TY - JOUR A1 - Wiegand, K. A1 - Schmidt, H. A1 - Jeltsch, Florian A1 - Ward, D. T1 - Linking a spatially-explicit model of acacias to GIS and remotely-sensed data Y1 - 2000 ER - TY - JOUR A1 - Wiegand, K. A1 - Ward, D. A1 - Thulke, Hans-Hermann A1 - Jeltsch, Florian T1 - From snap-shot information to long-term population dynamics of Acacias by a simulation model Y1 - 2000 ER - TY - JOUR A1 - Wiegand, T. A1 - Jeltsch, Florian T1 - Long-term dynamics in arid and semi-arid ecosystems : synthesis of a workshop Y1 - 2000 ER - TY - JOUR A1 - Wiegmann, Alex A1 - Rutschmann, Ronja A1 - Willemsen, Pascale T1 - Empirically investigating the concept of lying JF - Journal of Indian Council of Philosophical Research N2 - Lying is an everyday moral phenomenon about which philosophers have written a lot. Not only the moral status of lying has been intensively discussed but also what it means to lie in the first place. Perhaps the most important criterion for an adequate definition of lying is that it fits with people’s understanding and use of this concept. In this light, it comes as a surprise that researchers only recently started to empirically investigate the folk concept of lying. In this paper, we describe three experimental studies which address the following questions: Does a statement need to be objectively false in order to constitute lying? Does lying necessarily include the intention to deceive? Can one lie by omitting relevant facts? KW - Concept of lying KW - Lying KW - Definition of lying KW - Experimental philosophy Y1 - 2017 U6 - https://doi.org/10.1007/s40961-017-0112-z SN - 0970-7794 SN - 2363-9962 VL - 34 SP - 591 EP - 609 PB - Springer CY - New Dehli ER - TY - JOUR A1 - Wiemann, Annika A1 - Andersen, Liselotte W. A1 - Berggren, Per A1 - Siebert, Ursula A1 - Benke, Harald A1 - Teilmann, Jonay A1 - Lockyer, Christina A1 - Pawliczka, Iwona A1 - Skora, Krysztof A1 - Roos, Aanna A1 - Lyrholm, Thomas A1 - Paulus, Kirsten B. A1 - Ketmaier, Valerio T1 - Mitochondrial Control Region and microsatellite analyses on harbour porpoise (Phocoena phocoena) unravel population differentiation in the Baltic Sea and adjacent waters N2 - The population status of the harbour porpoise (Phocoena phocoena) in the Baltic area has been a continuous matter of debate. Here we present the by far most comprehensive genetic population structure assessment to date for this region, both with regard to geographic coverage and sample size: 497 porpoise samples from North Sea, Skagerrak, Kattegat, Belt Sea, and Inner Baltic Sea were sequenced at the mitochondrial Control Region and 305 of these specimens were typed at 15 polymorphic microsatellite loci. Samples were stratified according to sample type (stranding vs. by- caught), sex, and season (breeding vs. non-breeding season). Our data provide ample evidence for a population split between the Skagerrak and the Belt Sea, with a transition zone in the Kattegat area. Among other measures, this was particularly visible in significant frequency shifts of the most abundant mitochondrial haplotypes. A particular haplotype almost absent in the North Sea was the most abundant in Belt Sea and Inner Baltic Sea. Microsatellites yielded a similar pattern (i.e., turnover in occurrence of clusters identified by STRUCTURE). Moreover, a highly significant association between microsatellite assignment and unlinked mitochondrial haplotypes further indicates a split between North Sea and Baltic porpoises. For the Inner Baltic Sea, we consistently recovered a small, but significant separation from the Belt Sea population. Despite recent arguments that separation should exceed a predefined threshold before populations shall be managed separately, we argue in favour of precautionary acknowledging the Inner Baltic porpoises as a separate management unit, which should receive particular attention, as it is threatened by various factors, in particular local fishery measures. Y1 - 2010 UR - http://www.springerlink.com/content/105709 U6 - https://doi.org/10.1007/s10592-009-0023-x SN - 1566-0621 ER - TY - JOUR A1 - Wienhold, Sandra-Maria A1 - Macri, Mario A1 - Nouailles, Geraldine A1 - Dietert, Kristina A1 - Gurtner, Corinne A1 - Gruber, Achim D. A1 - Heimesaat, Markus M. A1 - Lienau, Jasmin A1 - Schumacher, Fabian A1 - Kleuser, Burkhard A1 - Opitz, Bastian A1 - Suttorp, Norbert A1 - Witzenrath, Martin A1 - Müller-Redetzky, Holger C. T1 - Ventilator-induced lung injury is aggravated by antibiotic mediated microbiota depletion in mice JF - Critical Care N2 - BackgroundAntibiotic exposure alters the microbiota, which can impact the inflammatory immune responses. Critically ill patients frequently receive antibiotic treatment and are often subjected to mechanical ventilation, which may induce local and systemic inflammatory responses and development of ventilator-induced lung injury (VILI). The aim of this study was to investigate whether disruption of the microbiota by antibiotic therapy prior to mechanical ventilation affects pulmonary inflammatory responses and thereby the development of VILI.MethodsMice underwent 6-8weeks of enteral antibiotic combination treatment until absence of cultivable bacteria in fecal samples was confirmed. Control mice were housed equally throughout this period. VILI was induced 3 days after completing the antibiotic treatment protocol, by high tidal volume (HTV) ventilation (34ml/kg; positive end-expiratory pressure=2 cmH(2)O) for 4h. Differences in lung function, oxygenation index, pulmonary vascular leakage, macroscopic assessment of lung injury, and leukocyte and lymphocyte differentiation were assessed. Control groups of mice ventilated with low tidal volume and non-ventilated mice were analyzed accordingly.ResultsAntibiotic-induced microbiota depletion prior to HTV ventilation led to aggravation of VILI, as shown by increased pulmonary permeability, increased oxygenation index, decreased pulmonary compliance, enhanced macroscopic lung injury, and increased cytokine/chemokine levels in lung homogenates.ConclusionsDepletion of the microbiota by broad-spectrum antibiotics prior to HTV ventilation renders mice more susceptible to developing VILI, which could be clinically relevant for critically ill patients frequently receiving broad-spectrum antibiotics. KW - Broad-spectrum antibiotic therapy KW - Ventilator-induced lung injury KW - Microbiota Y1 - 2018 U6 - https://doi.org/10.1186/s13054-018-2213-8 SN - 1466-609X SN - 1364-8535 VL - 22 IS - 282 PB - BMC CY - London ER - TY - JOUR A1 - Wiesner, Kerstin R. A1 - Loxdale, Hugh D. A1 - Köhler, Günter A1 - Schneider, Anja R. R. A1 - Tiedemann, Ralph A1 - Weisser, Wolfgang W. T1 - Patterns of local and regional genetic structuring in the meadow grasshopper, Chorthippus parallelus (Orthoptera: Acrididae), in Central Germany revealed using microsatellite markers JF - Biological journal of the Linnean Society : a journal of evolution N2 - The meadow grasshopper, Chorthippus parallelus (Zetterstedt), is common and widespread in Central Europe, with a low dispersal range per generation. A population study in Central Germany (Frankenwald and Thuringer Schiefergebirge) showed strong interpopulation differences in abundance and individual fitness. We examined genetic variability using microsatellite markers within and between 22 populations in a short-to long-distance sampling (19 populations, Frankenwald, Schiefergebirge, as well as a southern transect), and in the Erzgebirge region (three populations), with the latter aiming to check for effects as a result of historical forest cover. Of the 671 C. parallelus captured, none was macropterous (functionally winged). All populations showed a high level of expected and observed heterozygosity (mean 0.80-0.90 and 0.60-0.75, respectively), whereas there was evidence of inbreeding (F(IS) values all positive). Allelic richness for all locus-population combinations was high (mean 9.3-11.2), whereas alleles per locus ranged from 15-62. At a local level, genic and genotypic differences were significant. Pairwise F(ST) values were in the range 0.00-0.04, indicating little interpopulation genetic differentiation. Similarly, the calculated gene flow was very high, based on the respective F(ST) (19.5) and using private alleles (7.7). A Neighbour-joining tree using Nei's D(A) and principal coordinate analysis separated two populations that were collected in the Erzgebirge region. Populations from this region may have escaped the effects of the historical forest cover. The visualization of the spatial arrangement of genotypes revealed one geographical barrier to gene flow in the short-distance sampling. KW - adaptation KW - gene flow KW - diversity KW - landscape structure KW - wing polyphenism Y1 - 2011 U6 - https://doi.org/10.1111/j.1095-8312.2011.01698.x SN - 0024-4066 VL - 103 IS - 4 SP - 875 EP - 890 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Wiesner, Sebastian A1 - Salmikangas, Paula A1 - Auerbach, Daniel A1 - Himmel, Mirko A1 - Kempa, Stefan A1 - Hayes, Kathrin A1 - Pacholsky, Dirk A1 - Taivainen, Anu A1 - Schröder, Rolf A1 - Carpen, Olli A1 - Fürst, Dieter Oswald T1 - Indications for a novel muscular dystrophy pathway : gamma-filamin, the muscle-specific filamin isoform, intgeracts with myotilin Y1 - 2000 ER - TY - JOUR A1 - Wiethaus, Jessica A1 - Mueller, Alexandra A1 - Neumann, Meina A1 - Neumann, Sandra A1 - Leimkühler, Silke A1 - Narberhaus, Franz A1 - Masepohl, Bernd T1 - Specific interactions between four Molybdenum-binding proteins contribute to Mo-dependent gene regulation in Rhodobacter capsulatus N2 - The phototrophic purple bacterium Rhodobacter capsulatus encodes two transcriptional regulators, MopA and MopB, with partially overlapping and specific functions in molybdate-dependent gene regulation. Both MopA and MopB consist of an N-terminal DNA-binding helix-turn-helix domain and a C-terminal molybdate-binding di-MOP domain. They formed homodimers as apo-proteins and in the molybdate-bound state as shown by yeast two-hybrid (Y2H) studies, glutaraldehyde cross-linking, gel filtration chromatography, and copurification experiments. Y2H studies suggested that both the DNA- binding and the molybdate-binding domains contribute to dimer formation. Analysis of molybdate binding to MopA and MopB revealed a binding stoichiometry of four molybdate oxyanions per homodimer. Specific interaction partners of MopA and MopB were the molybdate transporter ATPase ModC and the molbindin-like Mop protein, respectively. Like other molbindins, the R. capsulatus Mop protein formed hexamers, which were stabilized by binding of six molybdate oxyanions per hexamer. Heteromer formation of MopA and MopB was shown by Y2H studies and copurification experiments. Reporter gene activity of a strictly MopA-dependent mop-lacZ fusion in mutant strains defective for either mopA, mopB, or both suggested that MopB negatively modulates expression of the mop promoter. We propose that depletion of the active MopA homodimer pool by formation of MopA-MopB heteromers might represent a fine-tuning mechanism controlling mop gene expression. Y1 - 2009 UR - http://jb.asm.org/ U6 - https://doi.org/10.1128/Jb.00526-09 SN - 0021-9193 ER - TY - JOUR A1 - Wildish, J. A1 - Pavesi, Laura A1 - Ketmaier, Valerio T1 - Talitrid amphipods (Crustacea: Amphipoda: Talitridae) and the driftwood ecological niche a morphological and molecular study JF - Journal of natural history : an international journal of systematics, interactive biology and biodiversity. - London : Taylor & Francis   1.1967 - N2 - Coastal regions of the North East Atlantic and Mediterranean Seas have four known species of driftwood talitrids. Records are extremely scanty, often limited to the type locality and dating to 1950. We were able to study three of them, all belonging to the genus Macarorchestia, using fresh and archived samples including type material. Allometric and molecular analyses support: (1) a close relationship among all the three classically defined Macarorchestia species, (2) Macarorchestia was well separated from non-driftwood taxa, and (3) a putative new driftwood talitrid discovered during this study was not closely related to Macarorchestia. Genetic divergence between the new species and Macarorchestia remyi is as high as the average distance among a number of talitrid species included in the study for comparison. A key is provided to identify all three of the presently known species of Macarorchestia, using morphological characters employed in the allometric study. KW - Macarorchestia remyi KW - Macarorchestia roffensis KW - Macarorchestia martini KW - Driftwood habitat KW - COI-DNA barcoding KW - allometry Y1 - 2012 U6 - https://doi.org/10.1080/00222933.2012.717971 SN - 0022-2933 VL - 46 IS - 43-44 SP - 2677 EP - 2700 PB - Routledge, Taylor & Francis Group CY - Abingdon ER - TY - JOUR A1 - Wilke, Liza A1 - Boeker, Sonja A1 - Mumm, Rebecca A1 - Groth, Detlef T1 - The Social status influences human growth BT - A summary and analysis of historical data from German school girls in 1914 with comparison to modern references JF - Human biology and public health N2 - Background: In the animal kingdom body size is often linked to dominance and subsequently the standing in social hierarchy. Similarly, human growth has been associated and linked to socioeconomic factors, including one’s social status. This has already been proposed in the early 1900s where data on young German school girls from different social strata have been compared. Objectives: This paper aims to summarize and analyze these results and make them accessible for non-German speakers. The full English translation of the historic work of Dikanski (Dikanski, 1914) is available as a supplement. Further, this work aims to compare the historical data with modern references, to test three hypotheses: (1) higher social class is positively associated with body height and weight, (2) affluent people from the used historical data match modern references in weight and height and (3) weight distributions are skewed in both modern and historical populations. Methods: Comparison of historical data from 1914 with WHO and 1980s German data. The data sets, for both body weight and height for 6.0- and 7.0-year-old girls, were fitted onto centile curves and quantile correlation coefficients were calculated. Results: In historical data social status is positively associated with body height and weight while both are also normally distributed, which marks a significant difference to modern references. Conclusion: Social status is positively associated with height, signaling social dominance, making children of affluent classes taller. Children from the historical data do not reach the average height of modern children, even under the best environmental conditions. The children of the upper social class were not skewed in weight distribution, although they had the means to become as obese as modern children. KW - Just so stories KW - Summer Schools KW - questioning solutions KW - repetition Y1 - 2022 U6 - https://doi.org/10.52905/hbph2021.3.22 SN - 2748-9957 VL - 2021 IS - 3, Summer School Supplement PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - JOUR A1 - Willi, Yvonne A1 - Fischer, Markus T1 - Genetic rescue effect in interconnected populations of small and large size of the self-incompatible Ranunculus reptans Y1 - 2005 ER - TY - JOUR A1 - Willi, Yvonne A1 - van Buskirk, J. A1 - Fischer, Markus T1 - A threefold genetic allee effect : Population size affects cross-compatibility, inbreeding depression and drift load in the self-incompatible Ranunculus reptans Y1 - 2005 SN - 0016-6731 ER - TY - JOUR A1 - Wilting, A. A1 - Patel, R. A1 - Pfestorf, Hans A1 - Kern, C. A1 - Sultan, K. A1 - Ario, A. A1 - Penaloza, F. A1 - Kramer-Schadt, S. A1 - Radchuk, Viktoriia A1 - Foerster, D. W. A1 - Fickel, Jörns T1 - Evolutionary history and conservation significance of the Javan leopard Panthera pardus melas JF - Journal of zoology : proceedings of the Zoological Society of London N2 - The leopard Panthera pardus is widely distributed across Africa and Asia; however, there is a gap in its natural distribution in Southeast Asia, where it occurs on the mainland and on Java but not on the interjacent island of Sumatra. Several scenarios have been proposed to explain this distribution gap. Here, we complemented an existing dataset of 68 leopard mtDNA sequences from Africa and Asia with mtDNA sequences (NADH5+ ctrl, 724bp) from 19 Javan leopards, and hindcasted leopard distribution to the Pleistocene to gain further insights into the evolutionary history of the Javan leopard. Our data confirmed that Javan leopards are evolutionarily distinct from other Asian leopards, and that they have been present on Java since the Middle Pleistocene. Species distribution projections suggest that Java was likely colonized via a Malaya-Java land bridge that by-passed Sumatra, as suitable conditions for leopards during Pleistocene glacial periods were restricted to northern and western Sumatra. As fossil evidence supports the presence of leopards on Sumatra at the beginning of the Late Pleistocene, our projections are consistent with a scenario involving the extinction of leopards on Sumatra as a consequence of the Toba super volcanic eruption (similar to 74kya). The impact of this eruption was minor on Java, suggesting that leopards managed to survive here. Currently, only a few hundred leopards still live in the wild and only about 50 are managed in captivity. Therefore, this unique and distinctive subspecies requires urgent, concerted conservation efforts, integrating insitu and ex situ conservation management activities in a One Plan Approach to species conservation management. KW - biogeography KW - evolutionary history KW - Felidae KW - Southeast Asia KW - Toba eruption KW - One Plan Approach KW - Pleistocene KW - Javan leopard Y1 - 2016 U6 - https://doi.org/10.1111/jzo.12348 SN - 0952-8369 SN - 1469-7998 VL - 299 SP - 239 EP - 250 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Wimmelbacher, Matthias A1 - Börnke, Frederik T1 - Redox activity of thioredoxin z and fructokinase-like protein 1 is dispensable for autotrophic growth of Arabidopsis thaliana JF - Journal of experimental botany N2 - Redox modulation of protein activity by thioredoxins (TRXs) plays a key role in cellular regulation. Thioredoxin z (TRX z) and its interaction partner fructokinase-like protein 1 (FLN1) represent subunits of the plastid-encoded RNA polymerase (PEP), suggesting a role of both proteins in redox regulation of chloroplast gene expression. Loss of TRX z or FLN1 expression generates a PEP-deficient phenotype and renders the plants incapable to grow autotrophically. This study shows that PEP function in trx z and fln1 plants can be restored by complementation with redox-inactive TRX z C106S and FLN1 C(105/106)A protein variants, respectively. The complemented plants showed wild-type levels of chloroplast gene expression and were restored in photosynthetic capacity, indicating that redox regulation of PEP through TRX z/FLN1 per se is not essential for autotrophic growth. Promoter-reporter gene studies indicate that TRX z and FLN1 are expressed during early phases of leaf development while expression ceases at maturation. Taken together, our data support a model in which TRX z and FLN1 are essential structural components of the PEP complex and their redox activity might only play a role in the fine tuning of PEP function. KW - Chloroplast transcription KW - FLN1 KW - plastid-encoded RNA polymerase KW - redox regulation KW - thioredoxins KW - TRX z Y1 - 2014 U6 - https://doi.org/10.1093/jxb/eru122 SN - 0022-0957 SN - 1460-2431 VL - 65 IS - 9 SP - 2405 EP - 2413 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Winck, Flavia V. A1 - Riano-Pachon, Diego M. A1 - Sommer, Frederik A1 - Rupprecht, Jens A1 - Müller-Röber, Bernd T1 - The nuclear proteome of the green alga Chlamydomonas reinhardtii JF - Proteomics N2 - Nuclear proteins play a central role in regulating gene expression. Their identification is important for understanding how the nuclear repertoire changes over time under different conditions. Nuclear proteins are often underrepresented in proteomic studies due to the frequently low abundance of proteins involved in regulatory processes. So far, only few studies describing the nuclear proteome of plant species have been published. Recently, the genome sequence of the unicellular green alga Chlamydomonas reinhardtii has been obtained and annotated, allowing the development of further detailed studies for this organism. However, a detailed description of its nuclear proteome has not been reported so far. Here, we present an analysis of the nuclear proteome of the sequenced Chlamydomonas strain cc503. Using LC-MS/MS, we identified 672 proteins from nuclei isolates with a maximum 1% peptide spectrum false discovery rate. Besides well-known proteins (e.g. histones), transcription factors and other transcriptional regulators (e.g. tubby and HMG) were identified. The presence of protein motifs in nuclear proteins was investigated by computational tools, and specific over-represented protein motifs were identified. This study provides new insights into the complexity of the nuclear environment and reveals novel putative protein targets for further studies of nuclear mechanisms. KW - Nuclear proteomics KW - Plant proteomics KW - Systems biology KW - Transcription factor Y1 - 2012 U6 - https://doi.org/10.1002/pmic.201000782 SN - 1615-9853 VL - 12 IS - 1 SP - 95 EP - 100 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Winck, Flavia Vischi A1 - Arvidsson, Samuel Janne A1 - Mauricio Riano-Pachon, Diego A1 - Hempel, Sabrina A1 - Koseska, Aneta A1 - Nikoloski, Zoran A1 - Urbina Gomez, David Alejandro A1 - Rupprecht, Jens A1 - Müller-Röber, Bernd T1 - Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga chlamydomonas reinhardtii under carbon deprivation JF - PLoS one N2 - The unicellular green alga Chlamydomonas reinhardtii is a long-established model organism for studies on photosynthesis and carbon metabolism-related physiology. Under conditions of air-level carbon dioxide concentration [CO2], a carbon concentrating mechanism (CCM) is induced to facilitate cellular carbon uptake. CCM increases the availability of carbon dioxide at the site of cellular carbon fixation. To improve our understanding of the transcriptional control of the CCM, we employed FAIRE-seq (formaldehyde-assisted Isolation of Regulatory Elements, followed by deep sequencing) to determine nucleosome-depleted chromatin regions of algal cells subjected to carbon deprivation. Our FAIRE data recapitulated the positions of known regulatory elements in the promoter of the periplasmic carbonic anhydrase (Cah1) gene, which is upregulated during CCM induction, and revealed new candidate regulatory elements at a genome-wide scale. In addition, time series expression patterns of 130 transcription factor (TF) and transcription regulator (TR) genes were obtained for cells cultured under photoautotrophic condition and subjected to a shift from high to low [CO2]. Groups of co-expressed genes were identified and a putative directed gene-regulatory network underlying the CCM was reconstructed from the gene expression data using the recently developed IOTA (inner composition alignment) method. Among the candidate regulatory genes, two members of the MYB-related TF family, Lcr1 (Low-CO2 response regulator 1) and Lcr2 (Low-CO2 response regulator 2), may play an important role in down-regulating the expression of a particular set of TF and TR genes in response to low [CO2]. The results obtained provide new insights into the transcriptional control of the CCM and revealed more than 60 new candidate regulatory genes. Deep sequencing of nucleosome-depleted genomic regions indicated the presence of new, previously unknown regulatory elements in the C. reinhardtii genome. Our work can serve as a basis for future functional studies of transcriptional regulator genes and genomic regulatory elements in Chlamydomonas. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0079909 SN - 1932-6203 VL - 8 IS - 11 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Winck, Flavia Vischi A1 - Kwasniewski, Miroslaw A1 - Wienkoop, Stefanie A1 - Müller-Röber, Bernd T1 - An optimized method for the isolation of nuclei from chlamydomas Reinhardtii (Chlorophyceae) JF - Journal of phycology N2 - The cell nucleus harbors a large number of proteins involved in transcription, RNA processing, chromatin remodeling, nuclear signaling, and ribosome assembly. The nuclear genome of the model alga Chlamydomonas reinhardtii P. A. Dang. was recently sequenced, and many genes encoding nuclear proteins, including transcription factors and transcription regulators, have been identified through computational discovery tools. However, elucidating the specific biological roles of nuclear proteins will require support from biochemical and proteomics data. Cellular preparations with enriched nuclei are important to assist in such analyses. Here, we describe a simple protocol for the isolation of nuclei from Chlamydomonas, based on a commercially available kit. The modifications done in the original protocol mainly include alterations of the differential centrifugation parameters and detergent-based cell lysis. The nuclei-enriched fractions obtained with the optimized protocol show low contamination with mitochondrial and plastid proteins. The protocol can be concluded within only 3 h, and the proteins extracted can be used for gel-based and non-gel-based proteomic approaches. KW - 2D gel electrophoresis KW - algae KW - Chlamydomonas KW - nuclear proteins KW - nucleus KW - proteomics Y1 - 2011 U6 - https://doi.org/10.1111/j.1529-8817.2011.00967.x SN - 0022-3646 VL - 47 IS - 2 SP - 333 EP - 340 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Winkler, Eckart A1 - Heinken, Thilo T1 - Spread of an ant-dispersed annual herb : an individual-based simulation study on population development of Melampyrum pratense L. N2 - The paper presents a simulation and parameter-estimation approach for evaluating stochastic patterns of population growth and spread of an annual forest herb, Melampyrum pratense (Orobanchaceae). The survival of a species during large-scale changes in land use and climate will depend, to a considerable extent, on its dispersal and colonisation abilities. Predictions on species migration need a combination of field studies and modelling efforts. Our study on the ability of M. pratense to disperse into so far unoccupied areas is based on experiments in secondary woodland in NE Germany. Experiments started in 1997 at three sites where the species was not yet present, with 300 seeds sown within 1m2. Population development was then recorded until 2001 by mapping of individuals with a resolution of 5 cm. Additional observations considered density dependence of seed production. We designed a spatially explicit individual-based computer simulation model to explain the spatial patterns of population development and to predict future population spread. Besides primary drop of seeds (barochory) it assumed secondary seed transport by ants (myrmecochory) with an exponentially decreasing dispersal tail. An important feature of population-pattern explanation was the simultaneous estimation of both population-growth and dispersal parameters from consistent spatio-temporal data sets. As the simulation model produced stochastic time series and random spatially discrete distributions of individuals we estimated parameters by minimising the expectation of weighted sum of squares. These sums of squares criteria considered population sizes, radial population distributions around the area of origin and distributions of individuals within squares of 25cm×25 cm, the range of density action. Optimal parameter values, together with the precision of the estimates, were obtained from calculating sum of squares in regular grids of parameter values. Our modelling results showed that transport of fractions of seeds by ants over distances of 1-2m was indispensable for explaining the observed population spread that led to distances of at most 8mfrom population origin within 3 years. Projections of population development over four additional years gave a diffusion-like increase of population area without any "outposts". This prediction generated by the simulation model gave a hypothesis which should be revised by additional field observations. Some structural deviations between observations and model output already indicated that for full understanding of population spread the set of dispersal mechanisms assumed in the model may have to be extended by additional features of plant-animal mutualism. Y1 - 2007 UR - http://www.sciencedirect.com/science/journal/03043800 SN - 0304-3800 ER - TY - JOUR A1 - Wischke, Christian A1 - Baehr, Elen A1 - Racheva, Miroslava A1 - Heuchel, Matthias A1 - Weigel, Thomas A1 - Lendlein, Andreas T1 - Surface immobilization strategies for tyrosinase as biocatalyst applicable to polymer network synthesis JF - MRS Advances N2 - Enzymes have recently attracted increasing attention in material research based on their capacity to catalyze the conversion of polymer-bound moieties for synthesizing polymer networks, particularly bulk hydrogels. hi this study. the surface immobilization of a relevant enzyme. mushroom tyrosinase, should be explored using glass as model surface. In a first step. the glass support was functionalized with silanes to introduce either amine or carboxyl groups, as confirmed e.g. by X-ray photoelectron spectroscopy. By applying glutaraldehyde and EDC/NHS chemistry, respectively, surfaces have been activated for subsequent successful coupling of tyrosinase. Via protein hydrolysis and amino acid characterization by HPLC, the quantity of bound tyrosinase was shown to correspond to a full surface coverage. Based on the visualized enzymatic conversion of a test substrate at the glass support. the functionalized surfaces may be explored for surface-associated material synthesis in the future. Y1 - 2018 U6 - https://doi.org/10.1557/adv.2018.630 SN - 2059-8521 VL - 3 IS - 63 SP - 3875 EP - 3881 PB - Cambridge Univ. Press CY - New York ER - TY - JOUR A1 - Wissel, Jörg A1 - Manack, Aubrey A1 - Brainin, Michael T1 - Toward an epidemiology of poststroke spasticity JF - Neurology : official journal of the American Academy of Neurology N2 - Poststroke spasticity (PSS)-related disability is emerging as a significant health issue for stroke survivors. There is a need for predictors and early identification of PSS in order to minimize complications and maladaptation from spasticity. Reviewing the literature on stroke and upper motor neuron syndrome, spasticity, contracture, and increased muscle tone measured with the Modified Ashworth Scale and the Tone Assessment Scale provided data on the dynamic time course of PSS. Prevalence estimates of PSS were highly variable, ranging from 4% to 42.6%, with the prevalence of disabling spasticity ranging from 2% to 13%. Data on phases of the PSS continuum revealed evidence of PSS in 4% to 27% of those in the early time course (1-4 weeks poststroke), 19% to 26.7% of those in the postacute phase (1-3 months poststroke), and 17% to 42.6% of those in the chronic phase (>3 months poststroke). Data also identified key risk factors associated with the development of spasticity, including lower Barthel Index scores, severe degree of paresis, stroke-related pain, and sensory deficits. Although such indices could be regarded as predictors of PSS and thus enable early identification and treatment, the different measures of PSS used in those studies limit the strength of the findings. To optimize evaluation in the different phases of care, the best possible assessment of PSS would make use of a combination of indicators for clinical impairment, motor performance, activity level, quality of life, and patient-reported outcome measures. Applying these recommended measures, as well as increasing our knowledge of the physiologic predictors of PSS, will enable us to perform clinical and epidemiologic studies that will facilitate identification and early, multimodal treatment. Y1 - 2013 SN - 0028-3878 VL - 80 IS - 1 SP - S13 EP - S19 PB - Lippincott Williams & Wilkins CY - Philadelphia ER - TY - JOUR A1 - Witt, B. A1 - Bornhorst, Julia A1 - Mitze, H. A1 - Ebert, Franziska A1 - Meyer, S. A1 - Francesconi, Kevin A. A1 - Schwerdtle, Tanja T1 - Arsenolipids exert less toxicity in a human neuron astrocyte co-culture as compared to the respective monocultures JF - Metallomics : integrated biometal science N2 - Arsenic-containing hydrocarbons (AsHCs), natural products found in seafood, have recently been shown to exert toxic effects in human neurons. In this study we assessed the toxicity of three AsHCs in cultured human astrocytes. Due to the high cellular accessibility and substantial toxicity observed astrocytes were identified as further potential brain target cells for arsenolipids. Thereby, the AsHCs exerted a 5-19-fold higher cytotoxicity in astrocytes as compared to arsenite. Next we compared the toxicity of the arsenicals in a co-culture model of the respective human astrocytes and neurons. Notably the AsHCs did not show any substantial toxic effects in the co-culture, while arsenite did. The arsenic accessibility studies indicated that in the co-culture astrocytes protect neurons against cellular arsenic accumulation especially after incubation with arsenolipids. In summary, these data underline the importance of the glial-neuron interaction when assessing the in vitro neurotoxicity of new unclassified metal species. Y1 - 2017 U6 - https://doi.org/10.1039/c7mt00036g SN - 1756-5901 SN - 1756-591X VL - 9 SP - 442 EP - 446 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Witt, Isabell A1 - Zanor, Maria Ines A1 - Müller-Röber, Bernd T1 - Transcription factor function search : how do individual factors regulate agronomical important processes in plants? (Subproject A) Y1 - 2004 SN - 3-00-011587-0 ER - TY - JOUR A1 - Witzel, Katja A1 - Abu Risha, Marua A1 - Albers, Philip A1 - Börnke, Frederik A1 - Hanschen, Franziska S. T1 - Corrigendum : Identification and characterization of three epithiospecifier protein isoforms in Brassica oleracea / Witzel, Katja; Abu Risha, Marua; Albers, Philip; Börnke, Frederike; Hanschen, Franziska S. - Lausanne: Frontiers Media, 2019. - Frontiers in plant science : FPLS. - 10 (2019) art. 1552. - doi: 10.3389/fpls.2019.01552 JF - Frontiers in plant science : FPLS KW - epithionitrile KW - expression profile KW - functional complementation KW - glucosinolate hydrolysis KW - nitrile KW - specifier proteins KW - tissue KW - specificity Y1 - 2020 U6 - https://doi.org/10.3389/fpls.2020.00523 SN - 1664-462X VL - 11 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Witzel, Katja A1 - Abu Risha, Marua A1 - Albers, Philip A1 - Börnke, Frederik A1 - Hanschen, Franziska S. T1 - Identification and Characterization of Three Epithiospecifier Protein Isoforms in Brassica oleracea JF - Frontiers in plant science N2 - Glucosinolates present in Brassicaceae play a major role in herbivory defense. Upon tissue disruption, glucosinolates come into contact with myrosinase, which initiates their breakdown to biologically active compounds. Among these, the formation of epithionitriles is triggered by the presence of epithiospecifier protein (ESP) and a terminal double bond in the glucosinolate side chain. One ESP gene is characterized in the model plant Arabidopsis thaliana (AtESP; At1g54040.2). However, Brassica species underwent genome triplication since their divergence from the Arabidopsis lineage. This indicates the presence of multiple ESP isoforms in Brassica crops that are currently poorly characterized. We identified three B. oleracea ESPs, specifically BoESP1 (LOC106296341), BoESP2 (LOC106306810), and BoESP3 (LOC106325105) based on in silico genome analysis. Transcript and protein abundance were assessed in shoots and roots of four B. oleracea vegetables, namely broccoli, kohlrabi, white, and red cabbage, because these genotypes showed a differential pattern for the formation of glucosinolate hydrolysis products as well for their ESP activity. BoESP1 and BoESP2 were expressed mainly in shoots, while BoESP3 was abundant in roots. Biochemical characterization of heterologous expressed BoESP isoforms revealed different substrate specificities towards seven glucosinolates: all isoforms showed epithiospecifier activity on alkenyl glucosinolates, but not on non-alkenyl glucosinolates. The pH-value differently affected BoESP activity: while BoESP1 and BoESP2 activities were optimal at pH 6-7, BoESP3 activity remained relatively stable from pH 4 to 7. In order test their potential for the in vivo modification of glucosinolate breakdown, the three isoforms were expressed in A. thaliana Hi-0, which lacks AtESP expression, and analyzed for the effect on their respective hydrolysis products. The BoESPs altered the hydrolysis of allyl glucosinolate in the A. thaliana transformants to release 1-cyano-2,3-epithiopropane and reduced formation of the corresponding 3-butenenitrile and allyl isothiocyanate. Plants expressing BoESP2 showed the highest percentage of released epithionitriles. Given these results, we propose a model for isoform-specific roles of B. oleracea ESPs in glucosinolate breakdown. KW - epithionitrile KW - expression profile KW - functional complementation KW - glucosinolate hydrolysis KW - nitrile KW - specifier proteins KW - tissue specificity Y1 - 2019 U6 - https://doi.org/10.3389/fpls.2019.01552 SN - 1664-462X VL - 10 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Wojcik, Laurie Anne A1 - Ceulemans, Ruben A1 - Gaedke, Ursula T1 - Functional diversity buffers the effects of a pulse perturbation on the dynamics of tritrophic food webs JF - Ecology and Evolution N2 - Biodiversity decline causes a loss of functional diversity, which threatens ecosystems through a dangerous feedback loop: This loss may hamper ecosystems’ ability to buffer environmental changes, leading to further biodiversity losses. In this context, the increasing frequency of human-induced excessive loading of nutrients causes major problems in aquatic systems. Previous studies investigating how functional diversity influences the response of food webs to disturbances have mainly considered systems with at most two functionally diverse trophic levels. We investigated the effects of functional diversity on the robustness, that is, resistance, resilience, and elasticity, using a tritrophic—and thus more realistic—plankton food web model. We compared a non-adaptive food chain with no diversity within the individual trophic levels to a more diverse food web with three adaptive trophic levels. The species fitness differences were balanced through trade-offs between defense/growth rate for prey and selectivity/half-saturation constant for predators. We showed that the resistance, resilience, and elasticity of tritrophic food webs decreased with larger perturbation sizes and depended on the state of the system when the perturbation occurred. Importantly, we found that a more diverse food web was generally more resistant and resilient but its elasticity was context-dependent. Particularly, functional diversity reduced the probability of a regime shift toward a non-desirable alternative state. The basal-intermediate interaction consistently determined the robustness against a nutrient pulse despite the complex influence of the shape and type of the dynamical attractors. This relationship was strongly influenced by the diversity present and the third trophic level. Overall, using a food web model of realistic complexity, this study confirms the destructive potential of the positive feedback loop between biodiversity loss and robustness, by uncovering mechanisms leading to a decrease in resistance, resilience, and potentially elasticity as functional diversity declines. KW - functional diversity KW - nutrient spike KW - pulse perturbation KW - regime shift KW - robustness KW - tritrophic food web Y1 - 2021 U6 - https://doi.org/10.1002/ece3.8214 SN - 2045-7758 N1 - Wojcik and Ceulemans shared first authorship. VL - 11 IS - 22 SP - 15639 EP - 15663 PB - John Wiley & Sons, Inc. CY - Hoboken (New Jersey) ER - TY - JOUR A1 - Wolff, Martin A1 - Gast, Klaus A1 - Evers, Andreas A1 - Kurz, Michael A1 - Pfeiffer-Marek, Stefania A1 - Schüler, Anja A1 - Seckler, Robert A1 - Thalhammer, Anja T1 - A Conserved Hydrophobic Moiety and Helix-Helix Interactions Drive the Self-Assembly of the Incretin Analog Exendin-4 JF - Biomolecules N2 - Exendin-4 is a pharmaceutical peptide used in the control of insulin secretion. Structural information on exendin-4 and related peptides especially on the level of quaternary structure is scarce. We present the first published association equilibria of exendin-4 directly measured by static and dynamic light scattering. We show that exendin-4 oligomerization is pH dependent and that these oligomers are of low compactness. We relate our experimental results to a structural hypothesis to describe molecular details of exendin-4 oligomers. Discussion of the validity of this hypothesis is based on NMR, circular dichroism and fluorescence spectroscopy, and light scattering data on exendin-4 and a set of exendin-4 derived peptides. The essential forces driving oligomerization of exendin-4 are helix–helix interactions and interactions of a conserved hydrophobic moiety. Our structural hypothesis suggests that key interactions of exendin-4 monomers in the experimentally supported trimer take place between a defined helical segment and a hydrophobic triangle constituted by the Phe22 residues of the three monomeric subunits. Our data rationalize that Val19 might function as an anchor in the N-terminus of the interacting helix-region and that Trp25 is partially shielded in the oligomer by C-terminal amino acids of the same monomer. Our structural hypothesis suggests that the Trp25 residues do not interact with each other, but with C-terminal Pro residues of their own monomers. KW - biophysics KW - diabetes KW - peptides KW - oligomerization KW - conformational change KW - molecular modeling KW - static and dynamic light scattering KW - spectroscopy Y1 - 2021 U6 - https://doi.org/10.3390/biom11091305 SN - 2218-273X VL - 11 IS - 9 PB - MDPI CY - Basel ER - TY - JOUR A1 - Wolff, Martin A1 - Schüler, Anja A1 - Gast, Klaus A1 - Seckler, Robert A1 - Evers, Andreas A1 - Pfeiffer-Marek, Stefania A1 - Kurz, Michael A1 - Nagel, Norbert A1 - Haack, Torsten A1 - Wagner, Michael A1 - Thalhammer, Anja T1 - Self-Assembly of Exendin-4-Derived Dual Peptide Agonists is Mediated by Acylation and Correlated to the Length of Conjugated Fatty Acyl Chains JF - Molecular pharmaceutics N2 - Dual glucagon-like peptide-1/glucagon receptor agonists have emerged as promising candidates for the treatment of diabetes and obesity. Issues of degradation sensitivity and rapid renal clearance are addressed, for example, by the conjugation of peptides to fatty acid chains, promoting reversible albumin binding. We use combined dynamic and static light scattering to directly measure the self-assembly of a set of dual peptide agonists based on the exendin-4 structure with varying fatty acid chain lengths in terms of apparent molecular mass and hydrodynamic radius (R-S). We use NMR spectroscopy to gain an insight into the molecular architecture of the assembly. We investigate conformational changes of the monomeric subunits resulting from peptide self-assembly and assembly stability as a function of the fatty acid chain length using circular dichroism and fluorescence spectroscopy. Our results demonstrate that self-assembly of the exendin-4-derived dual agonist peptides is essentially driven by hydrophobic interactions involving the conjugated acyl chains. The fatty acid chain length affects assembly equilibria and the assembly stability, although the peptide subunits in the assembly retain a dynamic secondary structure. The assembly architecture is characterized by juxtaposition of the fatty acyl side chains and a hydrophobic cluster of the peptide moiety. This cluster experiences local conformational changes in the assembly compared to the monomeric unit leading to a reduction in solvent exposure. The N-terminal half of the peptide and a C-terminal loop are not in contact with neighboring peptide subunits in the assemblies. Altogether, our study contributes to a thorough understanding of the association characteristics and the tendency toward self-assembly in response to lipidation. This is important not only to achieve the desired bioavailability but also with respect to the physical stability of peptide solutions. KW - dual GLP-1/glucagon receptor agonist KW - self-assembly KW - light scattering KW - molecular architecture KW - lipidation KW - exendin-4 Y1 - 2020 U6 - https://doi.org/10.1021/acs.molpharmaceut.9b01195 SN - 1543-8384 SN - 1543-8392 VL - 17 IS - 3 SP - 965 EP - 978 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Wolff, Martin A1 - Schüler, Anja A1 - Gast, Klaus A1 - Seckler, Robert A1 - Evers, Andreas A1 - Pfeiffer-Marek, Stefania A1 - Kurz, Michael A1 - Nagel, Norbert A1 - Haack, Torsten A1 - Wagner, Michael A1 - Thalhammer, Anja T1 - Self-Assembly of Exendin-4-Derived Dual Peptide Agonists is Mediated by Acylation and Correlated to the Length of Conjugated Fatty Acyl Chains JF - Molecular pharmaceutics N2 - Dual glucagon-like peptide-1/glucagon receptor agonists have emerged as promising candidates for the treatment of diabetes and obesity. Issues of degradation sensitivity and rapid renal clearance are addressed, for example, by the conjugation of peptides to fatty acid chains, promoting reversible albumin binding. We use combined dynamic and static light scattering to directly measure the self-assembly of a set of dual peptide agonists based on the exendin-4 structure with varying fatty acid chain lengths in terms of apparent molecular mass and hydrodynamic radius (R-S). We use NMR spectroscopy to gain an insight into the molecular architecture of the assembly. We investigate conformational changes of the monomeric subunits resulting from peptide self-assembly and assembly stability as a function of the fatty acid chain length using circular dichroism and fluorescence spectroscopy. Our results demonstrate that self-assembly of the exendin-4-derived dual agonist peptides is essentially driven by hydrophobic interactions involving the conjugated acyl chains. The fatty acid chain length affects assembly equilibria and the assembly stability, although the peptide subunits in the assembly retain a dynamic secondary structure. The assembly architecture is characterized by juxtaposition of the fatty acyl side chains and a hydrophobic cluster of the peptide moiety. This cluster experiences local conformational changes in the assembly compared to the monomeric unit leading to a reduction in solvent exposure. The N-terminal half of the peptide and a C-terminal loop are not in contact with neighboring peptide subunits in the assemblies. Altogether, our study contributes to a thorough understanding of the association characteristics and the tendency toward self-assembly in response to lipidation. This is important not only to achieve the desired bioavailability but also with respect to the physical stability of peptide solutions. KW - dual GLP-1/glucagon receptor agonist KW - self-assembly KW - light scattering KW - molecular architecture KW - lipidation KW - exendin-4 Y1 - 2020 U6 - https://doi.org/10.1021/acs.molpharmaceut.9b01195 SN - 1543-8384 VL - 17 IS - 3 SP - 965 EP - 978 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Wolff, Martin A1 - Zhang-Haagen, Bo A1 - Decker, Christina A1 - Barz, Bogdan A1 - Schneider, Mario A1 - Biehl, Ralf A1 - Radulescu, Aurel A1 - Strodel, Birgit A1 - Willbold, Dieter A1 - Nagel-Steger, Luitgard T1 - A beta 42 pentamers/hexamers are the smallest detectable oligomers in solution JF - Scientific reports Y1 - 2017 U6 - https://doi.org/10.1038/s41598-017-02370-3 SN - 2045-2322 VL - 7 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Wollenberger, Ursula T1 - Electrochemical biosensors - ways to improve sensor performance Y1 - 1995 ER - TY - JOUR A1 - Wollenberger, Ursula A1 - Drungiliene, A. A1 - Stöcklein, Walter F. M. A1 - Kulys, J. A1 - Scheller, Frieder W. T1 - Direct electrocatalytic determination of dissolved peroxidases Y1 - 1996 ER - TY - JOUR A1 - Wollenberger, Ursula A1 - Hintsche, R. A1 - Scheller, Frieder W. T1 - Biosensors for analytical microsystems Y1 - 1995 ER - TY - JOUR A1 - Wollenberger, Ursula A1 - Lisdat, Fred A1 - Scheller, Frieder W. T1 - Enzymatic substrade recycling electrodes Y1 - 1997 ER - TY - JOUR A1 - Wollenberger, Ursula A1 - Neumann, B. T1 - Quinoprotein glucose dehydrogenase modified carbon paste electrode for detection of phenolic compounds Y1 - 1997 ER - TY - JOUR A1 - Wollenberger, Ursula A1 - Neumann, B. A1 - Riedel, K. A1 - Scheller, Frieder W. T1 - Enzyme and microbial sensors for phosphate, phenols, pesticides and peroxides Y1 - 1994 ER - TY - JOUR A1 - Wollenberger, Ursula A1 - Neumann, B. A1 - Scheller, Frieder W. T1 - Development of a biomimetic alkane sensor f Y1 - 1998 ER - TY - JOUR A1 - Wollenberger, Ursula A1 - Neumann, B. A1 - Scheller, Frieder W. T1 - Enzyme and microbial sensors for environmental Monitoring Y1 - 1993 ER - TY - JOUR A1 - Wollenberger, Ursula A1 - Scheller, Frieder W. T1 - Enzyme activation for activator and enzyme activity measurement Y1 - 1993 ER - TY - JOUR A1 - Wollenberger, Ursula A1 - Schubert, Florian A1 - Pfeiffer, Dorothea A1 - Scheller, Frieder W. T1 - Recycling sensors based on kinases : proceedings of Mosbach Symposion on Biochemical Technology Y1 - 1996 ER - TY - JOUR A1 - Wollenberger, Ursula A1 - Schubert, Florian A1 - Pfeiffer, Dorothea A1 - Scheller, Frieder W. T1 - Enhancing biosensor performance using multienzyme systems Y1 - 1993 ER - TY - JOUR A1 - Wolters, Steffen A1 - Bittmann, Felix A1 - Kummer, Volker T1 - The first subfossil records of Urtica kioviensis Rogow. and their consequences for palaeoecological interpretations N2 - Among plant remains from Mesolithic layers dating from 9249 to 7779 B.C. at the excavation site of Friesack IV in north-eastern Germany, nutlets of Urtica kioviensis were identified. Morphological studies have shown that they clearly differed from all other European Urtica species investigated. In contrast, pollen morphological investigations revealed only slight differences between the central European Urtica species, which could hardly have been noticed during routine or normal pollen analyses. The records of U. kioviensis nutlets are the first subfossil finds reported and prove the indigenous status of this taxon in north-eastern Germany. The records are discussed in the context of the overall species spectrum of the Mesolithic layers and consequences for the interpretation of pollen analytical studies concerning human impact are pointed out Y1 - 2005 ER - TY - JOUR A1 - Wong-Ekkabut, Jirasak A1 - Miettinen, Markus S. A1 - Dias, Christiano A1 - Karttunen, Mikko T1 - Static charges cannot drive a continuous flow of water molecules through a carbon nanotube Y1 - 2010 UR - http://www.nature.com/nnano U6 - https://doi.org/10.1038/nnano.2010.152 SN - 1748-3387 ER - TY - JOUR A1 - Wonke, Gundula A1 - Wallschläger, Hans-Dieter T1 - Song dialects in the yellowhammer Emberiza citrinella : bioacoustic variation between and within dialects N2 - The yellowhammer Emberiza citrinella is a common European bird that sings in dialects that for decades have been distinguished by the existence of one single element (called a "specific''). In this study we looked into other possibilities for dialect discrimination, measuring 24 different variables. For the first time, multivariate statistics were used to discriminate dialect in yellowhammer song. Two similar dialects (XlB and XsB) that are not clearly defined in the literature were studied. Statistics incorporated (1) all variables, ( 2) no variables of "specific'' elements, and (3) no variables under the influence of these "specific'' variables. Multivariate statistics support dialect discrimination by ear and confirmed that only one element in yellowhammer song characterises dialect. In addition, we looked for local differences within two dialects and found that one local observation area showed a higher separation than the other sites (Meck1). However, as yet there is insufficient evidence for the existence of a new subdialect. Y1 - 2009 UR - http://www.springerlink.com/content/110831 U6 - https://doi.org/10.1007/s10336-008-0326-6 SN - 0021-8375 ER - TY - JOUR A1 - Wood, C. C. A1 - Poree, Fabien A1 - Dreyer, Ingo A1 - Koehler, G. J. A1 - Udvardi, M. K. T1 - Mechanisms of ammonium transport, accumulation, and retention in ooyctes and yeast cells expressing Arabidopsis AtAMT1; 1 N2 - Ammonium is a primary source of N for plants, so knowing how it is transported, stored, and assimilated in plant cells is important for rational approaches to optimise N-use in agriculture. Electrophysiological studies of Arabidopsis AtAMT1;1 expressed in oocytes revealed passive, Delta psi-driven transport of NH4+ through this protein. Expression of AtAMT1;1 in a novel yeast mutant defective in endogenous ammonium transport and vacuolar acidification supported the above mechanism for AtAMT1;1 and revealed a central role for acid vacuoles in storage and retention of ammonia in cells. These results highlight the mechanistic differences between plant AMT proteins and related transporters in bacteria and animal cells, and suggest novel strategies to enhance nitrogen use efficiency in agriculture. (c) 2006 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved Y1 - 2006 UR - http://www.sciencedirect.com/science/article/pii/S0014579306007332 U6 - https://doi.org/10.1016/j.febslet.2006.06.026 ER - TY - JOUR A1 - Wright, Justin P. A1 - Ames, Gregory M. A1 - Mitchelll, Rachel M. T1 - The more things change, the more they stay the same? When is trait variability important for stability of ecosystem function in a changing environment JF - Philosophical transactions of the Royal Society of London : B, Biological sciences N2 - The importance of intraspecific trait variability for community dynamics and ecosystem functioning has been underappreciated. There are theoretical reasons for predicting that species that differ in intraspecific trait variability will also differ in their effects on ecosystem functioning, particularly in variable environments. We discuss whether species with greater trait variability are likely to exhibit greater temporal stability in their population dynamics, and under which conditions this might lead to stability in ecosystem functioning. Resolving this requires us to consider several questions. First, are species with high levels of variation for one trait equally variable in others? In particular, is variability in response and effects traits typically correlated? Second, what is the relative contribution of local adaptation and phenotypic plasticity to trait variability? If local adaptation dominates, then stability in function requires one of two conditions: (i) individuals of appropriate phenotypes present in the environment at high enough frequencies to allow for populations to respond rapidly to the changing environment, and (ii) high levels of dispersal and gene flow. While we currently lack sufficient information on the causes and distribution of variability in functional traits, filling in these key data gaps should increase our ability to predict how changing biodiversity will alter ecosystem functioning. KW - biodiversity KW - intraspecific variation KW - ecosystem function KW - functional traits KW - phenotypic plasticity Y1 - 2016 U6 - https://doi.org/10.1098/rstb.2015.0272 SN - 0962-8436 SN - 1471-2970 VL - 371 PB - Royal Society CY - London ER - TY - JOUR A1 - Wronski, Torsten A1 - Apio, Ann A1 - Plath, Martin T1 - The communicatory significance of localised defecation sites in bushbuck (Tragelaphus scriptus) N2 - Like several other mammals, bushbuck (Tragelaphus scriptus) deposit faeces in specific localised defecation sites (LDS). A previous study has ruled out a function of LDS in the context of parasite avoidance. In this study, we investigated the communicatory significance of LDS. In a free ranging population, we tested whether LDS serve to demarcate home ranges, and/or if LDS are used for communication in a non-territorial context. In both sexes, LDS increased significantly in number towards the periphery of individual home ranges. However, the distribution pattern of LDS, as revealed by a nearest-neighbour mapping technique (nearest distances between LDS), did not support the idea that LDS serve home range/territory-demarcation because LDS did not follow a pattern of minimal nearest-neighbour distances along the margins of home ranges. We found females to urinate more often in LDS than males. Notably, information transfer was most frequent between sending (urinating or defecating) females and receiving/responding males (urination or defecation at places where a female had previously signalled). Our results suggest that LDS mainly serve for inter- sexual communication in bushbuck Y1 - 2006 UR - http://www.springerlink.com/content/517tm6115561t421/ U6 - https://doi.org/10.1007/s00265-006-0174-4 ER - TY - JOUR A1 - Wronski, Torsten A1 - Apio, Ann A1 - Plath, Martin T1 - Absence of a dominance hierarchy confirms territorial organization in male bushbuck (Tragelaphus scriptus Pallas, 1766) N2 - It has been suggested that all species of spiral-horned antelopes (Tragelaphini) lack territoriality. Furthermore, some authors suggested that bushbuck (Tragelpahus scriptus) males form dominance hierarchies. In this study, we investigated the dominance relationships in two groups of free-ranging bushbuck males in Queen Elizabeth National Park, Uganda. Adult males dominated young-adult bachelors and subadult males, but no distinct dominance relationships were found among adult males. Landau's index of linearity revealed no linear dominance hierarchy in the study populations. Our results support the idea that adult males are territorial, and overt aggression is directed almost exclusively towards bachelors that challenge territory holders. Y1 - 2009 UR - http://www3.interscience.wiley.com/cgi-bin/issn?DESCRIPTOR=PRINTISSN&VALUE=0141-6707 U6 - https://doi.org/10.1111/j.1365-2028.2007.00876.x SN - 0141-6707 ER - TY - JOUR A1 - Wronski, Torsten A1 - Apio, Ann A1 - Plath, Martin T1 - Activity patterns of bushbuck (Tragelaphus scriptus) in Queen Elizabeth National Park JF - Behavioural processes N2 - Activity patterns and time budgets of bushbuck (Tragelaphus scriptus) were studied in a free-ranging population in Queen Elizabeth National Park, Uganda from August 2000 to January 2002. We investigated differences in activity patterns in relation to daytime, season, sun radiation, moonlight, age and sex. Bushbuck were found to show peak activities around sunrise and at dawn. No difference in the mean activity rates was found between the dry and wet season. Daytime activity was not predicted by differences in sun radiation, nor was nighttime activity predicted by the presence or absence of moonlight. We found the activity of adult territorial males to be strongly positively correlated with that of females, whereas the activity of young-adult non-territorial males was not significantly correlated with the activity of females. This suggests that young-adult males shift their peak activity to phases when adult territorial males are less active. KW - activity patterns KW - bushbuck KW - tragelaphini KW - ungulate behaviour KW - Uganda Y1 - 2006 U6 - https://doi.org/10.1016/j.beproc.2006.08.003 SN - 0376-6357 VL - 73 IS - 3 SP - 333 EP - 341 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Wronski, Torsten A1 - Apio, Ann A1 - Plath, Martin A1 - Averbeck, Christiane T1 - Do ecotypes of bushbuck differ in grouping patterns? N2 - Grouping patterns within the genus Tragelaphus suggest that species inhabiting open areas tend to live in larger groups, while species preferring dense habitats live solitarily or in small family groups. We asked if similar variation would be concealed in the within-species variation of bushbuck (Tragelaphus scriptus). Recent molecular phylogeographic analyses revealed several locally adapted forms of bushbuck in different ecoregions on the African continent. We compared group sizes of south-eastern bushbuck (Tragelaphus sylvaticus) among six different populations ("ecotypes"). To date, most data on the social organization of bushbuck have been collected from only one population in Queen Elizabeth National Park (QENP) in Uganda. This particular population, however, inhabits an unusual-comparatively open-habitat type, while bushbuck otherwise inhabit dense habitats, leaving doubt whether data collected in QENP are representative of the entire species. We, therefore, compared grouping patterns between ecotypes inhabiting rather open habitats (e.g., dianae and haywoodi) and ecotypes occupying rather dense habitats (e.g., massaicus and ornatus). In bachelor groups and in all-female (spinster) groups, single sightings were the most frequent "group type" in all populations examined. We detected no significant difference among ecotypes in relative frequencies of group size categories in the case of bachelor groups. Spinster group sizes were slightly (albeit significantly) smaller in QENP than in all other areas. Moreover, a comparison of two areas inside (low human pursuit) and outside Lake Mburo National Park (high hunting pressure) in Uganda revealed no significant difference in grouping patterns in response to human pursuit (as reported for impala [Aepyceros melampus] inhabiting the same area). Altogether, our results suggest that group sizes in bushbuck are not dependent on the habitat type they inhabit; neither does human nuisance have an impact on grouping patterns. Hence, an "almost solitary" lifestyle appears to be a characteristic of the entire taxon. Y1 - 2009 UR - http://www.springerlink.com/content/103882 U6 - https://doi.org/10.1007/s10211-009-0058-5 SN - 0873-9749 ER - TY - JOUR A1 - Wronski, Torsten A1 - Apio, Ann A1 - Wanker, R A1 - Plath, Martin T1 - Behavioural repertoire of the bushbuck (Tragelaphus scriptus): agonistic interactions, mating behaviour and parent-offspring relations N2 - A free-ranging bushbuck (Tragelaphus scriptus) population was observed over a period of 3 years, thereby enabling a detailed description of the behavioural repertoire of this widespread but barely investigated solitary African antelope species. Agonistic and submissive behaviour patterns are described, among them several hitherto un- described behaviour patterns - such as "escorting", where territorial males guide intruders to the periphery of their territory - and "push-up position", an extreme form of submissive behaviour. Furthermore, we report on behaviour patterns of males and females during mating as well as on behaviour patterns of parents directed towards their offspring. Again, we describe a hitherto unknown behaviour: the protection of calves by adult males, which may be a socio-positive behaviour directed towards their offspring led by kin selection Y1 - 2006 UR - http://www.springerlink.com/content/h4v41315l1717v87/ U6 - https://doi.org/10.1007/s10164-005-0186-y ER - TY - JOUR A1 - Wronski, Torsten A1 - Tiedemann, Ralph A1 - Apio, Ann A1 - Plath, Martin T1 - Cover, food, competitors and individual densities within bushbuck Tragelaphus scriptus female clan home ranges N2 - We examined factors predicting female densities within the common home ranges of related females ("clans") in bushbuck Tragelaphus scriptus Pallas, 1776. In this species, each female forms an individual home range, but the home ranges of matrilineal clan members strongly overlap. We found female densities to increase in areas with high canopy cover. Moreover, individual home range sizes tended to decrease with increasing cover. Food plant availability and intruder pressure by two heterospecific competitors did not significantly affect female densities. Apparently, canopy cover is the major limited resource in this species. A possible explanation is that both adult bushbuck and - even more markedly - fawns hide from predators in dense vegetation, in particular in thicket clumps and coalescences. The study shows an effect of habitat properties (eg sufficient canopy cover) on a within-population level in bushbuck, where female densities differ even among proximate clan areas Y1 - 2006 ER - TY - JOUR A1 - Wronski, Torsten A1 - Wacher, Timothy A1 - Hammond, Robert L. A1 - Winney, Bruce A1 - Hundertmark, Kris J. A1 - Blacket, Mark J. A1 - Mohammed, Osama B. A1 - Flores, Benito A1 - Omer, Sawsan A. A1 - Macasero, William A1 - Plath, Martin A1 - Tiedemann, Ralph A1 - Bleidorn, Christoph T1 - Two reciprocally monophyletic mtDNA lineages elucidate the taxonomic status of Mountain gazelles (Gazella gazella) N2 - Mountain gazelles (Gazella gazella) rank among the most critically endangered mammals on the Arabian Peninsula. Past conservation efforts have been plagued by confusion about the phylogenetic relationship among various 'phenotypically discernable' populations, and even the question of species boundaries was far from being certain. This lack of knowledge has had a direct impact on conservation measures, especially ex situ breeding programmes, hampering the assignment of captive stocks to potential conservation units. Here, we provide a phylogenetic framework, based on the analysis of mtDNA sequences (360 bp cytochrome b and 213 bp Control Region) of 126 individuals collected from the wild throughout the Arabian Peninsula and from captive stocks. Our analyses revealed two reciprocally monophyletic genetic lineages within the presumed species Gazella gazella: one 'northern clade' on the Golan Heights (Israel/Syrian border) and one genetically diverse larger clade from the rest of the Arabian Peninsula including the Arava Valley (Negev, Israel). Applying the Strict Phylogenetic Species Concept (sensu Mishler & Theriot, 2000) allows assigning species status to these two major clades. Y1 - 2010 UR - http://www.informaworld.com/smpp/title~content=t913521959~db=all U6 - https://doi.org/10.1080/14772001003613192 SN - 1477-2000 ER - TY - JOUR A1 - Wu, Anhui A1 - Allu, Annapurna Devi A1 - Garapati, Prashanth A1 - Siddiqui, Hamad A1 - Dortay, Hakan A1 - Zanor, Maria-Ines A1 - Asensi-Fabado, Maria Amparo A1 - Munne-Bosch, Sergi A1 - Antonio, Carla A1 - Tohge, Takayuki A1 - Fernie, Alisdair R. A1 - Kaufmann, Kerstin A1 - Xue, Gang-Ping A1 - Müller-Röber, Bernd A1 - Balazadeh, Salma T1 - Jungbrunnen1, a reactive oxygen species-responsive NAC transcription factor, regulates longevity in arabidopsis JF - The plant cell N2 - The transition from juvenility through maturation to senescence is a complex process that involves the regulation of longevity. Here, we identify JUNGBRUNNEN1 (JUB1), a hydrogen peroxide (H2O2)-induced NAC transcription factor, as a central longevity regulator in Arabidopsis thaliana. JUB1 overexpression strongly delays senescence, dampens intracellular H2O2 levels, and enhances tolerance to various abiotic stresses, whereas in jub1-1 knockdown plants, precocious senescence and lowered abiotic stress tolerance are observed. A JUB1 binding site containing a RRYGCCGT core sequence is present in the promoter of DREB2A, which plays an important role in abiotic stress responses. JUB1 transactivates DREB2A expression in mesophyll cell protoplasts and transgenic plants and binds directly to the DREB2A promoter. Transcriptome profiling of JUB1 overexpressors revealed elevated expression of several reactive oxygen species-responsive genes, including heat shock protein and glutathione S-transferase genes, whose expression is further induced by H2O2 treatment. Metabolite profiling identified elevated Pro and trehalose levels in JUB1 overexpressors, in accordance with their enhanced abiotic stress tolerance. We suggest that JUB1 constitutes a central regulator of a finely tuned control system that modulates cellular H2O2 level and primes the plants for upcoming stress through a gene regulatory network that involves DREB2A. Y1 - 2012 U6 - https://doi.org/10.1105/tpc.111.090894 SN - 1040-4651 VL - 24 IS - 2 SP - 482 EP - 506 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Wu, Hao A1 - Han, Yijie A1 - Rodriguez Sillke, Yasmina A1 - Deng, Hongzhang A1 - Siddiqui, Sophiya A1 - Treese, Christoph A1 - Schmidt, Franziska A1 - Friedrich, Marie A1 - Keye, Jacqueline A1 - Wan, Jiajia A1 - Qin, Yue A1 - Kühl, Anja A. A1 - Qin, Zhihai A1 - Siegmund, Britta A1 - Glauben, Rainer T1 - Lipid droplet-dependent fatty acid metabolism controls the immune suppressive phenotype of tumor-associated macrophages JF - EMBO molecular medicine N2 - Tumor-associated macrophages (TAMs) promote tumor growth and metastasis by suppressing tumor immune surveillance. Herein, we provide evidence that the immunosuppressive phenotype of TAMs is controlled by long-chain fatty acid metabolism, specifically unsaturated fatty acids, here exemplified by oleate. Consequently, en-route enriched lipid droplets were identified as essential organelles, which represent effective targets for chemical inhibitors to block in vitro polarization of TAMs and tumor growth in vivo. In line, analysis of human tumors revealed that myeloid cells infiltrating colon cancer but not gastric cancer tissue indeed accumulate lipid droplets. Mechanistically, our data indicate that oleate-induced polarization of myeloid cells depends on the mammalian target of the rapamycin pathway. Thus, our findings reveal an alternative therapeutic strategy by targeting the pro-tumoral myeloid cells on a metabolic level. KW - cancer immunotherapy KW - lipid droplets KW - lipid metabolism KW - tumor microenvironment KW - tumor-associated macrophage Y1 - 2019 U6 - https://doi.org/10.15252/emmm.201910698 SN - 1757-4676 SN - 1757-4684 VL - 11 IS - 11 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Wu, Yabin A1 - Stoddart, Martin J. A1 - Wuertz-Kozak, Karin A1 - Grad, Sibylle A1 - Alini, Mauro A1 - Ferguson, Stephen J. T1 - Hyaluronan supplementation as a mechanical regulator of cartilage tissue development under joint-kinematic-mimicking loading JF - Interface : journal of the Royal Society KW - synovial fluid KW - cartilage tissue engineering KW - mechanical loading KW - non-Newtonian fluid KW - hyaluronic acid supplementation Y1 - 2017 U6 - https://doi.org/10.1098/rsif.2017.0255 SN - 1742-5689 SN - 1742-5662 VL - 14 PB - Royal Society CY - London ER - TY - JOUR A1 - Wu, Yunhua A1 - Wollenberger, Ursula A1 - Hofrichter, Martin A1 - Ullrich, Rene A1 - Scheibner, Katrin A1 - Scheller, Frieder W. T1 - Direct electron transfer of Agrocybe aegerita peroxygenase at electrodes modified with chitosan-capped Au nanoparticles and its bioelectrocatalysis to aniline JF - Sensors and actuators : B, Chemical N2 - Three different sizes of chitosan-capped Au nanoparticles were synthesized and were used to incorporate Agrocybe aegerita peroxygenase (AaeAPO) onto the surface of glassy carbon electrode. The direct electron transfer of AaeAPO was achieved in all films. The highest amount of electroactive enzyme and highest electron transfer rate constant k(s) of AaeAPO were obtained in the film with the smallest size of chitosan-capped Au nanoparticles. In anaerobic solutions, quasi-reversible oxidation and reduction are obtained with a formal potential of -0.280V vs. Ag/AgCl 1 M KCl in 100 mM (pH 7.0) PBS at scan rate of 1 V s(-1). Bioelectrocatalytic reduction currents can be obtained with the AaeAPO-modified electrode on addition of hydrogen peroxide. This reaction was suppressed when sodium azide, an inhibitor of AaeAPO, was present. Furthermore, the peroxide-dependent conversion of aniline was characterized and it was found that a polymer product via p-aminophenol is formed. And the AaeAPO biosensor was applied to determine aniline and p-aminophenol. KW - Agrocybe aegerita peroxygenase KW - Au nanoparticles KW - Direct electron transfer KW - Aniline biosensor KW - Bioelectrocatalysis Y1 - 2011 U6 - https://doi.org/10.1016/j.snb.2011.09.090 SN - 0925-4005 VL - 160 IS - 1 SP - 1419 EP - 1426 PB - Elsevier CY - Lausanne ER - TY - JOUR A1 - Wulf, Monika A1 - Rujner, Hendrik T1 - A GIS-based method for the reconstruction of the late eighteenth century forest vegetation in the Prignitz region (NE Germany) JF - Landscape ecology N2 - Our goal was to reconstruct the late eighteenth century forest vegetation of the Prignitz region (NE Germany) at a scale of 1:50,000. We also wanted to relate the historical forest vegetation to the actual and potential natural vegetation. For these purposes, we selected 15 woody species and transferred relevant data found in historical records from various sources together with the recent localities of (very) old individuals belonging to these woody species into ArcView GIS. Following multi-step data processing including the generation of a point density layer using a moving window with kernel estimation and derivation of vegetation units applying Boolean algebra rules together with information on site conditions, we derived 17 forest communities corresponding to the potential natural vegetation. We were able to reconstruct the historical forest vegetation for 90% of the forest area ca. 1780. Only two of the 17 forest communities covered large parts of the forested area. The oak forest with Agrostis capillaris covered about 44% of the total forest area, and alder forests on fenland made up about 37%. Oak-hornbeam forests with Stellaria holostea comprised slightly less than 6% of the forest area, while all other forest communities comprised less than 1%. The historical forest vegetation is more similar to the potential forest vegetation and quite different from the actual forest vegetation because coniferous tree species currently cover approximately two-thirds of the actual forest area. The most beneficial result of this study is the map of high-resolution historical vegetation units that may serve as the basis for various further studies, e.g., modelling long-term changes in biodiversity at the landscape scale. KW - Boolean algebra KW - Historical ecology KW - Kernel estimation KW - Moving window KW - Point density KW - Potential natural vegetation KW - Schmettau map KW - Toponymy KW - Vegetation map Y1 - 2011 U6 - https://doi.org/10.1007/s10980-010-9555-1 SN - 0921-2973 VL - 26 IS - 2 SP - 153 EP - 168 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Wurzbacher, Christian A1 - Attermeyer, Katrin A1 - Kettner, Marie Therese A1 - Flintrop, Clara A1 - Warthmann, Norman A1 - Hilt, Sabine A1 - Grossart, Hans-Peter A1 - Monaghan, Michael T. T1 - DNA metabarcoding of unfractionated water samples relates phyto-, zoo- and bacterioplankton dynamics and reveals a single-taxon bacterial bloom JF - Environmental microbiology reports N2 - Most studies of aquatic plankton focus on either macroscopic or microbial communities, and on either eukaryotes or prokaryotes. This separation is primarily for methodological reasons, but can overlook potential interactions among groups. Here we tested whether DNA metabarcoding of unfractionated water samples with universal primers could be used to qualitatively and quantitatively study the temporal dynamics of the total plankton community in a shallow temperate lake. Significant changes in the relative proportions of normalized sequence reads of eukaryotic and prokaryotic plankton communities over a 3-month period in spring were found. Patterns followed the same trend as plankton estimates measured using traditional microscopic methods. The bloom of a conditionally rare bacterial taxon belonging to Arcicella was characterized, which rapidly came to dominate the whole lake ecosystem and would have remained unnoticed without metabarcoding. The data demonstrate the potential of universal DNA metabarcoding applied to unfractionated samples for providing a more holistic view of plankton communities. Y1 - 2017 U6 - https://doi.org/10.1111/1758-2229.12540 SN - 1758-2229 VL - 9 SP - 383 EP - 388 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Wurzbacher, Christian A1 - Fuchs, Andrea A1 - Attermeyer, Katrin A1 - Frindte, Katharina A1 - Grossart, Hans-Peter A1 - Hupfer, Michael A1 - Casper, Peter A1 - Monaghan, Michael T. T1 - Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment JF - Microbiome N2 - Background: Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments. Methods: We analyzed four replicate sediment cores taken from 30-m depth in oligo-mesotrophic Lake Stechlin in northern Germany. Each 30-cm core spanned ca. 170 years of sediment accumulation according to Cs-137 dating and was sectioned into layers 1-4 cm thick. We examined a full suite of biogeochemical parameters and used DNA metabarcoding to examine community composition of microbial Archaea, Bacteria, and Eukaryota. Results: Community beta-diversity indicated nearly complete turnover within the uppermost 30 cm. We observed a pronounced shift from Eukaryota- and Bacteria-dominated upper layers (<5 cm) to Bacteria-dominated intermediate layers (5-14 cm) and to deep layers (>14 cm) dominated by enigmatic Archaea that typically occur in deep-sea sediments. Taxonomic replacement was the prevalent mechanism in structuring the community composition and was linked to parameters indicative of microbial activity (e.g., CO2 and CH4 concentration, bacterial protein production). Richness loss played a lesser role but was linked to conservative parameters (e.g., C, N, P) indicative of past conditions. Conclusions: By including all three domains, we were able to directly link the exponential decay of eukaryotes with the active sediment microbial community. The dominance of Archaea in deeper layers confirms earlier findings from marine systems and establishes freshwater sediments as a potential low-energy environment, similar to deep sea sediments. We propose a general model of sediment structure and function based on microbial characteristics and burial processes. An upper "replacement horizon" is dominated by rapid taxonomic turnover with depth, high microbial activity, and biotic interactions. A lower "depauperate horizon" is characterized by low taxonomic richness, more stable "low-energy" conditions, and a dominance of enigmatic Archaea. KW - Archaea KW - Eukaryota KW - Bacteria KW - Community KW - Freshwater KW - Lake KW - DNA metabarcoding KW - Beta-diversity KW - Sediment KW - Turnover Y1 - 2017 U6 - https://doi.org/10.1186/s40168-017-0255-9 SN - 2049-2618 VL - 5 PB - BioMed Central CY - London ER - TY - JOUR A1 - Wurzbacher, Christian A1 - Roesel, Stefan A1 - Rychla, Anna A1 - Grossart, Hans-Peter T1 - Importance of saprotrophic freshwater fungi for pollen degradation JF - PLoS one N2 - Fungi and bacteria are the major organic matter (OM) decomposers in aquatic ecosystems. While bacteria are regarded as primary mineralizers in the pelagic zone of lakes and oceans, fungi dominate OM decomposition in streams and wetlands. Recent findings indicate that fungal communities are also active in lakes, but little is known about their diversity and interactions with bacteria. Therefore, the decomposer niche overlap of saprotrophic fungi and bacteria was studied on pollen (as a seasonally recurring source of fine particulate OM) by performing microcosm experiments with three different lake types. Special emphasis was placed on analysis of fungal community composition and diversity. We hypothesized that (I) pollen select for small saprotrophic fungi and at the same time for typical particle-associated bacteria; (II) fungal communities form specific free-living and attached sub-communities in each lake type; (III) the ratio between fungi or bacteria on pollen is controlled by the lake's chemistry. Bacteria-to-fungi ratios were determined by quantitative PCR (qPCR), and bacterial and fungal diversity were studied by clone libraries and denaturing gradient gel electrophoresis (DGGE) fingerprints. A protease assay was used to identify functional differences between treatments. For generalization, systematic differences in bacteria-to-fungi ratios were analyzed with a dataset from the nearby Baltic Sea rivers. High abundances of Chytridiomycota as well as occurrences of Cryptomycota and yeast-like fungi confirm the decomposer niche overlap of saprotrophic fungi and bacteria on pollen. As hypothesized, microbial communities consistently differed between the lake types and exhibited functional differences. Bacteria-to-fungi ratios correlated well with parameters such as organic carbon and pH. The importance of dissolved organic carbon and nitrogen for bacteria-to-fungi ratios was supported by the Baltic Sea river dataset. Our findings highlight the fact that carbon-to-nitrogen ratios may also control fungal contributions to OM decomposition in aquatic ecosystems. Y1 - 2014 U6 - https://doi.org/10.1371/journal.pone.0094643 SN - 1932-6203 VL - 9 IS - 4 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Wurzbacher, Christian A1 - Salka, Ivette A1 - Grossart, Hans-Peter T1 - Environmental actinorhodopsin expression revealed by a new in situ filtration and fixation sampler JF - Environmental microbiology reports N2 - Freshwater Actinobacteria are an important and dominant group of bacterioplankton in most temperate freshwater systems. Recently, metagenomic studies discovered rhodopsin-like protein-coding sequences present in Actinobacteria which could be a decisive hint for their success in freshwater ecosystems. We analysed the diversity of actinorhodopsin (ActR) in Lake Stechlin (northern Germany) and assessed the actR expression profile during a diurnal cycle. We obtained 85 positive actR clones which could be subsequently grouped to 17 operational taxonomic units assuming a 90% sequence similarity. The phylogenetic analysis points to a close relationship of all obtained sequences to the acI lineage of Actinobacteria, forming six independent clusters. For the first time, we followed in situ transcription of actR in Lake Stechlin revealing a rather constitutive circadian gene expression. For analysing in situ expression patterns of functional genes in aquatic ecosystems, such as actR, we invented a new in situ filtration and fixation sampler (IFFS). The IFFS enables the representative investigation of microbial transcriptomes in any aquatic ecosystem at all water depths. The IFFS sampler is simple and inexpensive, and we provide all engineering plans for an easy rebuild. Consequently, our IFFS is suitable to reliably study expression of any known functional gene of any aquatic microorganism. Y1 - 2012 U6 - https://doi.org/10.1111/j.1758-2229.2012.00350.x SN - 1758-2229 VL - 4 IS - 5 SP - 491 EP - 497 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Wurzbacher, Christian A1 - Warthmann, Norman A1 - Bourne, Elizabeth Charlotte A1 - Attermeyer, Katrin A1 - Allgaier, Martin A1 - Powell, Jeff R. A1 - Detering, Harald A1 - Mbedi, Susan A1 - Grossart, Hans-Peter A1 - Monaghan, Michael T. T1 - High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany) JF - MycoKeys N2 - Freshwater fungi are a poorly studied ecological group that includes a high taxonomic diversity. Most studies on aquatic fungal diversity have focused on single habitats, thus the linkage between habitat heterogeneity and fungal diversity remains largely unexplored. We took 216 samples from 54 locations representing eight different habitats in the meso-oligotrophic, temperate Lake Stechlin in North-East Germany. These included the pelagic and littoral water column, sediments, and biotic substrates. We performed high throughput sequencing using the Roche 454 platform, employing a universal eukaryotic marker region within the large ribosomal subunit (LSU) to compare fungal diversity, community structure, and species turnover among habitats. Our analysis recovered 1027 fungal OTUs (97% sequence similarity). Richness estimates were highest in the sediment, biofilms, and benthic samples (189-231 OTUs), intermediate in water samples (42-85 OTUs), and lowest in plankton samples (8 OTUs). NMDS grouped the eight studied habitats into six clusters, indicating that community composition was strongly influenced by turnover among habitats. Fungal communities exhibited changes at the phylum and order levels along three different substrate categories from littoral to pelagic habitats. The large majority of OTUs (> 75%) could not be classified below the order level due to the lack of aquatic fungal entries in public sequence databases. Our study provides a first estimate of lake-wide fungal diversity and highlights the important contribution of habitat heterogeneity to overall diversity and community composition. Habitat diversity should be considered in any sampling strategy aiming to assess the fungal diversity of a water body. KW - Freshwater fungi KW - aquatic fungi KW - metabarcoding KW - LSU KW - GMYC KW - habitat specificity KW - Chytridiomycota KW - Cryptomycota KW - Rozellomycota KW - community ecology KW - lake ecosystem KW - biofilm KW - sediment KW - plankton KW - water sample KW - benthos KW - reed KW - fungal diversity Y1 - 2016 U6 - https://doi.org/10.3897/mycokeys.16.9646 SN - 1314-4057 SN - 1314-4049 VL - 41 SP - 17 EP - 44 PB - Pensoft Publ. CY - Sofia ER - TY - JOUR A1 - Wuster, Wolfgang A1 - Chirio, Laurent A1 - Trape, Jean-Francois A1 - Ineich, Ivan A1 - Jackson, Kate A1 - Greenbaum, Eli A1 - Barron, Cesar A1 - Kusamba, Chifundera A1 - Nagy, Zoltan T. A1 - Storey, Richard A1 - Hall, Cara A1 - Wuster, Catharine E. A1 - Barlow, Axel A1 - Broadley, Donald G. T1 - Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae) JF - Zootaxa : an international journal of zootaxonomy ; a rapid international journal for animal taxonomists N2 - Cobras are among the most widely known venomous snakes, and yet their taxonomy remains incompletely understood, particularly in Africa. Here, we use a combination of mitochondrial and nuclear gene sequences and morphological data to diagnose species limits within the African forest cobra, Naja (Boulengerina) melanoleuca. Mitochondrial DNA sequences reveal deep divergences within this taxon. Congruent patterns of variation in mtDNA, nuclear genes and morphology support the recognition of five separate species, confirming the species status of N. subfulva and N. peroescobari, and revealing two previously unnamed West African species, which are described as new: Naja (Boulengerina) guineensis sp. nov. Broadley, Trape, Chirio, Ineich & Wuster, from the Upper Guinea forest of West Africa, and Naja (Boulengerina) savannula sp. nov. Broadley, Trape, Chirio & Wuster, a banded form from the savanna-forest mosaic of the Guinea and Sudanian savannas of West Africa. The discovery of cryptic diversity in this iconic group highlights our limited understanding of tropical African biodiversity, hindering our ability to conserve it effectively. KW - Integrative taxonomy KW - Africa KW - Naja melanoleuca KW - Naja guineensis sp nov. KW - Naja savannula sp nov. KW - Elapidae KW - systematics Y1 - 2018 U6 - https://doi.org/10.11646/zootaxa.4455.1.3 SN - 1175-5326 SN - 1175-5334 VL - 4455 IS - 1 SP - 68 EP - 98 PB - Magnolia Press CY - Auckland ER - TY - JOUR A1 - Wutke, Saskia A1 - Benecke, Norbert A1 - Sandoval-Castellanos, Edson A1 - Döhle, Hans-Jürgen A1 - Friederich, Susanne A1 - Gonzalez Soto, Javier Esteban A1 - Hallsson, Jon Hallsteinn A1 - Hofreiter, Michael A1 - Lougas, Lembi A1 - Magnell, Ola A1 - Morales-Muniz, Arturo A1 - Orlando, Ludovic A1 - Palsdottir, Albina Hulda A1 - Reissmann, Monika A1 - Ruttkay, Matej A1 - Trinks, Alexandra A1 - Ludwig, Arne T1 - Spotted phenotypes in horses lost attractiveness in the Middle Ages JF - Scientific reports N2 - Horses have been valued for their diversity of coat colour since prehistoric times; this is especially the case since their domestication in the Caspian steppe in similar to 3,500 BC. Although we can assume that human preferences were not constant, we have only anecdotal information about how domestic horses were influenced by humans. Our results from genotype analyses show a significant increase in spotted coats in early domestic horses (Copper Age to Iron Age). In contrast, medieval horses carried significantly fewer alleles for these phenotypes, whereas solid phenotypes (i.e., chestnut) became dominant. This shift may have been supported because of (i) pleiotropic disadvantages, (ii) a reduced need to separate domestic horses from their wild counterparts, (iii) a lower religious prestige, or (iv) novel developments in weaponry. These scenarios may have acted alone or in combination. However, the dominance of chestnut is a remarkable feature of the medieval horse population. Y1 - 2016 U6 - https://doi.org/10.1038/srep38548 SN - 2045-2322 VL - 6 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Wutke, Saskia A1 - Sandoval-Castellanos, Edson A1 - Benecke, Norbert A1 - Döhle, Hans-Jürgen A1 - Friederich, Susanne A1 - Gonzalez, Javier A1 - Hofreiter, Michael A1 - Lougas, Lembi A1 - Magnell, Ola A1 - Malaspinas, Anna-Sapfo A1 - Morales-Muniz, Arturo A1 - Orlando, Ludovic A1 - Reissmann, Monika A1 - Trinks, Alexandra A1 - Ludwig, Arne T1 - Decline of genetic diversity in ancient domestic stallions in Europe JF - Science Advances N2 - Present-day domestic horses are immensely diverse in their maternally inherited mitochondrial DNA, yet they show very little variation on their paternally inherited Y chromosome. Although it has recently been shown that Y chromosomal diversity in domestic horses was higher at least until the Iron Age, when and why this diversity disappeared remain controversial questions. We genotyped 16 recently discovered Y chromosomal single-nucleotide polymorphisms in 96 ancient Eurasian stallions spanning the early domestication stages (Copper and Bronze Age) to the Middle Ages. Using this Y chromosomal time series, which covers nearly the entire history of horse domestication, we reveal how Y chromosomal diversity changed over time. Our results also show that the lack of multiple stallion lineages in the extant domestic population is caused by neither a founder effect nor random demographic effects but instead is the result of artificial selection-initially during the Iron Age by nomadic people from the Eurasian steppes and later during the Roman period. Moreover, the modern domestic haplotype probably derived from another, already advantageous, haplotype, most likely after the beginning of the domestication. In line with recent findings indicating that the Przewalski and domestic horse lineages remained connected by gene flow after they diverged about 45,000 years ago, we present evidence for Y chromosomal introgression of Przewalski horses into the gene pool of European domestic horses at least until medieval times. Y1 - 2018 U6 - https://doi.org/10.1126/sciadv.aap9691 SN - 2375-2548 VL - 4 IS - 4 PB - American Assoc. for the Advancement of Science CY - Washington ER - TY - JOUR A1 - Wölfl, S. A1 - Tittel, Jörg A1 - Zippel, Barbara A1 - Kringel, R. T1 - Occurrence of an algal mass development in an acidic (pH 2.5), iron and aluminium-rich coal mining pond Y1 - 2000 ER - TY - JOUR A1 - Wüstenhagen, Doreen Anja A1 - Lukas, Phil A1 - Müller, Christian A1 - Aubele, Simone A. A1 - Hildebrandt, Jan-Peter A1 - Kubick, Stefan T1 - Cell-free synthesis of the hirudin variant 1 of the blood-sucking leech Hirudo medicinalis JF - Scientific reports N2 - Synthesis and purification of peptide drugs for medical applications is a challenging task. The leech-derived factor hirudin is in clinical use as an alternative to heparin in anticoagulatory therapies. So far, recombinant hirudin is mainly produced in bacterial or yeast expression systems. We describe the successful development and application of an alternative protocol for the synthesis of active hirudin based on a cell-free protein synthesis approach. Three different cell lysates were compared, and the effects of two different signal peptide sequences on the synthesis of mature hirudin were determined. The combination of K562 cell lysates and the endogenous wild-type signal peptide sequence was most effective. Cell-free synthesized hirudin showed a considerably higher anti-thrombin activity compared to recombinant hirudin produced in bacterial cells. Y1 - 2020 U6 - https://doi.org/10.1038/s41598-020-76715-w SN - 2045-2322 VL - 10 IS - 1 PB - Macmillan Publishers Limited, part of Springer Nature CY - London ER - TY - JOUR A1 - Xiang, Hai A1 - Gao, Jianqiang A1 - Yu, Baoquan A1 - Zhou, Hui A1 - Cai, Dawei A1 - Zhang, Youwen A1 - Chen, Xiaoyong A1 - Wang, Xi A1 - Hofreiter, Michael A1 - Zhao, Xingbo T1 - Early Holocene chicken domestication in northern China JF - Proceedings of the National Academy of Sciences of the United States of America N2 - Chickens represent by far the most important poultry species, yet the number, locations, and timings of their domestication have remained controversial for more than a century. Here we report ancient mitochondrial DNA sequences from the earliest archaeological chicken bones from China, dating back to similar to 10,000 B.P. The results clearly show that all investigated bones, including the oldest from the Nanzhuangtou site, are derived from the genus Gallus, rather than any other related genus, such as Phasianus. Our analyses also suggest that northern China represents one region of the earliest chicken domestication, possibly dating as early as 10,000 y B.P. Similar to the evidence from pig domestication, our results suggest that these early domesticated chickens contributed to the gene pool of modern chicken populations. Moreover, our results support the idea that multiple members of the genus Gallus, specifically Gallus gallus and Gallus sonneratii contributed to the gene pool of the modern domestic chicken. Our results provide further support for the growing evidence of an early mixed agricultural complex in northern China. KW - ancient DNA KW - chicken KW - domestication KW - species origin Y1 - 2014 U6 - https://doi.org/10.1073/pnas.1411882111 SN - 0027-8424 VL - 111 IS - 49 SP - 17564 EP - 17569 PB - National Acad. of Sciences CY - Washington ER - TY - JOUR A1 - Xiao, Shangbin A1 - Liu, Liu A1 - Wang, Wei A1 - Lorke, Andreas A1 - Woodhouse, Jason Nicholas A1 - Grossart, Hans-Peter T1 - A Fast-Response Automated Gas Equilibrator (FaRAGE) for continuous in situ measurement of CH4 and CO2 dissolved in water JF - Hydrology and earth system sciences : HESS N2 - Biogenic greenhouse gas emissions, e.g., of methane (CH4) and carbon dioxide (CO2) from inland waters, contribute substantially to global warming. In aquatic systems, dissolved greenhouse gases are highly heterogeneous in both space and time. To better understand the biological and physical processes that affect sources and sinks of both CH4 and CO2, their dissolved concentrations need to be measured with high spatial and temporal resolution. To achieve this goal, we developed the Fast-Response Automated Gas Equilibrator (FaRAGE) for real-time in situ measurement of dissolved CH4 and CO2 concentrations at the water surface and in the water column. FaRAGE can achieve an exceptionally short response time (t(95%) = 12 s when including the response time of the gas analyzer) while retaining an equilibration ratio of 62.6% and a measurement accuracy of 0.5% for CH4. A similar performance was observed for dissolved CO2 (t(95%) = 10 s, equilibration ratio 67.1 %). An equilibration ratio as high as 91.8% can be reached at the cost of a slightly increased response time (16 s). The FaRAGE is capable of continuously measuring dissolved CO2 and CH4 concentrations in the nM-to-submM (10(-9)-10(-3) mol L-1) range with a detection limit of subnM (10(-10) mol L-1), when coupling with a cavity ring-down greenhouse gas analyzer (Picarro GasScouter). FaRAGE allows for the possibility of mapping dissolved concentration in a "quasi" three-dimensional manner in lakes and provides an inexpensive alternative to other commercial gas equilibrators. It is simple to operate and suitable for continuous monitoring with a strong tolerance for suspended particles. While the FaRAGE is developed for inland waters, it can be also applied to ocean waters by tuning the gas-water mixing ratio. The FaRAGE is easily adapted to suit other gas analyzers expanding the range of potential applications, including nitrous oxide and isotopic composition of the gases. Y1 - 2020 U6 - https://doi.org/10.5194/hess-24-3871-2020 SN - 1027-5606 SN - 1607-7938 VL - 24 IS - 7 SP - 3871 EP - 3880 PB - European Geosciences Union (EGU) ; Copernicus CY - Munich ER - TY - JOUR A1 - Xie, B. A1 - Tang, X. A1 - Wollenberger, Ursula A1 - Johansson, G. A1 - Gorton, Lo A1 - Scheller, Frieder W. A1 - Danielsson, B. T1 - Hybrid biosensor for simultaneous electrochemical and thermal detection Y1 - 1997 ER - TY - JOUR A1 - Xie, J. A1 - Techritz, S. A1 - Haebel, Sophie A1 - Horn, A. A1 - Neitzel, H. A1 - Klose, J. A1 - Schuelke, M. T1 - A two-dimensional electrophoretic map of human mitochondrial proteins from immortalized lymphoblastoid cell lines: a prerequisite to study mitochondrial disorders in patients N2 - Mitochondrial diseases may be caused by numerous mutations that alter proteins of the respiratory chain and of other metabolic pathways in the mitochondrium. For clinicians this disease group poses a considerable diagnostic challenge due to ambiguous genotype-phenotype relationships. Until now, only 30 % of the mitochondriopathies can be diagnosed at the molecular level. We therefore need a new diagnostic tool that offers a wide view on the mitochondrial proteins. Here, we present a method to generate a high-resolution, large-gel two-dimensional gel electrophoretic (2-DE) map of a purified fraction of mitochondrial proteins from Epstein-Barr virus-immortalized lymphoblastoid cell line (LCL). LCLs can be easily obtained from patients and control subjects in a routine clinical setting. They often express the biochemical phenotype and can be cultured to high cell numbers, sufficient to gain enough purified material for 2- DE. In total we identified 166 mitochondrial proteins. Thirteen proteins were earlier not known to be of mitochondrial origin. Thirty-nine proteins were associated with human diseases ranging from respiratory chain enzyme deficiencies to disorders of P-oxidation and amino acid metabolism. This 2-DE map is intended to be the first step to diagnose mitochondrial diseases at the proteomic level Y1 - 2005 SN - 1615-9853 ER - TY - JOUR A1 - Xu, Huizhen A1 - Giannetti, Alessandro A1 - Sugiyama, Yuki A1 - Zheng, Wenna A1 - Schneider, René A1 - Watanabe, Yoichiro A1 - Oda, Yoshihisa A1 - Persson, Staffan T1 - Secondary cell wall patterning-connecting the dots, pits and helices JF - Open biology N2 - All plant cells are encased in primary cell walls that determine plant morphology, but also protect the cells against the environment. Certain cells also produce a secondary wall that supports mechanically demanding processes, such as maintaining plant body stature and water transport inside plants. Both these walls are primarily composed of polysaccharides that are arranged in certain patterns to support cell functions. A key requisite for patterned cell walls is the arrangement of cortical microtubules that may direct the delivery of wall polymers and/or cell wall producing enzymes to certain plasma membrane locations. Microtubules also steer the synthesis of cellulose-the load-bearing structure in cell walls-at the plasma membrane. The organization and behaviour of the microtubule array are thus of fundamental importance to cell wall patterns. These aspects are controlled by the coordinated effort of small GTPases that probably coordinate a Turing's reaction-diffusion mechanism to drive microtubule patterns. Here, we give an overview on how wall patterns form in the water-transporting xylem vessels of plants. We discuss systems that have been used to dissect mechanisms that underpin the xylem wall patterns, emphasizing the VND6 and VND7 inducible systems, and outline challenges that lay ahead in this field. KW - plant cell wall KW - microtubules KW - xylem KW - cell wall patterning KW - cellulose Y1 - 2022 U6 - https://doi.org/10.1098/rsob.210208 SN - 2046-2441 VL - 12 IS - 5 PB - Royal Society CY - London ER - TY - JOUR A1 - Xu, J. A1 - Brearley, C. A. A1 - Lin, W. H. A1 - Wang, Y. A1 - Ye, R. A1 - Müller-Röber, Bernd A1 - Xu, Z. H. A1 - Xue, H. W. T1 - A role of Arabidopsis inositol polyphosphate kinase, AtIPK2 alpha, in pollen germination and root growth N2 - Inositol polyphosphates, such as inositol trisphosphate, are pivotal intracellular signaling molecules in eukaryotic cells. In higher plants the mechanism for the regulation of the type and the level of these signaling molecules is poorly understood. In this study we investigate the physiological function of an Arabidopsis (Arabidopsis thaliana) gene encoding inositol polyphosphate kinase (AtIPK2alpha), which phosphorylates inositol 1,4,5-trisphosphate successively at the D-6 and D-3 positions, and inositol 1,3,4,5-tetrakisphosphate at D-6, resulting in the generation of inositol 1,3,4,5,6-pentakisphosphate. Semiquantitative reverse transcription-PCR and promoter-beta-glucuronidase reporter gene analyses showed that AtIPK2alpha is expressed in various tissues, including roots and root hairs, stem, leaf, pollen grains, pollen tubes, the flower stigma, and siliques. Transgenic Arabidopsis plants expressing the AtIPK2alpha antisense gene under its own promoter were generated. Analysis of several independent transformants exhibiting strong reduction in AtIPK2alpha transcript levels showed that both pollen germination and pollen tube growth were enhanced in the antisense lines compared to wild-type plants, especially in the presence of nonoptimal low Ca2+ concentrations in the culture medium. Furthermore, root growth and root hair development were also stimulated in the antisense lines, in the presence of elevated external Ca2+ concentration or upon the addition of EGTA. In addition, seed germination and early seedling growth was stimulated in the antisense lines. These observations suggest a general and important role of AtIPK2alpha, and hence inositol polyphosphate metabolism, in the regulation of plant growth most likely through the regulation of calcium signaling, consistent with the well-known function of inositol trisphosphate in the mobilization of intracellular calcium stores Y1 - 2005 SN - 0032-0889 ER - TY - JOUR A1 - Xu, Rudan A1 - Razaghi-Moghadam, Zahra A1 - Nikoloski, Zoran T1 - Maximization of non-idle enzymes improves the coverage of the estimated maximal in vivo enzyme catalytic rates in Escherichia coli JF - Bioinformatics N2 - Motivation: Constraint-based modeling approaches allow the estimation of maximal in vivo enzyme catalytic rates that can serve as proxies for enzyme turnover numbers. Yet, genome-scale flux profiling remains a challenge in deploying these approaches to catalogue proxies for enzyme catalytic rates across organisms. Results: Here, we formulate a constraint-based approach, termed NIDLE-flux, to estimate fluxes at a genome-scale level by using the principle of efficient usage of expressed enzymes. Using proteomics data from Escherichia coli, we show that the fluxes estimated by NIDLE-flux and the existing approaches are in excellent qualitative agreement (Pearson correlation > 0.9). We also find that the maximal in vivo catalytic rates estimated by NIDLE-flux exhibits a Pearson correlation of 0.74 with in vitro enzyme turnover numbers. However, NIDLE-flux results in a 1.4-fold increase in the size of the estimated maximal in vivo catalytic rates in comparison to the contenders. Integration of the maximum in vivo catalytic rates with publically available proteomics and metabolomics data provide a better match to fluxes estimated by NIDLE-flux. Therefore, NIDLE-flux facilitates more effective usage of proteomics data to estimate proxies for kcatomes. Y1 - 2021 U6 - https://doi.org/10.1093/bioinformatics/btab575 SN - 1367-4803 SN - 1460-2059 VL - 37 IS - 21 SP - 3848 EP - 3855 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Xu, Xuan A1 - Wollenberger, Ursula A1 - Qian, Jing A1 - Lettau, Katrin A1 - Jung, Christiane A1 - Liu, Songqin T1 - Electrochemically driven biocatalysis of the oxygenase domain of neuronal nitric oxide synthase in indium tin oxide nanoparticles/polyvinyl alcohol nanocomposite JF - Bioelectrochemistry : an international journal devoted to electrochemical aspects of biology and biological aspects of electrochemistry ; official journal of the Bioelectrochemical Society N2 - Nitric oxide synthase (NOS) plays a critical role in a number of key physiological and pathological processes. Investigation of electron-transfer reactions in NOS would contribute to a better understanding of the nitric oxide (NO) synthesis mechanism. Herein, we describe an electrochemically driven catalytic strategy, using a nanocomposite that consisted of the oxygenase domain of neuronal NOS (D290nNOSoxy), indium tin oxide (ITO) nanopartides and polyvinyl alcohol (PVA). Fast direct electron transfer between electrodes and D290nNOSoxy was observed with the heterogeneous electron transfer rate constant (k(er)) of 154.8 +/- 0.1 s(-1) at the scan rate of 5 V s(-1). Moreover, the substrate IV-hydroxy-L-arginine (NHA) was used to prove the concept of electrochemically driven biocatalysis of D290nNOSoxy. In the presence of the oxygen cosubstrate and tetrahydrobiopterin (BH4) cofactor, the addition of NHA caused the decreases of both oxidation current at + 0.1 V and reduction current at potentials ranging from -0.149 V to -0.549 V vs Ag/AgCl. Thereafter, a series of control experiments such as in the absence of BH4 or D290nNOSoxy were performed. All the results demonstrated that D290nNOSoxy biocatalysis was successfully driven by electrodes in the presence of BH4 and oxygen. This novel bioelectronic system showed potential for further investigation of NOS and biosensor applications. (C) 2013 Elsevier B.V. All rights reserved. KW - Nitric oxide synthase KW - Tetrahydrobiopterin KW - N-omega-hydroxy-L-arginine KW - Indium tin oxide nanoparticles KW - Biocatalysis Y1 - 2013 U6 - https://doi.org/10.1016/j.bioelechem.2013.04.005 SN - 1567-5394 SN - 1521-186X VL - 94 IS - 47 SP - 7 EP - 12 PB - Elsevier CY - Lausanne ER - TY - JOUR A1 - Xu, Xun A1 - Nie, Yan A1 - Wang, Weiwei A1 - Ullah, Imran A1 - Tung, Wing Tai A1 - Ma, Nan A1 - Lendlein, Andreas T1 - Generation of 2.5D lung bud organoids from human induced pluripotent stem cells JF - Clinical hemorheology and microcirculation : blood flow and vessels N2 - Human induced pluripotent stem cells (hiPSCs) are a promising cell source to generate the patient-specific lung organoid given their superior differentiation potential. However, the current 3D cell culture approach is tedious and time-consuming with a low success rate and high batch-to-batch variability. Here, we explored the establishment of lung bud organoids by systematically adjusting the initial confluence levels and homogeneity of cell distribution. The efficiency of single cell seeding and clump seeding was compared. Instead of the traditional 3D culture, we established a 2.5D organoid culture to enable the direct monitoring of the internal structure via microscopy. It was found that the cell confluence and distribution prior to induction were two key parameters, which strongly affected hiPSC differentiation trajectories. Lung bud organoids with positive expression of NKX 2.1, in a single-cell seeding group with homogeneously distributed hiPSCs at 70% confluence (SC 70% hom) or a clump seeding group with heterogeneously distributed cells at 90% confluence (CL 90% het), can be observed as early as 9 days post induction. These results suggest that a successful lung bud organoid formation with single-cell seeding of hiPSCs requires a moderate confluence and homogeneous distribution of cells, while high confluence would be a prominent factor to promote the lung organoid formation when seeding hiPSCs as clumps. 2.5D organoids generated with defined culture conditions could become a simple, efficient, and valuable tool facilitating drug screening, disease modeling and personalized medicine. KW - lung organoid KW - human induced pluripotent stem cell KW - cell culture Y1 - 2021 U6 - https://doi.org/10.3233/CH-219111 SN - 1386-0291 SN - 1875-8622 VL - 79 IS - 1 SP - 217 EP - 230 PB - IOS Press CY - Amsterdam ER - TY - JOUR A1 - Xu, Ying T1 - Study on transport mechanism of m5C-edited mRNAs Y1 - 2022 ER - TY - JOUR A1 - Yan, Jiawei A1 - Frøkjær, Emil Egede A1 - Engelbrekt, Christian A1 - Leimkühler, Silke A1 - Ulstrup, Jens A1 - Wollenberger, Ulla A1 - Xiao, Xinxin A1 - Zhang, Jingdong T1 - Voltammetry and single-molecule in situ scanning tunnelling microscopy of the redox metalloenzyme human sulfite oxidase JF - ChemElectroChem N2 - Human sulfite oxidase (hSO) is a homodimeric two-domain enzyme central in the biological sulfur cycle. A pyranopterin molybdenum cofactor (Moco) is the catalytic site and a heme b(5) group located in the N-terminal domain. The two domains are connected by a flexible linker region. Electrons produced at the Moco in sulfite oxidation, are relayed via heme b(5) to electron acceptors or an electrode surface. Inter-domain conformational changes between an open and a closed enzyme conformation, allowing "gated" electron transfer has been suggested. We first recorded cyclic voltammetry (CV) of hSO on single-crystal Au(111)-electrode surfaces modified by self-assembled monolayers (SAMs) both of a short rigid thiol, cysteamine and of a longer structurally flexible thiol, omega-amino-octanethiol (AOT). hSO on cysteamine SAMs displays a well-defined pair of voltammetric peaks around -0.207 V vs. SCE in the absence of sulfite substrate, but no electrocatalysis. hSO on AOT SAMs displays well-defined electrocatalysis, but only "fair" quality voltammetry in the absence of sulfite. We recorded next in situ scanning tunnelling spectroscopy (STS) of hSO on AOT modified Au(111)-electrodes, disclosing, a 2-5 % surface coverage of strong molecular scale contrasts, assigned to single hSO molecules, notably with no contrast difference in the absence and presence of sulfite. In situ STS corroborated this observation with a sigmoidal tunnelling current/overpotential correlation. KW - cyclic voltammetry KW - human sulfite oxidase KW - in  situ scanning KW - tunnelling spectroscopy KW - self-assembled molecular monolayers KW - single-crystal gold electrodes Y1 - 2021 U6 - https://doi.org/10.1002/celc.202001258 SN - 2196-0216 VL - 8 IS - 1 SP - 164 EP - 171 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Yan, Robert A1 - Friemel, Martin A1 - Aloisi, Claudia A1 - Huynen, Martijn A1 - Taylor, Ian A. A1 - Leimkühler, Silke A1 - Pastore, Annalisa T1 - The Eukaryotic-Specific ISD11 Is a Complex-Orphan Protein with Ability to Bind the Prokaryotic IscS JF - PLoS one N2 - The eukaryotic protein Isd11 is a chaperone that binds and stabilizes the central component of the essential metabolic pathway responsible for formation of iron-sulfur clusters in mitochondria, the desulfurase Nfs1. Little is known about the exact role of Isd11. Here, we show that human Isd11 (ISD11) is a helical protein which exists in solution as an equilibrium between monomer, dimeric and tetrameric species when in the absence of human Nfs1 (NFS1). We also show that, surprisingly, recombinant ISD11 expressed in E. coli co-purifies with the bacterial orthologue of NFS1, IscS. Binding is weak but specific suggesting that, despite the absence of Isd11 sequences in bacteria, there is enough conservation between the two desulfurases to retain a similar mode of interaction. This knowledge may inform us on the conservation of the mode of binding of Isd11 to the desulfurase. We used evolutionary evidence to suggest Isd11 residues involved in the interaction. Y1 - 2016 U6 - https://doi.org/10.1371/journal.pone.0157895 SN - 1932-6203 VL - 11 SP - 383 EP - 395 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Yan, Wan A1 - Fang, Liang A1 - Nöchel, Ulrich A1 - Gould, Oliver E. C. A1 - Behl, Marc A1 - Kratz, Karl A1 - Lendlein, Andreas T1 - Investigating the roles of crystallizable and glassy switching segments within multiblock copolymer shape-memory materials JF - MRS Advances N2 - The variation of the molecular architecture of multiblock copolymers has enabled the introduction of functional behaviour and the control of key mechanical properties. In the current study, we explore the synergistic relationship of two structural components in a shape-memory material formed of a multiblock copolymer with crystallizable poly(epsilon-caprolactone) and crystallizable polyfoligo(3S-iso-butylmorpholine-2,5-dione) segments (PCL-PIBMD). The thermal and structural properties of PCL-PIBMD films were compared with PCI.-PU and PMMD-PU investigated by means of DSC, SAXS and WARS measurements. The shape-memory properties were quantified by cyclic, thermomechanical tensile tests, where deformation strains up to 900% were applied for programming PCL-PIBMD films at 50 degrees C. Toluene vapor treatment experiments demonstrated that the temporary shape was fixed mainly by glassy PIBMD domains at strains lower than 600% with the PCL contribution to fixation increasing to 42 +/- 2% at programming strains of 900% This study into the shape-memory mechanism of PCL-PIBMD provides insight into the structure function relation in multiblock copolymers with both crystallizable and glassy switching segments. Y1 - 2018 U6 - https://doi.org/10.1557/adv.2018.590 SN - 2059-8521 VL - 3 IS - 63 SP - 3741 EP - 3749 PB - Cambridge Univ. Press CY - New York ER - TY - JOUR A1 - Yan, Wenhao A1 - Chen, Dijun A1 - Kaufmann, Kerstin T1 - Efficient multiplex mutagenesis by RNA-guided Cas9 and its use in the characterization of regulatory elements in the AGAMOUS gene JF - Plant methods N2 - Background The efficiency of multiplex editing in plants by the RNA-guided Cas9 system is limited by efficient introduction of its components into the genome and by their activity. The possibility of introducing large fragment deletions by RNA-guided Cas9 tool provides the potential to study the function of any DNA region of interest in its ‘endogenous’ environment. Results Here, an RNA-guided Cas9 system was optimized to enable efficient multiplex editing in Arabidopsis thaliana. We demonstrate the flexibility of our system for knockout of multiple genes, and to generate heritable large-fragment deletions in the genome. As a proof of concept, the function of part of the second intron of the flower development gene AGAMOUS in Arabidopsis was studied by generating a Cas9-free mutant plant line in which part of this intron was removed from the genome. Further analysis revealed that deletion of this intron fragment results 40 % decrease of AGAMOUS gene expression without changing the splicing of the gene which indicates that this regulatory region functions as an activator of AGAMOUS gene expression. Conclusions Our modified RNA-guided Cas9 system offers a versatile tool for the functional dissection of coding and non-coding DNA sequences in plants. KW - RNA-guided Cas9 KW - Multiplex mutagenesis KW - Large fragment deletion KW - Germline transmission Y1 - 2016 U6 - https://doi.org/10.1186/s13007-016-0125-7 SN - 1746-4811 VL - 12 SP - 1 EP - 9 PB - BioMed Central CY - London ER - TY - JOUR A1 - Yan, Wenhao A1 - Chen, Dijun A1 - Kaufmann, Kerstin T1 - Efficient multiplex mutagenesis by RNA-guided Cas9 and its use in the characterization of regulatory elements in the AGAMOUS gene JF - Plant Methods N2 - Results: Here, an RNA-guided Cas9 system was optimized to enable efficient multiplex editing in Arabidopsis thaliana. We demonstrate the flexibility of our system for knockout of multiple genes, and to generate heritable large-fragment deletions in the genome. As a proof of concept, the function of part of the second intron of the flower development gene AGAMOUS in Arabidopsis was studied by generating a Cas9-free mutant plant line in which part of this intron was removed from the genome. Further analysis revealed that deletion of this intron fragment results 40 % decrease of AGAMOUS gene expression without changing the splicing of the gene which indicates that this regulatory region functions as an activator of AGAMOUS gene expression. Conclusions: Our modified RNA-guided Cas9 system offers a versatile tool for the functional dissection of coding and non-coding DNA sequences in plants. KW - RNA-guided Cas9 KW - Multiplex mutagenesis KW - Large fragment deletion KW - Germline transmission Y1 - 2016 U6 - https://doi.org/10.1186/s13007-016-0125-7 SN - 1746-4811 VL - 12 SP - 2381 EP - 2389 PB - BioMed Central CY - London ER - TY - JOUR A1 - Yan, Wenhao A1 - Chen, Dijun A1 - Schumacher, Julia A1 - Durantini, Diego A1 - Engelhorn, Julia A1 - Chen, Ming A1 - Carles, Cristel C. A1 - Kaufmann, Kerstin T1 - Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis JF - Nature Communications N2 - Enhancers are critical for developmental stage-specific gene expression, but their dynamic regulation in plants remains poorly understood. Here we compare genome-wide localization of H3K27ac, chromatin accessibility and transcriptomic changes during flower development in Arabidopsis. H3K27ac prevalently marks promoter-proximal regions, suggesting that H3K27ac is not a hallmark for enhancers in Arabidopsis. We provide computational and experimental evidence to confirm that distal DNase. hypersensitive sites are predictive of enhancers. The predicted enhancers are highly stage-specific across flower development, significantly associated with SNPs for flowering-related phenotypes, and conserved across crucifer species. Through the integration of genome-wide transcription factor (TF) binding datasets, we find that floral master regulators and stage-specific TFs are largely enriched at developmentally dynamic enhancers. Finally, we show that enhancer clusters and intronic enhancers significantly associate with stage-specific gene regulation by floral master TFs. Our study provides insights into the functional flexibility of enhancers during plant development, as well as hints to annotate plant enhancers. Y1 - 2019 U6 - https://doi.org/10.1038/s41467-019-09513-2 SN - 2041-1723 VL - 10 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Yang, Lei A1 - Perrera, Valentina A1 - Saplaoura, Eleftheria A1 - Apelt, Federico A1 - Bahin, Mathieu A1 - Kramdi, Amira A1 - Olas, Justyna Jadwiga A1 - Müller-Röber, Bernd A1 - Sokolowska, Ewelina A1 - Zhang, Wenna A1 - Li, Runsheng A1 - Pitzalis, Nicolas A1 - Heinlein, Manfred A1 - Zhang, Shoudong A1 - Genovesio, Auguste A1 - Colot, Vincent A1 - Kragler, Friedrich T1 - m(5)C Methylation Guides Systemic Transport of Messenger RNA over Graft Junctions in Plants JF - Current biology N2 - In plants, transcripts move to distant body parts to potentially act as systemic signals regulating development and growth. Thousands of messenger RNAs (mRNAs) are transported across graft junctions via the phloem to distinct plant parts. Little is known regarding features, structural motifs, and potential base modifications of transported transcripts and how these may affect their mobility. We identified Arabidopsis thalianam RNAs harboring the modified base 5-methylcytosine (m(5)C) and found that these are significantly enriched in mRNAs previously described as mobile, moving over graft junctions to distinct plant parts. We confirm this finding with graft-mobile methylated mRNAs TRANSLATIONALLY CONTROLLED TUMOR PROTEIN 1 (TCTP1) and HEAT SHOCK COGNATE PROTEIN 70.1 (HSC70.1), whose mRNA transport is diminished in mutants deficient in m(5)C mRNA methylation. Together, our results point toward an essential role of cytosine methylation in systemic mRNA mobility in plants and that TCTP1 mRNA mobility is required for its signaling function. Y1 - 2019 U6 - https://doi.org/10.1016/j.cub.2019.06.042 SN - 0960-9822 SN - 1879-0445 VL - 29 IS - 15 SP - 2465 EP - 2476.e5 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Yannelli, Florencia A. A1 - Karrer, Gerhard A1 - Hall, Rea A1 - Kollmann, Johannes A1 - Heger, Tina T1 - Seed density is more effective than multi-trait limiting similarity in controlling grassland resistance against plant invasions in mesocosms JF - Applied vegetation science : official organ of the International Association for Vegetation Science N2 - QuestionDisturbed areas offer great opportunities for restoring native biodiversity, but they are also prone to invasion by alien plants. Following the limiting similarity hypothesis, we address the question of whether or not similarity of plant functional traits helps developing seed mixtures of native communities with high resistance to invasive species at an early stage of restoration. LocationCentre of Greenhouses and Laboratories Durnast, Technische Universitat Munchen, Freising, Germany. MethodsUsing a system of linear equations, we designed native communities maximizing the similarity between the native and two invasive species according to ten functional traits. We used native grassland plants, two invasive alien species that are often problematic in disturbed areas (i.e., Ambrosia artemisiifolia and Solidago gigantea) and trait information obtained from databases. The two communities were then tested for resistance against establishment of the two invaders separately in a greenhouse experiment. We measured height of the invasive species and above-ground biomass, along with leaf area index, 4 and 8months after sowing respectively. ResultsBoth invasive species were successfully reduced by the native community designed to suppress S. gigantea dominated by small-seeded species. These results could be considered as partial support for the limiting similarity hypothesis. However, given the success of this mixture against both invasive species, suppression was better explained by a seed density effect resulting from the smaller seed mass of the native species included in this mixture. Further, the dominance of a fast-developing competitive species could also contribute to its success. ConclusionsThere was no unequivocal support for the limiting similarity hypothesis in terms of the traits selected. Instead we found that increasing seeding density of native species and selecting species with a fast vegetative development is an effective way to suppress invasive plants during early stages of restoration. If limiting similarity is used to design communities for restoration, early life-history traits should be taken into account. KW - Achillea millefolium KW - Ambrosia artemisiifolia KW - biotic resistance KW - competition KW - density-driven suppression KW - disturbed areas KW - restoration KW - seed mixtures KW - Solidago gigantea Y1 - 2018 U6 - https://doi.org/10.1111/avsc.12373 SN - 1402-2001 SN - 1654-109X VL - 21 IS - 3 SP - 411 EP - 418 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Yarman, Aysu T1 - Electrosynthesized Molecularly Imprinted Polymer for Laccase Using the Inactivated Enzyme as the Target JF - Bulletin of the Korean chemical society N2 - The first molecularly imprinted polymer (MIP) for the recognition of the copper-enzyme laccase was successfully prepared by electropolymerizing scopoletin in the presence of alkaline-inactivated enzyme. Laccase-MIP and the control polymer without laccase (nonimprinted polymer, NIP) were characterized by voltammetry using the redox marker ferricyanide. After electropolymerization, the signals for ferricyanide for both the MIP and the NIP were almost completely suppressed and increased after removal of the target from the polymer layer. Rebinding of both inactivated and active laccase decreased the ferricyanide peak currents to almost equal extent. The relative decrease of signal suppression approached saturation above 10 nM. Furthermore, the surface activity of rebound laccase toward the oxidation of catechol was investigated. The surface activity approached saturation above 10 nM, a value close to the value of the measurements with ferricyanide. Interaction of NIP with laccase brought about a six times smaller signal of catechol oxidation. KW - Molecularly imprinted polymers KW - Biomimetic sensors KW - Laccase KW - Electropolymerization KW - Scopoletin Y1 - 2018 U6 - https://doi.org/10.1002/bkcs.11413 SN - 1229-5949 VL - 39 IS - 4 SP - 483 EP - 488 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Yarman, Aysu T1 - Development of a molecularly imprinted polymer-based electrochemical sensor for tyrosinase JF - Turkish journal of chemistry N2 - For the first time a molecularly imprinted polymer (MIP)-based sensor for tyrosinase is described. This sensor is based on the electropolymerization of scopoletin or o-phenylenediamine in the presence of tyrosinase from mushrooms, which has a high homology to the human enzyme. The template was removed either by treatment with proteinase Kor by alkaline treatment. The measuring signal was generated either by measuring the formation of a product by the target enzyme or by evaluation of the permeability of the redox marker ferricyanide. The o-phenylenediamine-based MIP sensor has a linear measuring range up to 50 nM of tyrosinase with a limit of detection of 3.97 nM (R 2 = 0.994) and shows good discrimination towards other proteins, e.g., bovine serum albumin and cytochrome c. KW - Molecularly imprinted polymers KW - biomimetic sensors KW - tyrosinase KW - electropolymerization KW - scopoletin KW - ophenylenediamine Y1 - 2017 U6 - https://doi.org/10.3906/kim-1708-68 SN - 1300-0527 VL - 42 IS - 2 SP - 346 EP - 354 PB - Türkiye Bilimsel ve Teknik Araştırma Kurumu CY - Ankara ER - TY - JOUR A1 - Yarman, Aysu A1 - Badalyan, Artavazd A1 - Gajovic-Eichelmann, Nenad A1 - Wollenberger, Ursula A1 - Scheller, Frieder W. T1 - Enzyme electrode for aromatic compounds exploiting the catalytic activities of microperoxidase-11 JF - Biosensors and bioelectronics : the principal international journal devoted to research, design development and application of biosensors and bioelectronics N2 - Microperoxidase-11 (MR-11) which has been immobilised in a matrix of chitosan-embedded gold nanoparticles on the surface of a glassy carbon electrode catalyzes the conversion of aromatic substances. This peroxide-dependent catalysis of microperoxidase has been applied in an enzyme electrode for the first time to indicate aromatic compounds such as aniline. 4-fluoroaniline, catechol and p-aminophenol. The electrode signal is generated by the cathodic reduction of the quinone or quinoneimine which is formed in the presence of both MP-II and peroxide from the substrate. The same sensor principle will be extended to aromatic drugs. KW - Microperoxidase-11 KW - Nanoparticles KW - p-Aminophenol KW - Aniline KW - Catechol KW - 4-Fluoroaniline KW - Biosensors Y1 - 2011 U6 - https://doi.org/10.1016/j.bios.2011.09.004 SN - 0956-5663 VL - 30 IS - 1 SP - 320 EP - 323 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Yarman, Aysu A1 - Gröbe, Glenn A1 - Neumann, Bettina A1 - Kinne, Mathias A1 - Gajovic-Eichelmann, Nenad A1 - Wollenberger, Ursula A1 - Hofrichter, Martin A1 - Ullrich, Rene A1 - Scheibner, Katrin A1 - Scheller, Frieder W. T1 - The aromatic peroxygenase from Marasmius rutola-a new enzyme for biosensor applications JF - Analytical & bioanalytical chemistry N2 - The aromatic peroxygenase (APO; EC 1.11.2.1) from the agraric basidomycete Marasmius rotula (MroAPO) immobilized at the chitosan-capped gold-nanoparticle-modified glassy carbon electrode displayed a pair of redox peaks with a midpoint potential of -278.5 mV vs. AgCl/AgCl (1 M KCl) for the Fe(2+)/Fe(3+) redox couple of the heme-thiolate-containing protein. MroAPO oxidizes aromatic substrates such as aniline, p-aminophenol, hydroquinone, resorcinol, catechol, and paracetamol by means of hydrogen peroxide. The substrate spectrum overlaps with those of cytochrome P450s and plant peroxidases which are relevant in environmental analysis and drug monitoring. In M. rotula peroxygenase-based enzyme electrodes, the signal is generated by the reduction of electrode-active reaction products (e.g., p-benzoquinone and p-quinoneimine) with electro-enzymatic recycling of the analyte. In these enzyme electrodes, the signal reflects the conversion of all substrates thus representing an overall parameter in complex media. The performance of these sensors and their further development are discussed. KW - Unspecific peroxygenase KW - Cytochrome P450 KW - Biosensors KW - Phenolic substances Y1 - 2012 U6 - https://doi.org/10.1007/s00216-011-5497-y SN - 1618-2642 VL - 402 IS - 1 SP - 405 EP - 412 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Yarman, Aysu A1 - Kurbanoğlu, Sevinç A1 - Zebger, Ingo A1 - Scheller, Frieder W. T1 - Simple and robust BT - the claims of protein sensing by molecularly imprinted polymers JF - Sensors and actuators : B, Chemical : an international journal devoted to research and development of chemical transducers N2 - A spectrum of 7562 publications on Molecularly Imprinted Polymers (MIPs) has been presented in literature within the last ten years (Scopus, September 7, 2020). Around 10 % of the papers published on MIPs describe the recognition of proteins. The straightforward synthesis of MIPs is a significant advantage as compared with the preparation of enzymes or antibodies. MIPs have been synthesized from only one up to six functional monomers while proteins are made up of 20 natural amino acids. Furthermore, they can be synthesized against structures of low immunogenicity and allow multi-analyte measurements via multi-target synthesis. Electrochemical methods allow simple polymer synthesis, removal of the template and readout. Among the different sensor configurations electrochemical MIP-sensors provide the broadest spectrum of protein analytes. The sensitivity of MIP-sensors is sufficiently high for biomarkers in the sub-nanomolar region, nevertheless the cross-reactivity of highly abundant proteins in human serum is still a challenge. MIPs for proteins offer innovative tools not only for clinical and environmental analysis, but also for bioimaging, therapy and protein engineering. KW - Molecularly imprinted polymer KW - Plastibodies KW - Functional scaffolds KW - Biomimetic sensors KW - Proteins Y1 - 2021 U6 - https://doi.org/10.1016/j.snb.2020.129369 SN - 0925-4005 SN - 1873-3077 VL - 330 PB - Elsevier Science CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Yarman, Aysu A1 - Scheller, Frieder W. T1 - Coupling biocatalysis with molecular imprinting in a biomimetic sensor JF - Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition KW - biomimetic sensors KW - electropolymers KW - enzymes KW - hierarchical structures KW - molecularly imprinted polymers Y1 - 2013 U6 - https://doi.org/10.1002/anie.201305368 SN - 1433-7851 SN - 1521-3773 VL - 52 IS - 44 SP - 11521 EP - 11525 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Yarman, Aysu A1 - Scheller, Frieder W. T1 - The first electrochemical MIP sensor for tamoxifen JF - Sensors N2 - We present an electrochemical MIP sensor for tamoxifen (TAM)-a nonsteroidal anti-estrogen-which is based on the electropolymerisation of an O-phenylenediamine. resorcinol mixture directly on the electrode surface in the presence of the template molecule. Up to now only. bulk. MIPs for TAM have been described in literature, which are applied for separation in chromatography columns. Electro-polymerisation of the monomers in the presence of TAM generated a film which completely suppressed the reduction of ferricyanide. Removal of the template gave a markedly increased ferricyanide signal, which was again suppressed after rebinding as expected for filling of the cavities by target binding. The decrease of the ferricyanide peak of the MIP electrode depended linearly on the TAM concentration between 1 and 100 nM. The TAM-imprinted electrode showed a 2.3 times higher recognition of the template molecule itself as compared to its metabolite 4-hydroxytamoxifen and no cross-reactivity with the anticancer drug doxorubucin was found. Measurements at + 1.1 V caused a fouling of the electrode surface, whilst pretreatment of TAM with peroxide in presence of HRP generated an oxidation product which was reducible at 0 mV, thus circumventing the polymer formation and electrochemical interferences. KW - molecularly imprinted polymers KW - anticancer drug KW - tamoxifen KW - electropolymerisation Y1 - 2014 U6 - https://doi.org/10.3390/s140507647 SN - 1424-8220 VL - 14 IS - 5 SP - 7647 EP - 7654 PB - MDPI CY - Basel ER - TY - JOUR A1 - Yarman, Aysu A1 - Scheller, Frieder W. T1 - MIP-esterase/Tyrosinase Combinations for Paracetamol and Phenacetin JF - Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis N2 - A new electrochemical MIP sensor for the most frequently used drug paracetamol (PAR) was prepared by electropolymerization of mixtures containing the template molecule and the functional monomers ophenylenediamine, resorcinol and aniline. The imprinting factor of 12 reflects the effective target binding to the MIP as compared with the non-imprinted electropolymer. Combination of the MIP with a nonspecific esterase allows the measurement of phenacetin - another analgesic drug. In the second approach the PAR containing sample solution was pretreated with tyrosinase in order to prevent electrochemical interferences by ascorbic acid and uric acid. Interference-free indication at a very low electrode potential without fouling of the electrode surface was achieved with the o-phenylenediamine: resorcinol-based MIP. KW - Paracetamol KW - Molecularly imprinted polymers KW - Electropolymerization KW - Tyrosinase KW - Esterase KW - Phenacetin Y1 - 2016 U6 - https://doi.org/10.1002/elan.201600042 SN - 1040-0397 SN - 1521-4109 VL - 28 SP - 2222 EP - 2227 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Yarman, Aysu A1 - Schulz, Christopher A1 - Sygmund, Cristoph A1 - Ludwig, Roland A1 - Gorton, Lo A1 - Wollenberger, Ursula A1 - Scheller, Frieder W. T1 - Third generation ATP sensor with enzymatic analyte recycling JF - Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis N2 - For the first time the direct electron transfer of an enzyme - cellobiose dehydrogenase, CDH - has been coupled with the hexokinase catalyzed competition for glucose in a sensor for ATP. To enhance the signal output for ATP, pyruvate kinase was coimmobilized to recycle ADP by the phosphoenolpyruvate driven reaction. The new sensor overcomes the limit of 1:1 stoichiometry of the sequential or competitive conversion of ATP by effective enzymatic recycling of the analyte. The anodic oxidation of the glucose converting CDH proceeds at electrode potentials below 0 mV vs. Ag vertical bar AgCl thus potentially interfering substances like ascorbic acid or catecholamines do not influence the measuring signal. The combination of direct electron transfer of CDH with the enzymatic recycling results in an interference-free and oxygen-independent measurement of ATP in the lower mu molar concentration range with a lower limit of detection of 63.3 nM (S/N=3). KW - ATP KW - Third generation sensor KW - Enzymatic recycling KW - Cellobiose dehydrogenase KW - Hexokinase KW - Pyruvate kinase Y1 - 2014 U6 - https://doi.org/10.1002/elan.201400231 SN - 1040-0397 SN - 1521-4109 VL - 26 IS - 9 SP - 2043 EP - 2048 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Yasuhara, Jiro A1 - Baumann, Otto A1 - Takeyasu, Kunio T1 - Localization of Na/K-ATPase in developing and adult Drosophila melanogaster photoreceptors N2 - Drosophila melanogaster photoreceptors are highly polarized cells and their plasma membrane is organized into distinct domains. Zonula adherens junctions separate a smooth peripheral surface, the equivalent of the basolateral surface in other epithelial cells, from the central surface (cong apical surface). The latter consists of the microvillar rhabdomere and the juxtarhabdomeric domain, a nonmicrovillar area between the rhabdomere and the zonulae adherens. The distribution of Na/K-ATPase over these domains was examined by immunocytochemical, developmental, and genetic approaches. Immunofluorescence and immunogold labeling of adult compound eyes reveal that the distribution of Na/ K-ATPase is concentrated at the peripheral surface in the photoreceptors R1-R6, but extends over the juxtarhabdomeric domain to the rhabdomere in the photoreceptors R7/R8. Developmental analysis demonstrates further that Na/K-ATPase is localized over the entire plasma membrane in all photoreceptors in early pupal eyes. Redistribution of Na/K-ATPase in R1- R6 occurs at about 78% of pupal life, coinciding with the onset of Rh1-rhodopsin expression on the central surface of these cells. Despite the essential role of Rh1 in structural development and intracellular trafficking, Rh1 mutations do not affect the distribution of Na/K-ATPase. These results suggest that Na/K-ATPase and rhodopsin are involved in distinct intracellular localization mechanisms, which are maintained independent of each other. Y1 - 2000 UR - http://www.link.springer.de/link/service/journals/00441/bibs/030002/03000239.htm ER - TY - JOUR A1 - Yates, Colin J. A1 - Elith, Jane A1 - Latimer, Andrew M. A1 - Le Maitre, David A1 - Midgley, Guy F. A1 - Schurr, Frank Martin A1 - West, Adam G. T1 - Projecting climate change impacts on species distributions in megadiverse South African Cape and Southwest Australian Floristic Regions : Opportunities and challenges N2 - Increasing evidence shows that anthropogenic climate change is affecting biodiversity. Reducing or stabilizing greenhouse gas emissions may slow global warming, but past emissions will continue to contribute to further unavoidable warming for more than a century. With obvious signs of difficulties in achieving effective mitigation worldwide in the short term at least, sound scientific predictions of future impacts on biodiversity will be required to guide conservation planning and adaptation. This is especially true in Mediterranean type ecosystems that are projected to be among the most significantly affected by anthropogenic climate change, and show the highest levels of confidence in rainfall projections. Multiple methods are available for projecting the consequences of climate change on the main unit of interest - the species - with each method having strengths and weaknesses. Species distribution models (SDMs) are increasingly applied for forecasting climate change impacts on species geographic ranges. Aggregation of models for different species allows inferences of impacts on biodiversity, though excluding the effects of species interactions. The modelling approach is based on several further assumptions and projections and should be treated cautiously. In the absence of comparable approaches that address large numbers of species, SDMs remain valuable in estimating the vulnerability of species. In this review we discuss the application of SDMs in predicting the impacts of climate change on biodiversity with special reference to the species-rich South West Australian Floristic Region and South African Cape Floristic Region. We discuss the advantages and challenges in applying SDMs in biodiverse regions with high levels of endemicity, and how a similar biogeographical history in both regions may assist us in understanding their vulnerability to climate change. We suggest how the process of predicting the impacts of climate change on biodiversity with SDMs can be improved and emphasize the role of field monitoring and experiments in validating the predictions of SDMs. Y1 - 2010 UR - http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1442-9993a U6 - https://doi.org/10.1111/j.1442-9993.2009.02044.x SN - 1442-9985 ER - TY - JOUR A1 - Yildirim-Semerci, Cigdem A1 - Benayahu, Dafna A1 - Adamovski, Miriam A1 - Wollenberger, Ursula T1 - An Electrochemical Assay for Monitoring Differentiation of the Osteoblastic Cell Line (MBA-15) on the Sensor Chip JF - Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis N2 - An electrochemical assay for the indication of the activity of the cell bound differentiation marker alkaline phosphatase (ALP) is proposed using voltammetry on an in-vitro cell culture. The basis of the assay is cultivation of cells on gold microelectrodes in wells of a microplate, catalytic hydrolysis of p-aminophenyl phosphate by ALP and indication of p-aminophenol oxidation by square wave voltammetry (SWV) with the sensors onto which the cells attached. The morphology of the bone marrow stromal cell line (MBA-15) on the electrode surface was investigated and it exhibited in vitro osteogenic characteristics. Since ALP is expressed on the cell surface in early differentiation stage of osteoblastic cells, its activity was followed after different culture times over a period of 144 h by recording repetitive voltammograms at different time points upon addition of the substrate p-aminophenyl phosphate. The ALP activity was estimated from the signal increase related to formation rate of p-aminophenol and the number of cells. The highest value was measured at 120 h, when the cells reached confluence. The results of the electrochemical activity assay are consistent with the colorimetric acquired value from p-nitrophenol formation rate. KW - Alkaline phosphatase KW - Osteoblast KW - Voltammetry KW - Biomarker KW - p-Aminophenol Y1 - 2015 U6 - https://doi.org/10.1002/elan.201400684 SN - 1040-0397 SN - 1521-4109 VL - 27 IS - 6 SP - 1350 EP - 1358 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Yildiz, Tugba A1 - Leimkühler, Silke T1 - TusA is a versatile protein that links translation efficiency to cell division in Escherichia coli JF - Journal of bacteriology N2 - To enable accurate and efficient translation, sulfur modifications are introduced posttranscriptionally into nucleosides in tRNAs. The biosynthesis of tRNA sulfur modifications involves unique sulfur trafficking systems for the incorporation of sulfur atoms in different nucleosides of tRNA. One of the proteins that is involved in inserting the sulfur for 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U34) modifications in tRNAs is the TusA protein. TusA, however, is a versatile protein that is also involved in numerous other cellular pathways. Despite its role as a sulfur transfer protein for the 2-thiouridine formation in tRNA, a fundamental role of TusA in the general physiology of Escherichia coli has also been discovered. Poor viability, a defect in cell division, and a filamentous cell morphology have been described previously for tusA-deficient cells. In this report, we aimed to dissect the role of TusA for cell viability. We were able to show that the lack of the thiolation status of wobble uridine (U-34) nucleotides present on Lys, Gln, or Glu in tRNAs has a major consequence on the translation efficiency of proteins; among the affected targets are the proteins RpoS and Fis. Both proteins are major regulatory factors, and the deregulation of their abundance consequently has a major effect on the cellular regulatory network, with one consequence being a defect in cell division by regulating the FtsZ ring formation.
IMPORTANCE More than 100 different modifications are found in RNAs. One of these modifications is the mnm(5)s(2)U modification at the wobble position 34 of tRNAs for Lys, Gln, and Glu. The functional significance of U34 modifications is substantial since it restricts the conformational flexibility of the anticodon, thus providing translational fidelity. We show that in an Escherichia coli TusA mutant strain, involved in sulfur transfer for the mnm(5)s(2)U34 thio modifications, the translation efficiency of RpoS and Fis, two major cellular regulatory proteins, is altered. Therefore, in addition to the transcriptional regulation and the factors that influence protein stability, tRNA modifications that ensure the translational efficiency provide an additional crucial regulatory factor for protein synthesis. KW - iron-sulfur clusters KW - tRNA thio modifications KW - FtsZ ring formation KW - cell KW - division KW - TusA KW - RpoS KW - Fis KW - FtsZ Y1 - 2021 U6 - https://doi.org/10.1128/JB.00659-20 SN - 1098-5530 VL - 203 IS - 7 PB - American Society for Microbiology CY - Washington ER - TY - JOUR A1 - Yoshida, Takehito A1 - Jones, Laura E. A1 - Ellner, Stephen P. A1 - Fussmann, Gregor F. A1 - Hairston, Jr. A1 - Nelson, G. T1 - Rapid evolution drives ecological dynamics in a predator-prey system N2 - Ecological and evolutionary dynamics can occur on similar timescales. However, theoretical predictions of how rapid evolution can affect ecological dynamics are inconclusive and often depend on untested model assumptions. Here we report that rapid prey evolution in response to oscillating predator density affects predator-prey (rotifer-algal) cycles in laboratory microcosms. Our experiments tested explicit predictions from a model for our system that allows prey evolution. We verified the predicted existence of an evolutionary tradeoff between algal competitive ability and defence against consumption, and examined its effects on cycle dynamics by manipulating the evolutionary potential of the prey population. Single-clone algal cultures (lacking genetic variability) produced short cycle periods and typical quarter-period phase lags between prey and predator densities, whereas multi-clonal (genetically variable) algal cultures produced long cycles with prey and predator densities nearly out of phase, exactly as predicted. These results confirm that prey evolution can substantially alter predator-prey dynamics, and therefore that attempts to understand population oscillations in nature cannot neglect potential effects from ongoing rapid evolution. Y1 - 2003 UR - http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v424/n6946/full/nature01767_fs.html ER -