@article{AllanBossdorfDormannetal.2014, author = {Allan, Eric and Bossdorf, Oliver and Dormann, Carsten F. and Prati, Daniel and Gossner, Martin M. and Tscharntke, Teja and Bl{\"u}thgen, Nico and Bellach, Michaela and Birkhofer, Klaus and Boch, Steffen and B{\"o}hm, Stefan and B{\"o}rschig, Carmen and Chatzinotas, Antonis and Christ, Sabina and Daniel, Rolf and Diek{\"o}tter, Tim and Fischer, Christiane and Friedl, Thomas and Glaser, Karin and Hallmann, Christine and Hodac, Ladislav and H{\"o}lzel, Norbert and Jung, Kirsten and Klein, Alexandra Maria and Klaus, Valentin H. and Kleinebecker, Till and Krauss, Jochen and Lange, Markus and Morris, E. Kathryn and M{\"u}ller, J{\"o}rg and Nacke, Heiko and Pasalic, Esther and Rillig, Matthias C. and Rothenwoehrer, Christoph and Schally, Peter and Scherber, Christoph and Schulze, Waltraud X. and Socher, Stephanie A. and Steckel, Juliane and Steffan-Dewenter, Ingolf and T{\"u}rke, Manfred and Weiner, Christiane N. and Werner, Michael and Westphal, Catrin and Wolters, Volkmar and Wubet, Tesfaye and Gockel, Sonja and Gorke, Martin and Hemp, Andreas and Renner, Swen C. and Sch{\"o}ning, Ingo and Pfeiffer, Simone and K{\"o}nig-Ries, Birgitta and Buscot, Francois and Linsenmair, Karl Eduard and Schulze, Ernst-Detlef and Weisser, Wolfgang W. and Fischer, Markus}, title = {Interannual variation in land-use intensity enhances grassland multidiversity}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {1}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1312213111}, pages = {308 -- 313}, year = {2014}, abstract = {Although temporal heterogeneity is a well-accepted driver of biodiversity, effects of interannual variation in land-use intensity (LUI) have not been addressed yet. Additionally, responses to land use can differ greatly among different organisms; therefore, overall effects of land-use on total local biodiversity are hardly known. To test for effects of LUI (quantified as the combined intensity of fertilization, grazing, and mowing) and interannual variation in LUI (SD in LUI across time), we introduce a unique measure of whole-ecosystem biodiversity, multidiversity. This synthesizes individual diversity measures across up to 49 taxonomic groups of plants, animals, fungi, and bacteria from 150 grasslands. Multidiversity declined with increasing LUI among grasslands, particularly for rarer species and aboveground organisms, whereas common species and belowground groups were less sensitive. However, a high level of interannual variation in LUI increased overall multidiversity at low LUI and was even more beneficial for rarer species because it slowed the rate at which the multidiversity of rare species declined with increasing LUI. In more intensively managed grasslands, the diversity of rarer species was, on average, 18\% of the maximum diversity across all grasslands when LUI was static over time but increased to 31\% of the maximum when LUI changed maximally over time. In addition to decreasing overall LUI, we suggest varying LUI across years as a complementary strategy to promote biodiversity conservation.}, language = {en} } @article{AlluSojaWuetal.2014, author = {Allu, Annapurna Devi and Soja, Aleksandra Maria and Wu, Anhui and Szymanski, Jedrzej and Balazadeh, Salma}, title = {Salt stress and senescence: identification of cross-talk regulatory components}, series = {Journal of experimental botany}, volume = {65}, journal = {Journal of experimental botany}, number = {14}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0022-0957}, doi = {10.1093/jxb/eru173}, pages = {3993 -- 4008}, year = {2014}, abstract = {Leaf senescence is an active process with a pivotal impact on plant productivity. It results from extensive signalling cross-talk coordinating environmental factors with intrinsic age-related mechanisms. Although many studies have shown that leaf senescence is affected by a range of external parameters, knowledge about the regulatory systems that govern the interplay between developmental programmes and environmental stress is still vague. Salinity is one of the most important environmental stresses that promote leaf senescence and thus affect crop yield. Improving salt tolerance by avoiding or delaying senescence under stress will therefore play an important role in maintaining high agricultural productivity. Experimental evidence suggests that hydrogen peroxide (H2O2) functions as a common signalling molecule in both developmental and salt-induced leaf senescence. In this study, microarray-based gene expression profiling on Arabidopsis thaliana plants subjected to long-term salinity stress to induce leaf senescence was performed, together with co-expression network analysis for H2O2-responsive genes that are mutually up-regulated by salt induced-and developmental leaf senescence. Promoter analysis of tightly co-expressed genes led to the identification of seven cis-regulatory motifs, three of which were known previously, namely CACGTGT and AAGTCAA, which are associated with reactive oxygen species (ROS)-responsive genes, and CCGCGT, described as a stress-responsive regulatory motif, while the others, namely ACGCGGT, AGCMGNC, GMCACGT, and TCSTYGACG were not characterized previously. These motifs are proposed to be novel elements involved in the H2O2-mediated control of gene expression during salinity stress-triggered and developmental senescence, acting through upstream transcription factors that bind to these sites.}, language = {en} } @misc{ArltSchwiebsJaptoketal.2014, author = {Arlt, Olga and Schwiebs, Anja and Japtok, Lukasz and Rueger, Katja and Katzy, Elisabeth and Kleuser, Burkhard and Radeke, Heinfried H.}, title = {Sphingosine-1-Phosphate modulates dendritic cell function: focus on non-migratory effects in vitro and in vivo}, series = {Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry and pharmacology}, volume = {34}, journal = {Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry and pharmacology}, number = {1}, publisher = {Karger}, address = {Basel}, issn = {1015-8987}, doi = {10.1159/000362982}, pages = {27 -- 44}, year = {2014}, abstract = {Dendritic cells (DCs) are the cutting edge in innate and adaptive immunity. The major functions of these antigen presenting cells are the capture, endosomal processing and presentation of antigens, providing them an exclusive ability to provoke adaptive immune responses and to induce and control tolerance. Immature DCs capture and process antigens, migrate towards secondary lymphoid organs where they present antigens to naive T cells in a well synchronized sequence of procedures referred to as maturation. Indeed, recent research indicated that sphingolipids are modulators of essential steps in DC homeostasis. It has been recognized that sphingolipids not only modulate the development of DC subtypes from precursor cells but also influence functional activities of DCs such as antigen capture, and cytokine profiling. Thus, it is not astonishing that sphingolipids and sphingolipid metabolism play a substantial role in inflammatory diseases that are modulated by DCs. Here we highlight the function of sphingosine 1-phosphate (S1P) on DC homeostasis and the role of SIP and SW metabolism in inflammatory diseases.}, language = {en} } @phdthesis{Arnold2014, author = {Arnold, Anne}, title = {Modeling photosynthesis and related metabolic processes : from detailed examination to consideration of the metabolic context}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72277}, school = {Universit{\"a}t Potsdam}, year = {2014}, abstract = {Mathematical modeling of biological systems is a powerful tool to systematically investigate the functions of biological processes and their relationship with the environment. To obtain accurate and biologically interpretable predictions, a modeling framework has to be devised whose assumptions best approximate the examined scenario and which copes with the trade-off of complexity of the underlying mathematical description: with attention to detail or high coverage. Correspondingly, the system can be examined in detail on a smaller scale or in a simplified manner on a larger scale. In this thesis, the role of photosynthesis and its related biochemical processes in the context of plant metabolism was dissected by employing modeling approaches ranging from kinetic to stoichiometric models. The Calvin-Benson cycle, as primary pathway of carbon fixation in C3 plants, is the initial step for producing starch and sucrose, necessary for plant growth. Based on an integrative analysis for model ranking applied on the largest compendium of (kinetic) models for the Calvin-Benson cycle, those suitable for development of metabolic engineering strategies were identified. Driven by the question why starch rather than sucrose is the predominant transitory carbon storage in higher plants, the metabolic costs for their synthesis were examined. The incorporation of the maintenance costs for the involved enzymes provided a model-based support for the preference of starch as transitory carbon storage, by only exploiting the stoichiometry of synthesis pathways. Many photosynthetic organisms have to cope with processes which compete with carbon fixation, such as photorespiration whose impact on plant metabolism is still controversial. A systematic model-oriented review provided a detailed assessment for the role of this pathway in inhibiting the rate of carbon fixation, bridging carbon and nitrogen metabolism, shaping the C1 metabolism, and influencing redox signal transduction. The demand of understanding photosynthesis in its metabolic context calls for the examination of the related processes of the primary carbon metabolism. To this end, the Arabidopsis core model was assembled via a bottom-up approach. This large-scale model can be used to simulate photoautotrophic biomass production, as an indicator for plant growth, under so-called optimal, carbon-limiting and nitrogen-limiting growth conditions. Finally, the introduced model was employed to investigate the effects of the environment, in particular, nitrogen, carbon and energy sources, on the metabolic behavior. This resulted in a purely stoichiometry-based explanation for the experimental evidence for preferred simultaneous acquisition of nitrogen in both forms, as nitrate and ammonium, for optimal growth in various plant species. The findings presented in this thesis provide new insights into plant system's behavior, further support existing opinions for which mounting experimental evidences arise, and posit novel hypotheses for further directed large-scale experiments.}, language = {en} } @article{ArnoldNikoloski2014, author = {Arnold, Anne and Nikoloski, Zoran}, title = {In search for an accurate model of the photosynthetic carbon metabolism}, series = {Mathematics and computers in simulation : transactions of IMACS}, volume = {96}, journal = {Mathematics and computers in simulation : transactions of IMACS}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0378-4754}, doi = {10.1016/j.matcom.2012.03.011}, pages = {171 -- 194}, year = {2014}, abstract = {The photosynthetic carbon metabolism, including the Calvin-Benson cycle, is the primary pathway in C-3-plants, producing starch and sucrose from CO2. Understanding the interplay between regulation and efficiency of this pathway requires the development of mathematical models which would explain the observed dynamics of metabolic transformations. Here, we address this question by casting the existing models of Calvin-Benson cycle and the end-product processes into an analysis framework which not only facilitates the comparison of the different models, but also allows for their ranking with respect to chosen criteria, including stability, sensitivity, robustness and/or compliance with experimental data. The importance of the photosynthetic carbon metabolism for the increase of plant biomass has resulted in many models with various levels of detail. We provide the largest compendium of 15 existing, well-investigated models together with a comprehensive classification as well as a ranking framework to determine the best-performing models for metabolic engineering and planning of in silica experiments. The classification can be additionally used, based on the model structure, as a tool to identify the models which match best the experimental design. The provided ranking is just one alternative to score models and, by changing the weighting factor, this framework also could be applied for selection of other criteria of interest.}, language = {en} } @phdthesis{Arnold2014, author = {Arnold, Stefanie}, title = {Epitop-Kartierung von PBP2A und Identifizierung MRSA-spezifischer immunodominanter Peptidsequenzen}, pages = {XIX, 120}, year = {2014}, language = {de} } @article{AttermeyerHornickKayleretal.2014, author = {Attermeyer, Katrin and Hornick, T. and Kayler, Z. E. and Bahr, A. and Zwirnmann, E. and Grossart, Hans-Peter and Premke, K.}, title = {Enhanced bacterial decomposition with increasing addition of autochthonous to allochthonous carbon without any effect on bacterial community composition}, series = {Biogeosciences}, volume = {11}, journal = {Biogeosciences}, number = {6}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {1726-4170}, doi = {10.5194/bg-11-1479-2014}, pages = {1479 -- 1489}, year = {2014}, abstract = {Dissolved organic carbon (DOC) concentrations - mainly of terrestrial origin - are increasing worldwide in inland waters. Heterotrophic bacteria are the main consumers of DOC and thus determine DOC temporal dynamics and availability for higher trophic levels. Our aim was to study bacterial carbon (C) turnover with respect to DOC quantity and chemical quality using both allochthonous and autochthonous DOC sources. We incubated a natural bacterial community with allochthonous C (C-13-labeled beech leachate) and increased concentrations and pulses (intermittent occurrence of organic matter input) of autochthonous C (phytoplankton lysate). We then determined bacterial C consumption, activities, and community composition together with the C flow through bacteria using stable C isotopes. The chemical analysis of single sources revealed differences in aromaticity and low-and high-molecular-weight substance fractions (LMWS and HMWS, respectively) between allochthonous and autochthonous C sources. Both DOC sources (allochthonous and autochthonous DOC) were metabolized at a high bacterial growth efficiency (BGE) around 50\%. In treatments with mixed sources, rising concentrations of added autochthonous DOC resulted in a further, significant increase in bacterial DOC consumption of up to 68\% when nutrients were not limiting. This rise was accompanied by a decrease in the humic substance (HS) fraction and an increase in bacterial biomass. Changes in DOC concentration and consumption in mixed treatments did not affect bacterial community composition (BCC), but BCC differed in single vs. mixed incubations. Our study highlights that DOC quantity affects bacterial C consumption but not BCC in nutrient-rich aquatic systems. BCC shifted when a mixture of allochthonous and autochthonous C was provided simultaneously to the bacterial community. Our results indicate that chemical quality rather than source of DOC per se (allochthonous vs. autochthonous) determines bacterial DOC turnover.}, language = {en} } @article{AudisioClineSolanoetal.2014, author = {Audisio, Paolo and Cline, Andrew R. and Solano, Emanuela and Mancini, Emiliano and Lamanna, Francesco and Antonini, Gloria and Trizzino, Marco}, title = {A peculiar new genus and species of pollen-beetle (Coleoptera, Nitidulidae) from eastern Africa, with a molecular phylogeny of related Meligethinae}, series = {Systematics and biodiversity}, volume = {12}, journal = {Systematics and biodiversity}, number = {1}, publisher = {Routledge, Taylor \& Francis Group}, address = {Abingdon}, issn = {1477-2000}, doi = {10.1080/14772000.2013.877539}, pages = {77 -- 91}, year = {2014}, language = {en} } @misc{AugusiakVandenBrinkGrimm2014, author = {Augusiak, Jacqueline and Van den Brink, Paul J. and Grimm, Volker}, title = {Merging validation and evaluation of ecological models to 'evaludation': A review of terminology and a practical approach}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {280}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2013.11.009}, pages = {117 -- 128}, year = {2014}, abstract = {Confusion about model validation is one of the main challenges in using ecological models for decision support, such as the regulation of pesticides. Decision makers need to know whether a model is a sufficiently good representation of its real counterpart and what criteria can be used to answer this question. Unclear terminology is one of the main obstacles to a good understanding of what model validation is, how it works, and what it can deliver. Therefore, we performed a literature review and derived a standard set of terms. 'Validation' was identified as a catch-all term, which is thus useless for any practical purpose. We introduce the term 'evaludation', a fusion of 'evaluation' and 'validation', to describe the entire process of assessing a model's quality and reliability. Considering the iterative nature of model development, the modelling cycle, we identified six essential elements of evaludation: (i) 'data evaluation' for scrutinising the quality of numerical and qualitative data used for model development and testing; (ii) 'conceptual model evaluation' for examining the simplifying assumptions underlying a model's design; (iii) 'implementation verification' for testing the model's implementation in equations and as a computer programme; (iv) 'model output verification' for comparing model output to data and patterns that guided model design and were possibly used for calibration; (v) 'model analysis' for exploring the model's sensitivity to changes in parameters and process formulations to make sure that the mechanistic basis of main behaviours of the model has been well understood; and (vi) 'model output corroboration' for comparing model output to new data and patterns that were not used for model development and parameterisation. Currently, most decision makers require 'validating' a model by testing its predictions with new experiments or data. Despite being desirable, this is neither sufficient nor necessary for a model to be useful for decision support. We believe that the proposed set of terms and its relation to the modelling cycle can help to make quality assessments and reality checks of ecological models more comprehensive and transparent. (C) 2013 Elsevier B.V. All rights reserved.}, language = {en} } @article{AzumaKuekenshoenerMaetal.2014, author = {Azuma, Yusuke and Kuekenshoener, Tim and Ma, Guangyong and Yasunaga, Jun-ichiro and Imanishi, Miki and Tanaka, Gen and Nakase, Ikuhiko and Maruno, Takahiro and Kobayashi, Yuji and Arndt, Katja Maren and Matsuoka, Masao and Futaki, Shiroh}, title = {Controlling leucine-zipper partner recognition in cells through modification of a-g interactions}, series = {Chemical communications}, volume = {50}, journal = {Chemical communications}, number = {48}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1359-7345}, doi = {10.1039/c4cc00555d}, pages = {6364 -- 6367}, year = {2014}, abstract = {By focusing on the a-g interactions, successful design and selection were accomplished to obtain a leucine-zipper segment that discriminates the appropriate partner over another that provides very similar patterns of electrostatic interactions.}, language = {en} } @misc{AzumaKuekenshoenerMaetal.2014, author = {Azuma, Yusuke and K{\"u}kensh{\"o}ner, Tim and Ma, Guangyong and Yasunaga, Jun-ichiro and Imanishi, Miki and Tanaka, Gen and Nakase, Ikuhiko and Maruno, Takahiro and Kobayashi, Yuji and Arndt, Katja Maren and Matsuoka, Masao and Futaki, Shiroh}, title = {Controlling leucine-zipper partner recognition in cells through modification of a-g interactions}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-98758}, pages = {4}, year = {2014}, abstract = {By focusing on the a-g interactions, successful design and selection were accomplished to obtain a leucine-zipper segment that discriminates the appropriate partner over another that provides very similar patterns of electrostatic interactions.}, language = {en} } @article{BadalyanDierichStibaetal.2014, author = {Badalyan, Artavazd and Dierich, Marlen and Stiba, Konstanze and Schwuchow, Viola and Leimk{\"u}hler, Silke and Wollenberger, Ulla}, title = {Electrical wiring of the aldehyde oxidoreductase PaoABC with a polymer containing osmium redox centers}, series = {Biosensors}, volume = {4}, journal = {Biosensors}, number = {4}, publisher = {MDPI}, address = {Basel}, doi = {10.3390/bios4040403}, pages = {403 -- 421}, year = {2014}, abstract = {Biosensors for the detection of benzaldehyde and g-aminobutyric acid (GABA) are reported using aldehyde oxidoreductase PaoABC from Escherichia coli immobilized in a polymer containing bound low potential osmium redox complexes. The electrically connected enzyme already electrooxidizes benzaldehyde at potentials below -0.15 V (vs. Ag|AgCl, 1 M KCl). The pH-dependence of benzaldehyde oxidation can be strongly influenced by the ionic strength. The effect is similar with the soluble osmium redox complex and therefore indicates a clear electrostatic effect on the bioelectrocatalytic efficiency of PaoABC in the osmium containing redox polymer. At lower ionic strength, the pH-optimum is high and can be switched to low pH-values at high ionic strength. This offers biosensing at high and low pH-values. A "reagentless" biosensor has been formed with enzyme wired onto a screen-printed electrode in a flow cell device. The response time to addition of benzaldehyde is 30 s, and the measuring range is between 10-150 µM and the detection limit of 5 µM (signal to noise ratio 3:1) of benzaldehyde. The relative standard deviation in a series (n = 13) for 200 µM benzaldehyde is 1.9\%. For the biosensor, a response to succinic semialdehyde was also identified. Based on this response and the ability to work at high pH a biosensor for GABA is proposed by coimmobilizing GABA-aminotransferase (GABA-T) and PaoABC in the osmium containing redox polymer.}, language = {en} } @misc{BadalyanDierichStibaetal.2014, author = {Badalyan, Artavazd and Dierich, Marlen and Stiba, Konstanze and Schwuchow, Viola and Leimk{\"u}hler, Silke and Wollenberger, Ulla}, title = {Electrical wiring of the aldehyde oxidoreductase PaoABC with a polymer containing osmium redox centers}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1082}, issn = {1866-8372}, doi = {10.25932/publishup-47507}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-475070}, pages = {21}, year = {2014}, abstract = {Biosensors for the detection of benzaldehyde and g-aminobutyric acid (GABA) are reported using aldehyde oxidoreductase PaoABC from Escherichia coli immobilized in a polymer containing bound low potential osmium redox complexes. The electrically connected enzyme already electrooxidizes benzaldehyde at potentials below -0.15 V (vs. Ag|AgCl, 1 M KCl). The pH-dependence of benzaldehyde oxidation can be strongly influenced by the ionic strength. The effect is similar with the soluble osmium redox complex and therefore indicates a clear electrostatic effect on the bioelectrocatalytic efficiency of PaoABC in the osmium containing redox polymer. At lower ionic strength, the pH-optimum is high and can be switched to low pH-values at high ionic strength. This offers biosensing at high and low pH-values. A "reagentless" biosensor has been formed with enzyme wired onto a screen-printed electrode in a flow cell device. The response time to addition of benzaldehyde is 30 s, and the measuring range is between 10-150 µM and the detection limit of 5 µM (signal to noise ratio 3:1) of benzaldehyde. The relative standard deviation in a series (n = 13) for 200 µM benzaldehyde is 1.9\%. For the biosensor, a response to succinic semialdehyde was also identified. Based on this response and the ability to work at high pH a biosensor for GABA is proposed by coimmobilizing GABA-aminotransferase (GABA-T) and PaoABC in the osmium containing redox polymer.}, language = {en} } @article{BaetenWartonVanCalsteretal.2014, author = {Baeten, Lander and Warton, David I. and Van Calster, Hans and De Frenne, Pieter and Verstraeten, Gorik and Bonte, Dries and Bernhardt-R{\"o}mermann, Markus and Cornelis, Johnny and Decocq, Guillaume and Eriksson, Ove and Hedl, Radim and Heinken, Thilo and Hermy, Martin and Hommel, Patrick and Kirby, Keith J. and Naaf, Tobias and Petrik, Petr and Walther, Gian-Reto and Wulf, Monica and Verheyen, Kris}, title = {A model-based approach to studying changes in compositional heterogeneity}, series = {Methods in ecology and evolution : an official journal of the British Ecological Society}, volume = {5}, journal = {Methods in ecology and evolution : an official journal of the British Ecological Society}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {2041-210X}, pages = {156 -- 164}, year = {2014}, language = {en} } @unpublished{Balazadeh2014, author = {Balazadeh, Salma}, title = {Stay-green not always stays green}, series = {Molecular plant}, volume = {7}, journal = {Molecular plant}, number = {8}, publisher = {Cell Press}, address = {Cambridge}, issn = {1674-2052}, doi = {10.1093/mp/ssu076}, pages = {1264 -- 1266}, year = {2014}, language = {en} } @article{BalazadehSchildhauerAraujoetal.2014, author = {Balazadeh, Salma and Schildhauer, Joerg and Araujo, Wagner L. and Munne-Bosch, Sergi and Fernie, Alisdair R. and Proost, Sebastian and Humbeck, Klaus and M{\"u}ller-R{\"o}ber, Bernd}, title = {Reversal of senescence by N resupply to N-starved Arabidopsis thaliana: transcriptomic and metabolomic consequences}, series = {Journal of experimental botany}, volume = {65}, journal = {Journal of experimental botany}, number = {14}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0022-0957}, doi = {10.1093/jxb/eru119}, pages = {3975 -- 3992}, year = {2014}, abstract = {Leaf senescence is a developmentally controlled process, which is additionally modulated by a number of adverse environmental conditions. Nitrogen shortage is a well-known trigger of precocious senescence in many plant species including crops, generally limiting biomass and seed yield. However, leaf senescence induced by nitrogen starvation may be reversed when nitrogen is resupplied at the onset of senescence. Here, the transcriptomic, hormonal, and global metabolic rearrangements occurring during nitrogen resupply-induced reversal of senescence in Arabidopsis thaliana were analysed. The changes induced by senescence were essentially in keeping with those previously described; however, these could, by and large, be reversed. The data thus indicate that plants undergoing senescence retain the capacity to sense and respond to the availability of nitrogen nutrition. The combined data are discussed in the context of the reversibility of the senescence programme and the evolutionary benefit afforded thereby. Future prospects for understanding and manipulating this process in both Arabidopsis and crop plants are postulated.}, language = {en} } @article{BaselHarmsPrechtletal.2014, author = {Basel, Nicolai and Harms, Ute and Prechtl, Helmut and Weiss, Thomas and Rothgangel, Martin}, title = {Students' arguments on the science and religion issue: the example of evolutionary theory and Genesis}, series = {Journal of biological education}, volume = {48}, journal = {Journal of biological education}, number = {4}, publisher = {Routledge, Taylor \& Francis Group}, address = {Abingdon}, issn = {0021-9266}, doi = {10.1080/00219266.2013.849286}, pages = {179 -- 187}, year = {2014}, abstract = {Treating creationism as a controversial topic within the science and religion issue in the science classroom has been widely discussed in the recent literature. Some researchers have proposed that this topic is best addressed by focusing on sociocognitive conflict. To prepare new learning opportunities for this approach, it is necessary to know the concrete arguments that students use in their discussions on this issue. Therefore, this study aimed to provide a systematic description of these arguments. For this purpose, upper secondary students (N=43) argued for either the acceptance of evolutionary theory or faith in Genesis in a written speech. The study was conducted during their regular biology and religious education classes. Generated arguments were analysed by qualitative content analysis. Three dimensions of the arguments were described: the content (science or religion), the valuation of the argument (positive or negative), and whether the argument consisted of a descriptive or normative argumentation. The results indicate that students found it easier to generate arguments about the scientific side of the issue; however, these arguments were negatively constructed. The results are discussed with regard to implications for educational approaches for teaching controversial issues at the high-school level.}, language = {en} } @article{BauerVosKlauschiesetal.2014, author = {Bauer, Barbara and Vos, Matthijs and Klauschies, Toni and Gaedke, Ursula}, title = {Diversity, functional similarity, and top-down control drive synchronization and the reliability of ecosystem function}, series = {The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences}, volume = {183}, journal = {The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences}, number = {3}, publisher = {Univ. of Chicago Press}, address = {Chicago}, issn = {0003-0147}, doi = {10.1086/674906}, pages = {394 -- 409}, year = {2014}, abstract = {The concept that diversity promotes reliability of ecosystem function depends on the pattern that community-level biomass shows lower temporal variability than species-level biomasses. However, this pattern is not universal, as it relies on compensatory or independent species dynamics. When in contrast within--trophic level synchronization occurs, variability of community biomass will approach population-level variability. Current knowledge fails to integrate how species richness, functional distance between species, and the relative importance of predation and competition combine to drive synchronization at different trophic levels. Here we clarify these mechanisms. Intense competition promotes compensatory dynamics in prey, but predators may at the same time increasingly synchronize, under increasing species richness and functional similarity. In contrast, predators and prey both show perfect synchronization under strong top-down control, which is promoted by a combination of low functional distance and high net growth potential of predators. Under such conditions, community-level biomass variability peaks, with major negative consequences for reliability of ecosystem function.}, language = {en} } @article{BecherGrimmThorbeketal.2014, author = {Becher, Matthias A. and Grimm, Volker and Thorbek, Pernille and Horn, Juliane and Kennedy, Peter J. and Osborne, Juliet L.}, title = {BEEHAVE: a systems model of honeybee colony dynamics and foraging to explore multifactorial causes of colony failure}, series = {Journal of applied ecology : an official journal of the British Ecological Society}, volume = {51}, journal = {Journal of applied ecology : an official journal of the British Ecological Society}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0021-8901}, doi = {10.1111/1365-2664.12222}, pages = {470 -- 482}, year = {2014}, abstract = {BEEHAVE offers a valuable tool for researchers to design and focus field experiments, for regulators to explore the relative importance of stressors to devise management and policy advice and for beekeepers to understand and predict varroa dynamics and effects of management interventions. We expect that scientists and stakeholders will find a variety of applications for BEEHAVE, stimulating further model development and the possible inclusion of other stressors of potential importance to honeybee colony dynamics.}, language = {en} } @article{BechiHerterMcKennaetal.2014, author = {Bechi, Beatrice and Herter, Susanne and McKenna, Shane and Riley, Christopher and Leimk{\"u}hler, Silke and Turner, Nicholas J. and Carnell, Andrew J.}, title = {Catalytic bio-chemo and bio-bio tandem oxidation reactions for amide and carboxylic acid synthesis}, series = {Green chemistry : an international journal and green chemistry resource}, volume = {16}, journal = {Green chemistry : an international journal and green chemistry resource}, number = {10}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9262}, doi = {10.1039/c4gc01321b}, pages = {4524 -- 4529}, year = {2014}, abstract = {A catalytic toolbox for three different water-based one-pot cascades to convert aryl alcohols to amides and acids and cyclic amines to lactams, involving combination of oxidative enzymes (monoamine oxidase, xanthine dehydrogenase, galactose oxidase and laccase) and chemical oxidants (TBHP or Cul(cat)/H2O2) at mild temperatures, is presented. Mutually compatible conditions were found to afford products in good to excellent yields.}, language = {en} } @misc{BechiHerterMcKennaetal.2014, author = {Bechi, Beatrice and Herter, Susanne and McKenna, Shane and Riley, Christopher and Leimk{\"u}hler, Silke and Turner, Nicholas J. and Carnell, Andrew J.}, title = {Catalytic bio-chemo and bio-bio tandem oxidation reactions for amide and carboxylic acid synthesis}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-99414}, year = {2014}, abstract = {A catalytic toolbox for three different water-based one-pot cascades to convert aryl alcohols to amides and acids and cyclic amines to lactams, involving combination of oxidative enzymes (monoamine oxidase, xanthine dehydrogenase, galactose oxidase and laccase) and chemical oxidants (TBHP or CuI(cat)/H2O2) at mild temperatures, is presented. Mutually compatible conditions were found to afford products in good to excellent yields.}, language = {en} } @inproceedings{BehlKratzNoecheletal.2014, author = {Behl, Marc and Kratz, Karl and N{\"o}chel, Ulrich and Sauter, Tilman and Lendlein, Andreas}, title = {Polymer networks capable of reversible shape-memory-effects}, series = {Abstracts of papers : joint conference / The Chemical Institute of Cananda, CIC, American Chemical Society, ACS}, volume = {248}, booktitle = {Abstracts of papers : joint conference / The Chemical Institute of Cananda, CIC, American Chemical Society, ACS}, publisher = {American Chemical Society}, address = {Washington}, issn = {0065-7727}, pages = {1}, year = {2014}, language = {en} } @article{BehrensFrankRaweletal.2014, author = {Behrens, Maik and Frank, Oliver and Rawel, Harshadrai Manilal and Ahuja, Gaurav and Potting, Christoph and Hofmann, Thomas and Meyerhof, Wolfgang and Korsching, Sigrun}, title = {ORA1, a Zebrafish Olfactory Receptor Ancestral to All Mammalian V1R Genes, Recognizes 4-Hydroxyphenylacetic Acid, a Putative Reproductive Pheromone}, series = {The journal of biological chemistry}, volume = {289}, journal = {The journal of biological chemistry}, number = {28}, publisher = {American Society for Biochemistry and Molecular Biology}, address = {Bethesda}, issn = {0021-9258}, doi = {10.1074/jbc.M114.573162}, pages = {19778 -- 19788}, year = {2014}, abstract = {The teleost v1r-related ora genes are a small, highly conserved olfactory receptor gene family of only six genes, whose direct orthologues can be identified in lineages as far as that of cartilaginous fish. However, no ligands for fish olfactory receptor class A related genes (ORA) had been uncovered so far. Here we have deorphanized the ORA1 receptor using heterologous expression and calcium imaging. We report that zebrafish ORA1 recognizes with high specificity and sensitivity 4-hydroxyphenylacetic acid. The carboxyl group of this compound is required in a particular distance from the aromatic ring, whereas the hydroxyl group in the para-position is not essential, but strongly enhances the binding efficacy. Low concentrations of 4-hydroxyphenylacetic acid elicit increases in oviposition frequency in zebrafish mating pairs. This effect is abolished by naris closure. We hypothesize that 4-hydroxyphenylacetic acid might function as a pheromone for reproductive behavior in zebrafish. ORA1 is ancestral to mammalian V1Rs, and its putative function as pheromone receptor is reminiscent of the role of several mammalian V1Rs as pheromone receptors.}, language = {en} } @article{BiancoKetmaier2014, author = {Bianco, Pier Giorgio and Ketmaier, Valerio}, title = {A revision of the Rutilus complex from Mediterranean Europe with description of a new genus, Sarmarutilus, and a new species, Rutilus stoumboudae (Teleostei: Cyprinidae)}, series = {Zootaxa : an international journal of zootaxonomy ; a rapid international journal for animal taxonomists}, volume = {3841}, journal = {Zootaxa : an international journal of zootaxonomy ; a rapid international journal for animal taxonomists}, number = {3}, publisher = {Magnolia Press}, address = {Auckland}, issn = {1175-5326}, pages = {379 -- 402}, year = {2014}, abstract = {By combining morphology, ecology, biology, and biogeography with the available molecular (sequence variation of the entire mitochondrial cytochrome b gene; cyt-b) and karyology data, the taxonomy of several species of the Rutilus complex inhabiting southern Europe is revised. Rutilus stoumboudae, new species, is described from Lake Volvi, Greece. It differs from Rutilus rutilus in possessing more total GR and less branched rays in both dorsal and anal fins and in its placement in the cyt-b based phylogeny of the genus. The resurrected genus Leucos Heckel, 1843 (type species Leucos aula, Bonaparte, 1841), which according to molecular data diverged from Rutilus more than 5 million years ago, during the Messinian salinity crisis, includes five species of small size, without spinous tubercles on scales and head in reproductive males, pharyngeal teeth formula 5-5, and all show a preference for still waters. Leucos aula is the Italian species endemic in the Padany-Venetian district: L. basak is widespread in Croatia, Albania, Montenegro and former Yugoslav Republic of Macedonia (FYROM); L. albus, recently described from Lake Skadar, Montenegro, is also found in rivers Moraca and Zeta (Montenegro). L. albus differs from L. basak, its closest relative, in having more scales on the LL and less anal-fin rays; L. panosi is endemic to the western-Greece district, and L. ylikiensis is endemic to lakes Yliki and Paralimni in eastern Greece (introduced in Lake Volvi). Among the nominal species examined, Rutilus karamani, R. ohridanus, R. prespensis and R. prespensis vukovici are all junior synonyms of Leucos basak. Rutilus vegariticus is definitively regarded as junior synonym for R. rutilus. Sarmarutilus n.gen. is a monotypic genus, with Sarmarutilus rubilio as the type species. According to phylogenetic data, Sarmarutilus rubilio is basal to a cluster of species that includes Leucos basak, L. albus, L. aula, L. panosi and L. ylikiensis. Sarmarutilus possibly evolved in pre-Messinian time, in the Lago Mare, entered the Mediterranean area during the Messinian Lago Mare phase of the Mediterranean Sea and survived only in the Tuscany-Latium district. This genus differs from Leucos in having large pearl organs on the central part of head and body scales in mature males and for the habitat preference, being a riverine-adapted species. It differs from Rutilus in pharyngeal teeth formula (5-5 in Sarmarutilus and 6-5 in Rutilus), size (small in Sarmarutilus and large in Rutilus) and for the preferential habitat (riverine vs. still water). Finally, lectotypes for Leucos basak, Leucos aula, and Sarmarutilus rubilio are designated.}, language = {en} } @article{BickelTangGrossart2014, author = {Bickel, Samantha L. and Tang, Kam W. and Grossart, Hans-Peter}, title = {Structure and function of zooplankton-associated bacterial communities in a temperate estuary change more with time than with zooplankton species}, series = {Aquatic microbial ecology : international journal}, volume = {72}, journal = {Aquatic microbial ecology : international journal}, number = {1}, publisher = {Institute of Mathematical Statistics}, address = {Oldendorf Luhe}, issn = {0948-3055}, doi = {10.3354/ame01676}, pages = {1 -- 15}, year = {2014}, abstract = {Zooplankton support distinct bacterial communities in high concentrations relative to the surrounding water, but little is known about how the compositions and functionalities of these bacterial communities change through time in relation to environmental conditions. We conducted a year-long field study of bacterial communities associated with common zooplankton groups as well as free-living bacterial communities in the York River, a tributary of Chesapeake Bay. Bacterial community genetic fingerprints and their carbon substrate usage were examined by denaturing gradient gel electrophoresis (DGGE) of amplified 16S rDNA and by Biolog EcoPlates, respectively. Zooplankton-associated communities were genetically distinct from free-living bacterial communities but utilized a similar array of carbon substrates. On average, bacteria associated with different zooplankton groups were genetically more similar to each other within each month (65.4\% similarity) than to bacterial communities of the same zooplankton group from different months (28 to 30\% similarity), which suggests the importance of ambient environmental conditions in shaping resident zooplankton-associated bacterial communities. Monthly changes in carbon substrate utilization were less variable for zooplankton-associated bacteria than for free-living bacteria, suggesting that the zooplankton microhabitat is more stable than the surrounding water and supports specific bacterial groups in the otherwise unfavorable conditions in the water column.}, language = {en} } @article{BizicIonescuAmannGrossart2014, author = {Bizic-Ionescu, Mina and Amann, Rudolf and Grossart, Hans-Peter}, title = {Massive regime shifts and high activity of heterotrophic bacteria in an ice-covered lake}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {11}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0113611}, pages = {17}, year = {2014}, abstract = {In winter 2009/10, a sudden under-ice bloom of heterotrophic bacteria occurred in the seasonally ice-covered, temperate, deep, oligotrophic Lake Stechlin (Germany). Extraordinarily high bacterial abundance and biomass were fueled by the breakdown of a massive bloom of Aphanizomenon flos-aquae after ice formation. A reduction in light resulting from snow coverage exerted a pronounced physiological stress on the cyanobacteria. Consequently, these were rapidly colonized, leading to a sudden proliferation of attached and subsequently of free-living heterotrophic bacteria. Total bacterial protein production reached 201 mg C L-1 d(-1), ca. five times higher than spring-peak values that year. Fluorescence in situ hybridization and denaturing gradient gel electrophoresis at high temporal resolution showed pronounced changes in bacterial community structure coinciding with changes in the physiology of the cyanobacteria. Pyrosequencing of 16S rRNA genes revealed that during breakdown of the cyanobacterial population, the diversity of attached and free-living bacterial communities were reduced to a few dominant families. Some of these were not detectable during the early stages of the cyanobacterial bloom indicating that only specific, well adapted bacterial communities can colonize senescent cyanobacteria. Our study suggests that in winter, unlike commonly postulated, carbon rather than temperature is the limiting factor for bacterial growth. Frequent phytoplankton blooms in ice-covered systems highlight the need for year-round studies of aquatic ecosystems including the winter season to correctly understand element and energy cycling through aquatic food webs, particularly the microbial loop. On a global scale, such knowledge is required to determine climate change induced alterations in carbon budgets in polar and temperate aquatic systems.}, language = {en} } @article{BocediZurellReinekingetal.2014, author = {Bocedi, Greta and Zurell, Damaris and Reineking, Bjoern and Travis, Justin M. J.}, title = {Mechanistic modelling of animal dispersal offers new insights into range expansion dynamics across fragmented landscapes}, series = {Ecography : pattern and diversity in ecology ; research papers forum}, volume = {37}, journal = {Ecography : pattern and diversity in ecology ; research papers forum}, number = {12}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0906-7590}, doi = {10.1111/ecog.01041}, pages = {1240 -- 1253}, year = {2014}, language = {en} } @article{BoehmerHartmannLeimkuehler2014, author = {Boehmer, Nadine and Hartmann, Tobias and Leimk{\"u}hler, Silke}, title = {The chaperone FdsC for Rhodobacter capsulatus formate dehydrogenase binds the bis-molybdopterin guanine dinucleotide cofactor}, series = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences}, volume = {588}, journal = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences}, number = {4}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0014-5793}, doi = {10.1016/j.febslet.2013.12.033}, pages = {531 -- 537}, year = {2014}, abstract = {Molybdoenzymes are complex enzymes in which the molybdenum cofactor (Moco) is deeply buried in the enzyme. Most molybdoenzymes contain a specific chaperone for the insertion of Moco. For the formate dehydrogenase FdsGBA from Rhodobacter capsulatus the two chaperones FdsC and FdsD were identified to be essential for enzyme activity, but are not a subunit of the mature enzyme. Here, we purified and characterized the FdsC protein after heterologous expression in Escherichia coli. We were able to copurify FdsC with the bound Moco derivate bis-molybdopterin guanine dinucleotide. This cofactor successfully was used as a source to reconstitute the activity of molybdoenzymes. Structured summary of protein interactions: FdsC and FdsC bind by molecular sieving (View interaction) FdsD binds to RcMobA by surface plasmon resonance (View interaction) FdsC binds to RcMobA by surface plasmon resonance (View interaction) FdsC binds to FdsA by surface plasmon resonance (View interaction)}, language = {en} } @misc{Boernke2014, author = {Boernke, Frederik}, title = {The complex becomes more complex: protein-protein interactions of SnRK1 with DUF581 family proteins provide a framework for cell- and stimulus type-specific SnRK1 signaling in plants (vol 5, 54, 2014)}, series = {Frontiers in plant science}, volume = {5}, journal = {Frontiers in plant science}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2014.00693}, pages = {1}, year = {2014}, language = {en} } @article{BoitGaedke2014, author = {Boit, Alice and Gaedke, Ursula}, title = {Benchmarking successional progress in a quantitative food web}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {2}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0090404}, pages = {25}, year = {2014}, abstract = {Central to ecology and ecosystem management, succession theory aims to mechanistically explain and predict the assembly and development of ecological communities. Yet processes at lower hierarchical levels, e. g. at the species and functional group level, are rarely mechanistically linked to the under-investigated system-level processes which drive changes in ecosystem properties and functioning and are comparable across ecosystems. As a model system for secondary succession, seasonal plankton succession during the growing season is readily observable and largely driven autogenically. We used a long-term dataset from large, deep Lake Constance comprising biomasses, auto-and heterotrophic production, food quality, functional diversity, and mass-balanced food webs of the energy and nutrient flows between functional guilds of plankton and partly fish. Extracting population-and system-level indices from this dataset, we tested current hypotheses about the directionality of successional progress which are rooted in ecosystem theory, the metabolic theory of ecology, quantitative food web theory, thermodynamics, and information theory. Our results indicate that successional progress in Lake Constance is quantifiable, passing through predictable stages. Mean body mass, functional diversity, predator-prey weight ratios, trophic positions, system residence times of carbon and nutrients, and the complexity of the energy flow patterns increased during succession. In contrast, both the mass-specific metabolic activity and the system export decreased, while the succession rate exhibited a bimodal pattern. The weighted connectance introduced here represents a suitable index for assessing the evenness and interconnectedness of energy flows during succession. Diverging from earlier predictions, ascendency and eco-exergy did not increase during succession. Linking aspects of functional diversity to metabolic theory and food web complexity, we reconcile previously disjoint bodies of ecological theory to form a complete picture of successional progress within a pelagic food web. This comprehensive synthesis may be used as a benchmark for quantifying successional progress in other ecosystems.}, language = {en} } @article{BrothersKoehlerAttermeyeretal.2014, author = {Brothers, Soren M. and Koehler, J. and Attermeyer, Katrin and Grossart, Hans-Peter and Mehner, T. and Meyer, N. and Scharnweber, Inga Kristin and Hilt, Sabine}, title = {A feedback loop links brownification and anoxia in a temperate, shallow lake}, series = {Limnology and oceanography}, volume = {59}, journal = {Limnology and oceanography}, number = {4}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0024-3590}, doi = {10.4319/lo.2014.59.4.1388}, pages = {1388 -- 1398}, year = {2014}, abstract = {This study examines a natural, rapid, fivefold increase in dissolved organic carbon (DOC) concentrations in a temperate shallow lake, describing the processes by which increased DOC resulted in anoxic conditions and altered existing carbon cycling pathways. High precipitation for two consecutive years led to rising water levels and the flooding of adjacent degraded peatlands. Leaching from the flooded soils provided an initial increase in DOC concentrations (from a 2010 mean of 12 +/- 1 mg L-1 to a maximum concentration of 53 mg L-1 by June 2012). Increasing water levels, DOC, and phytoplankton concentrations reduced light reaching the sediment surface, eliminating most benthic primary production and promoting anoxia in the hypolimnion. From January to June 2012 there was a sudden increase in total phosphorus (from 57 mg L-1 to 216 mg L-1), DOC (from 24.6 mg L-1 to 53 mg L-1), and iron (from 0.12 mg L-1 to 1.07 mg L-1) concentrations, without any further large fluxes in water levels. We suggest that anoxic conditions at the sediment surface and flooded soils produced a dramatic release of these chemicals that exacerbated brownification and eutrophication, creating anoxic conditions that persisted roughly 6 months below a water depth of 1 m and extended periodically to the water surface. This brownification-anoxia feedback loop resulted in a near-complete loss of macroinvertebrate and fish populations, and increased surface carbon dioxide (CO2) emissions by an order of magnitude relative to previous years.}, language = {en} } @article{BrustLehmannFettke2014, author = {Brust, Henrike and Lehmann, Tanja and Fettke, J{\"o}rg}, title = {Analysis of the functional interaction of arabidopsis starch synthase and branching enzyme isoforms reveals that the cooperative action of SSI and BEs results in glucans with polymodal chain length distribution similar to amylopectin}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {7}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0102364}, pages = {14}, year = {2014}, abstract = {Starch synthase (SS) and branching enzyme (BE) establish the two glycosidic linkages existing in starch. Both enzymes exist as several isoforms. Enzymes derived from several species were studied extensively both in vivo and in vitro over the last years, however, analyses of a functional interaction of SS and BE isoforms are missing so far. Here, we present data from in vitro studies including both interaction of leaf derived and heterologously expressed SS and BE isoforms. We found that SSI activity in native PAGE without addition of glucans was dependent on at least one of the two BE isoforms active in Arabidopsis leaves. This interaction is most likely not based on a physical association of the enzymes, as demonstrated by immunodetection and native PAGE mobility analysis of SSI, BE2, and BE3. The glucans formed by the action of SSI/BEs were analysed using leaf protein extracts from wild type and be single mutants (Atbe2 and Atbe3 mutant lines) and by different combinations of recombinant proteins. Chain length distribution (CLD) patterns of the formed glucans were irrespective of SSI and BE isoforms origin and still independent of assay conditions. Furthermore, we show that all SS isoforms (SSI-SSIV) were able to interact with BEs and form branched glucans. However, only SSI/BEs generated a polymodal distribution of glucans which was similar to CLD pattern detected in amylopectin of Arabidopsis leaf starch. We discuss the impact of the SSI/BEs interplay for the CLD pattern of amylopectin.}, language = {en} } @phdthesis{Buechner2014, author = {B{\"u}chner, Kerstin}, title = {Modifizierung und Charakterisierung von Wellenleitermaterialien f{\"u}r Biosensoranwendungen}, pages = {129}, year = {2014}, language = {de} } @article{CaronDeFrenneBrunetetal.2014, author = {Caron, Maria Mercedes and De Frenne, P. and Brunet, J. and Chabrerie, Olivier and Cousins, S. A. O. and De Backer, L. and Diekmann, M. and Graae, B. J. and Heinken, Thilo and Kolb, A. and Naaf, T. and Plue, J. and Selvi, F. and Strimbeck, G. R. and Wulf, Monika and Verheyen, Kris}, title = {Latitudinal variation in seeds characteristics of Acer platanoides and A. pseudoplatanus}, series = {Plant ecology : an international journal}, volume = {215}, journal = {Plant ecology : an international journal}, number = {8}, publisher = {Springer}, address = {Dordrecht}, issn = {1385-0237}, doi = {10.1007/s11258-014-0343-x}, pages = {911 -- 925}, year = {2014}, abstract = {Climate change will likely affect population dynamics of numerous plant species by modifying several aspects of the life cycle. Because plant regeneration from seeds may be particularly vulnerable, here we assess the possible effects of climate change on seed characteristics and present an integrated analysis of seven seed traits (nutrient concentrations, samara mass, seed mass, wing length, seed viability, germination percentage, and seedling biomass) of Acer platanoides and A. pseudoplatanus seeds collected along a wide latitudinal gradient from Italy to Norway. Seed traits were analyzed in relation to the environmental conditions experienced by the mother trees along the latitudinal gradient. We found that seed traits of A. platanoides were more influenced by the climatic conditions than those of A. pseudoplatanus. Additionally, seed viability, germination percentage, and seedling biomass of A. platanoides were strongly related to the seed mass and nutrient concentration. While A. platanoides seeds were more influenced by the environmental conditions (generally negatively affected by rising temperatures), compared to A. pseudoplatanus, A. platanoides still showed higher germination percentage and seedling biomass than A. pseudoplatanus. Thus, further research on subsequent life-history stages of both species is needed. The variation in seed quality observed along the climatic gradient highlights the importance of studying the possible impact of climate change on seed production and species demography.}, language = {en} } @misc{CencilNitschkeSteupetal.2014, author = {Cencil, Ugo and Nitschke, Felix and Steup, Martin and Minassian, Berge A. and Colleoni, Christophe and Ball, Steven G.}, title = {Transition from glycogen to starch metabolism in Archaeplastida}, series = {Trends in plant science}, volume = {19}, journal = {Trends in plant science}, number = {1}, publisher = {Elsevier}, address = {London}, issn = {1360-1385}, doi = {10.1016/j.tplants.2013.08.004}, pages = {18 -- 28}, year = {2014}, abstract = {In this opinion article we propose a scenario detailing how two crucial components have evolved simultaneously to ensure the transition of glycogen to starch in the cytosol of the Archaeplastida last common ancestor: (i) the recruitment of an enzyme from intracellular Chlamydiae pathogens to facilitate crystallization of alpha-glucan chains; and (ii) the evolution of novel types of polysaccharide (de)phosphorylating enzymes from preexisting glycogen (de)phosphorylation host pathways to allow the turnover of such crystals. We speculate that the transition to starch benefitted Archaeplastida in three ways: more carbon could be packed into osmotically inert material; the host could resume control of carbon assimilation from the chlamydial pathogen that triggered plastid endosymbiosis; and cyanobacterial photosynthate export could be integrated in the emerging Archaeplastida.}, language = {en} } @article{ChenWangWangetal.2014, author = {Chen, Yao and Wang, Guang and Wang, Xiao-yu and Ma, Zheng-lai and Chen, You-peng and Chuai, Manli and von Websky, Karoline and Hocher, Berthold and Yang, Xuesong}, title = {Effects of high salt-exposure on the development of retina and lens in 5.5-Day Chick Embryo}, series = {Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry and pharmacology}, volume = {34}, journal = {Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry and pharmacology}, number = {3}, publisher = {Karger}, address = {Basel}, issn = {1015-8987}, doi = {10.1159/000363044}, pages = {804 -- 817}, year = {2014}, abstract = {Background/Aims: Excess maternal salt intake during pregnancy may alter fetal development. However; our knowledge on how an increased salt intake during pregnancy influences fetal eye development is limited. In this study, we investigated the effects of high salt treatment on the developing eyes in chick embryos, especially focusing on the development of the retina and the lens. Methods: 5.5 day chick embryos were exposed to 280mosm/l (n=17), or 300mosm/l (n=16) NaCl. The treated embryos were then incubated for 96 hours before they were fixed with 4\% paraformaldehyde for H\&E staining, whole mount embryo immunostaining and TUNEL staining. BrdU and PH3 incorporation experiments were performed on the chick embryos after high salt treatment. RT-PCR analyses were conducted from chick retina tissues. Results: We demonstrated that high-salt treatment altered the size of eyes in chick embryos, induced malformation of the eyes and impaired the development of the lens and the retina. We found an impaired expression of Paired box 6 (PAX6) and neuronal cells in the developing retina as revealed by neurofilament immunofluorescent staining. There was a reduction in the number of BrdU-positive cells and PH3-positive cells in the retina, indicating an impaired cell proliferation with high salt treatment. High salt treatment also resulted in an increased number of TUNEL-positive cells in the retina, indicating a higher amount of cell death. RT-PCR data displayed that the expression of the pro-apoptotic molecule nerve growth factor (NGF) in chick retina was increased and CyclinD1 was reduced with high-salt treatment. The size of the lens was reduced and Pax6 expression in the lens was significantly inhibited. High salt treatment was detrimental to the migration of neural crest cells. Conclusion: Taken together; our study demonstrated that high salt exposure of 5.5 day chick embryos led to an impairment of retina and lens development, possibly through interfering with Pax6 expression.}, language = {en} } @article{ChipmanFerrierBrenaetal.2014, author = {Chipman, Ariel D. and Ferrier, David E. K. and Brena, Carlo and Qu, Jiaxin and Hughes, Daniel S. T. and Schroeder, Reinhard and Torres-Oliva, Montserrat and Znassi, Nadia and Jiang, Huaiyang and Almeida, Francisca C. and Alonso, Claudio R. and Apostolou, Zivkos and Aqrawi, Peshtewani and Arthur, Wallace and Barna, Jennifer C. J. and Blankenburg, Kerstin P. and Brites, Daniela and Capella-Gutierrez, Salvador and Coyle, Marcus and Dearden, Peter K. and Du Pasquier, Louis and Duncan, Elizabeth J. and Ebert, Dieter and Eibner, Cornelius and Erikson, Galina and Evans, Peter D. and Extavour, Cassandra G. and Francisco, Liezl and Gabaldon, Toni and Gillis, William J. and Goodwin-Horn, Elizabeth A. and Green, Jack E. and Griffiths-Jones, Sam and Grimmelikhuijzen, Cornelis J. P. and Gubbala, Sai and Guigo, Roderic and Han, Yi and Hauser, Frank and Havlak, Paul and Hayden, Luke and Helbing, Sophie and Holder, Michael and Hui, Jerome H. L. and Hunn, Julia P. and Hunnekuhl, Vera S. and Jackson, LaRonda and Javaid, Mehwish and Jhangiani, Shalini N. and Jiggins, Francis M. and Jones, Tamsin E. and Kaiser, Tobias S. and Kalra, Divya and Kenny, Nathan J. and Korchina, Viktoriya and Kovar, Christie L. and Kraus, F. Bernhard and Lapraz, Francois and Lee, Sandra L. and Lv, Jie and Mandapat, Christigale and Manning, Gerard and Mariotti, Marco and Mata, Robert and Mathew, Tittu and Neumann, Tobias and Newsham, Irene and Ngo, Dinh N. and Ninova, Maria and Okwuonu, Geoffrey and Ongeri, Fiona and Palmer, William J. and Patil, Shobha and Patraquim, Pedro and Pham, Christopher and Pu, Ling-Ling and Putman, Nicholas H. and Rabouille, Catherine and Ramos, Olivia Mendivil and Rhodes, Adelaide C. and Robertson, Helen E. and Robertson, Hugh M. and Ronshaugen, Matthew and Rozas, Julio and Saada, Nehad and Sanchez-Gracia, Alejandro and Scherer, Steven E. and Schurko, Andrew M. and Siggens, Kenneth W. and Simmons, DeNard and Stief, Anna and Stolle, Eckart and Telford, Maximilian J. and Tessmar-Raible, Kristin and Thornton, Rebecca and van der Zee, Maurijn and von Haeseler, Arndt and Williams, James M. and Willis, Judith H. and Wu, Yuanqing and Zou, Xiaoyan and Lawson, Daniel and Muzny, Donna M. and Worley, Kim C. and Gibbs, Richard A. and Akam, Michael and Richards, Stephen}, title = {The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima}, series = {PLoS biology}, volume = {12}, journal = {PLoS biology}, number = {11}, publisher = {PLoS}, address = {San Fransisco}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1002005}, pages = {24}, year = {2014}, abstract = {Myriapods (e. g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.}, language = {en} } @article{CortesAvizandaJovaniAntonioDonazaretal.2014, author = {Cortes-Avizanda, Ainara and Jovani, Roger and Antonio Donazar, Jose and Grimm, Volker}, title = {Bird sky networks: How do avian scavengers use social information to find carrion?}, series = {Ecology : a publication of the Ecological Society of America}, volume = {95}, journal = {Ecology : a publication of the Ecological Society of America}, number = {7}, publisher = {Wiley}, address = {Washington}, issn = {0012-9658}, pages = {1799 -- 1808}, year = {2014}, abstract = {The relative contribution of personal and social information to explain individual and collective behavior in different species and contexts is an open question in animal ecology. In particular, there is a major lack of studies combining theoretical and empirical approaches to test the relative relevance of different hypothesized individual behaviors to predict empirical collective patterns. We used an individual-based model to confront three hypotheses about the information transfer between social scavengers (Griffon Vultures, Gyps fulvus) when searching for carrion: (1) Vultures only use personal information during foraging ("nonsocial" hypothesis); (2) they create long chains of vultures by following both other vultures that are flying towards carcasses and vultures that are following other vultures that are flying towards carcasses ("chains of vultures" hypothesis); and (3) vultures are only attracted by other vultures that are sinking vertically to a carcass ("local enhancement" hypothesis). The chains of vultures hypothesis has been used in existing models, but never been confronted with field data. Testing is important, though, because these hypotheses could have different management implications. The model was parameterized to mimic the behavior and the densities of both Griffon Vultures and carcasses in a 10 000-km(2) study area in northeastern Spain. We compared the number of vultures attending simulated carcasses with those attending 25 continuously monitored experimental carcasses in the field. Social hypotheses outperformed the nonsocial hypothesis. The chains of vultures hypothesis overestimated the number of vultures feeding on carcasses; the local enhancement hypothesis fitted closely to the empirical data. Supported by our results, we discuss mechanistic and adaptive considerations that reveal that local enhancement may be the key social mechanism behind collective foraging in this and likely other avian scavengers and/or social birds. It also highlights the current need for more studies confronting alternative models of key behaviors with empirical patterns in order to understand how collective behavior emerges in animal societies.}, language = {en} } @phdthesis{Czesnick2014, author = {Czesnick, Hj{\"o}rdis}, title = {Functional specialization of Arabidopsis poly(A) polymerases in relation to flowering time and stress}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-78015}, school = {Universit{\"a}t Potsdam}, pages = {157}, year = {2014}, abstract = {Polyadenylation is a decisive 3' end processing step during the maturation of pre-mRNAs. The length of the poly(A) tail has an impact on mRNA stability, localization and translatability. Accordingly, many eukaryotic organisms encode several copies of canonical poly(A) polymerases (cPAPs). The disruption of cPAPs in mammals results in lethality. In plants, reduced cPAP activity is non-lethal. Arabidopsis encodes three nuclear cPAPs, PAPS1, PAPS2 and PAPS4, which are constitutively expressed throughout the plant. Recently, the detailed analysis of Arabidopsis paps1 mutants revealed a subset of genes that is preferentially polyadenylated by the cPAP isoform PAPS1 (Vi et al. 2013). Thus, the specialization of cPAPs might allow the regulation of different sets of genes in order to optimally face developmental or environmental challenges. To gain insights into the cPAP-based gene regulation in plants, the phenotypes of Arabidopsis cPAPs mutants under different conditions are characterized in detail in the following work. An involvement of all three cPAPs in flowering time regulation and stress response regulation is shown. While paps1 knockdown mutants flower early, paps4 and paps2 paps4 knockout mutants exhibit a moderate late-flowering phenotype. PAPS1 promotes the expression of the major flowering inhibitor FLC, supposedly by specific polyadenylation of an FLC activator. PAPS2 and PAPS4 exhibit partially overlapping functions and ensure timely flowering by repressing FLC and at least one other unidentified flowering inhibitor. The latter two cPAPs act in a novel regulatory pathway downstream of the autonomous pathway component FCA and act independently from the polyadenylation factors and flowering time regulators CstF64 and FY. Moreover, PAPS1 and PAPS2/PAPS4 are implicated in different stress response pathways in Arabidopsis. Reduced activity of the poly(A) polymerase PAPS1 results in enhanced resistance to osmotic and oxidative stress. Simultaneously, paps1 mutants are cold-sensitive. In contrast, PAPS2/PAPS4 are not involved in the regulation of osmotic or cold stress, but paps2 paps4 loss-of-function mutants exhibit enhanced sensitivity to oxidative stress provoked in the chloroplast. Thus, both PAPS1 and PAPS2/PAPS4 are required to maintain a balanced redox state in plants. PAPS1 seems to fulfil this function in concert with CPSF30, a polyadenylation factor that regulates alternative polyadenylation and tolerance to oxidative stress. The individual paps mutant phenotypes and the cPAP-specific genetic interactions support the model of cPAP-dependent polyadenylation of selected mRNAs. The high similarity of the polyadenylation machineries in yeast, mammals and plants suggests that similar regulatory mechanisms might be present in other organism groups. The cPAP-dependent developmental and physiological pathways identified in this work allow the design of targeted experiments to better understand the ecological and molecular context underlying cPAP-specialization.}, language = {en} } @article{DechtriratGajovicEichelmannWojciketal.2014, author = {Dechtrirat, Decha and Gajovic-Eichelmann, Nenad and Wojcik, Felix and Hartmann, Laura and Bier, Frank Fabian and Scheller, Frieder W.}, title = {Electrochemical displacement sensor based on ferrocene boronic acid tracer and immobilized glycan for saccharide binding proteins and E. coli}, series = {Biosensors and bioelectronics : the principal international journal devoted to research, design development and application of biosensors and bioelectronics}, volume = {58}, journal = {Biosensors and bioelectronics : the principal international journal devoted to research, design development and application of biosensors and bioelectronics}, publisher = {Elsevier}, address = {Oxford}, issn = {0956-5663}, doi = {10.1016/j.bios.2014.02.028}, pages = {1 -- 8}, year = {2014}, abstract = {Pathogens such as viruses and bacteria use their envelope proteins and their adhesin lectins to recognize the glycan residues presented on the cell surface of the target tissues. This principle of recognition is used in a new electrochemical displacement sensor for the protein concanavalin A (ConA). A gold electrode was first modified with a self-assembled monolayer of a thiolated mannose/OEG conjugate and a ferrocene boroxol derivative was pre-assembled as reporter molecule onto the mannose surface. The novel tracer molecule based on a 2-hydroxymethyl phenyl boronic acid derivative binds even at neutral pH to the saccharides which could expand the application towards biological samples (i.e., urine and feces). Upon the binding of ConA, the tracer was displaced and washed away from the sensor surface leading to a decrease in the electrochemical signal. Using square wave voltammetry (SWV), the concentration of ConA in the sample solution could be determined in the dynamic concentration range established from 38 nmol L-1 to 5.76 mu mol L-1 with a reproducible detection limit of 1 mu g mL(-1) (38 nmol L-1) based on the signal-to-noise ratio (S/N=3) with fast response of 15 min. The new reporter molecule showed a reduced non-specific displacement by BSA and ribonuclease A. The sensor was also successfully transferred to the first proof of principle for the detection of Escherichia coli exhibiting a detection limit of approximately 6 x 102 cells/mL Specificity of the displacement by target protein ConA and E. coli was demonstrated since the control proteins (i.e., BSA and RNaseA) and the control E. coli strain, which lack of type 1 fimbriae, were ineffective. (C) 2014 Elsevier B.V. All rights reserved.}, language = {en} } @article{DevosGraefField2014, author = {Devos, Damien P. and Gr{\"a}f, Ralph and Field, Mark C.}, title = {Evolution of the nucleus}, series = {Current opinion in cell biology : review articles, recommended reading, bibliography of the world literature}, volume = {28}, journal = {Current opinion in cell biology : review articles, recommended reading, bibliography of the world literature}, publisher = {Elsevier}, address = {London}, issn = {0955-0674}, doi = {10.1016/j.ceb.2014.01.004}, pages = {8 -- 15}, year = {2014}, abstract = {The nucleus represents a major evolutionary transition. As a consequence of separating translation from transcription many new functions arose, which likely contributed to the remarkable success of eukaryotic cells. Here we will consider what has recently emerged on the evolutionary histories of several key aspects of nuclear biology; the nuclear pore complex, the lamina, centrosomes and evidence for prokaryotic origins of relevant players.}, language = {en} } @article{DeyAdamovskiFriebeetal.2014, author = {Dey, Pradip and Adamovski, Miriam and Friebe, Simon and Badalyan, Artavazd and Mutihac, Radu-Cristian and Paulus, Florian and Leimk{\"u}hler, Silke and Wollenberger, Ursula and Haag, Rainer}, title = {Dendritic polyglycerol-poly(ethylene glycol)-based polymer networks for biosensing application}, series = {ACS applied materials \& interfaces}, volume = {6}, journal = {ACS applied materials \& interfaces}, number = {12}, publisher = {American Chemical Society}, address = {Washington}, issn = {1944-8244}, doi = {10.1021/am502018x}, pages = {8937 -- 8941}, year = {2014}, abstract = {This work describes the formation of a new dendritic polyglycerol-poly(ethylene glycol)-based 3D polymer network as a matrix for immobilization of the redox enzyme periplasmatic aldehyde oxidoreductase to create an electrochemical biosensor. The novel network is built directly on the gold surface, where it simultaneously stabilizes the enzyme for up to 4 days. The prepared biosensors can be used for amperometric detection of benzaldehyde in the range of 0.8-400 mu M.}, language = {en} } @article{DietrichLombardoAbdelilahSeyfried2014, author = {Dietrich, Ann-Christin and Lombardo, Veronica A. and Abdelilah-Seyfried, Salim}, title = {Blood flow and Bmp signaling control endocardial chamber morphogenesis}, series = {Developmental cell}, volume = {30}, journal = {Developmental cell}, number = {4}, publisher = {Cell Press}, address = {Cambridge}, issn = {1534-5807}, doi = {10.1016/j.devcel.2014.06.020}, pages = {367 -- 377}, year = {2014}, abstract = {During heart development, the onset of heartbeat and blood flow coincides with a ballooning of the cardiac chambers. Here, we have used the zebrafish as a vertebrate model to characterize chamber ballooning morphogenesis of the endocardium, a specialized population of endothelial cells that line the interior of the heart. By combining functional manipulations, fate mapping studies, and high-resolution imaging, we show that endocardial growth occurs without an influx of external cells. Instead, endocardial cell proliferation is regulated, both by blood flow and by Bmp signaling, in a manner independent of vascular endothelial growth factor (VEGF) signaling. Similar to myocardial cells, endocardial cells obtain distinct chamber-specific and inner- versus outer-curvature-specific surface area sizes. We find that the hemodynamic-sensitive transcription factor Klf2a is involved in regulating endocardial cell morphology. These findings establish the endocardium as the flow-sensitive tissue in the heart with a key role in adapting chamber growth in response to the mechanical stimulus of blood flow.}, language = {en} } @article{DolgenerFreudenbergerSchlucketal.2014, author = {Dolgener, N. and Freudenberger, L. and Schluck, M. and Schneeweiss, N. and Ibisch, P. L. and Tiedemann, Ralph}, title = {Environmental niche factor analysis (ENFA) relates environmental parameters to abundance and genetic diversity in an endangered amphibian, the fire-bellied-toad (Bombina bombina)}, series = {Conservation genetics}, volume = {15}, journal = {Conservation genetics}, number = {1}, publisher = {Springer}, address = {Dordrecht}, issn = {1566-0621}, doi = {10.1007/s10592-013-0517-4}, pages = {11 -- 21}, year = {2014}, abstract = {Increasing attempts are made to understand the factors responsible for both the demographic and genetic depletion in amphibian populations. Landscape genetics aims at a spatially explicit correlation of genetic population parameters to landscape features. Using data from the endangered fire-bellied toad Bombina bombina in Brandenburg (Northeastern Germany), we performed an environmental niche factor analysis (ENFA), relating demographic (abundance) and genetic (diversity at 17 microsatellite loci and partial sequences of the mitochondrial control region in 434 individuals from 16 populations) parameters to ecological and anthropogenic variables such as temperature, precipitation, soil wetness, water runoff, vegetation density, and road/traffic impact. We found significant correlations between road disturbance and observed heterozygosity and between soil wetness and mitochondrial diversity. As the influences of the environmental variables can differ between different indicators for genetic diversity, population size and abundance data, our ENFA-based landscape genetics approach allows us to put various aspects of long- versus short term effective population size and genetic connectivity into an ecological and spatially explicit context, enabling potentially even forecast assessment under future environmental scenarios.}, language = {en} } @article{DolgenerFreudenbergerSchneeweissetal.2014, author = {Dolgener, Nicola and Freudenberger, L. and Schneeweiss, N. and Ibisch, P. L. and Tiedemann, Ralph}, title = {Projecting current and potential future distribution of the Fire-bellied toad Bombina bombina under climate change in north-eastern Germany}, series = {Regional environmental change}, volume = {14}, journal = {Regional environmental change}, number = {3}, publisher = {Springer}, address = {Heidelberg}, issn = {1436-3798}, doi = {10.1007/s10113-013-0468-9}, pages = {1063 -- 1072}, year = {2014}, abstract = {Environmental change is likely to have a strong impact on biodiversity, and many species may shift their distribution in response. In this study, we aimed at projecting the availability of suitable habitat for an endangered amphibian species, the Fire-bellied toad Bombina bombina, in Brandenburg (north-eastern Germany). We modelled a potential habitat distribution map based on (1) a database with 10,581 presence records for Bombina from the years 1990 to 2009, (2) current estimates for ecogeographical variables (EGVs) and (3) the future projection of these EGVs according to the statistical regional model, respectively, the soil and water integrated model, applying the maximum entropy approach (Maxent). By comparing current and potential future distributions, we evaluated the projected change in distribution of suitable habitats and identified the environmental variables most associated with habitat suitability that turned out to be climatic variables related to the hydrological cycle. Under the applied scenario, our results indicate increasing habitat suitability in many areas and an extended range of suitable habitats. However, even if the environmental conditions in Brandenburg may change as predicted, it is questionable whether the Fire-bellied toad will truly benefit, as dispersal abilities of amphibian species are limited and strongly influenced by anthropogenic disturbances, that is, intensive agriculture, habitat destruction and fragmentation. Furthermore, agronomic pressure is likely to increase on productive areas with fertile soils and high water retention capacities, indeed those areas suitable for B. bombina. All these changes may affect temporary pond hydrology as well as the reproductive success and breeding phenology of toads.}, language = {en} } @article{DongYangLehnkuehleretal.2014, author = {Dong, Chao and Yang, Jing and Lehnkuehler, Silke and Kirk, Martin L.}, title = {Pyranopterin dithiolene distortions relevant to electron transfer in xanthine oxidase/dehydrogenase}, series = {Inorganic chemistry}, volume = {53}, journal = {Inorganic chemistry}, number = {14}, publisher = {American Chemical Society}, address = {Washington}, issn = {0020-1669}, doi = {10.1021/ic500873y}, pages = {7077 -- 7079}, year = {2014}, abstract = {The reducing substrates 4-thiolumazine and 2,4-dithiolumazine have been used to form Mo-IV-product complexes with xanthine oxidase (XO) and xanthine dehydrogenase. These Mo-IV-product complexes display an intense metal-to-ligand charge-transfer (MLCT) band in the near-infrared region of the spectrum. Optical pumping into this MLCT band yields resonance Raman spectra of the Mo site that are devoid of contributions from the highly absorbing FAD and 2Fe2S clusters in the protein. The resonance Raman spectra reveal in-plane bending modes of the bound product and low-frequency molybdenum dithiolene and pyranopterin dithiolene vibrational modes. This work provides keen insight into the role of the pyranopterin dithiolene in electron-transfer reactivity.}, language = {en} } @article{EccardLiesenjohann2014, author = {Eccard, Jana and Liesenjohann, Thilo}, title = {The importance of predation risk and missed opportunity costs for context-dependent foraging patterns}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {5}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0094107}, pages = {5}, year = {2014}, abstract = {Correct assessment of risks and costs of foraging is vital for the fitness of foragers. Foragers should avoid predation risk and balance missed opportunities. In risk-heterogeneous landscapes animals prefer safer locations over riskier, constituting a landscape of fear. Risk-uniform landscapes do not offer this choice, all locations are equally risky. Here we investigate the effects of predation risk in patches, travelling risk between patches, and missed social opportunities on foraging decisions in risk-uniform and risk-heterogeous landscapes. We investigated patch leaving decisions of 20 common voles (M. arvalis) in three experimental landscapes: safe risk-uniform, risky risk-uniform and risk-heterogeneous. We varied both the predation risk level and the predation risk distribution between two patches experimentally and in steps, assuming that our manipulation consequently yield different distributions and levels of risk while foraging, risk while travelling, and costs of missed, social opportunities (MSOCs). We measured mean GUDs (giving-up density of food left in the patch) for both patches as a measure of foraging gain, and delta GUD, the differences among patches, as a measure of the spatial distribution of foraging effort over a period of six hours. Distribution of foraging effort was most even in the safe risk-uniform landscapes and least even in the risk-heterogeneous landscape, with risky risk-uniform landscapes in between. Foraging gain was higher in the safe than in the two riskier landscapes (both uniform and heterogeneous). Results supported predictions for the effects of risk in foraging patches and while travelling between patches, however predictions for the effects of missed social opportunities were not met in this short term experiment. Thus, both travelling and foraging risk contribute to distinct patterns observable high risk, risk-uniform landscapes.}, language = {en} } @phdthesis{Eggers2014, author = {Eggers, Ute}, title = {Environmental impacts on white stork (Ciconia ciconia) breeding success}, school = {Universit{\"a}t Potsdam}, pages = {164}, year = {2014}, language = {en} } @phdthesis{Emadpour2014, author = {Emadpour, Masoumeh}, title = {Development of tools for inducible gene expression in choroplasts}, pages = {viii}, year = {2014}, language = {en} } @article{EngelPiontekGrossartetal.2014, author = {Engel, Anja and Piontek, Judith and Grossart, Hans-Peter and Riebesell, Ulf and Schulz, Kai Georg and Sperling, Martin}, title = {Impact of CO2 enrichment on organic matter dynamics during nutrient induced coastal phytoplankton blooms}, series = {Journal of plankton research}, volume = {36}, journal = {Journal of plankton research}, number = {3}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0142-7873}, doi = {10.1093/plankt/fbt125}, pages = {641 -- 657}, year = {2014}, abstract = {A mesocosm experiment was conducted to investigate the impact of rising fCO(2) on the build-up and decline of organic matter during coastal phytoplankton blooms. Five mesocosms (similar to 38 mA(3) each) were deployed in the Baltic Sea during spring (2009) and enriched with CO2 to yield a gradient of 355-862 A mu atm. Mesocosms were nutrient fertilized initially to induce phytoplankton bloom development. Changes in particulate and dissolved organic matter concentrations, including dissolved high-molecular weight (> 1 kDa) combined carbohydrates, dissolved free and combined amino acids as well as transparent exopolymer particles (TEP), were monitored over 21 days together with bacterial abundance, and hydrolytic extracellular enzyme activities. Overall, organic matter followed well-known bloom dynamics in all CO2 treatments alike. At high fCO(2,) higher Delta POC:Delta PON during bloom rise, and higher TEP concentrations during bloom peak, suggested preferential accumulation of carbon-rich components. TEP concentration at bloom peak was significantly related to subsequent sedimentation of particulate organic matter. Bacterial abundance increased during the bloom and was highest at high fCO(2). We conclude that increasing fCO(2) supports production and exudation of carbon-rich components, enhancing particle aggregation and settling, but also providing substrate and attachment sites for bacteria. More labile organic carbon and higher bacterial abundance can increase rates of oxygen consumption and may intensify the already high risk of oxygen depletion in coastal seas in the future.}, language = {en} } @article{FeherLisecRoemischMargletal.2014, author = {Feher, Kristen and Lisec, Jan and Roemisch-Margl, Lilla and Selbig, Joachim and Gierl, Alfons and Piepho, Hans-Peter and Nikoloski, Zoran and Willmitzer, Lothar}, title = {Deducing hybrid performance from parental metabolic profiles of young primary roots of maize by using a multivariate diallel approach}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {1}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0085435}, pages = {9}, year = {2014}, language = {en} } @article{FilipBauerHillebrandetal.2014, author = {Filip, Joanna and Bauer, Barbara and Hillebrand, Helmut and Beniermann, Anna and Gaedke, Ursula and Moorthi, Stefanie D.}, title = {Multitrophic diversity effects depend on consumer specialization and species-specific growth and grazing rates}, series = {Oikos}, volume = {123}, journal = {Oikos}, number = {8}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0030-1299}, doi = {10.1111/oik.01219}, pages = {912 -- 922}, year = {2014}, abstract = {Ecosystem functioning is affected by horizontal (within trophic groups) and vertical (across trophic levels) biodiversity. Theory predicts that the effects of vertical biodiversity depend on consumer specialization. In a microcosm experiment, we investigated ciliate consumer diversity and specialization effects on algal prey biovolume, evenness and composition, and on ciliate biovolume production. The experimental data was complemented by a process-based model further analyzing the ecological mechanisms behind the observed diversity effects. Overall, increasing consumer diversity had no significant effect on prey biovolume or evenness. However, consumer specialization affected the prey community. Specialist consumers showed a stronger negative impact on prey biovolume and evenness than generalists. The model confirmed that this pattern was mainly driven by a single specialist with a high per capita grazing rate, consuming the two most productive prey species. When these were suppressed, the prey assemblage became dominated by a less productive species, consequently decreasing prey biovolume and evenness. Consumer diversity increased consumer biovolume, which was stronger for generalists than for specialists and highest in mixed combinations, indicating that consumer functional diversity, i.e. more diverse feeding strategies, increased resource use efficiency. Overall, our results indicate that consumer diversity effects on prey and consumers strongly depend on species-specific growth and grazing rates, which may be at least equally important as consumer specialization in driving consumer diversity effects across trophic levels.}, language = {en} } @article{FraesdorfRadonLeimkuehler2014, author = {Fraesdorf, Benjamin and Radon, Christin and Leimk{\"u}hler, Silke}, title = {Characterization and interaction studies of two isoforms of the dual localized 3-mercaptopyruvate sulfurtransferase TUM1 from humans}, series = {The journal of biological chemistry}, volume = {289}, journal = {The journal of biological chemistry}, number = {50}, publisher = {American Society for Biochemistry and Molecular Biology}, address = {Bethesda}, issn = {0021-9258}, doi = {10.1074/jbc.M114.605733}, pages = {34543 -- 34556}, year = {2014}, abstract = {Background: Localization and identification of interaction partners of two splice variants of the human 3-mercaptopyruvate sulfurtransferase TUM1. Results: We show that TUM1 interacts with proteins involved in Moco and FeS cluster biosynthesis. Conclusion: Human TUM1 is a dual localized protein in the cytosol and mitochondria with distinct roles in sulfur transfer and interaction partners. Significance: The study contributes to the sulfur transfer pathway for the biosynthesis of sulfur-containing biofactors. The human tRNA thiouridine modification protein (TUM1), also designated as 3-mercaptopyruvate sulfurtransferase (MPST), has been implicated in a wide range of physiological processes in the cell. The roles range from an involvement in thiolation of cytosolic tRNAs to the generation of H2S as signaling molecule both in mitochondria and the cytosol. TUM1 is a member of the sulfurtransferase family and catalyzes the conversion of 3-mercaptopyruvate to pyruvate and protein-bound persulfide. Here, we purified and characterized two novel TUM1 splice variants, designated as TUM1-Iso1 and TUM1-Iso2. The purified proteins showed similar kinetic behavior and comparable pH and temperature dependence. Cellular localization studies, however, showed a different localization pattern between the isoforms. TUM1-Iso1 is exclusively localized in the cytosol, whereas TUM1-Iso2 showed a dual localization both in the cytosol and mitochondria. Interaction studies were performed with the isoforms both in vitro using the purified proteins and in vivo by fluorescence analysis in human cells, using the split-EGFP system. The studies showed that TUM1 interacts with the l-cysteine desulfurase NFS1 and the rhodanese-like protein MOCS3, suggesting a dual function of TUM1 both in sulfur transfer for the biosynthesis of the molybdenum cofactor, and for the thiolation of tRNA. Our studies point to distinct roles of each TUM1 isoform in the sulfur transfer processes in the cell, with different compartmentalization of the two splice variants of TUM1.}, language = {en} } @article{FrenchSimcockRolkeetal.2014, author = {French, Alice S. and Simcock, Kerry L. and Rolke, Daniel and Gartside, Sarah E. and Blenau, Wolfgang and Wright, Geraldine A.}, title = {The role of serotonin in feeding and gut contractions in the honeybee}, series = {Journal of insect physiology}, volume = {61}, journal = {Journal of insect physiology}, publisher = {Elsevier}, address = {Oxford}, issn = {0022-1910}, doi = {10.1016/j.jinsphys.2013.12.005}, pages = {8 -- 15}, year = {2014}, language = {en} } @article{FrescatadaRosaStanislasBackuesetal.2014, author = {Frescatada-Rosa, Marcia and Stanislas, Thomas and Backues, Steven K. and Reichardt, Ilka and Men, Shuzhen and Boutte, Yohann and Juergens, Gerd and Moritz, Thomas and Bednarek, Sebastian York and Grebe, Markus}, title = {High lipid order of Arabidopsis cell-plate membranes mediated by sterol and Dynamin-Related Protein 1A function}, series = {The plant journal}, volume = {80}, journal = {The plant journal}, number = {5}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0960-7412}, doi = {10.1111/tpj.12674}, pages = {745 -- 757}, year = {2014}, abstract = {Membranes of eukaryotic cells contain high lipid-order sterol-rich domains that are thought to mediate temporal and spatial organization of cellular processes. Sterols are crucial for execution of cytokinesis, the last stage of cell division, in diverse eukaryotes. The cell plate of higher-plant cells is the membrane structure that separates daughter cells during somatic cytokinesis. Cell-plate formation in Arabidopsis relies on sterol- and DYNAMIN-RELATED PROTEIN1A (DRP1A)-dependent endocytosis. However, functional relationships between lipid membrane order or lipid packing and endocytic machinery components during eukaryotic cytokinesis have not been elucidated. Using ratiometric live imaging of lipid order-sensitive fluorescent probes, we show that the cell plate of Arabidopsis thaliana represents a dynamic, high lipid-order membrane domain. The cell-plate lipid order was found to be sensitive to pharmacological and genetic alterations of sterol composition. Sterols co-localize with DRP1A at the cell plate, and DRP1A accumulates in detergent-resistant membrane fractions. Modifications of sterol concentration or composition reduce cell-plate membrane order and affect DRP1A localization. Strikingly, DRP1A function itself is essential for high lipid order at the cell plate. Our findings provide evidence that the cell plate represents a high lipid-order domain, and pave the way to explore potential feedback between lipid order and function of dynamin-related proteins during cytokinesis.}, language = {en} } @phdthesis{Fronton2014, author = {Fronton, Ludivine}, title = {Modeling approaches to characterize the disposition of monoclonal antibodies}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-76537}, school = {Universit{\"a}t Potsdam}, pages = {xxi, 133}, year = {2014}, abstract = {Monoclonal antibodies (mAbs) are engineered immunoglobulins G (IgG) used for more than 20 years as targeted therapy in oncology, infectious diseases and (auto-)immune disorders. Their protein nature greatly influences their pharmacokinetics (PK), presenting typical linear and non-linear behaviors. While it is common to use empirical modeling to analyze clinical PK data of mAbs, there is neither clear consensus nor guidance to, on one hand, select the structure of classical compartment models and on the other hand, interpret mechanistically PK parameters. The mechanistic knowledge present in physiologically-based PK (PBPK) models is likely to support rational classical model selection and thus, a methodology to link empirical and PBPK models is desirable. However, published PBPK models for mAbs are quite diverse in respect to the physiology of distribution spaces and the parameterization of the non-specific elimination involving the neonatal Fc receptor (FcRn) and endogenous IgG (IgGendo). The remarkable discrepancy between the simplicity of biodistribution data and the complexity of published PBPK models translates in parameter identifiability issues. In this thesis, we address this problem with a simplified PBPK model—derived from a hierarchy of more detailed PBPK models and based on simplifications of tissue distribution model. With the novel tissue model, we are breaking new grounds in mechanistic modeling of mAbs disposition: We demonstrate that binding to FcRn is indeed linear and that it is not possible to infer which tissues are involved in the unspecific elimination of wild-type mAbs. We also provide a new approach to predict tissue partition coefficients based on mechanistic insights: We directly link tissue partition coefficients (Ktis) to data-driven and species-independent published antibody biodistribution coefficients (ABCtis) and thus, we ensure the extrapolation from pre-clinical species to human with the simplified PBPK model. We further extend the simplified PBPK model to account for a target, relevant to characterize the non-linear clearance due to mAb-target interaction. With model reduction techniques, we reduce the dimensionality of the simplified PBPK model to design 2-compartment models, thus guiding classical model development with physiological and mechanistic interpretation of the PK parameters. We finally derive a new scaling approach for anatomical and physiological parameters in PBPK models that translates the inter-individual variability into the design of mechanistic covariate models with direct link to classical compartment models, specially useful for PK population analysis during clinical development.}, language = {en} } @article{FrontonPilariHuisinga2014, author = {Fronton, Ludivine and Pilari, Sabine and Huisinga, Wilhelm}, title = {Monoclonal antibody disposition: a simplified PBPK model and its implications for the derivation and interpretation of classical compartment models}, series = {Journal of pharmacokinetics and pharmacodynamics}, volume = {41}, journal = {Journal of pharmacokinetics and pharmacodynamics}, number = {2}, publisher = {Springer}, address = {New York}, issn = {1567-567X}, doi = {10.1007/s10928-014-9349-1}, pages = {87 -- 107}, year = {2014}, abstract = {The structure, interpretation and parameterization of classical compartment models as well as physiologically-based pharmacokinetic (PBPK) models for monoclonal antibody (mAb) disposition are very diverse, with no apparent consensus. In addition, there is a remarkable discrepancy between the simplicity of experimental plasma and tissue profiles and the complexity of published PBPK models. We present a simplified PBPK model based on an extravasation rate-limited tissue model with elimination potentially occurring from various tissues and plasma. Based on model reduction (lumping), we derive several classical compartment model structures that are consistent with the simplified PBPK model and experimental data. We show that a common interpretation of classical two-compartment models for mAb disposition-identifying the central compartment with the total plasma volume and the peripheral compartment with the interstitial space (or part of it)-is not consistent with current knowledge. Results are illustrated for the monoclonal antibodies 7E3 and T84.66 in mice.}, language = {en} } @article{FujikuraElsaesserBreuningeretal.2014, author = {Fujikura, Ushio and Elsaesser, Lore and Breuninger, Holger and Sanchez-Rodriguez, Clara and Ivakov, Alexander and Laux, Thomas and Findlay, Kim and Persson, Staffan and Lenhard, Michael}, title = {Atkinesin-13A modulates cell-wall synthesis and cell expansion in arabidopsis thaliana via the THESEUS1 pathway}, series = {PLoS Genetics : a peer-reviewed, open-access journal}, volume = {10}, journal = {PLoS Genetics : a peer-reviewed, open-access journal}, number = {9}, publisher = {PLoS}, address = {San Fransisco}, issn = {1553-7390}, doi = {10.1371/journal.pgen.1004627}, pages = {15}, year = {2014}, abstract = {Growth of plant organs relies on cell proliferation and expansion. While an increasingly detailed picture about the control of cell proliferation is emerging, our knowledge about the control of cell expansion remains more limited. We demonstrate the internal-motor kinesin AtKINESIN-13A (AtKIN13A) limits cell expansion and cell size in Arabidopsis thaliana, ion atkinl3a mutants forming larger petals with larger cells. The homolog, AtKINESIN-13B, also affects cell expansion and double mutants display growth, gametophytic and early embryonic defects, indicating a redundant role of he two genes. AtKIN13A is known to depolymerize microtubules and influence Golgi motility and distribution. Consistent his function, AtKIN13A interacts genetically with ANGUSTIFOLIA, encoding a regulator of Golgi dynamics. Reduced AtIGN13A activity alters cell wall structure as assessed by Fourier-transformed infrared-spectroscopy and triggers signalling he THESEUS1-dependent cell-wall integrity pathway, which in turn promotes the excess cell expansion in the atkinl3a mutant. Thus, our results indicate that the intracellular activity of AtKIN13A regulates cell expansion and wall architecture via THESEUS1, providing a compelling case of interplay between cell wall integrity sensing and expansion.}, language = {en} } @article{GabsiHammersWirtzGrimmetal.2014, author = {Gabsi, Faten and Hammers-Wirtz, Monika and Grimm, Volker and Schaeffer, Andreas and Preuss, Thomas G.}, title = {Coupling different mechanistic effect models for capturing individual- and population-level effects of chemicals: Lessons from a case where standard risk assessment failed}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {280}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2013.06.018}, pages = {18 -- 29}, year = {2014}, abstract = {Current environmental risk assessment (ERA) of chemicals for aquatic invertebrates relies on standardized laboratory tests in which toxicity effects on individual survival, growth and reproduction are measured. Such tests determine the threshold concentration of a chemical below which no population-level effects are expected. How well this procedure captures effects on individuals and populations, however, remains an open question. Here we used mechanistic effect models, combining individual-level reproduction and survival models with an individual-based population model (IBM), to understand the individuals' responses and extrapolate them to the population level. We used a toxicant (Dispersogen A) for which adverse effects on laboratory populations were detected at the determined threshold concentration and thus challenged the conservatism of the current risk assessment method. Multiple toxicity effects on reproduction and survival were reported, in addition to effects on the F1 generation. We extrapolated commonly tested individual toxicity endpoints, reproduction and survival, to the population level using the IBM. Effects on reproduction were described via regression models. To select the most appropriate survival model, the IBM was run assuming either stochastic death (SD) or individual tolerance (IT). Simulations were run for different scenarios regarding the toxicant's effects: survival toxicity, reproductive toxicity, or survival and reproductive toxicity. As population-level endpoints, we used population size and structure and extinction risk. We found that survival represented as SD explained population dynamics better than IT. Integrating toxicity effects on both reproduction and survival yielded more accurate predictions of population effects than considering isolated effects. To fully capture population effects observed at high toxicant concentrations, toxicity effects transmitted to the F1 generation had to be integrated. Predicted extinction risk was highly sensitive to the assumptions about individual-level effects. Our results demonstrate that the endpoints used in current standard tests may not be sufficient for assessing the risk of adverse effects on populations. A combination of laboratory population experiments with mechanistic effect models is a powerful tool to better understand and predict effects on both individuals and populations. Mechanistic effect modelling thus holds great potential to improve the accuracy of ERA of chemicals in the future. (C) 2013 The Authors. Published by Elsevier B.V. All rights reserved.}, language = {en} } @article{GambaJonesTeasdaleetal.2014, author = {Gamba, Cristina and Jones, Eppie R. and Teasdale, Matthew D. and McLaughlin, Russell L. and Gonz{\´a}lez-Fortes, Gloria M. and Mattiangeli, Valeria and Domboroczki, Laszlo and Kovari, Ivett and Pap, Ildiko and Anders, Alexandra and Whittle, Alasdair and Dani, Janos and Raczky, Pal and Higham, Thomas F. G. and Hofreiter, Michael and Bradley, Daniel G. and Pinhasi, Ron}, title = {Genome flux and stasis in a five millennium transect of European prehistory}, series = {Nature Communications}, volume = {5}, journal = {Nature Communications}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/ncomms6257}, pages = {9}, year = {2014}, abstract = {The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (similar to 22x) and seven to similar to 1x coverage, to investigate the impact of these on Europe's genetic landscape. These data suggest genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability. The earliest Neolithic context genome shows a European hunter-gatherer genetic signature and a restricted ancestral population size, suggesting direct contact between cultures after the arrival of the first farmers into Europe. The latest, Iron Age, sample reveals an eastern genomic influence concordant with introduced Steppe burial rites. We observe transition towards lighter pigmentation and surprisingly, no Neolithic presence of lactase persistence.}, language = {en} } @misc{GambaJonesTeasdaleetal.2014, author = {Gamba, Cristina and Jones, Eppie R. and Teasdale, Matthew D. and McLaughlin, Russell L. and Gonz{\´a}lez-Fortes, Gloria M. and Mattiangeli, Valeria and Dombor{\´o}czki, L{\´a}szl{\´o} and Kőv{\´a}ri, Ivett and Pap, Ildik{\´o} and Anders, Alexandra and Whittle, Alasdair and Dani, J{\´a}nos and Raczky, P{\´a}l and Higham, Thomas F. G. and Hofreiter, Michael and Bradley, Daniel G. and Pinhasi, Ron}, title = {Genome flux and stasis in a five millennium transect of European prehistory}, series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, volume = {5}, journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1332}, issn = {1866-8372}, doi = {10.25932/publishup-43799}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-437999}, pages = {9}, year = {2014}, abstract = {The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (similar to 22x) and seven to similar to 1x coverage, to investigate the impact of these on Europe's genetic landscape. These data suggest genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability. The earliest Neolithic context genome shows a European hunter-gatherer genetic signature and a restricted ancestral population size, suggesting direct contact between cultures after the arrival of the first farmers into Europe. The latest, Iron Age, sample reveals an eastern genomic influence concordant with introduced Steppe burial rites. We observe transition towards lighter pigmentation and surprisingly, no Neolithic presence of lactase persistence.}, language = {en} } @article{GarciaMcMahonGrossartetal.2014, author = {Garcia, Sarahi L. and McMahon, Katherine D. and Grossart, Hans-Peter and Warnecke, Falk}, title = {Successful enrichment of the ubiquitous freshwater acI Actinobacteria}, series = {Environmental microbiology reports}, volume = {6}, journal = {Environmental microbiology reports}, number = {1}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1758-2229}, doi = {10.1111/1758-2229.12104}, pages = {21 -- 27}, year = {2014}, abstract = {Actinobacteria of the acI lineage are often the numerically dominant bacterial phylum in surface freshwaters, where they can account for >50\% of total bacteria. Despite their abundance, there are no described isolates. In an effort to obtain enrichment of these ubiquitous freshwater Actinobacteria, diluted freshwater samples from Lake Grosse Fuchskuhle, Germany, were incubated in 96-well culture plates. With this method, a successful enrichment containing high abundances of a member of the lineage acI was established. Phylogenetic classification showed that the acIActinobacteria of the enrichment belonged to the acI-B2 tribe, which seems to prefer acidic lakes. This enrichment grows to low cell densities and thus the oligotrophic nature of acI-B2 was confirmed.}, language = {en} } @article{GattePicchiWeizIshidaetal.2014, author = {Gatte-Picchi, Douglas and Weiz, Annika and Ishida, Keishi and Hertweck, Christian and Dittmann-Th{\"u}nemann, Elke}, title = {Functional analysis of environmental DNA-derived microviridins provides new insights into the diversity of the tricyclic peptide family}, series = {Applied and environmental microbiology}, volume = {80}, journal = {Applied and environmental microbiology}, number = {4}, publisher = {American Society for Microbiology}, address = {Washington}, issn = {0099-2240}, doi = {10.1128/AEM.03502-13}, pages = {1380 -- 1387}, year = {2014}, abstract = {Microviridins represent a unique family of ribosomally synthesized cage-like depsipeptides from cyanobacteria with potent protease-inhibitory activities. The natural diversity of these peptides is largely unexplored. Here, we describe two methodologies that were developed to functionally characterize cryptic microviridin gene clusters from metagenomic DNA. Environmental samples were collected and enriched from cyanobacterial freshwater blooms of different geographical origins containing predominantly Microcystis sp. Microviridins were produced either directly from fosmid clones or after insertion of environmental DNA-derived gene cassettes into a minimal expression platform in Escherichia coli. Three novel microviridin variants were isolated and tested against different serine-type proteases. The comparison of the bioactivity profiles of the new congeners allows deduction of further structure-function relationships for microviridins. Moreover, this study provides new insights into microviridin processing and gene cluster organization.}, language = {en} } @misc{GechevHilleWoerdenbagetal.2014, author = {Gechev, Tsanko S. and Hille, Jacques and Woerdenbag, Herman J. and Benina, Maria and Mehterov, Nikolay and Toneva, Valentina and Fernie, Alisdair R. and M{\"u}ller-R{\"o}ber, Bernd}, title = {Natural products from resurrection plants: Potential for medical applications}, series = {Biotechnology advances : an international review journal ; research reviews and patent abstracts}, volume = {32}, journal = {Biotechnology advances : an international review journal ; research reviews and patent abstracts}, number = {6}, publisher = {Elsevier}, address = {Oxford}, issn = {0734-9750}, doi = {10.1016/j.biotechadv.2014.03.005}, pages = {1091 -- 1101}, year = {2014}, abstract = {Resurrection species are a group of land plants that can tolerate extreme desiccation of their vegetative tissues during harsh drought stress, and still quickly often within hours regain normal physiological and metabolic functions following rehydration. At the molecular level, this desiccation tolerance is attributed to basal cellular mechanisms including the constitutive expression of stress-associated genes and high levels of protective metabolites present already in the absence of stress, as well as to transcriptome and metabolome reconfigurations rapidly occurring during the initial phases of drought stress. Parts of this response are conferred by unique metabolites, including a diverse array of sugars, phenolic compounds, and polyols, some of which accumulate to high concentrations within the plant cell. In addition to drought stress, these metabolites are proposed to contribute to the protection against other abiotic stresses and to an increased oxidative stress tolerance. Recently, extracts of resurrection species and particular secondary metabolites therein were reported to display biological activities of importance to medicine, with e.g. antibacterial, anticancer, antifungal, and antiviral activities, rendering them possible candidates for the development of novel drug substances as well as for cosmetics. Herein, we provide an overview of the metabolite composition of resurrection species, summarize the latest reports related to the use of natural products from resurrection plants, and outline their potential for medical applications. (C) 2014 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/3.0/).}, language = {en} } @misc{GiladiMayRistowetal.2014, author = {Giladi, Itamar and May, Felix and Ristow, Michael and Jeltsch, Florian and Ziv, Yaron}, title = {Scale-dependent species-area and species-isolation relationships: a review and a test study from a fragmented semi-arid agro-ecosystem}, series = {Journal of biogeography}, volume = {41}, journal = {Journal of biogeography}, number = {6}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0305-0270}, doi = {10.1111/jbi.12299}, pages = {1055 -- 1069}, year = {2014}, abstract = {Aim Patterns that relate species richness with fragment area (the species-area relationship, SAR) and with isolation (the species-isolation relationship, SIR) are well documented. However, those that relate species density - the number of species within a standardized area - with fragment area (D-SAR) or isolation (D-SIR) have not been sufficiently explored, despite the potential for such an analysis to disentangle the underlying mechanisms of SARs and SIRs. Previous spatial theory predicts that a significant D-SAR or D-SIR is unlikely to emerge in taxa with high dispersal limitation, such as plants. Furthermore, a recent model predicts that the detection and the significance of D-SARs or D-SIRs may decrease with grain size. We combined a literature review with grain size-dependent sampling in a fragmented landscape to evaluate the prevalence and grain size-dependent nature of D-SARs and D-SIRs in plants. Location Worldwide (review) and a semi-arid agro-ecosystem in Israel (case study). Methods We combined an extensive literature review of 31 D-SAR studies of plants in fragmented landscapes with an empirical study in which we analysed grain size-dependent D-SARs and D-SIRs using a grain size-dependent hierarchical sampling of species density and species richness in a fragmented, semi-arid agro-ecosystem. Results We found that significantly increasing D-SARs are rare in plant studies. Furthermore, we found that the detection of a significant D-SAR is often possible only after the data have been stratified by species, habitat or landscape characteristics. The results from our case study indicated that the significance and the slopes of both D-SARs and D-SIRs increase as grain size decreases. Main conclusions These results call for a careful consideration of scale while analysing and interpreting the responses of species richness and species density to fragmentation. Our results suggest that grain size-dependent analyses of D-SARs and D-SIRs may help to disentangle the mechanisms that generate SARs and SIRs and may enable early detection of the effects of fragmentation on plant biodiversity.}, language = {en} } @phdthesis{Girbig2014, author = {Girbig, Dorothee}, title = {Analysing concerted criteria for local dynamic properties of metabolic systems}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72017}, school = {Universit{\"a}t Potsdam}, year = {2014}, abstract = {Metabolic systems tend to exhibit steady states that can be measured in terms of their concentrations and fluxes. These measurements can be regarded as a phenotypic representation of all the complex interactions and regulatory mechanisms taking place in the underlying metabolic network. Such interactions determine the system's response to external perturbations and are responsible, for example, for its asymptotic stability or for oscillatory trajectories around the steady state. However, determining these perturbation responses in the absence of fully specified kinetic models remains an important challenge of computational systems biology. Structural kinetic modeling (SKM) is a framework to analyse whether a metabolic steady state remains stable under perturbation, without requiring detailed knowledge about individual rate equations. It provides a parameterised representation of the system's Jacobian matrix in which the model parameters encode information about the enzyme-metabolite interactions. Stability criteria can be derived by generating a large number of structural kinetic models (SK-models) with randomly sampled parameter sets and evaluating the resulting Jacobian matrices. The parameter space can be analysed statistically in order to detect network positions that contribute significantly to the perturbation response. Because the sampled parameters are equivalent to the elasticities used in metabolic control analysis (MCA), the results are easy to interpret biologically. In this project, the SKM framework was extended by several novel methodological improvements. These improvements were evaluated in a simulation study using a set of small example pathways with simple Michaelis Menten rate laws. Afterwards, a detailed analysis of the dynamic properties of the neuronal TCA cycle was performed in order to demonstrate how the new insights obtained in this work could be used for the study of complex metabolic systems. The first improvement was achieved by examining the biological feasibility of the elasticity combinations created during Monte Carlo sampling. Using a set of small example systems, the findings showed that the majority of sampled SK-models would yield negative kinetic parameters if they were translated back into kinetic models. To overcome this problem, a simple criterion was formulated that mitigates such infeasible models and the application of this criterion changed the conclusions of the SKM experiment. The second improvement of this work was the application of supervised machine-learning approaches in order to analyse SKM experiments. So far, SKM experiments have focused on the detection of individual enzymes to identify single reactions important for maintaining the stability or oscillatory trajectories. In this work, this approach was extended by demonstrating how SKM enables the detection of ensembles of enzymes or metabolites that act together in an orchestrated manner to coordinate the pathways response to perturbations. In doing so, stable and unstable states served as class labels, and classifiers were trained to detect elasticity regions associated with stability and instability. Classification was performed using decision trees and relevance vector machines (RVMs). The decision trees produced good classification accuracy in terms of model bias and generalizability. RVMs outperformed decision trees when applied to small models, but encountered severe problems when applied to larger systems because of their high runtime requirements. The decision tree rulesets were analysed statistically and individually in order to explore the role of individual enzymes or metabolites in controlling the system's trajectories around steady states. The third improvement of this work was the establishment of a relationship between the SKM framework and the related field of MCA. In particular, it was shown how the sampled elasticities could be converted to flux control coefficients, which were then investigated for their predictive information content in classifier training. After evaluation on the small example pathways, the methodology was used to study two steady states of the neuronal TCA cycle with respect to their intrinsic mechanisms responsible for stability or instability. The findings showed that several elasticities were jointly coordinated to control stability and that the main source for potential instabilities were mutations in the enzyme alpha-ketoglutarate dehydrogenase.}, language = {en} } @article{GlaeserBerghoffStratmannetal.2014, author = {Glaeser, Stefanie P. and Berghoff, Bork A. and Stratmann, Verena and Grossart, Hans-Peter and Glaeser, Jens}, title = {Contrasting effects of singlet oxygen and hydrogen peroxide on bacterial community composition in a humic lake}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {3}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0092518}, pages = {19}, year = {2014}, abstract = {Light excitation of humic matter generates reactive oxygen species (ROS) in surface waters of aquatic ecosystems. Abundant ROS generated in humic matter rich lakes include singlet oxygen (O-1(2)) and hydrogen peroxide (H2O2). Because these ROS differ in half-life time and toxicity, we compared their effects on microbial activity (C-14-Leucine incorporation) and bacterial community composition (BCC) in surface waters of humic Lake Grosse Fuchskuhle (North-eastern Germany). For this purpose, experiments with water samples collected from the lake were conducted in July 2006, September 2008 and August 2009. Artificially increased O-1(2) and H2O2 concentrations inhibited microbial activity in water samples to a similar extent, but the effect of the respective ROS on BCC varied strongly. BCC analysis by 16S rRNA gene clone libraries and RT-PCR DGGE revealed ROS specific changes in relative abundance and activity of major bacterial groups and composition of dominating phylotypes. These changes were consistent in the three experiments performed in different years. The relative abundance of Polynucleobacter necessarius, Limnohabitans-related phylotypes (Betaproteobacteria), and Novosphingobium acidiphilum (Alphaproteobacteria) increased or was not affected by photo-sensitized O-1(2) exposure, but decreased after H2O2 exposure. The opposite pattern was found for Actinobacteria of the freshwater AcI-B cluster which were highly sensitive to O-1(2) but not to H2O2 exposure. Furthermore, group-specific RT-PCR DGGE analysis revealed that particle-attached P. necessarius and Limnohabitans-related phylotypes exhibit higher resistance to O-1(2) exposure compared to free-living populations. These results imply that O-1(2) acts as a factor in niche separation of closely affiliated Polynucleobacter and Limnohabitans-related phylotypes. Consequently, oxidative stress caused by photochemical ROS generation should be regarded as an environmental variable determining abundance, activity, and phylotype composition of environmentally relevant bacterial groups, in particular in illuminated and humic matter rich waters.}, language = {en} } @article{Gonzalez2014, author = {Gonzalez, Javier}, title = {Phylogenetic position of the most endangered Chilean bird: the Masafuera Rayadito (Aphrastura masafuerae; Furnariidae)}, series = {Tropical conservation science}, volume = {7}, journal = {Tropical conservation science}, number = {4}, publisher = {Mongabay.com}, address = {Menlo Park}, issn = {1940-0829}, pages = {677 -- 689}, year = {2014}, abstract = {Masafuera Rayadito (Aphrastura masafuerae; Furnariidae) is a Critically Endangered species endemic to Alejandro Selkirk Island (Juan Fernandez Archipelago, Chile). Categorized as probably extinct in 1980, later estimates, ranging from 140 (in 2002) to 500 individuals (in 2006-2007), showed a fluctuating population size of the species. The grazing of goats and cattle has increased habitat loss for the species. Other threats are lack of nesting sites, introduced species such as feral cats and rats (Rattus rattus and R. norvegicus), and increased populations of natural predators like the Masafuera Hawk. In order to increase the availability of nesting sites, 81 nest boxes were installed in different habitats in 2006, with evidence of use during subsequent breeding seasons. Despite conservation concerns, however, no genetic studies are yet available for this furnariid. This study reports for the first time the levels of genetic divergence of the species, based on nucleotide sequences of the mitochondrial DNA (cytochrome oxidase subunit 1 gene; COI). Aphrastura masafuerae is closely related to a widespread species of furnariid distributed mainly in Chile on the mainland, the Thorn-tailed Rayadito (A. spinicauda). The Masafuera Rayadito diverged from its mainland sister species probably during the Pleistocene 0.57 +/- 0.19 Myr ago. Consistent with mitochondrial and nuclear molecular clocks, the estimated time of the split between A. masafuerae and A. spinicauda is in perfect agreement with the geological origin of the Juan Fernandez Archipelago, which is of volcanic origin. In order to assess genetic variability within the population of this fragile bird, further studies using a multi-locus genetic approach at the population level are necessary.}, language = {en} } @article{GopalakrishnanMontazeriMenzetal.2014, author = {Gopalakrishnan, Sathej and Montazeri, Hesam and Menz, Stephan and Beerenwinkel, Niko and Huisinga, Wilhelm}, title = {Estimating HIV-1 fitness characteristics from cross-sectional genotype data}, series = {PLoS Computational Biology : a new community journal}, volume = {10}, journal = {PLoS Computational Biology : a new community journal}, number = {11}, publisher = {PLoS}, address = {San Fransisco}, issn = {1553-734X}, doi = {10.1371/journal.pcbi.1003886}, pages = {14}, year = {2014}, abstract = {Despite the success of highly active antiretroviral therapy (HAART) in the management of human immunodeficiency virus (HIV)-1 infection, virological failure due to drug resistance development remains a major challenge. Resistant mutants display reduced drug susceptibilities, but in the absence of drug, they generally have a lower fitness than the wild type, owing to a mutation-incurred cost. The interaction between these fitness costs and drug resistance dictates the appearance of mutants and influences viral suppression and therapeutic success. Assessing in vivo viral fitness is a challenging task and yet one that has significant clinical relevance. Here, we present a new computational modelling approach for estimating viral fitness that relies on common sparse cross-sectional clinical data by combining statistical approaches to learn drug-specific mutational pathways and resistance factors with viral dynamics models to represent the host-virus interaction and actions of drug mechanistically. We estimate in vivo fitness characteristics of mutant genotypes for two antiretroviral drugs, the reverse transcriptase inhibitor zidovudine (ZDV) and the protease inhibitor indinavir (IDV). Well-known features of HIV-1 fitness landscapes are recovered, both in the absence and presence of drugs. We quantify the complex interplay between fitness costs and resistance by computing selective advantages for different mutants. Our approach extends naturally to multiple drugs and we illustrate this by simulating a dual therapy with ZDV and IDV to assess therapy failure. The combined statistical and dynamical modelling approach may help in dissecting the effects of fitness costs and resistance with the ultimate aim of assisting the choice of salvage therapies after treatment failure.}, language = {en} } @article{GossnerPasalicLangeetal.2014, author = {Gossner, Martin M. and Pasalic, Esther and Lange, Markus and Lange, Patricia and Boch, Steffen and Hessenm{\"o}ller, Dominik and M{\"u}ller, J{\"o}rg and Socher, Stephanie A. and Fischer, Markus and Schulze, Ernst-Detlef and Weisser, Wolfgang W.}, title = {Differential responses of herbivores and herbivory to management in temperate Eeuropean beech}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {8}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0104876}, pages = {16}, year = {2014}, abstract = {Forest management not only affects biodiversity but also might alter ecosystem processes mediated by the organisms, i.e. herbivory the removal of plant biomass by plant-eating insects and other arthropod groups. Aiming at revealing general relationships between forest management and herbivory we investigated aboveground arthropod herbivory in 105 plots dominated by European beech in three different regions in Germany in the sun-exposed canopy of mature beech trees and on beech saplings in the understorey. We separately assessed damage by different guilds of herbivores, i.e. chewing, sucking and scraping herbivores, gall-forming insects and mites, and leaf-mining insects. We asked whether herbivory differs among different forest management regimes (unmanaged, uneven-aged managed, even-aged managed) and among age-classes within even-aged forests. We further tested for consistency of relationships between regions, strata and herbivore guilds. On average, almost 80\% of beech leaves showed herbivory damage, and about 6\% of leaf area was consumed. Chewing damage was most common, whereas leaf sucking and scraping damage were very rare. Damage was generally greater in the canopy than in the understorey, in particular for chewing and scraping damage, and the occurrence of mines. There was little difference in herbivory among differently managed forests and the effects of management on damage differed among regions, strata and damage types. Covariates such as wood volume, tree density and plant diversity weakly influenced herbivory, and effects differed between herbivory types. We conclude that despite of the relatively low number of species attacking beech; arthropod herbivory on beech is generally high. We further conclude that responses of herbivory to forest management are multifaceted and environmental factors such as forest structure variables affecting in particular microclimatic conditions are more likely to explain the variability in herbivory among beech forest plots.}, language = {en} } @article{GraccevaHerdeGroothuisetal.2014, author = {Gracceva, Giulia and Herde, Antje and Groothuis, Ton G. G. and Koolhaas, Jaap M. and Palme, Rupert and Eccard, Jana}, title = {Turning shy on a winter's day: Effects of season on personality and stress response in Microtus arvalis}, series = {Ethology}, volume = {120}, journal = {Ethology}, number = {8}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0179-1613}, doi = {10.1111/eth.12246}, pages = {753 -- 767}, year = {2014}, abstract = {Animal personalities are by definition stable over time, but to what extent they may change during development and in adulthood to adjust to environmental change is unclear. Animals of temperate environments have evolved physiological and behavioural adaptations to cope with the cyclic seasonal changes. This may also result in changes in personality: suites of behavioural and physiological traits that vary consistently among individuals. Winter, typically the adverse season challenging survival, may require individuals to have shy/cautious personality, whereas during summer, energetically favourable to reproduction, individuals may benefit from a bold/risk-taking personality. To test the effects of seasonal changes in early life and in adulthood on behaviours (activity, exploration and anxiety), body mass and stress response, we manipulated the photoperiod and quality of food in two experiments to simulate the conditions of winter and summer. We used the common voles (Microtus arvalis) as they have been shown to display personality based on behavioural consistency over time and contexts. Summer-born voles allocated to winter conditions at weaning had lower body mass, a higher corticosterone increase after stress and a less active, more cautious behavioural phenotype in adulthood compared to voles born in and allocated to summer conditions. In contrast, adult females only showed plasticity in stress-induced corticosterone levels, which were higher in the animals that were transferred to the winter conditions than to those staying in summer conditions. These results suggest a sensitive period for season-related behavioural plasticity in which juveniles shift over the bold-shy axis.}, language = {en} } @article{GrimmAugusiakFocksetal.2014, author = {Grimm, Volker and Augusiak, Jacqueline and Focks, Andreas and Frank, Beatrice M. and Gabsi, Faten and Johnston, Alice S. A. and Liu, Chun and Martin, Benjamin T. and Meli, Mattia and Radchuk, Viktoriia and Thorbek, Pernille and Railsback, Steven Floyd}, title = {Towards better modelling and decision support: Documenting model development, testing, and analysis using TRACE}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {280}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2014.01.018}, pages = {129 -- 139}, year = {2014}, abstract = {The potential of ecological models for supporting environmental decision making is increasingly acknowledged. However, it often remains unclear whether a model is realistic and reliable enough. Good practice for developing and testing ecological models has not yet been established. Therefore, TRACE, a general framework for documenting a model's rationale, design, and testing was recently suggested. Originally TRACE was aimed at documenting good modelling practice. However, the word 'documentation' does not convey TRACE's urgency. Therefore, we re-define TRACE as a tool for planning, performing, and documenting good modelling practice. TRACE documents should provide convincing evidence that a model was thoughtfully designed, correctly implemented, thoroughly tested, well understood, and appropriately used for its intended purpose. TRACE documents link the science underlying a model to its application, thereby also linking modellers and model users, for example stakeholders, decision makers, and developers of policies. We report on first experiences in producing TRACE documents. We found that the original idea underlying TRACE was valid, but to make its use more coherent and efficient, an update of its structure and more specific guidance for its use are needed. The updated TRACE format follows the recently developed framework of model 'evaludation': the entire process of establishing model quality and credibility throughout all stages of model development, analysis, and application. TRACE thus becomes a tool for planning, documenting, and assessing model evaludation, which includes understanding the rationale behind a model and its envisaged use. We introduce the new structure and revised terminology of TRACE and provide examples. (C) 2014 Elsevier B.V. All rights reserved.}, language = {en} } @unpublished{GrimmThorbek2014, author = {Grimm, Volker and Thorbek, Pernille}, title = {Population models for ecological risk assessment of chemicals: Short introduction and summary of a special issue}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {280}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2014.01.017}, pages = {1 -- 4}, year = {2014}, language = {en} } @article{GuoFuJuerchottetal.2014, author = {Guo, Ke-Tai and Fu, Peng and Juerchott, Kathrin and Motaln, Helena and Selbig, Joachim and Lah, Tamara T. and Tonn, J{\"o}rg-Christian and Schichor, Christian}, title = {The expression of Wnt-inhibitor DKK1 (Dickkopf 1) is determined by intercellular crosstalk and hypoxia in human malignant gliomas}, series = {Journal of cancer research and clinical oncology : official organ of the Deutsche Krebsgesellschaft}, volume = {140}, journal = {Journal of cancer research and clinical oncology : official organ of the Deutsche Krebsgesellschaft}, number = {8}, publisher = {Springer}, address = {New York}, issn = {0171-5216}, doi = {10.1007/s00432-014-1642-2}, pages = {1261 -- 1270}, year = {2014}, abstract = {Objective Wnt signalling pathways regulate proliferation, motility and survival in a variety of human cell types. Dickkopf 1 (DKK1) gene codes for a secreted Wnt inhibitory factor. It functions as tumour suppressor gene in breast cancer and as a pro-apoptotic factor in glioma cells. In this study, we aimed to demonstrate whether the different expression of DKK1 in human glioma-derived cells is dependent on microenvironmental factors like hypoxia and regulated by the intercellular crosstalk with bone-marrow-derived mesenchymal stem cells (bmMSCs). Methods Glioma cell line U87-MG, three cell lines from human glioblastoma grade IV (glioma-derived mesenchymal stem cells) and three bmMSCs were selected for the experiment. The expression of DKK1 in cell lines under normoxic/hypoxic environment or co-culture condition was measured using real-time PCR and enzyme-linked immunoadsorbent assay. The effect of DKK1 on cell migration and proliferation was evaluated by in vitro wound healing assays and sulphorhodamine assays, respectively. Results Glioma-derived cells U87-MG displayed lower DKK1 expression compared with bmMSCs. Hypoxia led to an overexpression of DKK1 in bmMSCs and U87-MG when compared to normoxic environment, whereas co-culture of U87-MG with bmMSCs induced the expression of DKK1 in both cell lines. Exogenous recombinant DKK1 inhibited cell migration on all cell lines, but did not have a significant effect on cell proliferation of bmMSCs and glioma cell lines. Conclusion In this study, we showed for the first time that the expression of DKK1 was hypoxia dependent in human malignant glioma cell lines. The induction of DKK1 by intracellular crosstalk or hypoxia stimuli sheds light on the intense adaption of glial tumour cells to environmental alterations.}, language = {en} } @article{HaemaelaeinenDammhahnAujardetal.2014, author = {Haemaelaeinen, Anni and Dammhahn, Melanie and Aujard, Fabienne and Eberle, Manfred and Hardy, Isabelle and Kappeler, Peter M. and Perret, Martine and Schliehe-Diecks, Susanne and Kraus, Cornelia}, title = {Senescence or selective disappearance? Age trajectories of body mass in wild and captive populations of a small-bodied primate}, series = {Proceedings of the Royal Society of London : B, Biological sciences}, volume = {281}, journal = {Proceedings of the Royal Society of London : B, Biological sciences}, number = {1791}, publisher = {Royal Society}, address = {London}, issn = {0962-8452}, doi = {10.1098/rspb.2014.0830}, pages = {10}, year = {2014}, abstract = {Classic theories of ageing consider extrinsic mortality (EM) a major factor in shaping longevity and ageing, yet most studies of functional ageing focus on species with low EM. This bias may cause overestimation of the influence of senescent declines in performance over condition-dependent mortality on demographic processes across taxa. To simultaneously investigate the roles of functional senescence (FS) and intrinsic, extrinsic and condition-dependent mortality in a species with a high predation risk in nature, we compared age trajectories of body mass (BM) in wild and captive grey mouse lemurs (Microcebus murinus) using longitudinal data (853 individuals followed through adulthood). We found evidence of non-random mortality in both settings. In captivity, the oldest animals showed senescence in their ability to regain lost BM, whereas no evidence of FS was found in the wild. Overall, captive animals lived longer, but a reversed sex bias in lifespan was observed between wild and captive populations. We suggest that even moderately condition-dependent EM may lead to negligible FS in the wild. While high EM may act to reduce the average lifespan, this evolutionary process may be counteracted by the increased fitness of the long-lived, high-quality individuals.}, language = {en} } @article{HagenBaumannWagneretal.2014, author = {Hagen, Sven and Baumann, Tobias and Wagner, Hanna J. and Morath, Volker and Kaufmann, Beate and Fischer, Adrian and Bergmann, Stefan and Schindler, Patrick and Arndt, Katja Maren and Mueller, Kristian M.}, title = {Modular adeno-associated virus (rAAV) vectors used for cellular virus-directed enzyme prodrug therapy}, series = {Scientific reports}, volume = {4}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep03759}, pages = {11}, year = {2014}, abstract = {The pre-clinical and clinical development of viral vehicles for gene transfer increased in recent years, and a recombinant adeno-associated virus (rAAV) drug took center stage upon approval in the European Union. However, lack of standardization, inefficient purification methods and complicated retargeting limit general usability. We address these obstacles by fusing rAAV-2 capsids with two modular targeting molecules (DARPin or Affibody) specific for a cancer cell-surface marker (EGFR) while simultaneously including an affinity tag (His-tag) in a surface-exposed loop. Equipping these particles with genes coding for prodrug converting enzymes (thymidine kinase or cytosine deaminase) we demonstrate tumor marker specific transduction and prodrug-dependent apoptosis of cancer cells. Coding terminal and loop modifications in one gene enabled specific and scalable purification. Our genetic parts for viral production adhere to a standardized cloning strategy facilitating rapid prototyping of virus directed enzyme prodrug therapy (VDEPT).}, language = {en} } @article{HagenMattayRaeuberetal.2014, author = {Hagen, Sven and Mattay, Dinah and Raeuber, Christina and Mueller, Kristian M. and Arndt, Katja Maren}, title = {Characterization and inhibition of AF10-mediated interaction}, series = {Journal of peptide science}, volume = {20}, journal = {Journal of peptide science}, number = {6}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1075-2617}, doi = {10.1002/psc.2626}, pages = {385 -- 397}, year = {2014}, abstract = {The non-random chromosomal translocations t(10;11)(p13;q23) and t(10;11)(p13;q14-21) result in leukemogenic fusion proteins comprising the coiled coil domain of the transcription factor AF10 and the proteins MLL or CALM, respectively, and subsequently cause certain types of acute leukemia. The AF10 coiled-coil domain, which is crucial for the leukemogenic effect, has been shown to interact with GAS41, a protein previously identified as the product of an amplified gene in glioblastoma. Using sequential synthetic peptides, we mapped the potential AF10/GAS41 interaction site, which was subsequently be used as scaffold for a library targeting the AF10 coiled-coil domain. Using phage display, we selected a peptide that binds the AF10 coiled-coil domain with higher affinity than the respective coiled-coil region of wild-type GAS41, as demonstrated by phage ELISA, CD, and PCAs. Furthermore, we were able to successfully deploy the inhibitory peptide in a mammalian cell line to lower the expression of Hoxa genes that have been described to be overexpressed in these leukemias. This work dissects molecular determinants mediating AF10-directed interactions in leukemic fusions comprising the N-terminal parts of the proteins MLL or CALM and the C-terminal coiled-coil domain of AF10. Furthermore, it outlines the first steps in recognizing and blocking the leukemia-associated AF10 interaction in histiocytic lymphoma cells and therefore, may have significant implications in future diagnostics and therapeutics. Copyright (c) 2014 European Peptide Society and John Wiley \& Sons, Ltd.}, language = {en} } @article{HahnReschkeLeimkuehleretal.2014, author = {Hahn, Aaron and Reschke, Stefan and Leimk{\"u}hler, Silke and Risse, Thomas}, title = {Ketoxime coupling of p-Acetylphenylalanine at neutral pH for site-directed spin labeling of human sulfite oxidase}, series = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, volume = {118}, journal = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, number = {25}, publisher = {American Chemical Society}, address = {Washington}, issn = {1520-6106}, doi = {10.1021/jp503471j}, pages = {7077 -- 7084}, year = {2014}, abstract = {Site-directed spin labeling of the unnatural amino acid p-acetylphenylalanine (p-AcPhe) using oxime based coupling chemistry is successfully applied to investigate human sulfite oxidase (hSO), a protein containing an essential cysteine residue, which impedes the use of thiol based coupling chemistry. The protein was found to be sensitive toward typical reaction conditions of oxime coupling, namely, acidic reaction conditions and elevated temperatures. Thus, coupling at neutral pH and room temperature is mandatory. Three catalysts described in the literature to accelerate the reaction rate have been tested. Best spin labeling efficiencies were observed for p-methoxyaniline, while the other catalysts described in the literature to have even better performance for oxime coupling at neutral pH were substantially less active or led to precipitation of the protein. A clear correlation of spin labeling efficiency with the local environment of the residue is found, shedding some light on the importance of the sterically demanding reaction complex between p-AcPhe, the aniline catalyst, and the spin label for the reaction rate. The analysis of the line shape has shown that its interpretation in terms of local environment is more challenging as compared to the well-established spin labels based on cysteine chemistry. To this end the results presented here indicate that the larger steric demand of the spin labeled p-AcPhe can induce structural effects instead of reporting on them.}, language = {en} } @article{HallReschkeCaoetal.2014, author = {Hall, James and Reschke, Stefan and Cao, Hongnan and Leimk{\"u}hler, Silke and Hille, Russ}, title = {The reductive half-reaction of xanthine dehydrogenase from rhodobacter capsulatus the role of GLU(232) in catalysis}, series = {The journal of biological chemistry}, volume = {289}, journal = {The journal of biological chemistry}, number = {46}, publisher = {American Society for Biochemistry and Molecular Biology}, address = {Bethesda}, issn = {0021-9258}, doi = {10.1074/jbc.M114.603456}, pages = {32121 -- 32130}, year = {2014}, abstract = {Background: Kinetic characterization of wild-type xanthine dehydrogenase and variants. Results: Comparison of the pH dependence of both k(red) and k(red)/K-d, as well as k(cat) and k(cat)/K-m. Conclusion: Ionized Glu(232) of wild-type enzyme plays an important role in catalysis by discriminating against the monoanionic form of xanthine. Significance: Examining the contributions of Glu(232) to catalysis is essential for understanding the mechanism of xanthine dehydrogenase. The kinetic properties of an E232Q variant of the xanthine dehydrogenase from Rhodobacter capsulatus have been examined to ascertain whether Glu(232) in wild-type enzyme is protonated or unprotonated in the course of catalysis at neutral pH. We find that k(red), the limiting rate constant for reduction at high [xanthine], is significantly compromised in the variant, a result that is inconsistent with Glu(232) being neutral in the active site of the wild-type enzyme. A comparison of the pH dependence of both k(red) and k(red)/K-d from reductive half-reaction experiments between wild-type and enzyme and the E232Q variant suggests that the ionized Glu(232) of wild-type enzyme plays an important role in catalysis by discriminating against the monoanionic form of substrate, effectively increasing the pK(a) of substrate by two pH units and ensuring that at physiological pH the neutral form of substrate predominates in the Michaelis complex. A kinetic isotope study of the wild-type R. capsulatus enzyme indicates that, as previously determined for the bovine and chicken enzymes, product release is principally rate-limiting in catalysis. The disparity in rate constants for the chemical step of the reaction and product release, however, is not as great in the bacterial enzyme as compared with the vertebrate forms. The results indicate that the bacterial and bovine enzymes catalyze the chemical step of the reaction to the same degree and that the faster turnover observed with the bacterial enzyme is due to a faster rate constant for product release than is seen with the vertebrate enzyme.}, language = {en} } @article{HeindorffBaumann2014, author = {Heindorff, Kristoffer and Baumann, Otto}, title = {Calcineurin is part of a negative feedback loop in the InsP(3)/Ca2+ signalling pathway in blowfly salivary glands}, series = {Cell calcium}, volume = {56}, journal = {Cell calcium}, number = {3}, publisher = {Churchill Livingstone}, address = {Edinburgh}, issn = {0143-4160}, doi = {10.1016/j.ceca.2014.07.009}, pages = {215 -- 224}, year = {2014}, abstract = {The ubiquitous InsP(3)/Ca2+ signalling pathway is modulated by diverse mechanisms, i.e. feedback of Ca2+ and interactions with other signalling pathways. In the salivary glands of the blowfly Calliphora vicina, the hormone serotonin (5-HT) causes a parallel rise in intracellular [Ca2+] and [cAMP] via two types of 5-HT receptors. We have shown recently that cAMP/protein kinase A (PKA) sensitizes InsP(3)-induced Ca2+ release. We have now identified the protein phosphatase that counteracts the effect of PKA on 5-HT-induced InsP(3)/Ca2+ signalling. We demonstrate that (1) tautomycin and okadaic acid, inhibitors of protein phosphatases PP1 and PP2A, have no effect on 5-HT-induced Ca2+ signals; (2) cyclosporin A and FK506, inhibitors of Ca2+/calmodulin-activated protein phosphatase calcineurin, cause an increase in the frequency of 5-HT-induced Ca2+ oscillations; (3) the sensitizing effect of cyclosporin A on 5-HT-induced Ca2+ responses does not involve Ca2+ entry into the cells; (4) cyclosporin A increases InsP(3)-dependent Ca2+ release; (5) inhibition of PKA abolishes the effect of cyclosporin A on the 5-HT-induced Ca2+ responses, indicating that PKA and calcineurin act antagonistically on the InsP(3)/Ca2+ signalling pathway. These findings suggest that calcineurin provides a negative feedback on InsP(3)/Ca2+ signalling in blowfly salivary glands, counteracting the effect of PKA and desensitizing the signalling cascade at higher 5-HT concentrations. (C) 2014 Elsevier Ltd. All rights reserved.}, language = {en} } @phdthesis{Heise2014, author = {Heise, Robert}, title = {Estimation of photosynthetic carbon fluxes in intact plants}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, school = {Universit{\"a}t Potsdam}, pages = {178}, year = {2014}, language = {en} } @article{HemmeVeyelMuehlhausetal.2014, author = {Hemme, Dorothea and Veyel, Daniel and Muehlhaus, Timo and Sommer, Frederik and Jueppner, Jessica and Unger, Ann-Katrin and Sandmann, Michael and Fehrle, Ines and Schoenfelder, Stephanie and Steup, Martin and Geimer, Stefan and Kopka, Joachim and Giavalisco, Patrick and Schroda, Michael}, title = {Systems-wide analysis of acclimation responses to long-term heat stress and recovery in the photosynthetic model organism Chlamydomonas reinhardtii}, series = {The plant cell}, volume = {26}, journal = {The plant cell}, number = {11}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {1040-4651}, doi = {10.1105/tpc.114.130997}, pages = {4270 -- 4297}, year = {2014}, abstract = {We applied a top-down systems biology approach to understand how Chlamydomonas reinhardtii acclimates to long-term heat stress (HS) and recovers from it. For this, we shifted cells from 25 to 42 degrees C for 24 h and back to 25 degrees C for >= 8 h and monitored abundances of 1856 proteins/protein groups, 99 polar and 185 lipophilic metabolites, and cytological and photosynthesis parameters. Our data indicate that acclimation of Chlamydomonas to long-term HS consists of a temporally ordered, orchestrated implementation of response elements at various system levels. These comprise (1) cell cycle arrest; (2) catabolism of larger molecules to generate compounds with roles in stress protection; (3) accumulation of molecular chaperones to restore protein homeostasis together with compatible solutes; (4) redirection of photosynthetic energy and reducing power from the Calvin cycle to the de novo synthesis of saturated fatty acids to replace polyunsaturated ones in membrane lipids, which are deposited in lipid bodies; and (5) when sinks for photosynthetic energy and reducing power are depleted, resumption of Calvin cycle activity associated with increased photorespiration, accumulation of reactive oxygen species scavengers, and throttling of linear electron flow by antenna uncoupling. During recovery from HS, cells appear to focus on processes allowing rapid resumption of growth rather than restoring pre-HS conditions.}, language = {en} } @misc{HepworthLenhard2014, author = {Hepworth, Jo and Lenhard, Michael}, title = {Regulation of plant lateral-organ growth by modulating cell number and size}, series = {Current opinion in plant biology}, volume = {17}, journal = {Current opinion in plant biology}, publisher = {Elsevier}, address = {London}, issn = {1369-5266}, doi = {10.1016/j.pbi.2013.11.005}, pages = {36 -- 42}, year = {2014}, abstract = {Leaves and floral organs grow to distinct, species-specific sizes and shapes. Research over the last few years has increased our understanding of how genetic pathways modulate cell proliferation and cell expansion to determine these sizes and shapes. In particular, the timing of proliferation arrest is an important point of control for organ size, and work on the regulators involved is showing how this control is achieved mechanistically and integrates environmental information. We are also beginning to understand how growth differs in different organs to produce their characteristic shapes, and how growth is integrated between different tissues that make up plant organs. Lastly, components of the general machinery in eukaryotic cells have been identified as having important roles in growth control.}, language = {en} } @article{HermanussenAltStaubetal.2014, author = {Hermanussen, Michael and Alt, Christoph and Staub, Kaspar and Aßmann, Christian and Groth, Detlef}, title = {The impact of physical connectedness on body height in Swiss conscripts}, series = {Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft f{\"u}r Anthropologie}, volume = {71}, journal = {Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft f{\"u}r Anthropologie}, number = {4}, publisher = {Schweizerbart}, address = {Stuttgart}, issn = {0003-5548}, doi = {10.1127/0003-5548/2014/0466}, pages = {313 -- 327}, year = {2014}, abstract = {Background: Human populations differ in height. Recent evidence suggests that social networks play an important role in the regulation of adolescent growth and adult height. We further investigated the effect of physical connectedness on height. Material and methods: We considered Switzerland as a geographic network with 169 nodes (district capitals) and 335 edges (connecting roads) and studied effects of connectedness on height in Swiss conscript from 1884-1891, 1908-1910, and 2004-2009. We also created exponential-family random graph models to separate possible unspecific effects of geographic vicinity. Results: In 1884-1891, in 1908-1910, and in 2004-2009, 1st, 2nd and 3rd order neighboring districts significantly correlate in height (p<0.01). The correlations depend on the order of connectedness, they decline with increasing distance. Short stature districts tend to have short, tall stature districts tend to have tall neighbors. Random network analyses suggest direct road effects on height. Whereas in 1884-1891, direct road effects were only visible between 1st order neighbors, direct road effects extended to 2nd and 3rd in 1908-1910, and in 2004-2009, also to 4th order neighbors, and might reflect historic improvements in transportation. The spatial correlations did not significantly change when height was controlled for goiter (1884-1889) and for median per capita income (2006), suggesting direct road effects also in goiter-allowed-for height and income-allowed-for height. Conclusion: Height in a district depends on height of physically connected neighboring districts. The association decreases with increasing distance in the net. The present data suggest that people can be short because their neighbors are short; or tall because their neighbors are tall (community effect on growth). Psycho-biological effects seem to control growth and development within communities that go far beyond our current understanding of growth regulation.}, language = {en} } @article{HeuvelingFrochauxZiomkowskaetal.2014, author = {Heuveling, Johanna and Frochaux, Violette and Ziomkowska, Joanna and Wawrzinek, Robert and Wessig, Pablo and Herrmann, Andreas and Schneider, Erwin}, title = {Conformational changes of the bacterial type I ATP-binding cassette importer HisQMP(2) at distinct steps of the catalytic cycle}, series = {Biochimica et biophysica acta : Biomembranes}, volume = {1838}, journal = {Biochimica et biophysica acta : Biomembranes}, number = {1}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0005-2736}, doi = {10.1016/j.bbamem.2013.08.024}, pages = {106 -- 116}, year = {2014}, abstract = {Prokaryotic solute binding protein-dependent ATP-binding cassette import systems are divided into type land type II and mechanistic differences in the transport process going along with this classification are under intensive investigation. Little is known about the conformational dynamics during the catalytic cycle especially concerning the transmembrane domains. The type I transporter for positively charged amino acids from Salmonella enterica serovar Typhimurium (1A0-Hi5QMP2) was studied by limited proteolysis in detergent solution in the absence and presence of co-factors including ATP, ADP, LAO/arginine, and Mg2+ ions. Stable peptide fragments could be obtained and differentially susceptible cleavage sites were determined by mass spectrometry as Lys-258 in the nucleotide-binding subunit, HisP, and Arg-217/Arg-218 in the transmembrane subunit, HisQ In contrast, transmembrane subunit HisM was gradually degraded but no stable fragment could be detected. HisP and HisQ were equally resistant under pre- and post-hydrolysis conditions in the presence of arginine-loaded solute-binding protein LAO and ATP/ADP. Some protection was also observed with LAO/arginine alone, thus reflecting binding to the transporter in the apo-state and transmembrane signaling. Comparable digestion patterns were obtained with the transporter reconstituted into proteoliposomes and nanodiscs. Fluorescence lifetime spectroscopy confirmed the change of HisQ(R218) to a more apolar microenvironment upon ATP binding and hydrolysis. Limited proteolysis was subsequently used as a tool to study the consequences of mutations on the transport cycle. Together, our data suggest similar conformational changes during the transport cycle as described for the maltose ABC transporter of Escherichia coli, despite distinct structural differences between both systems.}, language = {en} } @article{HeydariBullerWischerhoffetal.2014, author = {Heydari, Esmaeil and Buller, Jens and Wischerhoff, Erik and Laschewsky, Andr{\´e} and D{\"o}ring, Sebastian and Stumpe, Joachim}, title = {Label-Free biosensor based on an all-polymer DFB laser}, series = {Advanced optical materials}, volume = {2}, journal = {Advanced optical materials}, number = {2}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {2195-1071}, doi = {10.1002/adom.201300454}, pages = {137 -- 141}, year = {2014}, language = {en} } @article{HoppeBiervonNickischRosenegk2014, author = {Hoppe, Sebastian and Bier, Frank Fabian and von Nickisch-Rosenegk, Markus}, title = {Identification of antigenic proteins of the nosocomial pathogen klebsiella pneumoniae}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {10}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0110703}, pages = {16}, year = {2014}, abstract = {The continuous expansion of nosocomial infections around the globe has become a precarious situation. Key challenges include mounting dissemination of multiple resistances to antibiotics, the easy transmission and the growing mortality rates of hospital-acquired bacterial diseases. Thus, new ways to rapidly detect these infections are vital. Consequently, researchers around the globe pursue innovative approaches for point-of-care devices. In many cases the specific interaction of an antigen and a corresponding antibody is pivotal. However, the knowledge about suitable antigens is lacking. The aim of this study was to identify novel antigens as specific diagnostic markers. Additionally, these proteins might be aptly used for the generation of vaccines to improve current treatment options. Hence, a cDNA-based expression library was constructed and screened via microarrays to detect novel antigens of Klebsiella pneumoniae, a prominent agent of nosocomial infections well-known for its extensive antibiotics resistance, especially by extended-spectrum beta-lactamases (ESBL). After screening 1536 clones, 14 previously unknown immunogenic proteins were identified. Subsequently, each protein was expressed in full-length and its immunodominant character examined by ELISA and microarray analyses. Consequently, six proteins were selected for epitope mapping and three thereof possessed linear epitopes. After specificity analysis, homology survey and 3d structural modelling, one epitope sequence GAVVALSTTFA of KPN_00363, an ion channel protein, was identified harboring specificity for K. pneumoniae. The remaining epitopes showed ambiguous results regarding the specificity for K. pneumoniae. The approach adopted herein has been successfully utilized to discover novel antigens of Campylobacter jejuni and Salmonella enterica antigens before. Now, we have transferred this knowledge to the key nosocomial agent, K. pneumoniae. By identifying several novel antigens and their linear epitope sites, we have paved the way for crucial future research and applications including the design of point-of-care devices, vaccine development and serological screenings for a highly relevant nosocomial pathogen.}, language = {en} } @article{HornProstStilleretal.2014, author = {Horn, Susanne and Prost, Stefan and Stiller, Mathias and Makowiecki, Daniel and Kuznetsova, Tatiana and Benecke, Norbert and Pucher, Erich and Hufthammer, Anne K. and Schouwenburg, Charles and Shapiro, Beth and Hofreiter, Michael}, title = {Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe}, series = {Molecular ecology}, volume = {23}, journal = {Molecular ecology}, number = {7}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0962-1083}, doi = {10.1111/mec.12691}, pages = {1717 -- 1729}, year = {2014}, abstract = {After centuries of human hunting, the Eurasian beaver Castor fiber had disappeared from most of its original range by the end of the 19th century. The surviving relict populations are characterized by both low genetic diversity and strong phylogeographical structure. However, it remains unclear whether these attributes are the result of a human-induced, late Holocene bottleneck or already existed prior to this reduction in range. To investigate genetic diversity in Eurasian beaver populations during the Holocene, we obtained mitochondrial control region DNA sequences from 48 ancient beaver samples and added 152 modern sequences from GenBank. Phylogeographical analyses of the data indicate a differentiation of European beaver populations into three mitochondrial clades. The two main clades occur in western and eastern Europe, respectively, with an early Holocene contact zone in eastern Europe near a present-day contact zone. A divergent and previously unknown clade of beavers from the Danube Basin survived until at least 6000years ago, but went extinct during the transition to modern times. Finally, we identify a recent decline in effective population size of Eurasian beavers, with a stronger bottleneck signal in the western than in the eastern clade. Our results suggest that the low genetic diversity and the strong phylogeographical structure in recent beavers are artefacts of human hunting-associated population reductions. While beaver populations have been growing rapidly since the late 19th century, genetic diversity within modern beaver populations remains considerably reduced compared to what was present prior to the period of human hunting and habitat reduction.}, language = {en} } @article{HovestaedtMemczakPleineretal.2014, author = {Hovestaedt, Marc and Memczak, Henry and Pleiner, Dennis and Zhang, Xin and Rappich, Joerg and Bier, Frank Fabian and St{\"o}cklein, Walter F. M.}, title = {Characterization of a new maleimido functionalization of gold for surface plasmon resonance spectroscopy}, series = {Journal of molecular recognition : an international journal devoted to research on specific molecular recognition in chemistry, biology, biotechnology and medicine}, volume = {27}, journal = {Journal of molecular recognition : an international journal devoted to research on specific molecular recognition in chemistry, biology, biotechnology and medicine}, number = {12}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0952-3499}, doi = {10.1002/jmr.2396}, pages = {707 -- 713}, year = {2014}, abstract = {Para-maleimidophenyl (p-MP) modified gold surfaces have been prepared by one-step electrochemical deposition and used in surface plasmon resonance (SPR) studies. Therefore, a FITC mimotope peptide (MP1, 12 aa), a human mucin 1 epitope peptide (MUC, 9 aa) and a protein with their specific antibodies were used as model systems. The peptides were modified with an N-terminal cysteine for covalent and directed coupling to the maleimido functionalized surface by means of Michael addition. The coupling yield of the peptide, the binding characteristics of antibody and the unspecific adsorption of the analytes were investigated. The results expand the spectrum of biosensors usable with p-MP by widely used SPR and support its potential to be versatile for several electrochemical and optical biosensors. This allows the combination of an electrochemical and optical read-out for a broad variety of biomolecular interactions on the same chip. Copyright (c) 2014 John Wiley \& Sons, Ltd.}, language = {en} } @misc{HuynenSuzukiOguraetal.2014, author = {Huynen, Leon and Suzuki, Takayuki and Ogura, Toshihiko and Watanabe, Yusuke and Millar, Craig D. and Hofreiter, Michael and Smith, Craig and Mirmoeini, Sara and Lambert, David M.}, title = {Reconstruction and in vivo analysis of the extinct tbx5 gene from ancient wingless moa (Aves: Dinornithiformes)}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1117}, issn = {1866-8372}, doi = {10.25932/publishup-43159}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431599}, pages = {10}, year = {2014}, abstract = {Background The forelimb-specific gene tbx5 is highly conserved and essential for the development of forelimbs in zebrafish, mice, and humans. Amongst birds, a single order, Dinornithiformes, comprising the extinct wingless moa of New Zealand, are unique in having no skeletal evidence of forelimb-like structures. Results To determine the sequence of tbx5 in moa, we used a range of PCR-based techniques on ancient DNA to retrieve all nine tbx5 exons and splice sites from the giant moa, Dinornis. Moa Tbx5 is identical to chicken Tbx5 in being able to activate the downstream promotors of fgf10 and ANF. In addition we show that missexpression of moa tbx5 in the hindlimb of chicken embryos results in the formation of forelimb features, suggesting that Tbx5 was fully functional in wingless moa. An alternatively spliced exon 1 for tbx5 that is expressed specifically in the forelimb region was shown to be almost identical between moa and ostrich, suggesting that, as well as being fully functional, tbx5 is likely to have been expressed normally in moa since divergence from their flighted ancestors, approximately 60 mya. Conclusions The results suggests that, as in mice, moa tbx5 is necessary for the induction of forelimbs, but is not sufficient for their outgrowth. Moa Tbx5 may have played an important role in the development of moa's remnant forelimb girdle, and may be required for the formation of this structure. Our results further show that genetic changes affecting genes other than tbx5 must be responsible for the complete loss of forelimbs in moa.}, language = {en} } @article{HuynenSuzukiOguraetal.2014, author = {Huynen, Leon and Suzuki, Takayuki and Ogura, Toshihiko and Watanabe, Yusuke and Millar, Craig D. and Hofreiter, Michael and Smith, Craig and Mirmoeini, Sara and Lambert, David M.}, title = {Reconstruction and in vivo analysis of the extinct tbx5 gene from ancient wingless moa (Aves: Dinornithiformes)}, series = {BMC evolutionary biology}, volume = {14}, journal = {BMC evolutionary biology}, publisher = {BioMed Central}, address = {London}, issn = {1471-2148}, doi = {10.1186/1471-2148-14-75}, pages = {8}, year = {2014}, abstract = {Background: The forelimb-specific gene tbx5 is highly conserved and essential for the development of forelimbs in zebrafish, mice, and humans. Amongst birds, a single order, Dinornithiformes, comprising the extinct wingless moa of New Zealand, are unique in having no skeletal evidence of forelimb-like structures. Results: To determine the sequence of tbx5 in moa, we used a range of PCR-based techniques on ancient DNA to retrieve all nine tbx5 exons and splice sites from the giant moa, Dinornis. Moa Tbx5 is identical to chicken Tbx5 in being able to activate the downstream promotors of fgf10 and ANF. In addition we show that missexpression of moa tbx5 in the hindlimb of chicken embryos results in the formation of forelimb features, suggesting that Tbx5 was fully functional in wingless moa. An alternatively spliced exon 1 for tbx5 that is expressed specifically in the forelimb region was shown to be almost identical between moa and ostrich, suggesting that, as well as being fully functional, tbx5 is likely to have been expressed normally in moa since divergence from their flighted ancestors, approximately 60 mya.}, language = {en} } @phdthesis{Huebner2014, author = {H{\"u}bner, Sandra}, title = {Molekulare Grundlagen der Bittergeschmackswahrnehmung in der Maus}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-77720}, school = {Universit{\"a}t Potsdam}, pages = {X, 171, iii}, year = {2014}, abstract = {Der Bittergeschmack dient S{\"a}ugern vermutlich zur Wahrnehmung und Vermeidung toxischer Substanzen. Bitterstoffe k{\"o}nnen jedoch auch gesund sein oder werden oft bereitwillig mit der Nahrung aufgenommen. Ob sie geschmacklich unterschieden werden k{\"o}nnen, ist allerdings umstritten. Detektiert werden Bitterstoffe von oralen Bittergeschmacksrezeptoren, den TAS2R (human) bzw. Tas2r (murin). In der Literatur gibt es aber immer mehr Hinweise darauf, dass {\"u}berdies Tas2r nicht nur in extragustatorischen Organen exprimiert werden, sondern dort auch wichtige Aufgaben erf{\"u}llen k{\"o}nnten, was wiederum die Aufkl{\"a}rung ihrer noch nicht vollst{\"a}ndig entschl{\"u}sselten Funktionsweisen erfordert. So ist noch unbekannt, ob alle bisher als funktionell identifizierten Tas2r wirklich gustatorische Funktionen erf{\"u}llen. Im Rahmen der Charakterisierung neu generierter, im Locus des Bittergeschmacksrezeptors Tas2r131 genetisch modifizierter Mauslinien, wurde in vorliegender Arbeit die gustatorische sowie extragustatorische Expression von Tas2r131 untersucht. Dass Tas2r131 nicht nur in Pilzpapillen, Wall- und Bl{\"a}tterpapillen (VP+FoP), Gaumen, Ductus nasopalatinus, Vomeronasalorgan und Kehldeckel, sondern auch in Thymus, Testes und Nebenhodenkopf, in Gehirnarealen sowie im Ganglion geniculatum nachgewiesen wurde, bildete die Grundlage f{\"u}r weiterf{\"u}hrende Studien. Die vorliegende Arbeit zeigt außerdem, dass Tas2r108, Tas2r126, Tas2r135, Tas2r137 und Tas2r143 in Blut exprimiert werden, was auf eine heterogene Funktion der Tas2r hindeutet. Dass zus{\"a}tzlich erstmals die Expression aller 35 als funktionell beschriebenen Tas2r im gustatorischen VP+FoP-Epithel von C57BL/6-M{\"a}usen nachgewiesen wurde, verweist auf deren Relevanz als funktionelle Geschmacksrezeptoren. Weiter zeigten Untersuchungen zur Aufkl{\"a}rung eines m{\"o}glichen Bitter-Unterscheidungsverm{\"o}gens in Geschmackspapillen von M{\"a}usen mit fluoreszenzmarkierten oder ablatierten Tas2r131-Zellen, dass Tas2r131 exprimierende Zellen eine Tas2r-Zellsubpopulation bilden. Dar{\"u}ber hinaus existieren innerhalb der Bitterzellen geordnete Tas2r-Expressionsmuster, die sich nach der chromosomalen Lage ihrer Gene richten. Isolierte Bitterzellen reagieren heterogen auf bekannte Bitterstoffe. Und M{\"a}use mit ablatierter Tas2r131-Zellpopulation besitzen noch andere Tas2r-Zellen und schmecken damit einige Bitterstoffe kaum noch, andere aber noch sehr gut. Diese Befunde belegen die Existenz verschiedener gustatorischer Tas2r-Zellpopulationen, welche die Voraussetzung bilden, Bitterstoffe heterogen zu detektieren. Ob dies die Grundlage f{\"u}r ein divergierendes Verhalten gegen{\"u}ber unvertr{\"a}glichen und harmlosen oder gar n{\"u}tzlichen Bitterstoffen darstellt, kann mit Hilfe der dargelegten Tas2r-Expressionsmuster k{\"u}nftig in Verhaltensexperimenten gepr{\"u}ft werden. Die Bittergeschmackswahrnehmung in S{\"a}ugetieren stellt sich als ein hochkomplexer Mechanismus dar, dessen Vielschichtigkeit durch die hier neu aufgezeigten heterogenen Tas2r-Expressions- und Funktionsmuster erneut verdeutlicht wird.}, language = {de} } @article{IvanovBeninaPetrovetal.2014, author = {Ivanov, Ivan and Benina, Maria and Petrov, Veselin and Gechev, Tsanko S. and Toneva, Valentina}, title = {Metabolic responses of gloxinia perennis to dehydration and rehydration}, series = {COMPTES RENDUS DE L ACADEMIE BULGARE DES SCIENCES}, volume = {67}, journal = {COMPTES RENDUS DE L ACADEMIE BULGARE DES SCIENCES}, number = {12}, publisher = {Publ. House of the Bulgarian Acad. of Sciences}, address = {Sofia}, issn = {1310-1331}, pages = {1657 -- 1662}, year = {2014}, abstract = {Gloxinia perennis is a species from the family Gesneriaceae with little known physiology, particularly in respect to responses to dehydration. G. perennis survived water deprivation for a month and then quickly recovered upon rehydration. The slow loss of water was in contrast with the quick dehydration of other Gesnerian species - Boea hygrometrica, Ramonda serbica, and Haber lea rhodopensis. Furthermore, a significant difference between older and younger leaves of G. perennis was observed. While the relative water content in the early stages of water deprivation was reduced to 65\% in the old leaves, it was not or slightly reduced in the young ones, implying a mechanism that protects specifically the younger leaves from dehydration. Water deprivation induced accumulation of gama-aminobutyric acid and sugars like sucrose and raffinose, but decreased the levels of amino acids such as glycine, leucine, and isoleucine. The levels of these amino acids recovered after rehydration and in some cases like glycine and isoleucine were even higher in rehydrated leaves compared with unstressed controls. We conclude that G.perennis can survive prolonged drought stress but its responses to dehydration are different from the resurrection species from Gesneriaceae. All this makes G. perennis a good model that can be used for comparative genomics and metabolomics of Gesneriads exposed to desiccation.}, language = {en} } @article{JoppSchefflerHermanussen2014, author = {Jopp, Eilin and Scheffler, Christiane and Hermanussen, Michael}, title = {Prevention and anthropology}, series = {Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft f{\"u}r Anthropologie}, volume = {71}, journal = {Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft f{\"u}r Anthropologie}, number = {1-2}, publisher = {Schweizerbart}, address = {Stuttgart}, issn = {0003-5548}, doi = {10.1127/0003-5548/2014/0384}, pages = {135 -- 141}, year = {2014}, abstract = {Screening is an important issue in medicine and is used to early identify unrecognised diseases in persons who are apparently in good health. Screening strongly relies on the concept of "normal values". Normal values are defined as values that are frequently observed in a population and usually range within certain statistical limits. Screening for obesity should start early as the prevalence of obesity consolidates already at early school age. Though widely practiced, measuring BMI is not the ultimate solution for detecting obesity. Children with high BMI may be "robust" in skeletal dimensions. Assessing skeletal robustness and in particularly assessing developmental tempo in adolescents are also important issues in health screening. Yet, in spite of the necessity of screening investigations, appropriate reference values are often missing. Meanwhile, new concepts of growth diagrams have been developed. Stage line diagrams are useful for tracking developmental processes over time. Functional data analyses have efficiently been used for analysing longitudinal growth in height and assessing the tempo of maturation. Convenient low-cost statistics have also been developed for generating synthetic national references.}, language = {en} } @phdthesis{Jueppner2014, author = {J{\"u}ppner, Jessica}, title = {Characterization of metabolomic dynamics in synchronized Chlamydomonas reinhardtii cell cultures and the impact of TOR inhibition on cell cycle, proliferation and growth}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-76923}, school = {Universit{\"a}t Potsdam}, pages = {VI, 153}, year = {2014}, abstract = {The adaptation of cell growth and proliferation to environmental changes is essential for the surviving of biological systems. The evolutionary conserved Ser/Thr protein kinase "Target of Rapamycin" (TOR) has emerged as a major signaling node that integrates the sensing of numerous growth signals to the coordinated regulation of cellular metabolism and growth. Although the TOR signaling pathway has been widely studied in heterotrophic organisms, the research on TOR in photosynthetic eukaryotes has been hampered by the reported land plant resistance to rapamycin. Thus, the finding that Chlamydomonas reinhardtii is sensitive to rapamycin, establish this unicellular green alga as a useful model system to investigate TOR signaling in photosynthetic eukaryotes. The observation that rapamycin does not fully arrest Chlamydomonas growth, which is different from observations made in other organisms, prompted us to investigate the regulatory function of TOR in Chlamydomonas in context of the cell cycle. Therefore, a growth system that allowed synchronously growth under widely unperturbed cultivation in a fermenter system was set up and the synchronized cells were characterized in detail. In a highly resolved kinetic study, the synchronized cells were analyzed for their changes in cytological parameters as cell number and size distribution and their starch content. Furthermore, we applied mass spectrometric analysis for profiling of primary and lipid metabolism. This system was then used to analyze the response dynamics of the Chlamydomonas metabolome and lipidome to TOR-inhibition by rapamycin The results show that TOR inhibition reduces cell growth, delays cell division and daughter cell release and results in a 50\% reduced cell number at the end of the cell cycle. Consistent with the growth phenotype we observed strong changes in carbon and nitrogen partitioning in the direction of rapid conversion into carbon and nitrogen storage through an accumulation of starch, triacylglycerol and arginine. Interestingly, it seems that the conversion of carbon into triacylglycerol occurred faster than into starch after TOR inhibition, which may indicate a more dominant role of TOR in the regulation of TAG biosynthesis than in the regulation of starch. This study clearly shows, for the first time, a complex picture of metabolic and lipidomic dynamically changes during the cell cycle of Chlamydomonas reinhardtii and furthermore reveals a complex regulation and adjustment of metabolite pools and lipid composition in response to TOR inhibition.}, language = {en} } @article{KabelitzKappelHennebergeretal.2014, author = {Kabelitz, Tina and Kappel, Christian and Henneberger, Kirstin and Benke, Eileen and Noeh, Christiane and B{\"a}urle, Isabel}, title = {eQTL mapping of transposon silencing reveals a position-dependent stable escape from epigenetic silencing and transposition of AtMu1 in thee arabidopsis lineage}, series = {The plant cell}, volume = {26}, journal = {The plant cell}, number = {8}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {1040-4651}, doi = {10.1105/tpc.114.128512}, pages = {3261 -- 3271}, year = {2014}, abstract = {Transposons are massively abundant in all eukaryotic genomes and are suppressed by epigenetic silencing. Transposon activity contributes to the evolution of species; however, it is unclear how much transposition-induced variation exists at a smaller scale and how transposons are targeted for silencing. Here, we exploited differential silencing of the AtMu1c transposon in the Arabidopsis thaliana accessions Columbia (Col) and Landsberg erecta (Ler). The difference persisted in hybrids and recombinant inbred lines and was mapped to a single expression quantitative trait locus within a 20-kb interval. In Ler only, this interval contained a previously unidentified copy of AtMu1c, which was inserted at the 39 end of a protein-coding gene and showed features of expressed genes. By contrast, AtMu1c(Col) was intergenic and associated with heterochromatic features. Furthermore, we identified widespread natural AtMu1c transposition from the analysis of over 200 accessions, which was not evident from alignments to the reference genome. AtMu1c expression was highest for insertions within 39 untranslated regions, suggesting that this location provides protection from silencing. Taken together, our results provide a species-wide view of the activity of one transposable element at unprecedented resolution, showing that AtMu1c transposed in the Arabidopsis lineage and that transposons can escape epigenetic silencing by inserting into specific genomic locations, such as the 3' end of genes.}, language = {en} } @phdthesis{Kamprad2014, author = {Kamprad, Fanny}, title = {Einfluss von Zink auf die intestinale Mikrobiota im Ferkel und der mono-assoziirten Maus}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, school = {Universit{\"a}t Potsdam}, pages = {VIII , 92}, year = {2014}, language = {de} } @inproceedings{KangBarbirzGohlkeetal.2014, author = {Kang, Yu and Barbirz, Stefanie and Gohlke, Ulrich and Santer, Mark}, title = {Molecular dynamics study on the interaction of O-antigen polysaccharides of the gram-negative bacterium Shigella flexneri with the tail-spike-protein of bacteriophage Sf6}, series = {Abstracts of papers : joint conference / The Chemical Institute of Cananda, CIC, American Chemical Society, ACS}, volume = {248}, booktitle = {Abstracts of papers : joint conference / The Chemical Institute of Cananda, CIC, American Chemical Society, ACS}, publisher = {American Chemical Society}, address = {Washington}, issn = {0065-7727}, pages = {1}, year = {2014}, language = {en} } @article{KannanKanabarSchryeretal.2014, author = {Kannan, Krishna and Kanabar, Pinal and Schryer, David and Florin, Tanja and Oh, Eugene and Bahroos, Neil and Tenson, Tanel and Weissman, Jonathan S. and Mankin, Alexander S.}, title = {The general mode of translation inhibition by macrolide antibiotics}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {45}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1417334111}, pages = {15958 -- 15963}, year = {2014}, language = {en} } @article{KedrackiChekiniMaronietal.2014, author = {Kedracki, Dawid and Chekini, Mahshid and Maroni, Plinio and Schlaad, Helmut and Nardin, Corinne}, title = {Synthesis and Self-Assembly of a DNA Molecular Brush}, series = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences}, volume = {15}, journal = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences}, number = {9}, publisher = {American Chemical Society}, address = {Washington}, issn = {1525-7797}, doi = {10.1021/bm5008713}, pages = {3375 -- 3382}, year = {2014}, abstract = {We report herein on the polymer-crystallization-assisted thiol-ene photosynthesis of an amphiphilic comb/graft DNA copolymer, or molecular brush, composed of a hydrophobic poly(2-oxazoline) backbone and hydrophilic short single-stranded nucleic acid grafts. Coupling efficiencies are above 60\% and thus higher as compared with the straight solid-phase-supported synthesis of amphiphilic DNA block copolymers. The DNA molecular brushes self-assemble into sub-micron-sized spherical structures in water as evidenced by light scattering as well as atomic force and electron microscopy imaging. The nucleotide sequences remain functional, as assessed by UV and fluorescence spectroscopy subsequent to isoindol synthesis at the surface of the structures. The determination of a vesicular morphology is supported by encapsulation and subsequent spectroscopy monitoring of the release of a water-soluble dye and spectroscopic quantification of the hybridization efficiency (30\% in average) of the functional nucleic acid strands engaged in structure formation: about one-half of the nucleotide sequences are available for hybridization, whereas the other half are hindered within the self-assembled structure. Because speciation between complementary and non complementary sequences in the medium could be ascertained by confocal laser scanning microscopy, the stable self-assembled molecular brushes demonstrate the potential for sensing applications.}, language = {en} }