated regions, suggesting that this location provides protection from silencing. Taken together, our results provide a species-wide view of the activity of one transposable element at unprecedented resolution, showing that AtMu1c transposed in the Arabidopsis lineage and that transposons can escape epigenetic silencing by inserting into specific genomic locations, such as the 3' end of genes. Y1 - 2014 U6 - https://doi.org/10.1105/tpc.114.128512 SN - 1040-4651 SN - 1532-298X VL - 26 IS - 8 SP - 3261 EP - 3271 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Koessl, M. A1 - Hechavarria, J. C. A1 - Voss, C. A1 - Macias, S. A1 - Mora, E. C. A1 - Vater, Marianne T1 - Neural maps for target range in the auditory cortex of echolocating bats JF - Current opinion in neurobiology : reviews of all advances ; evaluation of key references ; comprehensive listing of papers N2 - Computational brain maps as opposed to maps of receptor surfaces strongly reflect functional neuronal design principles. In echolocating bats, computational maps are established that topographically represent the distance of objects. These target range maps are derived from the temporal delay between emitted call and returning echo and constitute a regular representation of time (chronotopy). Basic features of these maps are innate, and in different bat species the map size and precision varies. An inherent advantage of target range maps is the implementation of mechanisms for lateral inhibition and excitatory feedback. Both can help to focus target ranging depending on the actual echolocation situation. However, these maps are not absolutely necessary for bat echolocation since there are bat species without cortical target-distance maps, which use alternative ensemble computation mechanisms. Y1 - 2014 U6 - https://doi.org/10.1016/j.conb.2013.08.016 SN - 0959-4388 SN - 1873-6882 VL - 24 SP - 68 EP - 75 PB - Elsevier CY - London ER - TY - JOUR A1 - Austin, Gina A1 - Groppe, Karoline A1 - Elsner, Birgit T1 - The reciprocal relationship between executive function and theory of mind in middle childhood: a 1-year longitudinal perspective JF - Frontiers in psychology N2 - There is robust evidence showing a link between executive function (EF) and theory of mind (ToM) in 3-to 5-year-olds. However, it is unclear whether this relationship extends to middle childhood. In addition, there has been much discussion about the nature of this relationship. Whereas some authors claim that ToM is needed for EF, others argue that ToM requires EF. To date, however, studies examining the longitudinal relationship between distinct sub components of EF [i.e., attention shifting, working memory (WM) updating, inhibition] and ToM in middle childhood are rare. The present study examined (1) the relationship between three EF subcomponents (attention shifting, WM updating, inhibition) and ToM in middle childhood, and (2) the longitudinal reciprocal relationships between the EF subcomponents and ToM across a 1-year period. EF and ToM measures were assessed experimentally in a sample of 1,657 children (aged 6-11 years) at time point one (t1) and 1 year later at time point two (t2). Results showed that the concurrent relationships between all three EF subcomponents and ToM pertained in middle childhood at t1 and t2, respectively, even when age, gender, and fluid intelligence were partialle dout. Moreover, cross-lagged structural equation modeling (again, controlling for age, gender, and fluid intelligence, as well as for the earlier levels of the target variables), revealed partial support for the view that early ToM predictslater EF, but stronger evidence for the assumption that early EF predictslater ToM. The latter was found for attention shifting and WM updating, but not for inhibition. This reveals the importance of studying the exact interplay of ToM and EF across childhood development, especially with regard to different EF subcomponents. Most likely, understanding others' mental states at different levels of perspective-taking requires specific EF subcomponents, suggesting developmental change in the relations between EF and ToM across childhood. KW - executive function KW - theory of mind KW - longitudinal KW - middle childhood KW - attention shifting KW - inhibition KW - working memory updating Y1 - 2014 U6 - https://doi.org/10.3389/fpsyg.2014.00655 SN - 1664-1078 VL - 5 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Primus, Philipp-Alexander A1 - Ritschel, Thomas A1 - Sigueenza, Pilar Y. A1 - Cauqui, Miguel Angel A1 - Hernandez-Garrido, Juan Carlos A1 - Kumke, Michael Uwe T1 - High-resolution spectroscopy of europium-doped ceria as a tool to correlate structure and catalytic activity JF - The journal of physical chemistry : C, Nanomaterials and interfaces N2 - Site-selective emission spectra of Eu3+-doped CeO2 nanoparticles up to the D-5(0) - F-7(5) transition were recorded under cryogenic conditions to identify the local structure around the Eu3+ dopants in ceria. It is found that pretreatment conditions are crucial for the redistribution of dopants from a broad variety of environments to six well-defined lattice sites. The influence of the dopant and the host structure on the catalytic activity was investigated. A relationship between structure and reactivity is discussed. It is shown that oxygen transport is most efficient in particles with a pronounced amorphous character. Y1 - 2014 U6 - https://doi.org/10.1021/jp505467r SN - 1932-7447 VL - 118 IS - 40 SP - 23349 EP - 23360 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Devos, Damien P. A1 - Gräf, Ralph A1 - Field, Mark C. T1 - Evolution of the nucleus JF - Current opinion in cell biology : review articles, recommended reading, bibliography of the world literature N2 - The nucleus represents a major evolutionary transition. As a consequence of separating translation from transcription many new functions arose, which likely contributed to the remarkable success of eukaryotic cells. Here we will consider what has recently emerged on the evolutionary histories of several key aspects of nuclear biology; the nuclear pore complex, the lamina, centrosomes and evidence for prokaryotic origins of relevant players. Y1 - 2014 U6 - https://doi.org/10.1016/j.ceb.2014.01.004 SN - 0955-0674 SN - 1879-0410 VL - 28 SP - 8 EP - 15 PB - Elsevier CY - London ER - TY - JOUR A1 - Ifenthaler, Dirk T1 - Challenges of a Holistic Learning Analytics Project JF - E-Learning Symposium 2014 : Mobil und vernetzt – studieren im digitalen Zeitalter ; Potsdam, 14. November 2014 N2 - Recently, interest in collecting and mining large sets of educational data on student background and performance to conduct research on learning and instruction has developed as an area generally referred to as learning analytics. Higher education leaders are recognising the value of learning analytics for improving not only learning and teaching but also the entire educational arena. However, theoretical concepts and empirical evidence need to be generated within the fast evolving field of learning analytics. In this paper, we introduce a holistic learning analytics framework. Based on this framework, student, learning, and curriculum profiles have been developed which include relevant static and dynamic parameters for facilitating the learning analytics framework. Based on the theoretical model, an empirical study was conducted to empirically validate the parameters included in the student profile. The paper concludes with practical implications and issues for future research. Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-442303 SP - 15 EP - 28 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - JOUR A1 - Putra, Sulistyo Emantoko Dwi A1 - Neuber, Corinna A1 - Reichetzeder, Christoph A1 - Hocher, Berthold A1 - Kleuser, Burkhard T1 - Analysis of genomic DNA methylation levels in human placenta using liquid Chromatography-Electrospray ionization tandem mass spectrometry JF - Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry and pharmacology N2 - Background: DNA-methylation is a common epigenetic tool which plays a crucial role in gene regulation and is essential for cell differentiation and embryonic development. The placenta is an important organ where gene activity can be regulated by epigenetic DNA modifications, including DNA methylation. This is of interest as, the placenta is the interface between the fetus and its environment, the mother. Exposure to environmental toxins and nutrition during pregnancy may alter DNA methylation of the placenta and subsequently placental function and as a result the phenotype of the offspring. The aim of this study was to develop a reliable method to quantify DNA methylation in large clinical studies. This will be a tool to analyze the degree of DNA methylation in the human placenta in relationship to clinical readouts. Methods: Liquid chromatography-electrospray ionization/multi-stage mass spectrometry (LC-ESI/MS/MS) technique was used for the quantification of the 5dmC/dG ratio in placentas from 248 healthy pregnancies. We were able to demonstrate that this method is a reliable and stable way to determine global placental DNA methylation in large clinical trials. Results/Conclusion: The degree of placental DNA methylation seen in our pilot study varies substantially from 2% to 5%. The clinical implications of this variation need to be demonstrated in adequately powered large studies. KW - Pregnancy KW - Placenta KW - Methylation KW - Global KW - LC-MS/MS KW - Fetal programming KW - Clinical Y1 - 2014 U6 - https://doi.org/10.1159/000358666 SN - 1015-8987 SN - 1421-9778 VL - 33 IS - 4 SP - 945 EP - 952 PB - Karger CY - Basel ER - TY - JOUR A1 - Risse, Sarah T1 - Effects of visual span on reading speed and parafoveal processing in eye movements during sentence reading JF - Journal of vision KW - eyetracking KW - reading KW - visual span profiles KW - crowding KW - reading speed KW - preview benefit KW - parafoveal vision Y1 - 2014 U6 - https://doi.org/10.1167/14.8.11 SN - 1534-7362 VL - 14 IS - 8 PB - Association for Research in Vision and Opthalmology CY - Rockville ER - TY - JOUR A1 - Schulze, Nicole A1 - Appelhans, D. A1 - Tiersch, Brigitte A1 - Koetz, Joachim T1 - Morphological transformation of vesicles into tubular structures by adding polyampholytes or dendritic glycopolymers JF - Colloids and surfaces : an international journal devoted to the principles and applications of colloid and interface science ; A, Physicochemical and engineering aspects N2 - For the first time tubulating properties of spherical dendritic glycopolymers and linear alternating polyampholytes against non-uniform negatively charged giant vesicles are proven by light microscopy and cryo-scanning electron microscopy study. Real time observation of the morphological transformation from giant vesicles to tubular structures, simulating morphogenesis in living cells, is given by using the cationic and H-bond active dendritic glycopolymer accompanied by reducing the size of the giant vesicles and the evidence of vesicle-vesicle interaction which was only postulated in a previous study. Similar morphogenesis of non-uniform giant vesicles into tubular network structure can be observed by using a polyampholyte in the stretched conformation at pH 9. Pearl necklace and tubular network structure formation are also observed by applying anionic vesicles of significant smaller dimensions with average size dimensions of 35 nm, after adding the polyampholyte at pH 9. However, the fitting accuracy between the functional groups along the backbone chain of the polyampholyte on one side and the vesicle surface on the other side is of high importance for the transformation process by using polyampholytes. The resulting tubular and network structures offer new fields of application as microfluidic transport channels or template phases for the shape controlled formation of nanoparticles. (C) 2014 Elsevier B.V. All rights reserved. KW - Alternating polyampholytes KW - Maltose-modified PEI KW - Network structure KW - Template phase KW - Cryo-SEM KW - DLS Y1 - 2014 U6 - https://doi.org/10.1016/j.colsurfa.2014.06.007 SN - 0927-7757 SN - 1873-4359 VL - 457 SP - 326 EP - 332 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Groppe, Karoline A1 - Elsner, Birgit T1 - Executive function and food approach behavior in middle childhood JF - Frontiers in psychology N2 - Executive function (EF) has long been considered to be a unitary, domain-general cognitive ability. However, recent research suggests differentiating "hot" affective and "cool" cognitive aspects of EF. Yet, findings regarding this two-factor construct are still inconsistent. In particular, the development of this factor structure remains unclear and data on school-aged children is lacking. Furthermore, studies linking EF and overweight or obesity suggest that EF contributes to the regulation of eating behavior. So far, however, the links between EF and eating behavior have rarely been investigated in children and non-clinical populations. First, we examined whether EF can be divided into hot and cool factors or whether they actually correspond to a unitary construct in middle childhood. Second, we examined how hot and cool EF are associated with different eating styles that put children at risk of becoming overweight during development. Hot and cool EF were assessed experimentally in a non-clinical population of 1657 elementary-school children (aged 6-11 years). The "food approach" behavior was rated mainly via parent questionnaires. Findings indicate that hot EF is distinguishable from cool EF. However, only cool EF seems to represent a coherent functional entity, whereas hot EF does not seem to be a homogenous construct. This was true for a younger and an older subgroup of children. Furthermore, different EF components were correlated with eating styles, such as responsiveness to food, desire to drink, and restrained eating in girls but not in boys. This shows that lower levels of EF are not only seen in clinical populations of obese patients but are already associated with food approach styles in a normal population of elementary school-aged girls. Although the direction of effect still has to be clarified, results point to the possibility that EF constitutes a risk factor for eating styles contributing to the development of overweight in the long-term. KW - hot and cool executive function KW - eating behavior KW - food approach KW - overweight KW - middle childhood Y1 - 2014 U6 - https://doi.org/10.3389/fpsyg.2014.00447 SN - 1664-1078 VL - 5 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Rofes, Adria A1 - Bastiaanse, Roelien A1 - Martinez-Ferreiro, Silvia T1 - Conditional and future tense impairment in non-fluent aphasia JF - Aphasiology : an international, interdisciplinary journal N2 - Background: Morphological errors of tense and agreement are salient in agrammatic aphasia. The PADILIH predicts impairments in discourse linking that translate to greater difficulties in referring to a past event time than to a future or a present event time. In Catalan, the Periphrastic conditional tense (e.g., if the man had had time, he would have...) refers to the past and the Simple conditional tense refers to the future (e.g., if the man had time, he would...). These two tenses refer to an event that may happen (irrealis).Aims: We fill in the gap of the conditional tense and provide further data to study contrasts in verb inflection for time reference. We predict that verb forms that refer to an irrealis past event (Periphrastic conditional) are more impaired than forms that refer to an irrealis future event (Simple conditional and Future). We also predict that there are no differences between verb forms that refer to an irrealis future event (Simple conditional and Future). We also assessed whether problems in time reference extend to individuals with non-fluent aphasia that are not typical agrammatic Broca aphasia.Methods & Procedures: A sentence completion task that included 60 sentences (20 per type) of equal length in a Conditional structure (if-sentences) was designed. We tested three sentence types: Periphrastic conditional, Simple conditional and Future. The task was administered to nine participants with non-fluent aphasia and nine age-matched non-brain-damaged participants.Outcomes & Results: The Control group scored at ceiling on the three sentence types. Participants with non-fluent aphasia were most impaired in the production of the Periphrastic conditional as compared with the Simple conditional and the Future.Conclusions: When irrealis event times are compared, past events are more impaired than future events. These results can be explained by a deficit in time reference as predicted by the PADILIH. Our data reveal that the predictions of the PADILIH also hold for non-fluent speakers who have been diagnosed with Transcortical motor aphasia. KW - Time reference KW - Conditional tense KW - Future tense KW - Realis KW - Irrealis KW - Non-fluent aphasia KW - Catalan KW - PADILIH Y1 - 2014 U6 - https://doi.org/10.1080/02687038.2013.850650 SN - 0268-7038 SN - 1464-5041 VL - 28 IS - 1 SP - 99 EP - 115 PB - Routledge, Taylor & Francis Group CY - Abingdon ER - TY - JOUR A1 - Neuschaefer-Rube, Frank A1 - Lieske, Stefanie A1 - Kuna, Manuela A1 - Henkel, Janin A1 - Perry, Rachel J. A1 - Erion, Derek M. A1 - Pesta, Dominik A1 - Willmes, Diana M. A1 - Brachs, Sebastian A1 - von Loeffelholz, Christian A1 - Tolkachov, Alexander A1 - Schupp, Michael A1 - Pathe-Neuschaefer-Rube, Andrea A1 - Pfeiffer, Andreas F. H. A1 - Shulman, Gerald I. A1 - Püschel, Gerhard Paul A1 - Birkenfeld, Andreas L. T1 - The mammalian INDY homolog is induced by CREB in a rat model of type 2 diabetes JF - Diabetes : a journal of the American Diabetes Association Y1 - 2014 SN - 0012-1797 SN - 1939-327X VL - 63 IS - 3 SP - 1048 EP - 1057 PB - American Diabetes Association CY - Alexandria ER - TY - JOUR A1 - Ivanov, Ivan A1 - Benina, Maria A1 - Petrov, Veselin A1 - Gechev, Tsanko S. A1 - Toneva, Valentina T1 - Metabolic responses of gloxinia perennis to dehydration and rehydration JF - COMPTES RENDUS DE L ACADEMIE BULGARE DES SCIENCES N2 - Gloxinia perennis is a species from the family Gesneriaceae with little known physiology, particularly in respect to responses to dehydration. G. perennis survived water deprivation for a month and then quickly recovered upon rehydration. The slow loss of water was in contrast with the quick dehydration of other Gesnerian species - Boea hygrometrica, Ramonda serbica, and Haber lea rhodopensis. Furthermore, a significant difference between older and younger leaves of G. perennis was observed. While the relative water content in the early stages of water deprivation was reduced to 65% in the old leaves, it was not or slightly reduced in the young ones, implying a mechanism that protects specifically the younger leaves from dehydration. Water deprivation induced accumulation of gama-aminobutyric acid and sugars like sucrose and raffinose, but decreased the levels of amino acids such as glycine, leucine, and isoleucine. The levels of these amino acids recovered after rehydration and in some cases like glycine and isoleucine were even higher in rehydrated leaves compared with unstressed controls. We conclude that G.perennis can survive prolonged drought stress but its responses to dehydration are different from the resurrection species from Gesneriaceae. All this makes G. perennis a good model that can be used for comparative genomics and metabolomics of Gesneriads exposed to desiccation. KW - Gloxinia perennis KW - drought stress KW - metabolome analysis Y1 - 2014 SN - 1310-1331 VL - 67 IS - 12 SP - 1657 EP - 1662 PB - Publ. House of the Bulgarian Acad. of Sciences CY - Sofia ER - TY - JOUR A1 - Csatlós, Erzsébet ED - Badó, Attila ED - Belling, Detlev W. ED - Bóka, János ED - Mezei, Péter T1 - The Application of International Law as an Instrument of Interpretation in Hungary – the Practice of the Constitutional Court and Ordinary Courts in a Comparative Approach JF - Internationale Konferenz zum zehnjährigen Bestehen des Instituts für Rechtsvergleichung der Universität Szeged Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-73683 IS - 1 SP - 127 EP - 142 ER - TY - JOUR A1 - Haßler, Gerda T1 - Evidentiality and the expression of speaker’s stance in Romance languages and German JF - Discourse Studies : an interdisciplinary journal for the study of text and talk N2 - In recent years, the category of evidentiality has also come into use for the description of Romance languages and of German. This has been contingent on a change in its interpretation from a typological category to a semantic-pragmatic category, which allows an application to languages lacking specialised morphemes for the expression of evidentiality. We consider evidentiality to be a structural dimension of grammar, the values of which are expressed by types of constructions that code the source of information which a speaker imparts. If we look at the situation in Romance languages and in German, drawing a boundary between epistemic modality and evidentiality presents problems that are difficult to solve. Adding markers of the source of the speaker’s knowledge often limits the degree of responsibility of the speaker for the content of the utterance. Evidential adverbs are a frequently used means of marking the source of the speaker’s knowledge. The evidential meaning is generalised to marking any source of knowledge, what can be regarded as a result of a process of pragmaticalisation. The use of certain means which also carry out evidential markings can even contribute to the blurring of the different kinds of evidentiality. German also has modal verbs which in conjunction with the perfect tense of the verb have a predominantly evidential use (sollen and wollen). But even here the evidential marking is not without influence on the modality of the utterance. The Romance languages, however, do not have such specialised verbs for expressing evidentiality in certain contexts. To do this, they mark evidentiality – often context bound – by verb forms such as the conditional and the imperfect tense. This article shall contrast the different architectures used in expressing evidentiality in German and in the Romance languages. KW - Adverbs KW - evidentiality KW - modal verbs KW - modality KW - pragmaticalisation Y1 - 2015 UR - http://journals.sagepub.com/doi/abs/10.1177/1461445614564522 U6 - https://doi.org/10.1177/1461445614564522 SN - 1461-4456 SN - 1461-7080 VL - 17 IS - 2 SP - 182 EP - 209 PB - Sage Publications CY - London ER - TY - JOUR A1 - Kelemen, Katalin A1 - Balázs, Fekete ED - Badó, Attila ED - Belling, Detlev W. ED - Bóka, János ED - Mezei, Péter T1 - How Should the Legal Systems of Eastern Europe Be Classified Today? JF - Internationale Konferenz zum zehnjährigen Bestehen des Instituts für Rechtsvergleichung der Universität Szeged Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-73748 IS - 1 SP - 197 EP - 223 ER - TY - JOUR A1 - Bóka, János ED - Badó, Attila ED - Belling, Detlev W. ED - Bóka, János ED - Mezei, Péter T1 - Use of the Comparative Method by the Hungarian Constitutional Court - Conceptual and Methodological Framework for an Ongoing Research Project JF - Internationale Konferenz zum zehnjährigen Bestehen des Instituts für Rechtsvergleichung der Universität Szeged Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-73632 IS - 1 SP - 93 EP - 107 ER - TY - JOUR A1 - Günther, Oliver T1 - Big Data: What is it? And what does it mean for science, economy and society? JF - Informatik-Spektrum Y1 - 2014 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84897396415&partnerID=MN8TOARS U6 - https://doi.org/10.1007/s00287-014-0783-7 SN - 0170-6012 VL - 37 IS - 2 SP - 85 EP - 86 PB - Springer Verlag CY - Heidelberg ER - TY - JOUR A1 - Hemme, Dorothea A1 - Veyel, Daniel A1 - Muehlhaus, Timo A1 - Sommer, Frederik A1 - Jueppner, Jessica A1 - Unger, Ann-Katrin A1 - Sandmann, Michael A1 - Fehrle, Ines A1 - Schoenfelder, Stephanie A1 - Steup, Martin A1 - Geimer, Stefan A1 - Kopka, Joachim A1 - Giavalisco, Patrick A1 - Schroda, Michael T1 - Systems-wide analysis of acclimation responses to long-term heat stress and recovery in the photosynthetic model organism Chlamydomonas reinhardtii JF - The plant cell N2 - We applied a top-down systems biology approach to understand how Chlamydomonas reinhardtii acclimates to long-term heat stress (HS) and recovers from it. For this, we shifted cells from 25 to 42 degrees C for 24 h and back to 25 degrees C for >= 8 h and monitored abundances of 1856 proteins/protein groups, 99 polar and 185 lipophilic metabolites, and cytological and photosynthesis parameters. Our data indicate that acclimation of Chlamydomonas to long-term HS consists of a temporally ordered, orchestrated implementation of response elements at various system levels. These comprise (1) cell cycle arrest; (2) catabolism of larger molecules to generate compounds with roles in stress protection; (3) accumulation of molecular chaperones to restore protein homeostasis together with compatible solutes; (4) redirection of photosynthetic energy and reducing power from the Calvin cycle to the de novo synthesis of saturated fatty acids to replace polyunsaturated ones in membrane lipids, which are deposited in lipid bodies; and (5) when sinks for photosynthetic energy and reducing power are depleted, resumption of Calvin cycle activity associated with increased photorespiration, accumulation of reactive oxygen species scavengers, and throttling of linear electron flow by antenna uncoupling. During recovery from HS, cells appear to focus on processes allowing rapid resumption of growth rather than restoring pre-HS conditions. Y1 - 2014 U6 - https://doi.org/10.1105/tpc.114.130997 SN - 1040-4651 SN - 1532-298X VL - 26 IS - 11 SP - 4270 EP - 4297 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Cisek, Richard A1 - Tokarz, Danielle A1 - Krouglov, Serguei A1 - Steup, Martin A1 - Emes, Michael J. A1 - Tetlow, Ian J. A1 - Barzda, Virginijus T1 - Second harmonic generation mediated by aligned water in starch granules JF - The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces & biophysical chemistry N2 - The origin of second harmonic generation (SHG) in starch granules was investigated using ab initio quantum mechanical modeling and experimentally examined using polarization-in, polarization-out (PIPO) second harmonic generation microscopy. Ab initio calculations revealed that the largest contribution to the SHG signal from A- and B-type allomorphs of starch originates from the anisotropic organization of hydroxide and hydrogen bonds mediated by aligned water found in the polymers. The hypothesis was experimentally tested by imaging maize starch granules under various hydration and heat treatment conditions that alter the hydrogen bond network. The highest SHG intensity was found in fully hydrated starch granules, and heat treatment diminished the SHG intensity. The PIPO SHG imaging showed that dried starch granules have a much higher nonlinear optical susceptibility component ratio than fully hydrated granules. In contrast, deuterated starch granules showed a smaller susceptibility component ratio demonstrating that SHG is highly sensitive to the organization of the hydroxyl and hydrogen bond network. The polarization SHG imaging results of potato starch granules, representing starch allomorph B, were compared to those of maize starch granules representing allomorph A. The results showed that the amount of aligned water was higher in the maize granules. Nonlinear microscopy of starch granules provides evidence that varying hydration conditions leads to significant changes in the nonlinear susceptibility ratio as well as the SHG intensity, supporting the hypothesis from ab initio calculations that the dominant contribution to SHG is due to the ordered hydroxide and hydrogen bond network. Y1 - 2014 U6 - https://doi.org/10.1021/jp508751s SN - 1520-6106 VL - 118 IS - 51 SP - 14785 EP - 14794 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Tenenboim, Hezi A1 - Smirnova, Julia A1 - Willmitzer, Lothar A1 - Steup, Martin A1 - Brotman, Yariv T1 - VMP1-deficient Chlamydomonas exhibits severely aberrant cell morphology and disrupted cytokinesies JF - BMC plant biology N2 - Background: The versatile Vacuole Membrane Protein 1 (VMP1) has been previously investigated in six species. It has been shown to be essential in macroautophagy, where it takes part in autophagy initiation. In addition, VMP1 has been implicated in organellar biogenesis; endo-, exo- and phagocytosis, and protein secretion; apoptosis; and cell adhesion. These roles underly its proven involvement in pancreatitis, diabetes and cancer in humans. Results: In this study we analyzed a VMP1 homologue from the green alga Chlamydomonas reinhardtii. CrVMP1 knockdown lines showed severe phenotypes, mainly affecting cell division as well as the morphology of cells and organelles. We also provide several pieces of evidence for its involvement in macroautophagy. KW - VMP1 KW - Autophagy KW - Cytokinesis Y1 - 2014 U6 - https://doi.org/10.1186/1471-2229-14-121 SN - 1471-2229 VL - 14 PB - BioMed Central CY - London ER - TY - JOUR A1 - Lukas, Marcus A1 - Wacker, Alexander T1 - Constraints by oxygen and food quality on carbon pathway regulation: a co-limitation study with an aquatic key herbivore JF - Ecology : a publication of the Ecological Society of America N2 - In food webs, herbivores are often constrained by low food quality in terms of mineral and biochemical limitations, which in aquatic ecosystems can co-occur with limited oxygen conditions. As low food quality implies that carbon (C) is available in excess, and therefore a regulation to get rid of excess C is crucial for the performance of consumers, we examined the C pathways (ingestion, feces release, excretion, and respiration) of a planktonic key herbivore (Daphnia magna). We tested whether consumer C pathways increase due to mineral (phosphorus, P) or biochemical (cholesterol and fatty acid) limitations and how these regulations vary when in addition oxygen is low. Under such conditions, at least the capability of the upregulation of respiration may be restricted. Furthermore, we discussed the potential role of the oxygen-transporting protein hemoglobin (Hb) in the regulation of C budgets. Different food quality constraints led to certain C regulation patterns to increase the removal of excess dietary C: P-limited D. magna increased excretion and respiration, while cholesterol-limited Daphnia in addition upregulated the release of feces. In contrast, the regulative effort was low and only feces release increased when D. magna was limited by a long-chain polyunsaturated fatty acid (eicosapentaenoic acid, EPA). Co-limiting oxygen did not always impact the discharge of excess C. We found the food-quality-induced upregulation of respiration was still present at low oxygen. In contrast, higher excretion of excess C was diminished at low oxygen supply. Besides the effect that the Hb concentration increased under low oxygen, our results indicate a low food-quality-induced increase in the Hb content of the animals. Overall, C budgeting is phenotypically plastic towards different (co-) limiting scenarios. These trigger specific regulation responses that could be the result of evolutionary adaptations. KW - carbon budget KW - carbon stoichiometry KW - cholesterol KW - co-limitation KW - Daphnia KW - EPA KW - hemoglobin KW - oxygen KW - phosphorus KW - polyunsaturated fatty acid KW - zooplankton Y1 - 2014 SN - 0012-9658 SN - 1939-9170 VL - 95 IS - 11 SP - 3068 EP - 3079 PB - Wiley CY - Washington ER - TY - JOUR A1 - Spijkerman, Elly A1 - Stojkovic, Slobodanka A1 - Beardall, John T1 - CO2 acquisition in Chlamydomonas acidophila is influenced mainly by CO2, not phosphorus, availability JF - Photosynthesis research N2 - The extremophilic green microalga Chlamydomonas acidophila grows in very acidic waters (pH 2.3-3.4), where CO2 is the sole inorganic carbon source. Previous work has revealed that the species can accumulate inorganic carbon (Ci) and exhibits high affinity CO2 utilization under low-CO2 (air-equilibrium) conditions, similar to organisms with an active CO2 concentrating mechanism (CCM), whereas both processes are down-regulated under high CO2 (4.5 % CO2) conditions. Responses of this species to phosphorus (Pi)-limited conditions suggested a contrasting regulation of the CCM characteristics. Therefore, we measured external carbonic anhydrase (CA(ext)) activities and protein expression (CAH1), the internal pH, Ci accumulation, and CO2-utilization in cells adapted to high or low CO2 under Pi-replete and Pi-limited conditions. Results reveal that C. acidophila expressed CA(ext) activity and expressed a protein cross-reacting with CAH1 (the CA(ext) from Chlamydomonas reinhardtii). Although the function of this CA remains unclear, CA(ext) activity and high affinity CO2 utilization were the highest under low CO2 conditions. C. acidophila accumulated Ci and expressed the CAH1 protein under all conditions tested, and C. reinhardtii also contained substantial amounts of CAH1 protein under Pi-limitation. In conclusion, Ci utilization is optimized in C. acidophila under ecologically relevant conditions, which may enable optimal survival in its extreme Ci- and Pi-limited habitat. The exact physiological and biochemical acclimation remains to be further studied. KW - CO2 concentrating mechanism KW - Inorganic phosphorus limitation KW - Varying CO2 condition KW - Extremophilic green alga KW - Co-limitation KW - Internal pH KW - Inorganic carbon accumulation KW - Affinity for CO2 uptake Y1 - 2014 U6 - https://doi.org/10.1007/s11120-014-0016-6 SN - 0166-8595 SN - 1573-5079 VL - 121 IS - 2-3 SP - 213 EP - 221 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Lukas, Marcus A1 - Wacker, Alexander T1 - Daphnia's dilemma: adjustment of carbon budgets in the face of food and cholesterol limitation JF - The journal of experimental biology N2 - We studied the carbon (C) metabolism in Daphnia when the amount of C (food quantity) and/or the content of biochemical nutrients (food quality) was limiting. Growth performances and C budgets of Daphnia magna (assimilation, faeces egestion, excretion and respiration measured by [C-14]-tracing) were analysed when animals were raised on different food quantities and concentrations of cholesterol, an essential biochemical food compound. Cholesterol is of special interest because it not only acts as limiting nutrient but also contributes to the overall C pool of the animals. As the tissue cholesterol concentration in Daphnia is quite low, we hypothesized the selective exclusion of cholesterol from C budgeting and tested this using radiolabelled cholesterol. Somatic growth rates of D. magna were highest at high quantity and quality and were reduced to a moderate value if either the food quantity or the cholesterol concentration was low. Growth was lowest at low food quantity and quality. The measurements of C budgets revealed high regulative response to low food quality at high food quantity only. Here, low dietary cholesterol caused bulk C assimilation efficiency (AE) to decrease and assimilated (excess) C to be increasingly respired. Additionally, Daphnia enhanced efficient adjustment of C budgets when facing cholesterol limitation by (1) increasing the AE of the cholesterol itself and (2) not changing cholesterol respiration, which was still not detectable. In contrast, at low food quantity, Daphnia is unable to adjust for low food quality, emphasizing that food limitation could overrule food quality effects. KW - Biochemical limitation KW - Carbon budgets KW - Zooplankton KW - Carbon pathway KW - Food quality KW - Food quantity Y1 - 2014 U6 - https://doi.org/10.1242/jeb.094151 SN - 0022-0949 SN - 1477-9145 VL - 217 IS - 7 SP - 1079 EP - 1086 PB - Company of Biologists Limited CY - Cambridge ER - TY - JOUR A1 - Lukas, Marcus A1 - Wacker, Alexander T1 - Acclimation to dietary shifts impacts the carbon budgets of Daphnia magna JF - Journal of plankton research N2 - Daphnia responds to low availability of carbon (food quantity) or limiting concentrations of nutrients relative to carbon (C) in excess (food quality) by respectively saving or discharging C via different pathways. We investigated which kind of food limitation leads to a faster regulation in Daphnia C budgets, and whether the pre-assimilative C pathways, ingestion and faeces egestion and the post-assimilative C pathways, excretion and respiration, are regulated concurrently. Daphnia magna were exposed to dietary shifts in different food quantities or qualities; food quality was varied in terms of the essential component, cholesterol. After acclimation to the new diet ranging from 0 to 96 h, C budgets were measured by a radiotracer technique. Dietary shifts in quantity and quality caused Daphnia to quickly adjust their C budgets within 6 h, but different C pathways were affected. A shift to low food quantity reduced Daphnia respiration indicating C retention. In contrast, sudden low quality food caused increased faeces egestion to discharge excess C. Furthermore, we observed a delayed increase in excretion but no change in respiration within the time frame studied. Such time-shifted responses appear to be an appropriate means to keep the costs of physiological adjustments relatively low, which in turn would benefit Daphnia performance. KW - carbon pathway KW - cholesterol KW - zooplankton KW - food quality KW - food quantity Y1 - 2014 U6 - https://doi.org/10.1093/plankt/fbu018 SN - 0142-7873 SN - 1464-3774 VL - 36 IS - 3 SP - 848 EP - 858 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Seifert, Linda I. A1 - de Castro, Francisco A1 - Marquart, Arnim A1 - Gaedke, Ursula A1 - Weithoff, Guntram A1 - Vos, Matthijs T1 - Heated relations: temperature-mediated shifts in consumption across trophic levels JF - PLoS one N2 - A rise in temperature will intensify the feeding links involving ectotherms in food webs. However, it is unclear how the effects will quantitatively differ between the plant-herbivore and herbivore-carnivore interface. To test how warming could differentially affect rates of herbivory and carnivory, we studied trophic interaction strength in a food chain comprised of green algae, herbivorous rotifers and carnivorous rotifers at 10, 15, 20 and 25 degrees C. We found significant warming-induced changes in feeding by both herbivorous and carnivorous rotifers, but these responses occurred at different parts of the entire temperature gradient. The strongest response of the per capita herbivore's ingestion rate occurred due to an increase in temperature from 15 to 20 degrees C (1.9 fold: from 834 to 1611 algal cells per h(-1)) and of the per capita carnivore's ingestion rate from 20 to 25 degrees C (1.6 fold: from 1.5 to 2.5 prey h(-1)). Handling time, an important component of a consumer's functional response, significantly decreased from 15 to 20 degrees C in herbivorous rotifers. In contrast, it decreased from 20 to 25 degrees C in carnivorous rotifers. Attack rates significantly and strongly increased from 10 to 25 degrees C in the herbivorous animals, but not at all in the carnivores. Our results exemplify how the relative forces of top-down control exerted by herbivores and carnivores may strongly shift under global warming. But warming, and its magnitude, are not the only issue: If our results would prove to be representative, shifts in ectotherm interactions will quantitatively differ when a 5 degrees C increase starts out from a low, intermediate or high initial temperature. This would imply that warming could have different effects on the relative forces of carnivory and herbivory in habitats differing in average temperature, as would exist at different altitudes and latitudes. Y1 - 2014 U6 - https://doi.org/10.1371/journal.pone.0095046 SN - 1932-6203 VL - 9 IS - 5 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Zimmermann, Andreas A1 - Sener, Meltem T1 - Chemical weapons and the international criminal court JF - American journal of international law Y1 - 2014 U6 - https://doi.org/10.5305/amerjintelaw.108.3.0436 SN - 0002-9300 SN - 2161-7953 VL - 108 IS - 3 SP - 436 EP - 448 PB - American Society of International Law CY - Washington ER - TY - JOUR A1 - Noble, Andrew T1 - Ultraschall Berlin BT - Festival für neue Musik, 2014 JF - Tempo: a quarterly review of modern music Y1 - 2014 U6 - https://doi.org/10.1017/S004029821400014X SN - 1478-2286 VL - 68 IS - 269 SP - 76 EP - 78 PB - Cambidge University Press CY - Cambridge ER - TY - JOUR A1 - Filip, Joanna A1 - Bauer, Barbara A1 - Hillebrand, Helmut A1 - Beniermann, Anna A1 - Gaedke, Ursula A1 - Moorthi, Stefanie D. T1 - Multitrophic diversity effects depend on consumer specialization and species-specific growth and grazing rates JF - Oikos N2 - Ecosystem functioning is affected by horizontal (within trophic groups) and vertical (across trophic levels) biodiversity. Theory predicts that the effects of vertical biodiversity depend on consumer specialization. In a microcosm experiment, we investigated ciliate consumer diversity and specialization effects on algal prey biovolume, evenness and composition, and on ciliate biovolume production. The experimental data was complemented by a process-based model further analyzing the ecological mechanisms behind the observed diversity effects. Overall, increasing consumer diversity had no significant effect on prey biovolume or evenness. However, consumer specialization affected the prey community. Specialist consumers showed a stronger negative impact on prey biovolume and evenness than generalists. The model confirmed that this pattern was mainly driven by a single specialist with a high per capita grazing rate, consuming the two most productive prey species. When these were suppressed, the prey assemblage became dominated by a less productive species, consequently decreasing prey biovolume and evenness. Consumer diversity increased consumer biovolume, which was stronger for generalists than for specialists and highest in mixed combinations, indicating that consumer functional diversity, i.e. more diverse feeding strategies, increased resource use efficiency. Overall, our results indicate that consumer diversity effects on prey and consumers strongly depend on species-specific growth and grazing rates, which may be at least equally important as consumer specialization in driving consumer diversity effects across trophic levels. Y1 - 2014 U6 - https://doi.org/10.1111/oik.01219 SN - 0030-1299 SN - 1600-0706 VL - 123 IS - 8 SP - 912 EP - 922 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Dietrich, Ann-Christin A1 - Lombardo, Veronica A. A1 - Abdelilah-Seyfried, Salim T1 - Blood flow and Bmp signaling control endocardial chamber morphogenesis JF - Developmental cell N2 - During heart development, the onset of heartbeat and blood flow coincides with a ballooning of the cardiac chambers. Here, we have used the zebrafish as a vertebrate model to characterize chamber ballooning morphogenesis of the endocardium, a specialized population of endothelial cells that line the interior of the heart. By combining functional manipulations, fate mapping studies, and high-resolution imaging, we show that endocardial growth occurs without an influx of external cells. Instead, endocardial cell proliferation is regulated, both by blood flow and by Bmp signaling, in a manner independent of vascular endothelial growth factor (VEGF) signaling. Similar to myocardial cells, endocardial cells obtain distinct chamber-specific and inner- versus outer-curvature-specific surface area sizes. We find that the hemodynamic-sensitive transcription factor Klf2a is involved in regulating endocardial cell morphology. These findings establish the endocardium as the flow-sensitive tissue in the heart with a key role in adapting chamber growth in response to the mechanical stimulus of blood flow. Y1 - 2014 U6 - https://doi.org/10.1016/j.devcel.2014.06.020 SN - 1534-5807 SN - 1878-1551 VL - 30 IS - 4 SP - 367 EP - 377 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Otrelo-Cardoso, Ana Rita A1 - da Silva Correia, Marcia Alexandra A1 - Schwuchow, Viola A1 - Svergun, Dmitri I. A1 - Romao, Maria Joao A1 - Leimkühler, Silke A1 - Santos-Silva, Teresa T1 - Structural Data on the Periplasmic Aldehyde Oxidoreductase PaoABC from Escherichia coli: SAXS and Preliminary X-ray Crystallography Analysis JF - International journal of molecular sciences N2 - The periplasmic aldehyde oxidoreductase PaoABC from Escherichia coli is a molybdenum enzyme involved in detoxification of aldehydes in the cell. It is an example of an heterotrimeric enzyme of the xanthine oxidase family of enzymes which does not dimerize via its molybdenum cofactor binding domain. In order to structurally characterize PaoABC, X-ray crystallography and small angle X-ray scattering (SAXS) have been carried out. The protein crystallizes in the presence of 20% (w/v) polyethylene glycol 3350 using the hanging-drop vapour diffusion method. Although crystals were initially twinned, several experiments were done to overcome twinning and lowering the crystallization temperature (293 K to 277 K) was the solution to the problem. The non-twinned crystals used to solve the structure diffract X-rays to beyond 1.80 angstrom and belong to the C2 space group, with cell parameters a = 109.42 angstrom, b = 78.08 angstrom, c = 151.77 angstrom, = 99.77 degrees, and one molecule in the asymmetric unit. A molecular replacement solution was found for each subunit separately, using several proteins as search models. SAXS data of PaoABC were also collected showing that, in solution, the protein is also an heterotrimer. KW - periplasmic aldehyde oxidoreductase KW - X-ray crystallography KW - small angle X-ray scattering KW - crystal twinning Y1 - 2014 U6 - https://doi.org/10.3390/ijms15022223 SN - 1422-0067 VL - 15 IS - 2 SP - 2223 EP - 2236 PB - MDPI CY - Basel ER - TY - JOUR A1 - Martin-Creuzburg, Dominik A1 - Oexle, Sarah A1 - Wacker, Alexander T1 - Thresholds for sterol-limited growth of Daphnia magna: A comparative approach using 10 different sterols JF - Journal of chemical ecology N2 - Arthropods are incapable of synthesizing sterols de novo and thus require a dietary source to cover their physiological demands. The most prominent sterol in animal tissues is cholesterol, which is an indispensable structural component of cell membranes and serves as precursor for steroid hormones. Instead of cholesterol, plants and algae contain a variety of different phytosterols. Consequently, herbivorous arthropods have to metabolize dietary phytosterols to cholesterol to meet their requirements for growth and reproduction. Here, we investigated sterol-limited growth responses of the freshwater herbivore Daphnia magna by supplementing a sterol-free diet with increasing amounts of 10 different phytosterols and comparing thresholds for sterol-limited growth. In addition, we analyzed the sterol composition of D. magna to explore sterol metabolic constraints and bioconversion capacities. We show that dietary phytosterols strongly differ in their potential to support somatic growth of D. magna. The dietary threshold concentrations obtained by supplementing the different sterols cover a wide range (3.5-34.4 mu g mg C-1) and encompass the one for cholesterol (8.9 mu g mg C-1), indicating that certain phytosterols are more efficient in supporting somatic growth than cholesterol (e.g., fucosterol, brassicasterol) while others are less efficient (e.g., dihydrocholesterol, lathosterol). The dietary sterol concentration gradients revealed that the poor quality of particular sterols can be alleviated partially by increasing dietary concentrations, and that qualitative differences among sterols are most pronounced at low to moderate dietary concentrations. We infer that the dietary sterol composition has to be considered in zooplankton nutritional ecology to accurately assess potential sterol limitations under field conditions. KW - Cholesterol KW - Daphnia KW - Food quality KW - Nutrition KW - Phytosterols KW - Sterols Y1 - 2014 U6 - https://doi.org/10.1007/s10886-014-0486-1 SN - 0098-0331 SN - 1573-1561 VL - 40 IS - 9 SP - 1039 EP - 1050 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Hovestaedt, Marc A1 - Memczak, Henry A1 - Pleiner, Dennis A1 - Zhang, Xin A1 - Rappich, Joerg A1 - Bier, Frank Fabian A1 - Stöcklein, Walter F. M. T1 - Characterization of a new maleimido functionalization of gold for surface plasmon resonance spectroscopy JF - Journal of molecular recognition : an international journal devoted to research on specific molecular recognition in chemistry, biology, biotechnology and medicine N2 - Para-maleimidophenyl (p-MP) modified gold surfaces have been prepared by one-step electrochemical deposition and used in surface plasmon resonance (SPR) studies. Therefore, a FITC mimotope peptide (MP1, 12 aa), a human mucin 1 epitope peptide (MUC, 9 aa) and a protein with their specific antibodies were used as model systems. The peptides were modified with an N-terminal cysteine for covalent and directed coupling to the maleimido functionalized surface by means of Michael addition. The coupling yield of the peptide, the binding characteristics of antibody and the unspecific adsorption of the analytes were investigated. The results expand the spectrum of biosensors usable with p-MP by widely used SPR and support its potential to be versatile for several electrochemical and optical biosensors. This allows the combination of an electrochemical and optical read-out for a broad variety of biomolecular interactions on the same chip. Copyright (c) 2014 John Wiley & Sons, Ltd. KW - biosensor KW - surface plasmon resonance KW - diazonium coupling KW - maleimidophenyl KW - cys-peptide KW - aryl diazonium salts Y1 - 2014 U6 - https://doi.org/10.1002/jmr.2396 SN - 0952-3499 SN - 1099-1352 VL - 27 IS - 12 SP - 707 EP - 713 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Kersting, Sebastian A1 - Rausch, Valentina A1 - Bier, Frank Fabian A1 - von Nickisch-Rosenegk, Markus T1 - Rapid detection of Plasmodium falciparum with isothermal recombinase polymerase amplification and lateral flow analysis JF - Malaria journal N2 - Background: Nucleic acid amplification is the most sensitive and specific method to detect Plasmodium falciparum. However the polymerase chain reaction remains laboratory-based and has to be conducted by trained personnel. Furthermore, the power dependency for the thermocycling process and the costly equipment necessary for the read-out are difficult to cover in resource-limited settings. This study aims to develop and evaluate a combination of isothermal nucleic acid amplification and simple lateral flow dipstick detection of the malaria parasite for point-of-care testing. Methods: A specific fragment of the 18S rRNA gene of P. falciparum was amplified in 10 min at a constant 38 C using the isothermal recombinase polymerase amplification (RPA) method. With a unique probe system added to the reaction solution, the amplification product can be visualized on a simple lateral flow strip without further labelling. The combination of these methods was tested for sensitivity and specificity with various Plasmodium and other protozoa/bacterial strains, as well as with human DNA. Additional investigations were conducted to analyse the temperature optimum, reaction speed and robustness of this assay. Results: The lateral flow RPA (LF-RPA) assay exhibited a high sensitivity and specificity. Experiments confirmed a detection limit as low as 100 fg of genomic P. falciparum DNA, corresponding to a sensitivity of approximately four parasites per reaction. All investigated P. falciparum strains (n = 77) were positively tested while all of the total 11 non-Plasmodium samples, showed a negative test result. The enzymatic reaction can be conducted under a broad range of conditions from 30-45 degrees C with high inhibitory concentration of known PCR inhibitors. A time to result of 15 min from start of the reaction to read-out was determined. Conclusions: Combining the isothermal RPA and the lateral flow detection is an approach to improve molecular diagnostic for P. falciparum in resource-limited settings. The system requires none or only little instrumentation for the nucleic acid amplification reaction and the read-out is possible with the naked eye. Showing the same sensitivity and specificity as comparable diagnostic methods but simultaneously increasing reaction speed and dramatically reducing assay requirements, the method has potential to become a true point-of-care test for the malaria parasite. KW - Plasmodium falciparum KW - Recombinase polymerase amplification KW - RPA KW - PCR KW - Lateral flow KW - Point-of-care testing KW - Rapid test KW - Isothermal nucleic acid amplification Y1 - 2014 U6 - https://doi.org/10.1186/1475-2875-13-99 SN - 1475-2875 VL - 13 PB - BioMed Central CY - London ER - TY - JOUR A1 - Hoppe, Sebastian A1 - Bier, Frank Fabian A1 - von Nickisch-Rosenegk, Markus T1 - Identification of antigenic proteins of the nosocomial pathogen klebsiella pneumoniae JF - PLoS one N2 - The continuous expansion of nosocomial infections around the globe has become a precarious situation. Key challenges include mounting dissemination of multiple resistances to antibiotics, the easy transmission and the growing mortality rates of hospital-acquired bacterial diseases. Thus, new ways to rapidly detect these infections are vital. Consequently, researchers around the globe pursue innovative approaches for point-of-care devices. In many cases the specific interaction of an antigen and a corresponding antibody is pivotal. However, the knowledge about suitable antigens is lacking. The aim of this study was to identify novel antigens as specific diagnostic markers. Additionally, these proteins might be aptly used for the generation of vaccines to improve current treatment options. Hence, a cDNA-based expression library was constructed and screened via microarrays to detect novel antigens of Klebsiella pneumoniae, a prominent agent of nosocomial infections well-known for its extensive antibiotics resistance, especially by extended-spectrum beta-lactamases (ESBL). After screening 1536 clones, 14 previously unknown immunogenic proteins were identified. Subsequently, each protein was expressed in full-length and its immunodominant character examined by ELISA and microarray analyses. Consequently, six proteins were selected for epitope mapping and three thereof possessed linear epitopes. After specificity analysis, homology survey and 3d structural modelling, one epitope sequence GAVVALSTTFA of KPN_00363, an ion channel protein, was identified harboring specificity for K. pneumoniae. The remaining epitopes showed ambiguous results regarding the specificity for K. pneumoniae. The approach adopted herein has been successfully utilized to discover novel antigens of Campylobacter jejuni and Salmonella enterica antigens before. Now, we have transferred this knowledge to the key nosocomial agent, K. pneumoniae. By identifying several novel antigens and their linear epitope sites, we have paved the way for crucial future research and applications including the design of point-of-care devices, vaccine development and serological screenings for a highly relevant nosocomial pathogen. Y1 - 2014 U6 - https://doi.org/10.1371/journal.pone.0110703 SN - 1932-6203 VL - 9 IS - 10 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Dechtrirat, Decha A1 - Gajovic-Eichelmann, Nenad A1 - Wojcik, Felix A1 - Hartmann, Laura A1 - Bier, Frank Fabian A1 - Scheller, Frieder W. T1 - Electrochemical displacement sensor based on ferrocene boronic acid tracer and immobilized glycan for saccharide binding proteins and E. coli JF - Biosensors and bioelectronics : the principal international journal devoted to research, design development and application of biosensors and bioelectronics N2 - Pathogens such as viruses and bacteria use their envelope proteins and their adhesin lectins to recognize the glycan residues presented on the cell surface of the target tissues. This principle of recognition is used in a new electrochemical displacement sensor for the protein concanavalin A (ConA). A gold electrode was first modified with a self-assembled monolayer of a thiolated mannose/OEG conjugate and a ferrocene boroxol derivative was pre-assembled as reporter molecule onto the mannose surface. The novel tracer molecule based on a 2-hydroxymethyl phenyl boronic acid derivative binds even at neutral pH to the saccharides which could expand the application towards biological samples (i.e., urine and feces). Upon the binding of ConA, the tracer was displaced and washed away from the sensor surface leading to a decrease in the electrochemical signal. Using square wave voltammetry (SWV), the concentration of ConA in the sample solution could be determined in the dynamic concentration range established from 38 nmol L-1 to 5.76 mu mol L-1 with a reproducible detection limit of 1 mu g mL(-1) (38 nmol L-1) based on the signal-to-noise ratio (S/N=3) with fast response of 15 min. The new reporter molecule showed a reduced non-specific displacement by BSA and ribonuclease A. The sensor was also successfully transferred to the first proof of principle for the detection of Escherichia coli exhibiting a detection limit of approximately 6 x 102 cells/mL Specificity of the displacement by target protein ConA and E. coli was demonstrated since the control proteins (i.e., BSA and RNaseA) and the control E. coli strain, which lack of type 1 fimbriae, were ineffective. (C) 2014 Elsevier B.V. All rights reserved. KW - Ferrocene benzoboroxol biosensor KW - Concanavalin A KW - Displacement KW - Escherichia coli KW - Ferrocene boronic acid KW - Self-assembled monolayer Y1 - 2014 U6 - https://doi.org/10.1016/j.bios.2014.02.028 SN - 0956-5663 SN - 1873-4235 VL - 58 SP - 1 EP - 8 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Scheller, Frieder W. A1 - Yarman, Aysu A1 - Bachmann, Till A1 - Hirsch, Thomas A1 - Kubick, Stefan A1 - Renneberg, Reinhard A1 - Schumacher, Soeren A1 - Wollenberger, Ursula A1 - Teller, Carsten A1 - Bier, Frank Fabian ED - Gu, MB ED - Kim, HS T1 - Future of biosensors: a personal view JF - Advances in biochemical engineering, biotechnology JF - Advances in Biochemical Engineering-Biotechnology N2 - Biosensors representing the technological counterpart of living senses have found routine application in amperometric enzyme electrodes for decentralized blood glucose measurement, interaction analysis by surface plasmon resonance in drug development, and to some extent DNA chips for expression analysis and enzyme polymorphisms. These technologies have already reached a highly advanced level and need minor improvement at most. The dream of the "100-dollar' personal genome may come true in the next few years provided that the technological hurdles of nanopore technology or of polymerase-based single molecule sequencing can be overcome. Tailor-made recognition elements for biosensors including membrane-bound enzymes and receptors will be prepared by cell-free protein synthesis. As alternatives for biological recognition elements, molecularly imprinted polymers (MIPs) have been created. They have the potential to substitute antibodies in biosensors and biochips for the measurement of low-molecular-weight substances, proteins, viruses, and living cells. They are more stable than proteins and can be produced in large amounts by chemical synthesis. Integration of nanomaterials, especially of graphene, could lead to new miniaturized biosensors with high sensitivity and ultrafast response. In the future individual therapy will include genetic profiling of isoenzymes and polymorphic forms of drug-metabolizing enzymes especially of the cytochrome P450 family. For defining the pharmacokinetics including the clearance of a given genotype enzyme electrodes will be a useful tool. For decentralized online patient control or the integration into everyday "consumables' such as drinking water, foods, hygienic articles, clothing, or for control of air conditioners in buildings and cars and swimming pools, a new generation of "autonomous' biosensors will emerge. KW - Biosensors KW - Molecularly imprinted polymers KW - Personalized medicine Y1 - 2014 SN - 978-3-642-54143-8; 978-3-642-54142-1 U6 - https://doi.org/10.1007/10_2013_251 SN - 0724-6145 VL - 140 SP - 1 EP - 28 PB - Springer CY - Berlin ER - TY - JOUR A1 - Kersting, Sebastian A1 - Rausch, Valentina A1 - Bier, Frank Fabian A1 - von Nickisch-Rosenegk, Markus T1 - Multiplex isothermal solid-phase recombinase polymerase amplification for the specific and fast DNA-based detection of three bacterial pathogens JF - Microchimica acta : analytical sciences based on micro- and nanomaterials N2 - We report on the development of an on-chip RPA (recombinase polymerase amplification) with simultaneous multiplex isothermal amplification and detection on a solid surface. The isothermal RPA was applied to amplify specific target sequences from the pathogens Neisseria gonorrhoeae, Salmonella enterica and methicillin-resistant Staphylococcus aureus (MRSA) using genomic DNA. Additionally, a positive plasmid control was established as an internal control. The four targets were amplified simultaneously in a quadruplex reaction. The amplicon is labeled during on-chip RPA by reverse oligonucleotide primers coupled to a fluorophore. Both amplification and spatially resolved signal generation take place on immobilized forward primers bount to expoxy-silanized glass surfaces in a pump-driven hybridization chamber. The combination of microarray technology and sensitive isothermal nucleic acid amplification at 38 degrees C allows for a multiparameter analysis on a rather small area. The on-chip RPA was characterized in terms of reaction time, sensitivity and inhibitory conditions. A successful enzymatic reaction is completed in < 20 min and results in detection limits of 10 colony-forming units for methicillin-resistant Staphylococcus aureus and Salmonella enterica and 100 colony-forming units for Neisseria gonorrhoeae. The results show this method to be useful with respect to point-of-care testing and to enable simplified and miniaturized nucleic acid-based diagnostics. KW - Isothermal amplification KW - RPA KW - Microchip KW - DNA sensor KW - Point-of-care Y1 - 2014 U6 - https://doi.org/10.1007/s00604-014-1198-5 SN - 0026-3672 SN - 1436-5073 VL - 181 IS - 13-14 SP - 1715 EP - 1723 PB - Springer CY - Wien ER - TY - JOUR A1 - Kedracki, Dawid A1 - Chekini, Mahshid A1 - Maroni, Plinio A1 - Schlaad, Helmut A1 - Nardin, Corinne T1 - Synthesis and Self-Assembly of a DNA Molecular Brush JF - Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences N2 - We report herein on the polymer-crystallization-assisted thiol-ene photosynthesis of an amphiphilic comb/graft DNA copolymer, or molecular brush, composed of a hydrophobic poly(2-oxazoline) backbone and hydrophilic short single-stranded nucleic acid grafts. Coupling efficiencies are above 60% and thus higher as compared with the straight solid-phase-supported synthesis of amphiphilic DNA block copolymers. The DNA molecular brushes self-assemble into sub-micron-sized spherical structures in water as evidenced by light scattering as well as atomic force and electron microscopy imaging. The nucleotide sequences remain functional, as assessed by UV and fluorescence spectroscopy subsequent to isoindol synthesis at the surface of the structures. The determination of a vesicular morphology is supported by encapsulation and subsequent spectroscopy monitoring of the release of a water-soluble dye and spectroscopic quantification of the hybridization efficiency (30% in average) of the functional nucleic acid strands engaged in structure formation: about one-half of the nucleotide sequences are available for hybridization, whereas the other half are hindered within the self-assembled structure. Because speciation between complementary and non complementary sequences in the medium could be ascertained by confocal laser scanning microscopy, the stable self-assembled molecular brushes demonstrate the potential for sensing applications. Y1 - 2014 U6 - https://doi.org/10.1021/bm5008713 SN - 1525-7797 SN - 1526-4602 VL - 15 IS - 9 SP - 3375 EP - 3382 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Zhao, Qiang A1 - Dunlop, John William Chapman A1 - Qiu, Xunlin A1 - Huang, Feihe A1 - Zhang, Zibin A1 - Heyda, Jan A1 - Dzubiella, Joachim A1 - Antonietti, Markus A1 - Yuan, Jiayin T1 - An instant multi-responsive porous polymer actuator driven by solvent molecule sorption JF - Nature Communications N2 - Fast actuation speed, large-shape deformation and robust responsiveness are critical to synthetic soft actuators. A simultaneous optimization of all these aspects without trade-offs remains unresolved. Here we describe porous polymer actuators that bend in response to acetone vapour (24 kPa, 20 degrees C) at a speed of an order of magnitude faster than the state-of-the-art, coupled with a large-scale locomotion. They are meanwhile multi-responsive towards a variety of organic vapours in both the dry and wet states, thus distinctive from the traditional gel actuation systems that become inactive when dried. The actuator is easy-to-make and survives even after hydrothermal processing (200 degrees C, 24 h) and pressing-pressure (100 MPa) treatments. In addition, the beneficial responsiveness is transferable, being able to turn 'inert' objects into actuators through surface coating. This advanced actuator arises from the unique combination of porous morphology, gradient structure and the interaction between solvent molecules and actuator materials. Y1 - 2014 U6 - https://doi.org/10.1038/ncomms5293 SN - 2041-1723 VL - 5 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Piekarczyk, Andreas A1 - Bald, Ilko A1 - Flosadottir, Helga D. A1 - Omarsson, Benedikt A1 - Lafosse, Anne A1 - Ingolfsson, Oddur T1 - Influence of metal ion complexation on the metastable fragmentation of DNA hexamers JF - The European physical journal : D, Atomic, molecular, optical and plasma physics N2 - Here, we study the metastable decay of 5'-d(TTGCTT) in the presence of 0-6 alkaline metal ions (Li+, Na+, K+, Rb+) and 0-3 alkaline earth metal ions (Mg2+ and Ca2+), which replace the corresponding number of protons in the oligonucleotide. We find that all ions studied here stabilize the oligonucleotide with respect to simple 3'-C-O backbone cleavage, but at the same time these metal ions promote a central oligonucleotide deletion accompanied by a concomitant recombination of the terminal d(TT) groups. We find that the quenching of the 3'-C-O backbone cleavage is not ion specific, since it is due to the removal of the phosphate protons upon replacement with the respective metal ions. The central nucleotide deletion competes with the 3'-C-O backbone cleavage channels and is thus promoted through the replacement of the exchangeable protons against metal ions. However, with increasing positive charge density of the metal ions the yield of the central nucleotide deletion further increases. We attribute this effect to the necessity of sufficient proximity of the terminal d(TT) group to allow for their recombination on this reaction path. Hence, the formation of a reactive conformer is mediated by the metal ions. Y1 - 2014 U6 - https://doi.org/10.1140/epjd/e2014-40838-7 SN - 1434-6060 SN - 1434-6079 VL - 68 IS - 6 PB - Springer CY - New York ER - TY - JOUR A1 - Kopyra, Janina A1 - Keller, A. A1 - Bald, Ilko T1 - On the role of fluoro-substituted nucleosides in DNA radiosensitization for tumor radiation therapy JF - RSC Advances Y1 - 2014 U6 - https://doi.org/10.1039/c3ra46735j SN - 2046-2069 VL - 4 IS - 13 SP - 6825 EP - 6829 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Zhang, Xiaoqing A1 - Zhang, Xinwu A1 - You, Qiong A1 - Sessler, Gerhard M. T1 - Low- cost, large- area, stretchable piezoelectric films based on irradiation- crosslinked poly ( propylene) JF - Macromolecular materials and engineering N2 - Low cost, large area, lightweight, stretchable piezoelectric films, based on space-charge electret with a foam structure (i.e., ferroelectrets or piezoelectrets), have been fabricated by using commercially available irradiation cross-linked poly(propylene) (IXPP) foam sheets. Piezoelectric d(33) coefficients are as high as 100pCN(-1). The piezoelectric performance in such IXPP films is well preserved for repeated strains of less than 10%. Piezoelectric d(33) coefficients are frequency independent in the range from 2 to 100Hz. Such new class materials may be applied in sensory skins, smart clothing, bio-inspired systems, microenergy harvesters, and so on. KW - crosslinked poly(propylene) KW - ferroelectret KW - piezoelectricity KW - stretchability Y1 - 2014 U6 - https://doi.org/10.1002/mame.201300161 SN - 1438-7492 SN - 1439-2054 VL - 299 IS - 3 SP - 290 EP - 295 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Otrelo-Cardoso, Ana Rita A1 - Schwuchow, Viola A1 - Rodrigues, David A1 - Cabrita, Eurico J. A1 - Leimkühler, Silke A1 - Romao, Maria Joao A1 - Santos-Silva, Teresa T1 - Biochemical, stabilization and crystallization studies on a molecular chaperone (PaoD) involved in the maturation of molybdoenzymes JF - PLoS one N2 - Molybdenum and tungsten enzymes require specific chaperones for folding and cofactor insertion. PaoD is the chaperone of the periplasmic aldehyde oxidoreductase PaoABC. It is the last gene in the paoABCD operon in Escherichia coli and its presence is crucial for obtaining mature enzyme. PaoD is an unstable, 35 kDa, protein. Our biochemical studies showed that it is a dimer in solution with a tendency to form large aggregates, especially after freezing/thawing cycles. In order to improve stability, PaoD was thawed in the presence of two ionic liquids [C(4)mim]Cl and [C(2)OHmim]PF6 and no protein precipitation was observed. This allowed protein concentration and crystallization using polyethylene glycol or ammonium sulfate as precipitating agents. Saturation transfer difference - nuclear magnetic resonance (STD-NMR) experiments have also been performed in order to investigate the effect of the ionic liquids in the stabilization process, showing a clear interaction between the acidic ring protons of the cation and, most likely, negatively charged residues at the protein surface. DLS assays also show a reduction of the overall size of the protein aggregates in presence of ionic liquids. Furthermore, cofactor binding studies on PaoD showed that the protein is able to discriminate between molybdenum and tungsten bound to the molybdenum cofactor, since only a Mo-MPT form of the cofactor remained bound to PaoD. Y1 - 2014 U6 - https://doi.org/10.1371/journal.pone.0087295 SN - 1932-6203 VL - 9 IS - 1 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Flöel, Agnes A1 - Werner, Cordula A1 - Grittner, Ulrike A1 - Hesse, Stefan A1 - Jöbges, Michael A1 - Knauss, Janet A1 - Seifert, Michael A1 - Steinhagen-Thiessen, Elisabeth A1 - Goevercin, Mehmet A1 - Dohle, Christian A1 - Fischer, Wolfgang A1 - Schlieder, Regina A1 - Nave, Alexander Heinrich A1 - Meisel, Andreas A1 - Ebinger, Martin A1 - Wellwood, Ian T1 - Physical fitness training in Subacute Stroke (PHYS-STROKE) - study protocol for a randomised controlled trial JF - Trials N2 - Background: Given the rising number of strokes worldwide, and the large number of individuals left with disabilities after stroke, novel strategies to reduce disability, increase functions in the motor and the cognitive domains, and improve quality of life are of major importance. Physical activity is a promising intervention to address these challenges but, as yet, there is no study demonstrating definite outcomes. Our objective is to assess whether additional treatment in the form of physical fitness-based training for patients early after stroke will provide benefits in terms of functional outcomes, in particular gait speed and the Barthel Index (co-primary outcome measures) reflecting activities of daily living (ADL). We will gather secondary functional outcomes as well as mechanistic parameters in an exploratory approach. Methods/Design: Our phase III randomised controlled trial will recruit 215 adults with moderate to severe limitations of walking and ADL 5 to 45 days after stroke onset. Participants will be stratified for the prognostic variables of "centre", "age", and "stroke severity", and randomly assigned to one of two groups. The interventional group receives physical fitness training delivered as supported or unsupported treadmill training (cardiovascular active aerobic training; five times per week, over 4 weeks; each session 50 minutes; total of 20 additional physical fitness training sessions) in addition to standard rehabilitation treatment. The control intervention consists of relaxation sessions (non-cardiovascular active; five times per week week, over 4 weeks; each session 50 minutes) in addition to standard rehabilitation treatment. Co-primary efficacy endpoints will be gait speed (in m/s, 10 m walk) and the Barthel Index (100 points total) at 3 months post-stroke, compared to baseline measurements. Secondary outcomes include standard measures of quality of life, sleep and mood, cognition, arm function, maximal oxygen uptake, and cardiovascular risk factors including blood pressure, pulse, waist-to-hip ratio, markers of inflammation, immunity and the insulin-glucose pathway, lipid profile, and others. Discussion: The goal of this endpoint-blinded, phase III randomised controlled trial is to provide evidence to guide post-stroke physical fitness-based rehabilitation programmes, and to elucidate the mechanisms underlying this intervention. Y1 - 2014 U6 - https://doi.org/10.1186/1745-6215-15-45 SN - 1745-6215 VL - 15 PB - BioMed Central CY - London ER - TY - JOUR A1 - Schaefer, Kevin A1 - Lantuit, Hugues A1 - Romanovsky, Vladimir E. A1 - Schuur, Edward A. G. A1 - Witt, Ronald T1 - The impact of the permafrost carbon feedback on global climate JF - Environmental research letters N2 - Degrading permafrost can alter ecosystems, damage infrastructure, and release enough carbon dioxide (CO2) and methane (CH4) to influence global climate. The permafrost carbon feedback (PCF) is the amplification of surface warming due to CO2 and CH4 emissions from thawing permafrost. An analysis of available estimates PCF strength and timing indicate 120 +/- 85 Gt of carbon emissions from thawing permafrost by 2100. This is equivalent to 5.7 +/- 4.0% of total anthropogenic emissions for the Intergovernmental Panel on Climate Change (IPCC) representative concentration pathway (RCP) 8.5 scenario and would increase global temperatures by 0.29 +/- 0.21 degrees C or 7.8 +/- 5.7%. For RCP4.5, the scenario closest to the 2 degrees C warming target for the climate change treaty, the range of cumulative emissions in 2100 from thawing permafrost decreases to between 27 and 100 Gt C with temperature increases between 0.05 and 0.15 degrees C, but the relative fraction of permafrost to total emissions increases to between 3% and 11%. Any substantial warming results in a committed, long-term carbon release from thawing permafrost with 60% of emissions occurring after 2100, indicating that not accounting for permafrost emissions risks overshooting the 2 degrees C warming target. Climate projections in the IPCC Fifth Assessment Report (AR5), and any emissions targets based on those projections, do not adequately account for emissions from thawing permafrost and the effects of the PCF on global climate. We recommend the IPCC commission a special assessment focusing on the PCF and its impact on global climate to supplement the AR5 in support of treaty negotiation. KW - permafrost carbon feedback KW - permafrost KW - global climate Y1 - 2014 U6 - https://doi.org/10.1088/1748-9326/9/8/085003 SN - 1748-9326 VL - 9 IS - 8 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Schmidt, Christian A1 - Behl, Marc A1 - Lendlein, Andreas A1 - Beuermann, Sabine T1 - Synthesis of high molecular weight polyglycolide in supercritical carbon dioxide JF - RSC Advances N2 - Polyglycolide (PGA) is a biodegradable polymer with multiple applications in the medical sector. Here the synthesis of high molecular weight polyglycolide by ring-opening polymerization of diglycolide is reported. For the first time stabilizer free supercritical carbon dioxide (scCO(2)) was used as a reaction medium. scCO(2) allowed for a reduction in reaction temperature compared to conventional processes. Together with the lowering of monomer concentration and consequently reduced heat generation compared to bulk reactions thermal decomposition of the product occurring already during polymerization is strongly reduced. The reaction temperatures and pressures were varied between 120 and 150 degrees C and 145 to 1400 bar. Tin(II) ethyl hexanoate and 1-dodecanol were used as catalyst and initiator, respectively. The highest number average molecular weight of 31 200 g mol(-1) was obtained in 5 hours from polymerization at 120 degrees C and 530 bar. In all cases the products were obtained as a dry white powder. Remarkably, independent of molecular weight the melting temperatures were always at (219 +/- 2)degrees C. Y1 - 2014 U6 - https://doi.org/10.1039/c4ra06815g SN - 2046-2069 VL - 4 IS - 66 SP - 35099 EP - 35105 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Ghobadi, Ehsan A1 - Heuchel, Matthias A1 - Kratz, Karl A1 - Lendlein, Andreas T1 - Atomistic simulation of the shape-memory effect in dry and water swollen Poly[(rac-lactide)-co-glycolide] and copolyester urethanes thereof JF - Macromolecular chemistry and physics N2 - An atomistic molecular dynamics simulation approach is applied to model the influence of urethane linker units as well as the addition of water molecules on the simulated shape-memory properties of poly[(rac-lactide)-co-glycolide] (PLGA) and PLGA-based copolyester urethanes comprising different urethane linkers. The shape-memory performance of these amorphous packing models is explored in a simulated heating-deformation-cooling-heating procedure. Depending on the type of incorporated urethane linker, the mechanical properties of the dry copolyester urethanes are found to be significantly improved compared with PLGA, which can be attributed to the number of intermolecular hydrogen bonds between the urethane units. Good shape-memory properties are observed for all the modeled systems. In the dry state, the shape fixation is found to be improved by implementation of urethane units. After swelling of the copolymer models with water, which results in a reduction of their glass transition temperatures, the relaxation kinetics during unloading and shape recovery are found to be substantially accelerated. KW - molecular dynamics simulations KW - polyesterurethane KW - shape-memory effect Y1 - 2014 U6 - https://doi.org/10.1002/macp.201300507 SN - 1022-1352 SN - 1521-3935 VL - 215 IS - 1 SP - 65 EP - 75 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Martinez-Garzon, Patricia A1 - Kwiatek, Grzegorz A1 - Sone, Hiroki A1 - Bohnhoff, Marco A1 - Dresen, Georg A1 - Hartline, Craig T1 - Spatiotemporal changes, faulting regimes, and source parameters of induced seismicity: A case study from the Geysers geothermal field JF - Journal of geophysical research : Solid earth N2 - The spatiotemporal, kinematic, and source characteristics of induced seismicity occurring at different fluid injection rates are investigated to determine the predominant physical mechanisms responsible for induced seismicity at the northwestern part of The Geysers geothermal field, California. We analyze a relocated hypocenter catalog from a seismicity cluster where significant variations of the stress tensor orientation were previously observed to correlate with injection rates. We find that these stress tensor orientation changes may be related to increased pore pressure and the corresponding changes in poroelastic stresses at reservoir depth. Seismic events during peak injections tend to occur at greater distances from the injection well, preferentially trending parallel to the maximum horizontal stress direction. In contrast, at lower injection rates the seismicity tends to align in a different direction which suggests the presence of a local fault. During peak injection intervals, the relative contribution of strike-slip faulting mechanisms increases. Furthermore, increases in fluid injection rates also coincide with a decrease in b values. Our observations suggest that regardless of the injection stage, most of the induced seismicity results from thermal fracturing of the reservoir rock. However, during peak injection intervals, the increase in pore pressure may likewise be responsible for the induced seismicity. By estimating the thermal and hydraulic diffusivities of the reservoir, we confirm that the characteristic diffusion length for pore pressure is much greater than the corresponding length scale for temperature and also more consistent with the spatial extent of seismicity observed during different injection rates. KW - thermal effect KW - focal mechanisms KW - geothermal KW - pore pressure KW - fluid-induced seismicity KW - reservoir characterization Y1 - 2014 U6 - https://doi.org/10.1002/2014JB011385 SN - 2169-9313 SN - 2169-9356 VL - 119 IS - 11 SP - 8378 EP - 8396 PB - American Geophysical Union CY - Washington ER - TY - JOUR A1 - Friess, Fabian A1 - Lendlein, Andreas A1 - Wischke, Christian T1 - Photoinduced synthesis of polyester networks from methacrylate functionalized precursors: analysis of side reactions JF - Polymers for advanced technologies N2 - Polyester networks can be prepared by ultraviolet (UV)-light-induced radical polymerization of methacrylate functionalized oligo(epsilon-caprolactone)s. The properties and functions of the obtained materials depend on defined network structures and may be altered, if crosslinking would occur by side reactions in other positions than the methacrylate endgroups. In order to explore whether and to which extent such side reactions occur, network synthesis as well as related model reactions were performed in the absence of photoinitiator. Hereby precursor structures (linear and four-arm star-shaped) and reaction conditions (in solution and in the melt) were varied. Unspecific side reactions were found only upon extensive UV irradiation for 60min (26 mW cm(-2)) with minor but detectable alterations of physicochemical properties of the networks. The analysis of model reactions suggested minor photolytic cleavage of ester bonds during polymer network synthesis. However, the effect of these side reactions on network properties and functions appeared to be less relevant than an incomplete precursor integration because of a too short UV irradiation for crosslinking. Copyright (c) 2014 John Wiley & Sons, Ltd. KW - poly(epsilon-caprolactone) methacrylate KW - crosslinking KW - excimer UV light KW - side reaction KW - photoinduced radical polymerization Y1 - 2014 U6 - https://doi.org/10.1002/pat.3313 SN - 1042-7147 SN - 1099-1581 VL - 25 IS - 11 SP - 1285 EP - 1292 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Schwarze, Thomas A1 - Müller, Holger A1 - Ast, Sandra A1 - Steinbrück, Dörte A1 - Eidner, Sascha A1 - Geißler, Felix A1 - Kumke, Michael Uwe A1 - Holdt, Hans-Jürgen ED - Kumke, Michael Uwe T1 - Fluorescence lifetime-based sensing of sodium by an optode JF - Chemical Communications N2 - We report a 1,2,3-triazol fluoroionophore for detecting Na+ that shows in vitro enhancement in the Na+-induced fluorescence intensity and decay time. The Na+-selective molecule 1 was incorporated into a hydrogel as a part of a fiber optical sensor. This sensor allows the direct determination of Na+ in the range of 1–10 mM by measuring reversible fluorescence decay time changes. KW - ion optodes KW - sensors KW - indicators KW - chromoionophore KW - ionophore KW - membrane KW - switches KW - systems KW - samples KW - green Y1 - 2014 SN - 0022-4936 SN - 0009-241X SP - 14167 EP - 14170 PB - The Royal Society Chemistry CY - Cambridge ER - TY - JOUR A1 - Baier, Heiko A1 - Metzner, Philipp A1 - Körzdörfer, Thomas A1 - Kelling, Alexandra A1 - Holdt, Hans-Jürgen T1 - Efficient palladium(II) precatalysts bearing 4,5-dicyanoimidazol-2-ylidene for the Mizoroki-Heck reaction JF - European journal of inorganic chemistry : a journal of ChemPubSoc Europe N2 - The new N-heterocyclic carbene (NHC) complex [PdCl2{(CN)(2)IMes}(PPh3)] (2) ({(CN)(2)IMes}: 4,5-dicyano-1,3-dimesitylimidazol-2-ylidene) and the NHC palladacycle [PdCl(dmba){(CN)(2)IMes}] (3) (dmba: N,N-dimethylbenzylamine) have been synthesized by thermolysis of 4,5-dicyano-1,3-dimesityl-2-(pentafluorophenyl) imidazoline (1) in the presence of suitable palladium(II) precursors. The acyclic complex 2 was formed by ligand exchange using the mononuclear precursor [PdCl2(PPh3)(2)] and the palladacycle 3 was formed by cleavage of the dinuclear chloro-bridged precursor [Pd(mu-Cl)(dmba)](2). The new NHC precursor 1-benzyl-4,5-dicyano-2-(pentafluorophenyl)-3-picolylimidazoline (5) was formed by condensation of pentafluorobenzaldehyde with N-benzyl-N'-picolyldiaminomaleonitrile (4). The NHC palladacycle [PdCl2{(CN)(2)IBzPic}] (6) ({(CN)(2)IBzPic}: 1-benzyl-4,5-dicyano-3-picolylimidazol-2-ylidene) was prepared by in situ thermolysis of 5 in the presence of [PdCl2(PhCN)(2)]. The three palladium(II) complexes were characterized by NMR and IR spectroscopy, mass spectrometry and elemental analysis. In addition, the molecular structures of 2 and 3 were determined by X-ray diffraction. The pi-acidity of (CN)(2)IBzPic was compared with (CN)(2)IMes and perviously reported pi-acidic imidazol-2-ylidenes by NBO analysis. The Mizoroki-Heck (MH) reactions of various aryl halides with n-butyl acrylate were performed in the presence of complexes 2, 3 and 6. The new precatalysts showed high activity in the MH reactions giving good-to-excellent product yields with 0.1 mol-% pre-catalyst. The nature of the catalytically active species of 2, 3 and 6 was investigated by poisoning experiments with mercury and transmission electron microscopy. It was found that palladium nanoparticles formed from the precatalysts were involved in the catalytic process. KW - Homogeneous catalysis KW - Palladium KW - Cross coupling KW - Carbene ligands Y1 - 2014 U6 - https://doi.org/10.1002/ejic.201402040 SN - 1434-1948 SN - 1099-0682 IS - 18 SP - 2952 EP - 2960 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Trautmann, Michael A1 - Lubahn, Susanne A1 - Holdt, Hans-Jürgen T1 - Preparation, characterisation and properties of sulphoxide modified polystyrene resins for solid-phase extraction of Pt-IV, Ru-III and Ru-IV from hydrochloric acid JF - Reactive & functional polymers N2 - New sulphoxide modified resins were synthesized using poly(styrene-co-divinylbenzene) (PS-DVB) as matrix. Infrared spectroscopy and elemental analysis were used for characterisation. Solid-phase extraction of Pt-IV, Ru-III and Ru-IV from acidic chloride solutions was performed via batch experiments. Influence of spacer length between sulphoxide and matrix (ethylene, hexamethylene), substitution of sulphoxide (R-1: ethyl, hexyl, phenyl) and bead size of PS-DVB (spherical beads: d(50) < 155 mu m, d(50) < 80 mu m; powder: d(50) < 30 mu m) on adsorption was investigated subjected to acidity. Experimental results showed that ethyl substituted sulphoxide immobilised onto ground PS-DVB and hexamethylene spacer exhibited best adsorption properties. Different kinetic models and isotherms were fitted to the experimental data to identify extraction mechanism. Pt-IV was quantitative sorbed at [HCl] <= 0.1 mol/L whereas Ru-III and Ru-IV sorption ranged between 90% and 95% at [HCl] 5 mol/L. Desorption was reached using a solution of 0.5 M thiourea (Tu) in 0.1 M HCl at 90 degrees C. Separation of Pt-IV and Rum occurred at [HCl] <= 0.1 mol/L whereas Pt-IV was extracted and Ru-III remained in solution. A further separation was achieved by extracting Pt-IV and Ru-IV at 5 M HCl followed by sequential elution of Pt-IV with concentrated HCl and Ru-IV with 0.5 M Tu in 0.1 M HCl at 90 degrees C. 2014 Elsevier B.V. All rights reserved. KW - Solid-phase extraction KW - Platinum group metals KW - Polystyrene-divinylbenzene KW - Sulphoxide KW - Adsorption kinetic Y1 - 2014 U6 - https://doi.org/10.1016/j.reactfunctpolym.2014.07.001 SN - 1381-5148 SN - 1873-166X VL - 83 SP - 84 EP - 97 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Schwarze, Thomas A1 - Mueller, Holger A1 - Ast, Sandra A1 - Steinbrück, Dorte A1 - Eidner, Sascha A1 - Geißler, Felix A1 - Kumke, Michael Uwe A1 - Holdt, Hans-Jürgen T1 - Fluorescence lifetime-based sensing of sodium by an optode JF - Chemical communications N2 - We report a 1,2,3-triazol fluoroionophore for detecting Na+ that shows in vitro enhancement in the Na+-induced fluorescence intensity and decay time. The Na+-selective molecule 1 was incorporated into a hydrogel as a part of a fiber optical sensor. This sensor allows the direct determination of Na+ in the range of 1-10 mM by measuring reversible fluorescence decay time changes. Y1 - 2014 U6 - https://doi.org/10.1039/c4cc06112h SN - 1359-7345 SN - 1364-548X VL - 50 IS - 91 SP - 14167 EP - 14170 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Schwarze, Thomas A1 - Garz, Andreas A1 - Teuchner, Klaus A1 - Menzel, Ralf A1 - Holdt, Hans-Jürgen T1 - Two-photon probes for metal ions based on phenylaza[18]crown-6 ethers and 1,2,3-triazoles as pi-linkers JF - ChemPhysChem : a European journal of chemical physics and physical chemistry KW - absorption KW - cations KW - click chemistry KW - dyes/pigments KW - fluorescence Y1 - 2014 U6 - https://doi.org/10.1002/cphc.201402232 SN - 1439-4235 SN - 1439-7641 VL - 15 IS - 12 SP - 2436 EP - 2439 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Korup, Oliver A1 - Hayakawa, Yuichi A1 - Codilean, Alexandru T. A1 - Matsushi, Yuki A1 - Saito, Hitoshi A1 - Oguchi, Takashi A1 - Matsuzaki, Hiroyuki T1 - Japan's sediment flux to the Pacific Ocean revisited JF - Earth science reviews : the international geological journal bridging the gap between research articles and textbooks N2 - Quantifying volumes and rates of delivery of terrestrial sediment from island arcs to subduction zones is indispensable for refining estimates of the thickness of trench fills that may eventually control the location and timing of submarine landslides and tsunami-generating mega-earthquakes. Despite these motivating insights, knowledge about the rates of erosion and sediment export from the Japanese islands to their Pacific subduction zones remains patchy regardless of the increasing availability of highly resolved data on surface deformation, climate, geology, and topography. Traditionally, natural erosion rates across the island arc have been estimated from regression of topographic catchment metrics and reservoir sedimentation rates that were recorded over several years to decades. We review current research in this context, correct for a systematic bias in one of the most widely used predictions, and present new estimates of decadal to millennial-scale erosion rates of Japan's terrestrial inner forearc. We draw on several independent and unprecedented inventories of mass wasting, reservoir sedimentation, and concentrations of cosmogenic Be-10 in river sands. We find that natural Be-10-derived denudation rates of several mm yr(-1) in the Japanese Alps have been sustained over several centuries to millennia, and are, within error, roughly consistent with sediment yields inferred from artificial reservoir sedimentation. Local exceptions may likely result from release of sediment storage or regional landsliding episodes that trigger transient sediment pulses. Our synopsis further reveals that catchments draining Japan's eastern seaboard differ distinctly in their tectonic, lithological, topographic, and climatic characteristics between the Tohoku, Japanese Alps, and Nankai inner forearc segments, which is underscored by a marked asymmetric pattern of erosion rates along the island arc. Erosion rates are highest (up to at least 3 mm yr(-1)) in the Japanese Alps that mark the collision of two subduction zones, where high topographic relief, hillslope and bedrock-channel steepness foster rapid denudation by mass wasting. Comparable, if slightly lower, erosion rates characterise the Nankai inner forearc in southwest Japan, most likely due to higher typhoon-driven rainfall totals and variability rather than its high topographic relief. In contrast, our estimated erosion and flux rates are lowest in the Tohoku inner forearc catchments that feed sediment into the Japan Trench. We conclude that collisional mountain building of the Japanese Alps drives some of the highest erosion rates in the island arc despite similar uplift and precipitation controls in southwest Japan. We infer that, prior to extensive river damming, reservoir construction, and coastal works, the gross of Japan's total sediment export to the Pacific Ocean entered the accretionary margin of the Nankai Trough as opposed to the comparatively sediment-starved Japan Trench. Compared to documented contemporary rates of sediment flux from mountainous catchments elsewhere in the Pacific, the rivers draining Japan's inner forearc take an intermediate position despite high relief, steep slopes, very high seismicity, and frequent rainstorms. However, the average rates of millennial-scale denudation in the Japanese Alps particularly are amongst the highest reported worldwide. Local mismatches between these late Holocene and modern rates emphasise the anthropogenic fingerprint on sediment retention that may have significantly reduced the island arc's mass flux to its subduction zones, as is the case elsewhere in east and southeast Asia. (C) 2014 Elsevier B.V. All rights reserved. KW - Erosion KW - Japan KW - Subduction zone KW - Landslides KW - Cosmogenic nuclides KW - Sediment budget Y1 - 2014 U6 - https://doi.org/10.1016/j.earscirev.2014.03.004 SN - 0012-8252 SN - 1872-6828 VL - 135 SP - 1 EP - 16 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Bloethe, Jan H. A1 - Munack, Henry A1 - Korup, Oliver A1 - Fuelling, Alexander A1 - Garzanti, Eduardo A1 - Resentini, Alberto A1 - Kubik, Peter W. T1 - Late Quaternary valley infill and dissection in the Indus River, western Tibetan Plateau margin JF - Quaternary science reviews : the international multidisciplinary research and review journal N2 - The Indus, one of Earth's major rivers, drains large parts of the NW Himalaya and the Transhimalayan ranges that form part of the western Tibetan Plateau margin. In the western Himalayan syntaxis, where local topographic relief exceeds 7 km, the Indus has incised a steep bedrock gorge at rates of several mm yr(-1). Upstream, however, the upper Indus and its tributaries alternate between bedrock gorges and broad alluvial flats flanked by the Ladakh and Zanskar ranges. We review the late Quaternary valley history in this region with a focus on the confluence of the Indus and Zanskar Rivers, where vast alluvial terrace staircases and lake sediments record major episodes of aggradation and incision. New absolute dating of high-level fluvial terrace remnants using cosmogenic Be-10, optically and infrared stimulated luminescence (OSL, IRSL) indicates at least two phases of late Quaternary valley infilling. These phases commenced before similar to 200 ka and similar to 50-20 ka, judging from terrace treads stranded >150 m and similar to 30-40 m above modern river levels, respectively. Numerous stacks of lacustrine sediments that straddle the Indus River >200 km between the city of Leh and the confluence with the Shyok River share a distinct horizontal alignment. Constraints from IRSL samples of lacustrine sequences from the Leh-Spituk area reveal a protracted lake phase from >177 ka to 72 ka, locally accumulating >50-m thick deposits. In the absence of tectonic faulting, major lithological differences, and stream capture, we attribute the formation of this and other large lakes in the region to natural damming by large landslides, glaciers, and alluvial fans. The overall patchy landform age constraints from earlier studies can be reconciled by postulating a major deglacial control on sediment flux, valley infilling, and subsequent incision that has been modulated locally by backwater effects of natural damming. While comparison with Pleistocene monsoon proxies reveals no obvious correlation, a lateor post-glacial sediment pulse seems a more likely source of this widespread sedimentation that has partly buried the dissected bedrock topography. Overall, the long residence times of fluvial, alluvial and lacustrine deposits in the region (>500 ka) support previous studies, but remain striking given the dominantly steep slopes and deeply carved valleys that characterise this high-altitude mountain desert. Recalculated late Quaternary rates of fluvial bedrock incision in the Indus and Zanskar of 1.5 +/- 0.2 mm yr(-1) are at odds with the longevity of juxtaposed valley-fill deposits, unless a lack of decisive lateral fluvial erosion helps to preserve these late Pleistocene sedimentary archives. We conclude that alternating, similar to 10(4)-yr long, phases of massive infilling and incision have dominated the late Quaternary history of the Indus valley below the western Tibetan Plateau margin. (C) 2014 Elsevier Ltd. All rights reserved. KW - Himalaya KW - Indus KW - Valley fills KW - Glaciation KW - Erosion KW - Lake sediment Y1 - 2014 U6 - https://doi.org/10.1016/j.quascirev.2014.04.011 SN - 0277-3791 VL - 94 SP - 102 EP - 119 PB - Elsevier CY - Oxford ER -