@phdthesis{Zulawski2013, author = {Zulawski, Monika Anna}, title = {Die Rolle der Phosphorylierung in der Regulation pflanzlicher Proteine}, address = {Potsdam}, pages = {160 S.}, year = {2013}, language = {de} } @article{ZhangPaijmansChangetal.2013, author = {Zhang, Hucai and Paijmans, Johanna L. A. and Chang, Fengqin and Wu, Xiaohong and Chen, Guangjie and Lei, Chuzhao and Yang, Xiujuan and Wei, Zhenyi and Bradley, Daniel G. and Orlando, Ludovic and O'Connor, Terry and Hofreiter, Michael}, title = {Morphological and genetic evidence for early Holocene cattle management in northeastern China}, series = {Nature Communications}, volume = {4}, journal = {Nature Communications}, number = {6}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/ncomms3755}, pages = {7}, year = {2013}, abstract = {The domestication of cattle is generally accepted to have taken place in two independent centres: around 10,500 years ago in the Near East, giving rise to modern taurine cattle, and two millennia later in southern Asia, giving rise to zebu cattle. Here we provide firmly dated morphological and genetic evidence for early Holocene management of taurine cattle in northeastern China. We describe conjoining mandibles from this region that show evidence of oral stereotypy, dated to the early Holocene by two independent C-14 dates. Using Illumina high-throughput sequencing coupled with DNA hybridization capture, we characterize 15,406 bp of the mitogenome with on average 16.7-fold coverage. Phylogenetic analyses reveal a hitherto unknown mitochondrial haplogroup that falls outside the known taurine diversity. Our data suggest that the first attempts to manage cattle in northern China predate the introduction of domestic cattle that gave rise to the current stock by several thousand years.}, language = {en} } @phdthesis{Zauber2013, author = {Zauber, Henrik}, title = {A systems biology driven approach for analyzing lipid protein interactions in sterol biosynthesis mutants}, address = {Potsdam}, pages = {126 S.}, year = {2013}, language = {en} } @article{ZarattiniMuraKetmaier2013, author = {Zarattini, Paola and Mura, Graziella and Ketmaier, Valerio}, title = {Intra-specific variability in the thirteen known populations of the fairy shrimp Chirocephalus ruffoi (Crustacea: Anostraca) - resting egg morphometrics and mitochondrial DNA reveal decoupled patterns of deep divergence}, series = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica}, volume = {713}, journal = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica}, number = {1}, publisher = {Springer}, address = {Dordrecht}, issn = {0018-8158}, doi = {10.1007/s10750-013-1487-8}, pages = {19 -- 34}, year = {2013}, abstract = {Chirocephalus ruffoi is a fairy shrimp endemic to the Italian peninsula, where it is known only from thirteen high mountain locations. Twelve of these are in the Northern Apennines while the thirteenth is about 700 km away in the Calabrian Apennines (Southern Italy). We quantified degree of genetic divergence within the species by sequencing a fragment of the mitochondrial DNA encoding for Cytochrome Oxidase I. We then combined genetic data with the re-analysis of two different datasets on the morphometrics of the resting eggs (cysts) produced by the species as an adaptation to survive seasonal droughts. Genetic data revealed profound divergence; we identified four clusters of haplotypes within the species phylogeography, three in the Northern Apennines and one in the Calabrian Apennines with most of the genetic variation (a parts per thousand 70\%) being apportioned among haplogroups. We found high variability in cyst morphometrics, especially in cyst size and height of the spines ornamenting the surface. Genetic and morphometric data are decoupled suggesting that cyst morphology is either under selection or a plastic trait. We, therefore, caution against using cyst morphology for taxonomic purposes in anostracans.}, language = {en} } @article{ZakharovaNikoloskiKoseska2013, author = {Zakharova, A. and Nikoloski, Zoran and Koseska, Aneta}, title = {Dimensionality reduction of bistable biological systems}, series = {Bulletin of mathematical biology : official journal of the Society for Mathematical Biology}, volume = {75}, journal = {Bulletin of mathematical biology : official journal of the Society for Mathematical Biology}, number = {3}, publisher = {Springer}, address = {New York}, issn = {0092-8240}, doi = {10.1007/s11538-013-9807-8}, pages = {373 -- 392}, year = {2013}, abstract = {Time hierarchies, arising as a result of interactions between system's components, represent a ubiquitous property of dynamical biological systems. In addition, biological systems have been attributed switch-like properties modulating the response to various stimuli across different organisms and environmental conditions. Therefore, establishing the interplay between these features of system dynamics renders itself a challenging question of practical interest in biology. Existing methods are suitable for systems with one stable steady state employed as a well-defined reference. In such systems, the characterization of the time hierarchies has already been used for determining the components that contribute to the dynamics of biological systems. However, the application of these methods to bistable nonlinear systems is impeded due to their inherent dependence on the reference state, which in this case is no longer unique. Here, we extend the applicability of the reference-state analysis by proposing, analyzing, and applying a novel method, which allows investigation of the time hierarchies in systems exhibiting bistability. The proposed method is in turn used in identifying the components, other than reactions, which determine the systemic dynamical properties. We demonstrate that in biological systems of varying levels of complexity and spanning different biological levels, the method can be effectively employed for model simplification while ensuring preservation of qualitative dynamical properties (i.e., bistability). Finally, by establishing a connection between techniques from nonlinear dynamics and multivariate statistics, the proposed approach provides the basis for extending reference-based analysis to bistable systems.}, language = {en} } @article{YarmanScheller2013, author = {Yarman, Aysu and Scheller, Frieder W.}, title = {Coupling biocatalysis with molecular imprinting in a biomimetic sensor}, series = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition}, volume = {52}, journal = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition}, number = {44}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1433-7851}, doi = {10.1002/anie.201305368}, pages = {11521 -- 11525}, year = {2013}, language = {en} } @article{XuWollenbergerQianetal.2013, author = {Xu, Xuan and Wollenberger, Ursula and Qian, Jing and Lettau, Katrin and Jung, Christiane and Liu, Songqin}, title = {Electrochemically driven biocatalysis of the oxygenase domain of neuronal nitric oxide synthase in indium tin oxide nanoparticles/polyvinyl alcohol nanocomposite}, series = {Bioelectrochemistry : an international journal devoted to electrochemical aspects of biology and biological aspects of electrochemistry ; official journal of the Bioelectrochemical Society}, volume = {94}, journal = {Bioelectrochemistry : an international journal devoted to electrochemical aspects of biology and biological aspects of electrochemistry ; official journal of the Bioelectrochemical Society}, number = {47}, publisher = {Elsevier}, address = {Lausanne}, issn = {1567-5394}, doi = {10.1016/j.bioelechem.2013.04.005}, pages = {7 -- 12}, year = {2013}, abstract = {Nitric oxide synthase (NOS) plays a critical role in a number of key physiological and pathological processes. Investigation of electron-transfer reactions in NOS would contribute to a better understanding of the nitric oxide (NO) synthesis mechanism. Herein, we describe an electrochemically driven catalytic strategy, using a nanocomposite that consisted of the oxygenase domain of neuronal NOS (D290nNOSoxy), indium tin oxide (ITO) nanopartides and polyvinyl alcohol (PVA). Fast direct electron transfer between electrodes and D290nNOSoxy was observed with the heterogeneous electron transfer rate constant (k(er)) of 154.8 +/- 0.1 s(-1) at the scan rate of 5 V s(-1). Moreover, the substrate IV-hydroxy-L-arginine (NHA) was used to prove the concept of electrochemically driven biocatalysis of D290nNOSoxy. In the presence of the oxygen cosubstrate and tetrahydrobiopterin (BH4) cofactor, the addition of NHA caused the decreases of both oxidation current at + 0.1 V and reduction current at potentials ranging from -0.149 V to -0.549 V vs Ag/AgCl. Thereafter, a series of control experiments such as in the absence of BH4 or D290nNOSoxy were performed. All the results demonstrated that D290nNOSoxy biocatalysis was successfully driven by electrodes in the presence of BH4 and oxygen. This novel bioelectronic system showed potential for further investigation of NOS and biosensor applications. (C) 2013 Elsevier B.V. All rights reserved.}, language = {en} } @article{WisselManackBrainin2013, author = {Wissel, J{\"o}rg and Manack, Aubrey and Brainin, Michael}, title = {Toward an epidemiology of poststroke spasticity}, series = {Neurology : official journal of the American Academy of Neurology}, volume = {80}, journal = {Neurology : official journal of the American Academy of Neurology}, number = {1}, publisher = {Lippincott Williams \& Wilkins}, address = {Philadelphia}, issn = {0028-3878}, pages = {S13 -- S19}, year = {2013}, abstract = {Poststroke spasticity (PSS)-related disability is emerging as a significant health issue for stroke survivors. There is a need for predictors and early identification of PSS in order to minimize complications and maladaptation from spasticity. Reviewing the literature on stroke and upper motor neuron syndrome, spasticity, contracture, and increased muscle tone measured with the Modified Ashworth Scale and the Tone Assessment Scale provided data on the dynamic time course of PSS. Prevalence estimates of PSS were highly variable, ranging from 4\% to 42.6\%, with the prevalence of disabling spasticity ranging from 2\% to 13\%. Data on phases of the PSS continuum revealed evidence of PSS in 4\% to 27\% of those in the early time course (1-4 weeks poststroke), 19\% to 26.7\% of those in the postacute phase (1-3 months poststroke), and 17\% to 42.6\% of those in the chronic phase (>3 months poststroke). Data also identified key risk factors associated with the development of spasticity, including lower Barthel Index scores, severe degree of paresis, stroke-related pain, and sensory deficits. Although such indices could be regarded as predictors of PSS and thus enable early identification and treatment, the different measures of PSS used in those studies limit the strength of the findings. To optimize evaluation in the different phases of care, the best possible assessment of PSS would make use of a combination of indicators for clinical impairment, motor performance, activity level, quality of life, and patient-reported outcome measures. Applying these recommended measures, as well as increasing our knowledge of the physiologic predictors of PSS, will enable us to perform clinical and epidemiologic studies that will facilitate identification and early, multimodal treatment.}, language = {en} } @phdthesis{Winkler2013, author = {Winkler, Andr{\´e}}, title = {Entstehung und ph{\"a}notyp anti - inflammatorischer IgG und ihre Verwendung zur Induktion von Toleranz in der Maus}, address = {Potsdam}, pages = {100 S.}, year = {2013}, language = {de} } @article{WinckArvidssonMauricioRianoPachonetal.2013, author = {Winck, Flavia Vischi and Arvidsson, Samuel Janne and Mauricio Riano-Pachon, Diego and Hempel, Sabrina and Koseska, Aneta and Nikoloski, Zoran and Urbina Gomez, David Alejandro and Rupprecht, Jens and M{\"u}ller-R{\"o}ber, Bernd}, title = {Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga chlamydomonas reinhardtii under carbon deprivation}, series = {PLoS one}, volume = {8}, journal = {PLoS one}, number = {11}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0079909}, pages = {16}, year = {2013}, abstract = {The unicellular green alga Chlamydomonas reinhardtii is a long-established model organism for studies on photosynthesis and carbon metabolism-related physiology. Under conditions of air-level carbon dioxide concentration [CO2], a carbon concentrating mechanism (CCM) is induced to facilitate cellular carbon uptake. CCM increases the availability of carbon dioxide at the site of cellular carbon fixation. To improve our understanding of the transcriptional control of the CCM, we employed FAIRE-seq (formaldehyde-assisted Isolation of Regulatory Elements, followed by deep sequencing) to determine nucleosome-depleted chromatin regions of algal cells subjected to carbon deprivation. Our FAIRE data recapitulated the positions of known regulatory elements in the promoter of the periplasmic carbonic anhydrase (Cah1) gene, which is upregulated during CCM induction, and revealed new candidate regulatory elements at a genome-wide scale. In addition, time series expression patterns of 130 transcription factor (TF) and transcription regulator (TR) genes were obtained for cells cultured under photoautotrophic condition and subjected to a shift from high to low [CO2]. Groups of co-expressed genes were identified and a putative directed gene-regulatory network underlying the CCM was reconstructed from the gene expression data using the recently developed IOTA (inner composition alignment) method. Among the candidate regulatory genes, two members of the MYB-related TF family, Lcr1 (Low-CO2 response regulator 1) and Lcr2 (Low-CO2 response regulator 2), may play an important role in down-regulating the expression of a particular set of TF and TR genes in response to low [CO2]. The results obtained provide new insights into the transcriptional control of the CCM and revealed more than 60 new candidate regulatory genes. Deep sequencing of nucleosome-depleted genomic regions indicated the presence of new, previously unknown regulatory elements in the C. reinhardtii genome. Our work can serve as a basis for future functional studies of transcriptional regulator genes and genomic regulatory elements in Chlamydomonas.}, language = {en} } @article{WeisseMoserScheffeletal.2013, author = {Weisse, Thomas and Moser, Michael and Scheffel, Ulrike and Stadler, Peter and Berendonk, Thomas U. and Weithoff, Guntram and Berger, Helmut}, title = {Systematics and species-specific response to pH of Oxytricha acidotolerans sp nov and Urosomoida sp (Ciliophora, Hypotricha) from acid mining lakes}, series = {European journal of protistology}, volume = {49}, journal = {European journal of protistology}, number = {2}, publisher = {Elsevier}, address = {Jena}, issn = {0932-4739}, doi = {10.1016/j.ejop.2012.08.001}, pages = {255 -- 271}, year = {2013}, abstract = {We investigated the morphology, phylogeny of the 18S rDNA, and pH response of Oxytricha acidotolerans sp. nov. and Urosomoida sp. (Ciliophora, Hypotricha) isolated from two chemically similar acid mining lakes (pH similar to 2.6) located at Langau, Austria, and in Lusatia, Germany. Oxytricha acidotolerans sp. nov. from Langau has 18 frontal-ventral-transverse cirri but a very indistinct kinety 3 fragmentation so that the assignment to Oxytricha is uncertain. The somewhat smaller species from Lusatia has a highly variable cirral pattern and the dorsal kineties arranged in the Urosomoida pattern and is, therefore, preliminary designated as Urosomoida sp. The pH response was measured as ciliate growth rates in laboratory experiments at pH ranging from 2.5 to 7.0. Our hypothesis was that the shape of the pH reaction norm would not differ between these closely related (3\% difference in their SSU rDNA) species. Results revealed a broad pH niche for O. acidotolerans, with growth rates peaking at moderately acidic conditions (pH 5.2). Cyst formation was positively and linearly related to pH. Urosomoida sp. was more sensitive to pH and did not survive at circumneutral pH. Accordingly, we reject our hypothesis that similar habitats would harbour ciliate species with virtually identical pH reaction norm.}, language = {en} } @article{WeisseLaufensteinWeithoff2013, author = {Weisse, Thomas and Laufenstein, Nicole and Weithoff, Guntram}, title = {Multiple environmental stressors confine the ecological niche of the rotifer Cephalodella acidophila}, series = {Freshwater biology}, volume = {58}, journal = {Freshwater biology}, number = {5}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0046-5070}, doi = {10.1111/fwb.12104}, pages = {1008 -- 1015}, year = {2013}, abstract = {1The planktonic food web in extremely acidic mining lakes is restricted to a few species that are either acidophilic or acidotolerant. Common metazoans inhabiting acidic mining lakes with a pH below 3 include rotifers in the genera Cephalodella and Elosa. 2The life history response of Cephalodella acidophila to three environmental key factors, pH (2, 3.5, 5.0 and 7.0), temperature (10, 17.5 and 25 degrees C) and food concentration (10000, 35000 and 50000algal cells per mL), was investigated in a full factorial design using life-table experiments. 3The effect of each of the three environmental variables investigated on the rotifer life cycle parameters (life span, fecundity and population growth rate) differed. C.acidophila is a stenoecious species with a pH optimum in the range 34 and a comparably high food threshold. Combining the laboratory results with field data, we conclude that C.acidophila is severely growth limited in its natural habitat. However, low pH alone is not harmful as long as temperatures are moderate to warm and food is abundant. 4The population of C.acidophila in the field is maintained mainly due to release from competitors and predators.}, language = {en} } @article{WatanabeBalazadehTohgeetal.2013, author = {Watanabe, Mutsumi and Balazadeh, Salma and Tohge, Takayuki and Erban, Alexander and Giavalisco, Patrick and Kopka, Joachim and M{\"u}ller-R{\"o}ber, Bernd and Fernie, Alisdair R. and H{\"o}fgen, Rainer}, title = {Comprehensive dissection of spatiotemporal metabolic shifts in primary, secondary, and lipid metabolism during developmental senescence in arabidopsis}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {162}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {3}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.113.217380}, pages = {1290 -- 1310}, year = {2013}, abstract = {Developmental senescence is a coordinated physiological process in plants and is critical for nutrient redistribution from senescing leaves to newly formed sink organs, including young leaves and developing seeds. Progress has been made concerning the genes involved and the regulatory networks controlling senescence. The resulting complex metabolome changes during senescence have not been investigated in detail yet. Therefore, we conducted a comprehensive profiling of metabolites, including pigments, lipids, sugars, amino acids, organic acids, nutrient ions, and secondary metabolites, and determined approximately 260 metabolites at distinct stages in leaves and siliques during senescence in Arabidopsis (Arabidopsis thaliana). This provided an extensive catalog of metabolites and their spatiotemporal cobehavior with progressing senescence. Comparison with silique data provides clues to source-sink relations. Furthermore, we analyzed the metabolite distribution within single leaves along the basipetal sink-source transition trajectory during senescence. Ceramides, lysolipids, aromatic amino acids, branched chain amino acids, and stress-induced amino acids accumulated, and an imbalance of asparagine/aspartate, glutamate/glutamine, and nutrient ions in the tip region of leaves was detected. Furthermore, the spatiotemporal distribution of tricarboxylic acid cycle intermediates was already changed in the presenescent leaves, and glucosinolates, raffinose, and galactinol accumulated in the base region of leaves with preceding senescence. These results are discussed in the context of current models of the metabolic shifts occurring during developmental and environmentally induced senescence. As senescence processes are correlated to crop yield, the metabolome data and the approach provided here can serve as a blueprint for the analysis of traits and conditions linking crop yield and senescence.}, language = {en} } @article{WasofLenoirGalletMoronetal.2013, author = {Wasof, Safaa and Lenoir, Jonathan and Gallet-Moron, Emilie and Jamoneau, Aurelien and Brunet, J{\"o}rg and Cousins, Sara A. O. and De Frenne, Pieter and Diekmann, Martin and Hermy, Martin and Kolb, Annette and Liira, Jaan and Verheyen, Kris and Wulf, Monika and Decocq, Guillaume}, title = {Ecological niche shifts of understorey plants along a latitudinal gradient of temperate forests in north-western Europe}, series = {Global ecology and biogeography : a journal of macroecology}, volume = {22}, journal = {Global ecology and biogeography : a journal of macroecology}, number = {10}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1466-822X}, doi = {10.1111/geb.12073}, pages = {1130 -- 1140}, year = {2013}, abstract = {Aim In response to environmental changes and to avoid extinction, species may either track suitable environmental conditions or adapt to the modified environment. However, whether and how species adapt to environmental changes remains unclear. By focusing on the realized niche (i.e. the actual space that a species inhabits and the resources it can access as a result of limiting biotic factors present in its habitat), we here examine shifts in the realized-niche width (i.e. ecological amplitude) and position (i.e. ecological optimum) of 26 common and widespread forest understorey plants across their distributional ranges. Location Temperate forests along a ca. 1800-km-long latitudinal gradient from northern France to central Sweden and Estonia. Methods We derived species' realized-niche width from a -diversity metric, which increases if the focal species co-occurs with more species. Based on the concept that species' scores in a detrended correspondence analysis (DCA) represent the locations of their realized-niche positions, we developed a novel approach to run species-specific DCAs allowing the focal species to shift its realized-niche position along the studied latitudinal gradient while the realized-niche positions of other species were held constant. Results None of the 26 species maintained both their realized-niche width and position along the latitudinal gradient. Few species (9 of 26: 35\%) shifted their realized-niche width, but all shifted their realized-niche position. With increasing latitude, most species (22 of 26: 85\%) shifted their realized-niche position for soil nutrients and pH towards nutrient-poorer and more acidic soils. Main conclusions Forest understorey plants shifted their realized niche along the latitudinal gradient, suggesting local adaptation and/or plasticity. This macroecological pattern casts doubt on the idea that the realized niche is stable in space and time, which is a key assumption of species distribution models used to predict the future of biodiversity, hence raising concern about predicted extinction rates.}, language = {en} } @phdthesis{Wang2013, author = {Wang, Ting}, title = {A novel R2R3 MYB-like transcription factor regulates ABA mediated stress response and leaf growth in Arabidopsis}, address = {Potsdam}, pages = {102 S.}, year = {2013}, language = {en} } @article{WangFritzschBernardingetal.2013, author = {Wang, Jing and Fritzsch, Claire and Bernarding, Johannes and Krause, Thomas and Mauritz, Karl-Heinz and Brunetti, Maddalena and Dohle, Christian}, title = {Cerebral activation evoked by the mirror illusion of the hand in stroke patients compared to normal subjects}, series = {Neurorehabilitation : an interdisciplinary journal}, volume = {33}, journal = {Neurorehabilitation : an interdisciplinary journal}, number = {4}, publisher = {IOS Press}, address = {Amsterdam}, issn = {1053-8135}, doi = {10.3233/NRE-130999}, pages = {593 -- 603}, year = {2013}, abstract = {BACKGROUND: Mirror therapy (MT) was found to improve motor function after stroke, but its neural mechanisms remain unclear, especially in single stroke patients. OBJECTIVES: The following imaging study was designed to compare brain activation patterns evoked by the mirror illusion in single stroke patients with normal subjects. METHODS: Fifteen normal volunteers and five stroke patients with severe arm paresis were recruited. Cerebral activations during movement mirroring by means of a video chain were recorded with functional magnetic resonance imaging (fMRI). Single-subject analysis was performed using SPM 8. RESULTS: For normal subjects, ten and thirteen subjects displayed lateralized cerebral activations evoked by the mirror illusion while moving their right and left hand respectively. The magnitude of this effect in the precuneus contralateral to the seen hand was not dependent on movement speed or subjective experience. Negative correlation of activation strength with age was found for the right hand only. The activation pattern in stroke patients is comparable to that of normal subjects and present in four out of five patients. CONCLUSIONS: In summary, the mirror illusion can elicit cerebral activation contralateral to the perceived hand in the majority of single normal subjects, but not in all of them. This is similar even in stroke patients with severe hemiparesis.}, language = {en} } @misc{WagnerHillebrandWackeretal.2013, author = {Wagner, Nicole D. and Hillebrand, Helmut and Wacker, Alexander and Frost, Paul C.}, title = {Nutritional indicators and their uses in ecology}, series = {Ecology letters}, volume = {16}, journal = {Ecology letters}, number = {4}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1461-023X}, doi = {10.1111/ele.12067}, pages = {535 -- 544}, year = {2013}, abstract = {The nutrition of animal consumers is an important regulator of ecological processes due to its effects on their physiology, life-history and behaviour. Understanding the ecological effects of poor nutrition depends on correctly diagnosing the nature and strength of nutritional limitation. Despite the need to assess nutritional limitation, current approaches to delineating nutritional constraints can be non-specific and imprecise. Here, we consider the need and potential to develop new complementary approaches to the study of nutritional constraints on animal consumers by studying and using a suite of established and emerging biochemical and molecular responses. These nutritional indicators include gene expression, transcript regulators, protein profiling and activity, and gross biochemical and elemental composition. The potential applications of nutritional indicators to ecological studies are highlighted to demonstrate the value that this approach would have to future studies in community and ecosystem ecology.}, language = {en} } @article{VossBolhuisFeweretal.2013, author = {Voss, Bj{\"o}rn and Bolhuis, Henk and Fewer, David P. and Kopf, Matthias and M{\"o}ke, Fred and Haas, Fabian and El-Shehawy, Rehab and Hayes, Paul and Bergman, Birgitta and Sivonen, Kaarina and Dittmann-Th{\"u}nemann, Elke and Scanlan, Dave J. and Hagemann, Martin and Stal, Lucas J. and Hess, Wolfgang R.}, title = {Insights into the physiology and ecology of the brackish-water-adapted cyanobacterium nodularia spumigena CCY9414 based on a genome-transcriptome analysis}, series = {PLoS one}, volume = {8}, journal = {PLoS one}, number = {3}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0060224}, pages = {22}, year = {2013}, abstract = {Nodularia spumigena is a filamentous diazotrophic cyanobacterium that dominates the annual late summer cyanobacterial blooms in the Baltic Sea. But N. spumigena also is common in brackish water bodies worldwide, suggesting special adaptation allowing it to thrive at moderate salinities. A draft genome analysis of N. spumigena sp. CCY9414 yielded a single scaffold of 5,462,271 nucleotides in length on which genes for 5,294 proteins were annotated. A subsequent strand-specific transcriptome analysis identified more than 6,000 putative transcriptional start sites (TSS). Orphan TSSs located in intergenic regions led us to predict 764 non-coding RNAs, among them 70 copies of a possible retrotransposon and several potential RNA regulators, some of which are also present in other N2-fixing cyanobacteria. Approximately 4\% of the total coding capacity is devoted to the production of secondary metabolites, among them the potent hepatotoxin nodularin, the linear spumigin and the cyclic nodulapeptin. The transcriptional complexity associated with genes involved in nitrogen fixation and heterocyst differentiation is considerably smaller compared to other Nostocales. In contrast, sophisticated systems exist for the uptake and assimilation of iron and phosphorus compounds, for the synthesis of compatible solutes, and for the formation of gas vesicles, required for the active control of buoyancy. Hence, the annotation and interpretation of this sequence provides a vast array of clues into the genomic underpinnings of the physiology of this cyanobacterium and indicates in particular a competitive edge of N. spumigena in nutrient-limited brackish water ecosystems.}, language = {en} } @article{vonderLippeBullockKowariketal.2013, author = {von der Lippe, Moritz and Bullock, James M. and Kowarik, Ingo and Knopp, Tatjana and Wichmann, Matthias}, title = {Human-mediated dispersal of seeds by the airflow of vehicles}, series = {PLoS one}, volume = {8}, journal = {PLoS one}, number = {1}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0052733}, pages = {10}, year = {2013}, abstract = {Human-mediated dispersal is known as an important driver of long-distance dispersal for plants but underlying mechanisms have rarely been assessed. Road corridors function as routes of secondary dispersal for many plant species but the extent to which vehicles support this process remains unclear. In this paper we quantify dispersal distances and seed deposition of plant species moved over the ground by the slipstream of passing cars. We exposed marked seeds of four species on a section of road and drove a car along the road at a speed of 48 km/h. By tracking seeds we quantified movement parallel as well as lateral to the road, resulting dispersal kernels, and the effect of repeated vehicle passes. Median distances travelled by seeds along the road were about eight meters for species with wind dispersal morphologies and one meter for species without such adaptations. Airflow created by the car lifted seeds and resulted in longitudinal dispersal. Single seeds reached our maximum measuring distance of 45 m and for some species exceeded distances under primary dispersal. Mathematical models were fit to dispersal kernels. The incremental effect of passing vehicles on longitudinal dispersal decreased with increasing number of passes as seeds accumulated at road verges. We conclude that dispersal by vehicle airflow facilitates seed movement along roads and accumulation of seeds in roadside habitats. Dispersal by vehicle airflow can aid the spread of plant species and thus has wide implications for roadside ecology, invasion biology and nature conservation.}, language = {en} } @phdthesis{Verhounig2013, author = {Verhounig, Andreas}, title = {Riboswitche f{\"u}r die konditionale Genexpression in Bakterien und Plastiden}, address = {Potsdam}, pages = {138 S.}, year = {2013}, language = {de} } @article{VanderMeerScottWaightetal.2013, author = {Van der Meer, Q. H. A. and Scott, James M. and Waight, T. E. and Sudo, Masafumi and Schersten, A. and Cooper, Alan F. and Spell, Terry L.}, title = {Magmatism during Gondwana break-up: new geochronological data from Westland, New Zealand}, series = {New Zealand journal of geology and geophysics : an international journal of pacific rim geosciences}, volume = {56}, journal = {New Zealand journal of geology and geophysics : an international journal of pacific rim geosciences}, number = {4}, publisher = {Routledge, Taylor \& Francis Group}, address = {Abingdon}, issn = {0028-8306}, doi = {10.1080/00288306.2013.826699}, pages = {229 -- 242}, year = {2013}, abstract = {Newly determined Late Cretaceous Ar-40/Ar-39 ages on megacrystic kaersutite from four lamprophyre dikes, and a U-Pb zircon age on a trachyte, from central and north Westland (New Zealand) are presented. These ages suggest that the intrusion of mafic dikes (88-86 and 69 Ma) was not necessarily restricted to the previously established narrow age range of 80-92 Ma. The younger lamprophyre and trachyte dikes (c. 68-70 Ma) imply that tensional stresses in the Western Province were either renewed at this time, or that extension and related magmatism continued during opening of the Tasman Sea. Extension-related magmatism in the region not only preceded Tasman seafloor spreading initiation (starting at c. 83 Ma, lasting to c. 53 Ma), but may have sporadically continued for up to 15 Ma after continental break-up.}, language = {en} } @article{ToepferCaldanaGrimbsetal.2013, author = {T{\"o}pfer, Nadine and Caldana, Camila and Grimbs, Sergio and Willmitzer, Lothar and Fernie, Alisdair R. and Nikoloski, Zoran}, title = {Integration of genome-scale modeling and transcript profiling reveals metabolic pathways underlying light and temperature acclimation in arabidopsis}, series = {The plant cell}, volume = {25}, journal = {The plant cell}, number = {4}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {1040-4651}, doi = {10.1105/tpc.112.108852}, pages = {1197 -- 1211}, year = {2013}, abstract = {Understanding metabolic acclimation of plants to challenging environmental conditions is essential for dissecting the role of metabolic pathways in growth and survival. As stresses involve simultaneous physiological alterations across all levels of cellular organization, a comprehensive characterization of the role of metabolic pathways in acclimation necessitates integration of genome-scale models with high-throughput data. Here, we present an integrative optimization-based approach, which, by coupling a plant metabolic network model and transcriptomics data, can predict the metabolic pathways affected in a single, carefully controlled experiment. Moreover, we propose three optimization-based indices that characterize different aspects of metabolic pathway behavior in the context of the entire metabolic network. We demonstrate that the proposed approach and indices facilitate quantitative comparisons and characterization of the plant metabolic response under eight different light and/or temperature conditions. The predictions of the metabolic functions involved in metabolic acclimation of Arabidopsis thaliana to the changing conditions are in line with experimental evidence and result in a hypothesis about the role of homocysteine-to-Cys interconversion and Asn biosynthesis. The approach can also be used to reveal the role of particular metabolic pathways in other scenarios, while taking into consideration the entirety of characterized plant metabolism.}, language = {en} } @article{TsukayaByrneHoriguchietal.2013, author = {Tsukaya, Hirokazu and Byrne, Mary E. and Horiguchi, Gorou and Sugiyama, Munetaka and Van Lijsebettens, Mieke and Lenhard, Michael}, title = {How do 'housekeeping' genes control organogenesis?-unexpected new findings on the role of housekeeping genes in cell and organ differentiation}, series = {Journal of plant research}, volume = {126}, journal = {Journal of plant research}, number = {1}, publisher = {Springer}, address = {Tokyo}, issn = {0918-9440}, doi = {10.1007/s10265-012-0518-2}, pages = {3 -- 15}, year = {2013}, abstract = {In recent years, an increasing number of mutations in what would appear to be 'housekeeping genes' have been identified as having unexpectedly specific defects in multicellular organogenesis. This is also the case for organogenesis in seed plants. Although it is not surprising that loss-of-function mutations in 'housekeeping' genes result in lethality or growth retardation, it is surprising when (1) the mutant phenotype results from the loss of function of a 'housekeeping' gene and (2) the mutant phenotype is specific. In this review, by defining housekeeping genes as those encoding proteins that work in basic metabolic and cellular functions, we discuss unexpected links between housekeeping genes and specific developmental processes. In a surprising number of cases housekeeping genes coding for enzymes or proteins with functions in basic cellular processes such as transcription, post-transcriptional modification, and translation affect plant development.}, language = {en} } @article{TikhonenkoMagidsonGraefetal.2013, author = {Tikhonenko, Irina and Magidson, Valentin and Gr{\"a}f, Ralph and Khodjakov, Alexey and Koonce, Michael P.}, title = {A kinesin-mediated mechanism that couples centrosomes to nuclei}, series = {Cellular and molecular life sciences}, volume = {70}, journal = {Cellular and molecular life sciences}, number = {7}, publisher = {Springer}, address = {Basel}, issn = {1420-682X}, doi = {10.1007/s00018-012-1205-0}, pages = {1285 -- 1296}, year = {2013}, abstract = {The M-type kinesin isoform, Kif9, has recently been implicated in maintaining a physical connection between the centrosome and nucleus in Dictyostelium discoideum. However, the mechanism by which Kif9 functions to link these two organelles remains obscure. Here we demonstrate that the Kif9 protein is localized to the nuclear envelope and is concentrated in the region underlying the centrosome point of attachment. Nuclear anchorage appears mediated through a specialized transmembrane domain located in the carboxyl terminus. Kif9 interacts with microtubules in in vitro binding assays and effects an endwise depolymerization of the polymer. These results suggest a model whereby Kif9 is anchored to the nucleus and generates a pulling force that reels the centrosome up against the nucleus. This is a novel activity for a kinesin motor, one important for progression of cells into mitosis and to ensure centrosome-nuclear parity in a multinuclear environment.}, language = {en} } @article{ThinesKummer2013, author = {Thines, Marco and Kummer, Volker}, title = {Diversity and species boundaries in floricolous downy mildews}, series = {Mycological progress : international journal of the German Mycological Society}, volume = {12}, journal = {Mycological progress : international journal of the German Mycological Society}, number = {2}, publisher = {Springer}, address = {Heidelberg}, issn = {1617-416X}, doi = {10.1007/s11557-012-0837-7}, pages = {321 -- 329}, year = {2013}, abstract = {Floricolous downy mildews are a monophyletic group of members of the genus Peronospora (Oomycota, Peronosporales). These downy mildews can be found on a variety of families of the Asteridae, including Asteraceae, Campanulaceae, Dipsacaceae, Lamiaceae, and Orobanchaceae. With the exception of Peronospora radii, which can also cause economically relevant losses, sporulation usually takes place only on floral parts of their hosts. However, only very few specimens of these mostly inconspicuous downy mildews have so far been included in molecular phylogenies. Focusing on Lamiaceae, we have investigated multiple specimens of floricolous downy mildews for elucidating species boundaries and host specificity in this group. Based on both mitochondrial and nuclear loci, it became apparent that phylogenetic lineages in the Lamiaceae seem to be host genus specific and significant sequence diversity could be found between lineages. Based on distinctiveness in both phylogenetic reconstructions and morphology, the downy mildew on flowers of Stachys palustris is introduced as a new species, Peronospora jagei sp. nov., which can be morphologically distinguished from Peronospora stigmaticola by broader and shorter conidiospores. The diversity of the floricolous down mildews might be higher than previously assumed, although specimens from a much broader set of samples will be needed to confirm this view.}, language = {en} } @article{ThammRolkeJordanetal.2013, author = {Thamm, Markus and Rolke, Daniel and Jordan, Nadine and Balfanz, Sabine and Schiffer, Christian and Baumann, Arnd and Blenau, Wolfgang}, title = {Function and distribution of 5-HT2 receptors in the honeybee (apis mellifera)}, series = {PLoS one}, volume = {8}, journal = {PLoS one}, number = {12}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0082407}, pages = {12}, year = {2013}, abstract = {Background: Serotonin plays a pivotal role in regulating and modulating physiological and behavioral processes in both vertebrates and invertebrates. In the honeybee (Apis mellifera), serotonin has been implicated in division of labor, visual processing, and learning processes. Here, we present the cloning, heterologous expression, and detailed functional and pharmacological characterization of two honeybee 5-HT2 receptors. Methods: Honeybee 5-HT2 receptor cDNAs were amplified from brain cDNA. Recombinant cell lines were established constitutively expressing receptor variants. Pharmacological properties of the receptors were investigated by Ca2+ imaging experiments. Quantitative PCR was applied to explore the expression patterns of receptor mRNAs. Results: The honeybee 5-HT2 receptor class consists of two subtypes, Am5-HT2 alpha and Am5-HT2 beta. Each receptor gene also gives rise to alternatively spliced mRNAs that possibly code for truncated receptors. Only activation of the full-length receptors with serotonin caused an increase in the intracellular Ca2+ concentration. The effect was mimicked by the agonists 5-methoxytryptamine and 8-OH-DPAT at low micromolar concentrations. Receptor activities were blocked by established 5-HT receptor antagonists such as clozapine, methiothepin, or mianserin. High transcript numbers were detected in exocrine glands suggesting that 5-HT2 receptors participate in secretory processes in the honeybee. Conclusions: This study marks the first molecular and pharmacological characterization of two 5-HT2 receptor subtypes in the same insect species. The results presented should facilitate further attempts to unravel central and peripheral effects of serotonin mediated by these receptors.}, language = {en} } @article{TaylanDiRussoRampinietal.2013, author = {Taylan, Mehmet Sait and Di Russo, Claudio and Rampini, Mauro and Ketmaier, Valerio}, title = {Molecular systematics of the genus Troglophilus (Rhaphidophoridae, Orthoptera) in Turkey mitochondrial 16S rDNA evidences}, series = {ZooKeys}, journal = {ZooKeys}, number = {257}, publisher = {Pensoft Publ.}, address = {Sofia}, issn = {1313-2989}, doi = {10.3897/zookeys.257.4133}, pages = {33 -- 46}, year = {2013}, abstract = {This study focuses on the evolutionary relationships among Turkish species of the cave cricket genus Troglophilus. Fifteen populations were studied for sequence variation in a fragment (543 base pairs) of the mitochondrial DNA (mtDNA) 16S rDNA gene (16S) to reconstruct their phylogenetic relationships and biogeographic history. Genetic data retrieved three main clades and at least three divergent lineages that could not be attributed to any of the taxa known for the area. Molecular time estimates suggest that the diversification of the group took place between the Messinian and the Plio-Pleistocene.}, language = {en} } @phdthesis{Tartivel2013, author = {Tartivel, Lucile}, title = {Design of hydrogels with inverse shape-memory function for biomedical applications}, address = {Potsdam}, pages = {150 S.}, year = {2013}, language = {en} } @article{TanentzapLeeSchulz2013, author = {Tanentzap, Andrew J. and Lee, William G. and Schulz, Katharina A. C.}, title = {Niches drive peaked and positive relationships between diversity and disturbance in natural ecosystems}, series = {Ecosphere : the magazine of the International Ecology University}, volume = {4}, journal = {Ecosphere : the magazine of the International Ecology University}, number = {11}, publisher = {Wiley}, address = {Washington}, issn = {2150-8925}, doi = {10.1890/ES13-00102.1}, pages = {28}, year = {2013}, abstract = {A unified understanding of the relationship between disturbance and biodiversity is needed to predict biotic responses to global change. Recent advances have identified the need to deconstruct traditional models of disturbance into intensity and frequency to reconcile empirical studies that appear to generate contradictory associations between species diversity and disturbance. We integrate results from theoretical simulation modelling, field-based surveys of 5176 vegetation plots from 48 transects across 6 sites, and experimental pot-based manipulations of flooding to identify how disturbance drives species diversity within ephemeral wetlands in South Island, New Zealand. We find empirical, hump-shaped and positive relationships between species diversity and both disturbance intensity and frequency, mirroring patterns from a simulation model in which species differed in their demographic responses to disturbance. More generally, our simulations show that the relationships between diversity and disturbance shift from positive to hump-shaped to negative as species that are favored at low disturbance because of their resistance strategies, defined by low mortality and recruitment, decline within communities relative to resilient species. Resilient species with higher mortality and recruitment rates are instead favored as disturbance intensity and frequency intensify. Our theoretical findings suggest that sites must also have a third group of unique species with intermediate resilience and resistance. Analyses of community composition along our disturbance gradients support this prediction, emphasizing that shifts in community-level resistance and resilience drive empirical associations between diversity and disturbance. Overall, terrestrial plants may be unable to resist intense and frequent flooding, even with specialized traits. Only fast-growing species with high regeneration from seed may respond once flooding subsides and dominate community composition in these situations, especially on nutrient-rich soils. However, different strategies can co-occur at intermediate disturbance, ultimately increasing species richness. As disturbances become more pervasive globally, our results suggest that differences in the niches of species, rather than demographic stochasticity, drive biodiversity patterns. These niche-based processes may especially prevail, without accompanying losses in species richness, where sites are initially dominated by resistant taxa or life history strategies that balance resistance and resilience.}, language = {en} } @article{SultanowWeber2013, author = {Sultanow, Eldar and Weber, Edzard}, title = {Pharmataxigraphie Model of a Hybrid System of RFID Technology and optical Methods}, series = {Die pharmazeutische Industrie}, volume = {75}, journal = {Die pharmazeutische Industrie}, number = {7}, publisher = {Editio-Cantor-Verl. f{\"u}r Medizin und Naturwiss.}, address = {Aulendorf}, issn = {0031-711X}, pages = {1197 -- +}, year = {2013}, language = {de} } @article{SulpiceNikoloskiTschoepetal.2013, author = {Sulpice, Ronan and Nikoloski, Zoran and Tschoep, Hendrik and Antonio, Carla and Kleessen, Sabrina and Larhlimi, Abdelhalim and Selbig, Joachim and Ishihara, Hirofumi and Gibon, Yves and Fernie, Alisdair R. and Stitt, Mark}, title = {Impact of the Carbon and Nitrogen Supply on Relationships and Connectivity between Metabolism and Biomass in a Broad Panel of Arabidopsis Accessions(1[W][OA])}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {162}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {1}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.112.210104}, pages = {347 -- 363}, year = {2013}, abstract = {Natural genetic diversity provides a powerful tool to study the complex interrelationship between metabolism and growth. Profiling of metabolic traits combined with network-based and statistical analyses allow the comparison of conditions and identification of sets of traits that predict biomass. However, it often remains unclear why a particular set of metabolites is linked with biomass and to what extent the predictive model is applicable beyond a particular growth condition. A panel of 97 genetically diverse Arabidopsis (Arabidopsis thaliana) accessions was grown in near-optimal carbon and nitrogen supply, restricted carbon supply, and restricted nitrogen supply and analyzed for biomass and 54 metabolic traits. Correlation-based metabolic networks were generated from the genotype-dependent variation in each condition to reveal sets of metabolites that show coordinated changes across accessions. The networks were largely specific for a single growth condition. Partial least squares regression from metabolic traits allowed prediction of biomass within and, slightly more weakly, across conditions (cross-validated Pearson correlations in the range of 0.27-0.58 and 0.21-0.51 and P values in the range of <0.001-<0.13 and <0.001-<0.023, respectively). Metabolic traits that correlate with growth or have a high weighting in the partial least squares regression were mainly condition specific and often related to the resource that restricts growth under that condition. Linear mixed-model analysis using the combined metabolic traits from all growth conditions as an input indicated that inclusion of random effects for the conditions improves predictions of biomass. Thus, robust prediction of biomass across a range of conditions requires condition-specific measurement of metabolic traits to take account of environment-dependent changes of the underlying networks.}, language = {en} } @inproceedings{SpijkermanBehrendFachetal.2013, author = {Spijkerman, Elly and Behrend, Hella and Fach, Bettina and Gaedke, Ursula}, title = {INDIRECT EFFECT ON ECOSYSTEM FUNCTIONING : DECREASED PHOSPHORUS INCORPORATION NOT IRON TOXICITY DECREASES PHOTOSYNTHESIS AND GROWTH IN A GREEN MICROALGA}, series = {Phycologia}, volume = {52}, booktitle = {Phycologia}, number = {4}, publisher = {International Phycological Society}, address = {Lawrence}, issn = {0031-8884}, pages = {104 -- 105}, year = {2013}, language = {en} } @article{SpeckRaeuberKuekenshoeneretal.2013, author = {Speck, Janina and R{\"a}uber, Christina and K{\"u}kensh{\"o}ner, Tim and Niem{\"o}ller, Christoph and Mueller, Katelyn J. and Schleberger, Paula and Dondapati, Padmarupa and Hecky, Jochen and Arndt, Katja Maren and M{\"u}ller, Kristian M.}, title = {TAT hitchhiker selection expanded to folding helpers, multimeric interactions and combinations with protein fragment complementation}, series = {Protein engineering design \& selection}, volume = {26}, journal = {Protein engineering design \& selection}, number = {3}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1741-0126}, doi = {10.1093/protein/gzs098}, pages = {225 -- 242}, year = {2013}, abstract = {The twin-arginine translocation (TAT) pathway of the bacterial cytoplasmic membrane mediates translocation only of proteins that accomplished a native-like conformation. We deploy this feature in modular selection systems for directed evolution, in which folding helpers as well as dimeric or oligomeric proteinprotein interactions enable TAT-dependent translocation of the resistance marker TEM -lactamase (L). Specifically, we demonstrate and analyze selection of (i) enhancers for folding by direct TAT translocation selection of a target protein interposed between the TorA signal sequence and L, (ii) dimeric or oligomeric proteinprotein interactions by hitchhiker translocation (HiT) selection of proteins fused to the TorA signal sequence and to the L, respectively and (iii) heterotrimeric proteinprotein interactions by combining HiT with protein fragment complementation selection of proteins fused to two split L fragments and TorA, respectively. The lactamase fragments were additionally engineered for improved activity and stability. Applicability was benchmarked with interaction partners of known affinity and multimerization whereby cellular fitness correlated well with biophysical protein properties. Ultimately, the HiT selection was employed to identify peptides, which specifically bind to leukemia- and melanoma-relevant target proteins (MITF and ETO) by coiled-coil or tetra-helix-bundle formation with high affinity. The various versions of TAT selection led to inhibiting peptides (iPEPs) of disease-promoting interactions and enabled so far difficult to achieve selections.}, language = {en} } @article{SollySchoeningBochetal.2013, author = {Solly, Emily and Sch{\"o}ning, Ingo and Boch, Steffen and Mueller, J. and Socher, S. A. and Trumbore, S. E. and Schrumpf, M.}, title = {Mean age of carbon in fine roots from temperate forests and grasslands with different management}, series = {Biogeosciences}, volume = {10}, journal = {Biogeosciences}, number = {7}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {1726-4170}, doi = {10.5194/bg-10-4833-2013}, pages = {4833 -- 4843}, year = {2013}, abstract = {Fine roots are the most dynamic portion of a plant's root system and a major source of soil organic matter. By altering plant species diversity and composition, soil conditions and nutrient availability, and consequently belowground allocation and dynamics of root carbon (C) inputs, land-use and management changes may influence organic C storage in terrestrial ecosystems. In three German regions, we measured fine root radiocarbon (C-14) content to estimate the mean time since C in root tissues was fixed from the atmosphere in 54 grassland and forest plots with different management and soil conditions. Although root biomass was on average greater in grasslands 5.1 +/- 0.8 g (mean +/- SE, n = 27) than in forests 3.1 +/- 0.5 g (n = 27) (p < 0.05), the mean age of C in fine roots in forests averaged 11.3 +/- 1.8 yr and was older and more variable compared to grasslands 1.7 +/- 0.4 yr (p < 0.001). We further found that management affects the mean age of fine root C in temperate grasslands mediated by changes in plant species diversity and composition. Fine root mean C age is positively correlated with plant diversity (r = 0.65) and with the number of perennial species (r = 0.77). Fine root mean C age in grasslands was also affected by study region with averages of 0.7 +/- 0.1 yr (n= 9) on mostly organic soils in northern Germany and of 1.8 +/- 0.3 yr (n = 9) and 2.6 +/- 0.3 (n = 9) in central and southern Germany (p < 0.05). This was probably due to differences in soil nutrient contents and soil moisture conditions between study regions, which affected plant species diversity and the presence of perennial species. Our results indicate more long-lived roots or internal redistribution of C in perennial species and suggest linkages between fine root C age and management in grasslands. These findings improve our ability to predict and model belowground C fluxes across broader spatial scales.}, language = {en} } @article{SocherPratiBochetal.2013, author = {Socher, Stephanie A. and Prati, Daniel and Boch, Steffen and M{\"u}ller, J{\"o}rg and Baumbach, Henryk and Gockel, Sonja and Hemp, Andreas and Sch{\"o}ning, Ingo and Wells, Konstans and Buscot, Francois and Kalko, Elisabeth K. V. and Linsenmair, Karl Eduard and Schulze, Ernst-Detlef and Weisser, Wolfgang W. and Fischer, Markus}, title = {Interacting effects of fertilization, mowing and grazing on plant species diversity of 1500 grasslands in Germany differ between regions}, series = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, volume = {14}, journal = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, number = {2}, publisher = {Elsevier}, address = {Jena}, issn = {1439-1791}, doi = {10.1016/j.baae.2012.12.003}, pages = {126 -- 136}, year = {2013}, abstract = {The relationship of different types of grassland use with plant species richness and composition ( functional groups of herbs, legumes, and grasses) has so far been studied at small regional scales or comprising only few components of land use. We comprehensively studied the relationship between abandonment, fertilization, mowing intensity, and grazing by different livestock types on plant diversity and composition of 1514 grassland sites in three regions in North-East, Central and South-West Germany. We further considered environmental site conditions including soil type and topographical situation. Fertilized grasslands showed clearly reduced plant species diversity (-15\% plant species richness, -0.1 Shannon diversity on fertilized grasslands plots of 16m(2)) and changed composition (-3\% proportion of herb species), grazing had the second largest effects and mowing the smallest ones. Among the grazed sites, the ones grazed by sheep had higher than average species richness (+27\%), and the cattle grazed ones lower (-42\%). Further, these general results were strongly modulated by interactions between the different components of land use and by regional context: land-use effects differed largely in size and sometimes even in direction between regions. This highlights the importance of comparing different regions and to involve a large number of plots}, language = {en} } @article{SnijmanKocyan2013, author = {Snijman, Deirdre A. and Kocyan, Alexander}, title = {The genus Pauridia (Hypoxidaceae) amplified to include Hypoxis sect. Ianthe, Saniella and Spiloxene, with revised nomenclature and typification}, series = {Phytotaxa : a rapid international journal for accelerating the publication of botanical taxonomy}, volume = {116}, journal = {Phytotaxa : a rapid international journal for accelerating the publication of botanical taxonomy}, number = {1}, publisher = {Magnolia Press}, address = {Auckland}, issn = {1179-3155}, doi = {10.11646/phytotaxa.116.1.2}, pages = {19 -- 33}, year = {2013}, abstract = {Recent phylogenetic analyses show that the species of the southern African genera Pauridia, Saniella and Spiloxene and the Australian, Tasmanian and New Zealand Hypoxis sect. Ianthe form a highly supported, monophyletic clade. In keeping with earlier suggestions that these taxa doubtfully warrant separate status, and to avoid the recognition of Hypoxis and Spiloxene as paraphyletic, we expand the circumscription of Pauridia to include Saniella, Spiloxene and Hypoxis sect. Ianthe. As a result 33 new combinations at specific and infraspecific level are proposed and one epitype, two neotypes and 30 lectotypes are newly designated. Three basionyms, of which Linnaeus, Linnaeus filius and Lamarck are the authors, are also typified (Amaryllis capensis, Hypoxis aquatica, and Hypoxis pumila).}, language = {en} } @inproceedings{SmithMattosBarbirz2013, author = {Smith, Mychal Daijon and Mattos, Carla and Barbirz, Stefanie}, title = {The multiple solvent crystal structures method of P22TSP}, series = {The FASEB journal : the official journal of the Federation of American Societies for Experimental Biology}, volume = {27}, booktitle = {The FASEB journal : the official journal of the Federation of American Societies for Experimental Biology}, number = {11}, publisher = {Federation of American Societies for Experimental Biology}, address = {Bethesda}, issn = {0892-6638}, pages = {1}, year = {2013}, language = {en} } @article{SivanesanLyAdamkiewiczetal.2013, author = {Sivanesan, Arumugam and Ly, Khoa H. and Adamkiewicz, Witold and Stiba, Konstanze and Leimk{\"u}hler, Silke and Weidinger, Inez M.}, title = {Tunable electric field enhancement and redox chemistry on TiO2 Island films via covalent attachment to Ag or Au nanostructures}, series = {The journal of physical chemistry : C, Nanomaterials and interfaces}, volume = {117}, journal = {The journal of physical chemistry : C, Nanomaterials and interfaces}, number = {22}, publisher = {American Chemical Society}, address = {Washington}, issn = {1932-7447}, doi = {10.1021/jp4032578}, pages = {11866 -- 11872}, year = {2013}, abstract = {Ag-TiO2 and Au-TiO2 hybrid electrodes were designed by covalent attachment of TiO2 nanoparticles to Ag or Au electrodes via an organic linker. The optical and electronic properties of these systems were investigated using the cytochrome b(5) (Cyt b(5)) domain of sulfite oxidase, exclusively attached to the TiO2 surface, as a Raman marker and model redox enzyme. Very strong SERR signals of Cyt b(5) were obtained for Ag-supported systems due to plasmonic field enhancement of Ag. Time-resolved surface-enhanced resonance Raman spectroscopic measurements yielded a remarkably fast electron transfer kinetic (k = 60 s(-1)) of Cyt b(5) to Ag. A much lower Raman intensity was observed for Au-supported systems with undefined and slow redox behavior. We explain this phenomenon on the basis of the different potential of zero charge of the two metals that largely influence the electronic properties of the TiO2 island film.}, language = {en} } @misc{SiblyGrimmMartinetal.2013, author = {Sibly, Richard M. and Grimm, Volker and Martin, Benjamin T. and Johnston, Alice S. A. and Kulakowska, Katarzyna and Topping, Christopher J. and Calow, Peter and Nabe-Nielsen, Jacob and Thorbek, Pernille and DeAngelis, Donald L.}, title = {Representing the acquisition and use of energy by individuals in agent-based models of animal populations}, series = {Methods in ecology and evolution : an official journal of the British Ecological Society}, volume = {4}, journal = {Methods in ecology and evolution : an official journal of the British Ecological Society}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {2041-210X}, doi = {10.1111/2041-210x.12002}, pages = {151 -- 161}, year = {2013}, abstract = {Agent-based models (ABMs) are widely used to predict how populations respond to changing environments. As the availability of food varies in space and time, individuals should have their own energy budgets, but there is no consensus as to how these should be modelled. Here, we use knowledge of physiological ecology to identify major issues confronting the modeller and to make recommendations about how energy budgets for use in ABMs should be constructed. Our proposal is that modelled animals forage as necessary to supply their energy needs for maintenance, growth and reproduction. If there is sufficient energy intake, an animal allocates the energy obtained in the order: maintenance, growth, reproduction, energy storage, until its energy stores reach an optimal level. If there is a shortfall, the priorities for maintenance and growth/reproduction remain the same until reserves fall to a critical threshold below which all are allocated to maintenance. Rates of ingestion and allocation depend on body mass and temperature. We make suggestions for how each of these processes should be modelled mathematically. Mortality rates vary with body mass and temperature according to known relationships, and these can be used to obtain estimates of background mortality rate. If parameter values cannot be obtained directly, then values may provisionally be obtained by parameter borrowing, pattern-oriented modelling, artificial evolution or from allometric equations. The development of ABMs incorporating individual energy budgets is essential for realistic modelling of populations affected by food availability. Such ABMs are already being used to guide conservation planning of nature reserves and shell fisheries, to assess environmental impacts of building proposals including wind farms and highways and to assess the effects on nontarget organisms of chemicals for the control of agricultural pests.}, language = {en} } @misc{SharmaDreyerRiedelsberger2013, author = {Sharma, Tripti and Dreyer, Ingo and Riedelsberger, Janin}, title = {The role of K+ channels in uptake and redistribution of potassium in the model plant Arabidopsis thaliana}, series = {Frontiers in plant science}, volume = {4}, journal = {Frontiers in plant science}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2013.00224}, pages = {16}, year = {2013}, abstract = {Potassium (K+) is inevitable for plant growth and development. It plays a crucial role in the regulation of enzyme activities, in adjusting the electrical membrane potential and the cellular turgor, in regulating cellular homeostasis and in the stabilization of protein synthesis. Uptake of K+ from the soil and its transport to growing organs is essential for a healthy plant development. Uptake and allocation of K+ are performed by K+ channels and transporters belonging to different protein families. In this review we summarize the knowledge on the versatile physiological roles of plant K+ channels and their behavior under stress conditions in the model plant Arabidopsis thaliana.}, language = {en} } @misc{SenguptaChattopadhyayGrossart2013, author = {Sengupta, Saswati and Chattopadhyay, Madhab K. and Grossart, Hans-Peter}, title = {The multifaceted roles of antibiotics and antibiotic resistance in nature}, series = {Frontiers in microbiology}, volume = {4}, journal = {Frontiers in microbiology}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-302X}, doi = {10.3389/fmicb.2013.00047}, pages = {13}, year = {2013}, abstract = {Antibiotics are chemotherapeutic agents, which have been a very powerful tool in the clinical management of bacterial diseases since the 1940s. However, benefits offered by these magic bullets have been substantially lost in subsequent days following the widespread emergence and dissemination of antibiotic-resistant strains. While it is obvious that excessive and imprudent use of antibiotics significantly contributes to the emergence of resistant strains, antibiotic resistance is also observed in natural bacteria of remote places unlikely to be impacted by human intervention. Both antibiotic biosynthetic genes and resistance-conferring genes have been known to evolve billions of years ago, long before clinical use of antibiotics. Hence it appears that antibiotics and antibiotics resistance determinants have some other roles in nature, which often elude our attention because of overemphasis on the therapeutic importance of antibiotics and the crisis imposed by the antibiotic resistance in pathogens. In the natural milieu, antibiotics are often found to be present in sub-inhibitory concentrations acting as signaling molecules supporting the process of quorum sensing and biofilm formation. They also play an important role in the production of virulence factors and influence host-parasite interactions (e.g., phagocytosis, adherence to the target cell, and so on). The evolutionary and ecological aspects of antibiotics and antibiotic resistance in the naturally occurring microbial community are little understood. Therefore, the actual role of antibiotics in nature warrants in-depth investigations. Studies on such an intriguing behavior of the microorganisms promise insight into the intricacies of the microbial physiology and are likely to provide some lead in controlling the emergence and subsequent dissemination of antibiotic resistance. This article highlights some of the recent findings on the role of antibiotics and the genes that confer resistance to antibiotics in nature.}, language = {en} } @article{SeifanSeifanSchiffersetal.2013, author = {Seifan, Merav and Seifan, Tal and Schiffers, Katja and Jeltsch, Florian and Tielboerger, Katja}, title = {Beyond the competition-colonization trade-off - linking multiple trait response to disturbance characteristics}, series = {The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences}, volume = {181}, journal = {The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences}, number = {2}, publisher = {Univ. of Chicago Press}, address = {Chicago}, issn = {0003-0147}, doi = {10.1086/668844}, pages = {151 -- 160}, year = {2013}, abstract = {Disturbances' role in shaping communities is well documented but highly disputed. We suggest replacing the overused two-trait trade-off approach with a functional group scheme, constructed from combinations of four key traits that represent four classes of species' responses to disturbances. Using model results and field observations from sites affected by two highly different disturbances, we demonstrated that popular dichotomous trade-offs are not sufficient to explain community dynamics, even if some emerge under certain conditions. Without disturbances, competition was only sufficient to predict species survival but not relative success, which required some escape mechanism (e.g., long-term dormancy). With highly predictable and large-scale disturbances, successful species showed a combination of high individual tolerance to disturbance and, more surprisingly, high competitive ability. When disturbances were less predictable, high individual tolerance and long-term seed dormancy were favored, due to higher environmental uncertainty. Our study demonstrates that theories relying on a small number of predefined trade-offs among traits (e.g., competition-colonization trade-off) may lead to unrealistic results. We suggest that the understanding of disturbance-community relationships can be significantly improved by employing sets of relevant trait assemblies instead of the currently common approach in which trade-offs are assumed in advance.}, language = {en} } @article{SchwarzerHeinkenLuthardtetal.2013, author = {Schwarzer, Christian and Heinken, Thilo and Luthardt, Vera and Joshi, Jasmin Radha}, title = {Latitudinal shifts in species interactions interfere with resistance of southern but not of northern bog-plant communities to experimental climate change}, series = {The journal of ecology}, volume = {101}, journal = {The journal of ecology}, number = {6}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0022-0477}, doi = {10.1111/1365-2745.12158}, pages = {1484 -- 1497}, year = {2013}, abstract = {The persistence of species under changed climatic conditions depends on adaptations and plastic responses to these conditions and on interactions with their local plant community resulting in direct and indirect effects of changed climatic conditions. Populations at species' range margins may be especially crucial in containing a gene pool comprising adaptations to extreme climatic conditions. Many species of northern European bog ecosystems reach their southern lowland range limit in central Europe. In a common-garden experiment, we experimentally assessed the impact of projected climatic changes on five bog-plant species (including peat moss Sphagnum magellanicum) sampled along a latitudinal gradient of 1400km from Scandinavia to the marginal lowland populations in Germany. Populations were cultivated in monocultures and in experimental communities composed of all five species from their local community, and exposed to five combinations of three climate treatments (warming, fluctuating water-tables, fertilization) in a southern common garden. Whereas most monocultures showed a decreasing biomass production from southern to northern origins under southern environmental conditions, in the experimental mixed-species communities, an increasing biomass production towards northern communities was observed together with a shift in interspecific interactions along the latitudinal gradient. While negative dominance effects prevailed in southern communities, higher net biodiversity effects were observed in northern subarctic communities. The combined effects of climate treatments increased biomass production in monocultures of most origins. In communities, however, overall the treatments did not result in significantly changed biomass production. Among individual treatments, water-table fluctuations caused a significant decrease in biomass production, but only in southern communities, indicating higher vulnerability to changed climatic conditions. Here, negative effects of climate treatments on graminoids were not compensated by the slightly increased growth of peat moss that benefited from interspecific interactions only in northern communities.Synthesis. We conclude that shifting interactions within multispecies communities caused pronounced responses to changed climatic conditions in wetland communities of temperate southern marginal, but not of northern subarctic origin. Therefore, future models investigating the impacts of climate change on plant communities should consider geographical variation in species interactions an important factor influencing community responses to changed climatic conditions.}, language = {en} } @article{SchwarteBrustSteupetal.2013, author = {Schwarte, Sandra and Brust, Henrike and Steup, Martin and Tiedemann, Ralph}, title = {Intraspecific sequence variation and differential expression in starch synthase genes of Arabidopsis thaliana}, doi = {10.1186/1756-0500-6-84}, year = {2013}, language = {en} } @misc{SchwarteBrustSteupetal.2013, author = {Schwarte, Sandra and Brust, Henrike and Steup, Martin and Tiedemann, Ralph}, title = {Intraspecific sequence variation and differential expression in starch synthase genes of Arabidopsis thaliana}, series = {BMC Research Notes}, journal = {BMC Research Notes}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-401128}, pages = {14}, year = {2013}, abstract = {Background Natural accessions of Arabidopsis thaliana are a well-known system to measure levels of intraspecific genetic variation. Leaf starch content correlates negatively with biomass. Starch is synthesized by the coordinated action of many (iso)enzymes. Quantitatively dominant is the repetitive transfer of glucosyl residues to the non-reducing ends of α-glucans as mediated by starch synthases. In the genome of A. thaliana, there are five classes of starch synthases, designated as soluble starch synthases (SSI, SSII, SSIII, and SSIV) and granule-bound synthase (GBSS). Each class is represented by a single gene. The five genes are homologous in functional domains due to their common origin, but have evolved individual features as well. Here, we analyze the extent of genetic variation in these fundamental protein classes as well as possible functional implications on transcript and protein levels. Findings Intraspecific sequence variation of the five starch synthases was determined by sequencing the entire loci including promoter regions from 30 worldwide distributed accessions of A. thaliana. In all genes, a considerable number of nucleotide polymorphisms was observed, both in non-coding and coding regions, and several amino acid substitutions were identified in functional domains. Furthermore, promoters possess numerous polymorphisms in potentially regulatory cis-acting regions. By realtime experiments performed with selected accessions, we demonstrate that DNA sequence divergence correlates with significant differences in transcript levels. Conclusions Except for AtSSII, all starch synthase classes clustered into two or three groups of haplotypes, respectively. Significant difference in transcript levels among haplotype clusters in AtSSIV provides evidence for cis-regulation. By contrast, no such correlation was found for AtSSI, AtSSII, AtSSIII, and AtGBSS, suggesting trans-regulation. The expression data presented here point to a regulation by common trans-regulatory transcription factors which ensures a coordinated action of the products of these four genes during starch granule biosynthesis. The apparent cis-regulation of AtSSIV might be related to its role in the initiation of de novo biosynthesis of granules.}, language = {en} } @article{SchradeScheffler2013, author = {Schrade, Lisa and Scheffler, Christiane}, title = {Assessing the applicability of the digital laser rangefinder GLM Professional (R) Bosch 250 VF for anthropometric field studies}, series = {Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft f{\"u}r Anthropologie}, volume = {70}, journal = {Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft f{\"u}r Anthropologie}, number = {2}, publisher = {Schweizerbart}, address = {Stuttgart}, issn = {0003-5548}, doi = {10.1127/0003-5548/2013/0223}, pages = {137 -- 145}, year = {2013}, abstract = {The digital laser rangefinder GLM Professional (R) BOSCH 250 VF was tested as a modified preproduction model with regard to its applicability of quantifying humans' height. The aim of this investigation was to determine and evaluate the instrument's precision, as well as its manageability within anthropometric field studies. Data collected by the digital laser rangefinder did not show a significant difference to data of control by an anthropometer. Furthermore, more than 96\% of the difference values are located within area of agreement. Nevertheless, the GLM Professional (R) is a highly sensitive instrument and mean SD within threefold data acquisition is twice as high as SD resulting from data collection by an anthropometer. However, due to the minimal percentage differences within data acquisition and compared to the standard method, the GLM Professional (R) is proved to be a reliable instrument and to be highly applicable for anthropometric field studies. Furthermore, due to its excellent manageability and compact size, the GLM Professional (R) shows a very good applicability even for less trained anthropometrists and thus ameliorates the possibilities of collecting reliable data within anthropometric field studies.}, language = {en} } @article{SchradeScheffler2013, author = {Schrade, Lisa and Scheffler, Christiane}, title = {Assessing the applicability of the digital laser rangefinder GLM Professional Bosch 250 VF for anthropometric field studies}, year = {2013}, language = {en} } @article{SchmitzHertzbergMakLaietal.2013, author = {Schmitz-Hertzberg, Sebastian-Tim and Mak, Wing Cheung and Lai, Kwok Kei and Teller, Carsten and Bier, Frank Fabian}, title = {Multifactorial design of Poly(D, L-lactic-co-glycolic acid) capsules with various release properties for differently sized filling agents}, series = {Journal of applied polymer science}, volume = {130}, journal = {Journal of applied polymer science}, number = {6}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0021-8995}, doi = {10.1002/app.39537}, pages = {4219 -- 4228}, year = {2013}, abstract = {The hydrolytic degradation and corresponding content release of capsules made of poly(d,l-lactic-co-glycolic acid) (PLGA) strongly depends on the composition and material properties of the initially applied copolymer. Consecutive or simultaneous release from capsule batches of combinable material compositions, therefore, offers high control over the bioavailability of an encapsulated drug. The keynote of this study was the creation of a superordinated database that addressed the correlation between the release kinetics of filling agents with different molecular weights from PLGA capsules of alternating composition. Fluorescein isothiocyanate (FITC)-dextran (with molecular weights of 4, 40, and 2000 kDa) was chosen as a model analyte, whereas the copolymers were taken from various 50:50 PLGA, 75:25 PLGA, and polylactide blends. With reference to recent publications, the capsule properties, such as the size, morphology, and encapsulation efficiency, were further modified during production. Hence, uniform microdisperse and polydisperse submicrometer nanocapsules were prepared by two different water-in-oil-in-water emulsification techniques, and additional effects on the size and morphology were achieved by capsule solidification in two different sodium salt buffers. The qualitative and quantitative examination of the physical capsule properties was performed by confocal laser scanning microscopy, scanning electron microscopy, and Coulter counting techniques to evaluate the capsule size distribution and the morphological appearance of the different batches. The corresponding agent release was quantified by fluorescence measurement of the FITC-dextran in the incubation media and by the direct measurement of the capsule brightness via fluorescence microscopy. In summary, the observed agent release showed a highly controllable flexibility depending on the PLGA blends, preparation methods, and molecular weight of the used filling substances. (c) 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 130: 4219-4228, 2013}, language = {en} } @phdthesis{SchmitzHertzberg2013, author = {Schmitz-Hertzberg, Sebastian-Tim}, title = {Entwicklung eines Verkapselungssystems f{\"u}r den Einsatz autonomer Biosensoren in der Bioprozesstechnik und medizinischen Diagnostik}, address = {Potsdam}, pages = {131 S.}, year = {2013}, language = {de} } @article{SchmiederNitschkeSteupetal.2013, author = {Schmieder, Peter and Nitschke, Felix and Steup, Martin and Mallow, Keven and Specker, Edgar}, title = {Determination of glucan phosphorylation using heteronuclear H-1,C-13 double and H-1,C-13,P-31 triple-resonance NMR spectra}, series = {Magnetic resonance in chemistry}, volume = {51}, journal = {Magnetic resonance in chemistry}, number = {10}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0749-1581}, doi = {10.1002/mrc.3996}, pages = {655 -- 661}, year = {2013}, abstract = {Phosphorylation and dephosphorylation of starch and glycogen are important for their physicochemical properties and also their physiological functions. It is therefore desirable to reliably determine the phosphorylation sites. Heteronuclear multidimensional NMR-spectroscopy is in principle a straightforward analytical approach even for complex carbohydrate molecules. With heterogeneous samples from natural sources, however, the task becomes more difficult because a full assignment of the resonances of the carbohydrates is impossible to obtain. Here, we show that the combination of heteronuclear H-1,C-13 and H-1,C-13,P-31 techniques and information derived from spectra of a set of reference compounds can lead to an unambiguous determination of the phosphorylation sites even in heterogeneous samples.}, language = {en} } @phdthesis{Schmidt2013, author = {Schmidt, Stefanie}, title = {Untersuchung des Einflusses der stressregulierten rei1 homologen Proteine auf die Physiologie und den Metabolismus von Arabidopsis thaliana}, address = {Potsdam}, pages = {106, XXII S.}, year = {2013}, language = {de} } @article{SchmidtSchippersMieuletetal.2013, author = {Schmidt, Romy and Schippers, Jos H. M. and Mieulet, Delphine and Obata, Toshihiro and Fernie, Alisdair R. and Guiderdoni, Emmanuel and M{\"u}ller-R{\"o}ber, Bernd}, title = {Multipass, a rice R2R3-type MYB transcription factor, regulates adaptive growth by integrating multiple hormonal pathways}, series = {The plant journal}, volume = {76}, journal = {The plant journal}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0960-7412}, doi = {10.1111/tpj.12286}, pages = {258 -- 273}, year = {2013}, abstract = {Growth regulation is an important aspect of plant adaptation during environmental perturbations. Here, the role of MULTIPASS (OsMPS), an R2R3-type MYB transcription factor of rice, was explored. OsMPS is induced by salt stress and expressed in vegetative and reproductive tissues. Over-expression of OsMPS reduces growth under non-stress conditions, while knockdown plants display increased biomass. OsMPS expression is induced by abscisic acid and cytokinin, but is repressed by auxin, gibberellin and brassinolide. Growth retardation caused by OsMPS over-expression is partially restored by auxin application. Expression profiling revealed that OsMPS negatively regulates the expression of EXPANSIN (EXP) and cell-wall biosynthesis as well as phytohormone signaling genes. Furthermore, the expression of OsMPS-dependent genes is regulated by auxin, cytokinin and abscisic acid. Moreover, we show that OsMPS is a direct upstream regulator of OsEXPA4, OsEXPA8, OsEXPB2, OsEXPB3, OsEXPB6 and the endoglucanase genes OsGLU5 and OsGLU14. The multiple responses of OsMPS and its target genes to various hormones suggest an integrative function of OsMPS in the cross-talk between phytohormones and the environment to regulate adaptive growth.}, language = {en} } @article{SchmidtMieuletHubbertenetal.2013, author = {Schmidt, Romy and Mieulet, Delphine and Hubberten, Hans-Michael and Obata, Toshihiro and H{\"o}fgen, Rainer and Fernie, Alisdair R. and Fisahn, Joachim and Segundo, Blanca San and Guiderdoni, Emmanuel and Schippers, Jos H. M. and M{\"u}ller-R{\"o}ber, Bernd}, title = {Salt-responsive ERF1 regulates reactive oxygen species-dependent signaling during the initial response to salt stress in rice}, series = {The plant cell}, volume = {25}, journal = {The plant cell}, number = {6}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {1040-4651}, doi = {10.1105/tpc.113.113068}, pages = {2115 -- 2131}, year = {2013}, abstract = {Early detection of salt stress is vital for plant survival and growth. Still, the molecular processes controlling early salt stress perception and signaling are not fully understood. Here, we identified SALT-RESPONSIVE ERF1 (SERF1), a rice (Oryza sativa) transcription factor (TF) gene that shows a root-specific induction upon salt and hydrogen peroxide (H2O2) treatment. Loss of SERF1 impairs the salt-inducible expression of genes encoding members of a mitogen-activated protein kinase (MAPK) cascade and salt tolerance-mediating TFs. Furthermore, we show that SERF1-dependent genes are H2O2 responsive and demonstrate that SERF1 binds to the promoters of MAPK KINASE KINASE6 (MAP3K6), MAPK5, DEHYDRATION-RESPONSIVE ELEMENT BINDING2A (DREB2A), and ZINC FINGER PROTEIN179 (ZFP179) in vitro and in vivo. SERF1 also directly induces its own gene expression. In addition, SERF1 is a phosphorylation target of MAPK5, resulting in enhanced transcriptional activity of SERF1 toward its direct target genes. In agreement, plants deficient for SERF1 are more sensitive to salt stress compared with the wild type, while constitutive overexpression of SERF1 improves salinity tolerance. We propose that SERF1 amplifies the reactive oxygen species-activated MAPK cascade signal during the initial phase of salt stress and translates the salt-induced signal into an appropriate expressional response resulting in salt tolerance.}, language = {en} } @misc{ScheinerAbramsonBrodschneideretal.2013, author = {Scheiner, Ricarda and Abramson, Charles I. and Brodschneider, Robert and Crailsheim, Karl and Farina, Walter M. and Fuchs, Stefan and Gr{\"u}newald, Bernd and Hahshold, Sybille and Karrer, Marlene and Koeniger, Gudrun and K{\"o}niger, Niko and Menzel, Randolf and Mujagic, Samir and Radspieler, Gerald and Schmickl, Thomas and Schneider, Christof and Siegel, Adam J. and Szopek, Martina and Thenius, Ronald}, title = {Standard methods for behavioural studies of Apis mellifera}, series = {Journal of apicultural research}, volume = {52}, journal = {Journal of apicultural research}, number = {4}, publisher = {International Bee Research Association}, address = {Cardiff}, issn = {0021-8839}, doi = {10.3896/IBRA.1.52.4.04}, pages = {58}, year = {2013}, abstract = {In this BEEBOOK paper we present a set of established methods for quantifying honey bee behaviour. We start with general methods for preparing bees for behavioural assays. Then we introduce assays for quantifying sensory responsiveness to gustatory, visual and olfactory stimuli. Presentation of more complex behaviours like appetitive and aversive learning under controlled laboratory conditions and learning paradigms under free-flying conditions will allow the reader to investigate a large range of cognitive skills in honey bees. Honey bees are very sensitive to changing temperatures. We therefore present experiments which aim at analysing honey bee locomotion in temperature gradients. The complex flight behaviour of honey bees can be investigated under controlled conditions in the laboratory or with sophisticated technologies like harmonic radar or RFID in the field. These methods will be explained in detail in different sections. Honey bees are model organisms in behavioural biology for their complex yet plastic division of labour. To observe the daily behaviour of individual bees in a colony, classical observation hives are very useful. The setting up and use of typical observation hives will be the focus of another section. The honey bee dance language has important characteristics of a real language and has been the focus of numerous studies. We here discuss the background of the honey bee dance language and describe how it can be studied. Finally, the mating of a honey bee queen with drones is essential to survival of the entire colony. We here give detailed and structured information how the mating behaviour of drones and queens can be observed and experimentally manipulated. The ultimate goal of this chapter is to provide the reader with a comprehensive set of experimental protocols for detailed studies on all aspects of honey bee behaviour including investigation of pesticide and insecticide effects.}, language = {en} } @article{SchefflerBegoTheouetal.2013, author = {Scheffler, Ingo and Bego, Ferdinand and Theou, Philippe and Podany, Milan and Pospischil, Reiner and H{\"u}bner, Sven}, title = {Ectoparasites of Bats in Albania Species Range and Host Preference Ektoparasiten der Fledermaeuse in Albanien - Artenspektren und Wirtsbindung}, year = {2013}, abstract = {279 bat specimens of 14 species were examined for ectoparasites during the autumnal swarming period in different cave roosts in Albania. A total of 550 ectoparasites were identified belonging to 19 species. The structure of the ectoparasite fauna and the influence of body mass index and body surface area on the parasite load were discussed for the most common bat species (Miniopterus schreibersii, Myotis myotis, M. capaccinii and Rhinolophus ferrumequinum). The ectoparasite fauna of the studied bats in Albania is qualitatively similar to northern Bulgaria (SCHEFFLER, 2011). The bat species Myotis myotis and M. daubentonii are infested with different ectoparasites in the Balkan region during the autumn swarming period than specimens of the same bat species in Central Europe. There is a strong need of further research for most host and ectoparasite species in the entire Balkan region.}, language = {en} } @article{Scheffler2013, author = {Scheffler, Christiane}, title = {Types of Body Shape}, series = {Auxology : Studying Human Growth and Development}, journal = {Auxology : Studying Human Growth and Development}, publisher = {Schweizerbart Science Publishers}, address = {Stuttgart}, isbn = {978-3-510-65278-5}, pages = {28 -- 29}, year = {2013}, language = {en} } @article{Scheffler2013, author = {Scheffler, Christiane}, title = {Variable and Invariable Proportions in the Ontogenesis of the Human Face}, year = {2013}, language = {en} } @article{Scheffler2013, author = {Scheffler, Christiane}, title = {Variable and invariable proportions in the ontogenesis of the human face}, series = {The journal of craniofacial surgery : an international journal dedicated to the practice of the art and science of craniofacial surgery ; official publication of the American Association of Pediatric Plastic Surgeons}, volume = {24}, journal = {The journal of craniofacial surgery : an international journal dedicated to the practice of the art and science of craniofacial surgery ; official publication of the American Association of Pediatric Plastic Surgeons}, number = {1}, publisher = {Lippincott Williams \& Wilkins}, address = {Philadelphia}, issn = {1049-2275}, doi = {10.1097/SCS.0b013e31826d07a3}, pages = {237 -- 241}, year = {2013}, abstract = {The human face shows individual features and features that are characteristic for sex and age (the loss of childlike characteristics during maturation). The analysis of facial dimensions is essential for identifying individual features also for forensic issues. The analysis of facial proportions was performed on photogrammetric data from front views of 125 children. The data were pooled from 2 different studies. The children's data were obtained from a longitudinal study and reduced by random generator to ensure the data of adults from a separate cross-sectional study. We applied principal component analysis on photogrammetric facial proportions of 169 individuals: 125 children (63 boys and 62 girls) aged 2-7 years and 44 adults (18 men and 26 women) aged 18-65 years. Facial proportions depend on age and sex. Three components described age: (1) proportions of facial height to head height, (2) proportions that involve endocanthal breadth, and (3) bigonial to bizygonial proportions. Proportions that associate with sex are connected with nasal distances and nasal to bizygonial distances. Twenty-three percent of the variance, particularly variance that are connected with proportions of lower and middle face heights to head height, do neither depend on sex nor on age and thus appear useful for screening purposes, eg, for dysmorphic genetic syndromes.}, language = {en} } @article{Scheffler2013, author = {Scheffler, Christiane}, title = {Body composition}, series = {Auxology : Studying Human Growth and Development}, journal = {Auxology : Studying Human Growth and Development}, editor = {Hermanussen, Michael}, publisher = {Schweizerbart Science Publishers}, address = {Stuttgart}, isbn = {978-3-510-65278-5}, pages = {30 -- 31}, year = {2013}, language = {en} } @article{Scheffler2013, author = {Scheffler, Christiane}, title = {Determining body composition in field studies}, series = {Auxology : Studying Human Growth and Development}, journal = {Auxology : Studying Human Growth and Development}, editor = {Hermanussen, Michael}, publisher = {Schweizerbart Science Publishers}, address = {Stuttgart}, isbn = {978-3-510-65278-5}, pages = {32 -- 33}, year = {2013}, language = {en} } @article{Scheffler2013, author = {Scheffler, Christiane}, title = {Comparative Biology and Human Life History}, series = {Auxology : Studying Human Growth and Development}, journal = {Auxology : Studying Human Growth and Development}, editor = {Hermanussen, Michael}, publisher = {Schweizerbart Science Publishers}, address = {Stuttgart}, isbn = {978-3-510-65278-5}, pages = {38 -- 41}, year = {2013}, language = {en} } @article{Scheffler2013, author = {Scheffler, Christiane}, title = {Biological age}, series = {Auxology : Studying Human Growth and Development}, journal = {Auxology : Studying Human Growth and Development}, editor = {Hermanussen, Michael}, publisher = {Schweizerbart Science Publishers}, address = {Stuttgart}, isbn = {978-3-510-65278-5}, pages = {44 -- 47}, year = {2013}, language = {en} } @article{SchaldachWimmerKochetal.2013, author = {Schaldach, R{\"u}diger and Wimmer, Florian and Koch, Jennifer and Volland, Jan and Geissler, Katja and K{\"o}chy, Martin}, title = {Model-based analysis of the environmental impacts of grazing management on Eastern Mediterranean ecosystems in Jordan}, series = {Journal of environmental management}, volume = {127}, journal = {Journal of environmental management}, number = {9}, publisher = {Elsevier}, address = {London}, issn = {0301-4797}, doi = {10.1016/j.jenvman.2012.11.024}, pages = {S84 -- S95}, year = {2013}, abstract = {Eastern Mediterranean ecosystems are prone to desertification when under grazing pressure. Therefore, management of grazing intensity plays a crucial role to avoid or to diminish land degradation and to sustain both livelihoods and ecosystem functioning. The dynamic land-use model LandSHIFT was applied to a case study on the country level for Jordan. The impacts of different stocking densities on the environment were assessed through a set of simulation experiments for various combinations of climate input and assumptions about the development of livestock numbers. Indicators used for the analysis include a set of landscape metrics to account for habitat fragmentation and the "Human Appropriation of Net Primary Production" (HANPP), i.e., the difference between the amount of net primary production (NPP) that would be available in a natural ecosystem and the amount of NPP that remains under human management. Additionally, the potential of the economic valuation of ecosystem services, including landscape and grazing services, as an analysis concept was explored. We found that lower management intensities had a positive effect on HANPP but at the same time resulted in a strong increase of grazing area. This effect was even more pronounced under climate change due to a predominantly negative effect on the biomass productivity of grazing land. Also Landscape metrics tend to indicate decreasing habitat fragmentation as a consequence of lower grazing pressure. The valuation of ecosystem services revealed that low grazing intensity can lead to a comparatively higher economic value on the country level average. The results from our study underline the importance of considering grazing management as an important factor to manage dry-land ecosystems in a sustainable manner.}, language = {en} } @inproceedings{SauterLuetzowSchossigetal.2013, author = {Sauter, Tilman and L{\"u}tzow, Karola and Schossig, Michael and Kosmella, Hans and Weigel, Thomas and Kratz, Karl and Lendlein, Andreas}, title = {Pore morphology as structural parameter to tailor the shape-memory effect of polyuetherurethane foams}, series = {Abstracts of papers : joint conference / The Chemical Institute of Cananda, CIC, American Chemical Society, ACS}, volume = {245}, 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 = {2013}, language = {en} } @article{SauterKratzLendlein2013, author = {Sauter, Tilman and Kratz, Karl and Lendlein, Andreas}, title = {Pore-size distribution controls shape-memory properties on the macro- and microscale of polymeric foams}, series = {Macromolecular chemistry and physics}, volume = {214}, journal = {Macromolecular chemistry and physics}, number = {11}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1022-1352}, doi = {10.1002/macp.201300062}, pages = {1184 -- 1188}, year = {2013}, abstract = {Open porous foams with identical foam density but different pore-size distributions (bimodal or monomodal) are prepared from a shape-memory polyetherurethane (PEU) by thermally induced phase separation. The shape-memory effect of the two PEU foams is explored by cyclic thermomechanical compression tests and microstructural analysis. The obtained results reveal that the PEU foam with a bimodal pore-size distribution exhibits an increased shape-recovery under stress-free conditions, both on the macro- (foam level) as well as the microscale (pore level). While bimodal pore-size distributions induce microscale bending during compression, buckling occurs in foams with monomodal pore-size distributions, leading to both a reduced and delayed shape recovery.}, language = {en} } @article{SarmentoJeltschThuilleretal.2013, author = {Sarmento, Juliano Sarmento and Jeltsch, Florian and Thuiller, Wilfried and Higgins, Steven and Midgley, Guy F. and Rebelo, Anthony G. and Rouget, Mathieu and Schurr, Frank Martin}, title = {Impacts of past habitat loss and future climate change on the range dynamics of South African Proteaceae}, series = {Diversity \& distributions : a journal of biological invasions and biodiversity}, volume = {19}, journal = {Diversity \& distributions : a journal of biological invasions and biodiversity}, number = {4}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1366-9516}, doi = {10.1111/ddi.12011}, pages = {363 -- 376}, year = {2013}, abstract = {Aim To assess how habitat loss and climate change interact in affecting the range dynamics of species and to quantify how predicted range dynamics depend on demographic properties of species and the severity of environmental change. Location South African Cape Floristic Region. Methods We use data-driven demographic models to assess the impacts of past habitat loss and future climate change on range size, range filing and abundances of eight species of woody plants (Proteaceae). The species-specific models employ a hybrid approach that simulates population dynamics and long-distance dispersal on top of expected spatio-temporal dynamics of suitable habitat. Results Climate change was mainly predicted to reduce range size and range filling (because of a combination of strong habitat shifts with low migration ability). In contrast, habitat loss mostly decreased mean local abundance. For most species and response measures, the combination of habitat loss and climate change had the most severe effect. Yet, this combined effect was mostly smaller than expected from adding or multiplying effects of the individual environmental drivers. This seems to be because climate change shifts suitable habitats to regions less affected by habitat loss. Interspecific variation in range size responses depended mostly on the severity of environmental change, whereas responses in range filling and local abundance depended mostly on demographic properties of species. While most surviving populations concentrated in areas that remain climatically suitable, refugia for multiple species were overestimated by simply overlying habitat models and ignoring demography. Main conclusions Demographic models of range dynamics can simultaneously predict the response of range size, abundance and range filling to multiple drivers of environmental change. Demographic knowledge is particularly needed to predict abundance responses and to identify areas that can serve as biodiversity refugia under climate change. These findings highlight the need for data-driven, demographic assessments in conservation biogeography.}, language = {en} } @inproceedings{SapirRoticsKaatzetal.2013, author = {Sapir, N. and Rotics, S. and Kaatz, M. and Davidson, S. and Zurell, Damaris and Eggers, U. and Jeltsch, Florian and Nathan, R. and Wikelski, M.}, title = {Multi-year tracking of white storks (Ciconia ciconia) how the environment shapes the movement and behavior of a soaring-gliding inter-continental migrant}, series = {Integrative and comparative biology}, volume = {53}, booktitle = {Integrative and comparative biology}, number = {3}, publisher = {Oxford Univ. Press}, address = {Cary}, issn = {1540-7063}, pages = {E189 -- E189}, year = {2013}, language = {en} } @phdthesis{Sandmann2013, author = {Sandmann, Michael}, title = {Biochemische und cytologische Marker der Zellentwicklung synchronisierter St{\"a}mme con Chlamydomonas reinhardtii}, address = {Potsdam}, pages = {121 S.}, year = {2013}, language = {de} } @misc{SammlerKetmaierHavensteinetal.2013, author = {Sammler, Svenja and Ketmaier, Valerio and Havenstein, Katja and Tiedemann, Ralph}, title = {Intraspecific rearrangement of duplicated mitochondrial control regions in the luzon tarictic hornbill penelopides manillae (Aves: Bucerotidae)}, series = {Journal of molecular evolution}, volume = {77}, journal = {Journal of molecular evolution}, number = {5-6}, publisher = {Springer}, address = {New York}, issn = {0022-2844}, doi = {10.1007/s00239-013-9591-y}, pages = {199 -- 205}, year = {2013}, abstract = {Philippine hornbills of the genera Aceros and Penelopides (Bucerotidae) are known to possess a large tandemly duplicated fragment in their mitochondrial genome, whose paralogous parts largely evolve in concert. In the present study, we surveyed the two distinguishable duplicated control regions in several individuals of the Luzon Tarictic Hornbill Penelopides manillae, compare their characteristics within and across individuals, and report on an intraspecific mitochondrial gene rearrangement found in one single specimen, i.e., an interchange between the two control regions. To our knowledge, this is the first observation of two distinct mitochondrial genome rearrangements within a bird species. We briefly discuss a possible evolutionary mechanism responsible for this pattern, and highlight potential implications for the application of control region sequences as a marker in population genetics and phylogeography.}, language = {en} } @article{SagollaLoehmannsroebenHille2013, author = {Sagolla, Kristina and L{\"o}hmannsr{\"o}ben, Hans-Gerd and Hille, Carsten}, title = {Time-resolved fluorescence microscopy for quantitative Ca2+ imaging in living cells}, series = {Analytical \& bioanalytical chemistry}, volume = {405}, journal = {Analytical \& bioanalytical chemistry}, number = {26}, publisher = {Springer}, address = {Heidelberg}, issn = {1618-2642}, doi = {10.1007/s00216-013-7290-6}, pages = {8525 -- 8537}, year = {2013}, abstract = {Calcium (Ca2+) is a ubiquitous intracellular second messenger and involved in a plethora of cellular processes. Thus, quantification of the intracellular Ca2+ concentration ([Ca2+](i)) and of its dynamics is required for a comprehensive understanding of physiological processes and potential dysfunctions. A powerful approach for studying [Ca2+](i) is the use of fluorescent Ca2+ indicators. In addition to the fluorescence intensity as a common recording parameter, the fluorescence lifetime imaging microscopy (FLIM) technique provides access to the fluorescence decay time of the indicator dye. The nanosecond lifetime is mostly independent of variations in dye concentration, allowing more reliable quantification of ion concentrations in biological preparations. In this study, the feasibility of the fluorescent Ca2+ indicator Oregon Green Bapta-1 (OGB-1) for two-photon fluorescence lifetime imaging microscopy (2P-FLIM) was evaluated. In aqueous solution, OGB-1 displayed a Ca2+-dependent biexponential fluorescence decay behaviour, indicating the presence of a Ca2+-free and Ca2+-bound dye form. After sufficient dye loading into living cells, an in situ calibration procedure has also unravelled the Ca2+-free and Ca2+-bound dye forms from a global biexponential fluorescence decay analysis, although the dye's Ca2+ sensitivity is reduced. Nevertheless, quantitative [Ca2+](i) recordings and its stimulus-induced changes in salivary gland cells could be performed successfully. These results suggest that OGB-1 is suitable for 2P-FLIM measurements, which can gain access to cellular physiology.}, language = {en} } @article{SachseWuestenhagenSamalikovaetal.2013, author = {Sachse, Rita and W{\"u}stenhagen, Doreen Anja and Samalikova, Maria and Gerrits, Michael and Bier, Frank Fabian and Kubick, Stefan}, title = {Synthesis of membrane proteins in eukaryotic cell-free systems}, series = {Engineering in life sciences : Industry, Environment, Plant, Food}, volume = {13}, journal = {Engineering in life sciences : Industry, Environment, Plant, Food}, number = {1}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1618-0240}, doi = {10.1002/elsc.201100235}, pages = {39 -- 48}, year = {2013}, abstract = {Cell-free protein synthesis (CFPS) is a valuable method for the fast expression of difficult-to-express proteins as well as posttranslationally modified proteins. Since cell-free systems circumvent possible cytotoxic effects caused by protein overexpression in living cells, they significantly enlarge the scale and variety of proteins that can be characterized. We demonstrate the high potential of eukaryotic CFPS to express various types of membrane proteins covering a broad range of structurally and functionally diverse proteins. Our eukaryotic cell-free translation systems are capable to provide high molecular weight membrane proteins, fluorescent-labeled membrane proteins, as well as posttranslationally modified proteins for further downstream analysis.}, language = {en} } @article{RuederSauterKratzetal.2013, author = {R{\"u}der, Constantin and Sauter, Tilman and Kratz, Karl and Haase, Tobias and Peter, Jan and Jung, Friedrich and Lendlein, Andreas and Zohlnh{\"o}fer, Dietlind}, title = {Influence of fibre diameter and orientation of electrospun copolyetheresterurethanes on smooth muscle and endothelial cell behaviour}, series = {Clinical hemorheology and microcirculation : blood flow and vessels}, volume = {55}, journal = {Clinical hemorheology and microcirculation : blood flow and vessels}, number = {4}, publisher = {IOS Press}, address = {Amsterdam}, issn = {1386-0291}, doi = {10.3233/CH-131787}, pages = {513 -- 522}, year = {2013}, abstract = {Polymers exhibiting cell-selective effects represent an extensive research field with high relevance for biomedical applications e.g. in the cardiovascular field supporting re-endothelialization while suppressing smooth muscle cell overgrowth. Such an endothelial cell-selective effect could be recently demonstrated for a copolyetheresterurethane (PDC) containing biodegradable poly(p-dioxanone) and poly(epsilon-caprolactone) segments, which selectively enhanced the adhesion of human umbilical vein endothelial cells (HUVEC) while suppressing the attachment of smooth muscle cells (SMC). In this study we investigated the influence of the fibre orientation (random and aligned) and fibre diameter (2 mu m and 500 nm) of electrospun PDC scaffolds on the adhesion, proliferation and apoptosis of HUVEC and SMC. Adhesion, viability and proliferation of HUVEC was diminished when the fibre diameter was reduced to a submicron scale, while the orientation of the microfibres did only slightly influence the cellular behaviour. In contrast, a submicron fibre diameter improved SMC viability. In conclusion, PDC scaffolds with micron-sized single fibres could be promising candidate materials for cell-selective stent coatings.}, language = {en} } @article{RuzanskiSmirnovaRejzeketal.2013, author = {Ruzanski, Christian and Smirnova, Julia and Rejzek, Martin and Cockburn, Darrell and Pedersen, Henriette L. and Pike, Marilyn and Willats, William G. T. and Svensson, Birte and Steup, Martin and Ebenh{\"o}h, Oliver and Smith, Alison M. and Field, Robert A.}, title = {A bacterial glucanotransferase can replace the complex maltose metabolism required for starch to sucrose conversion in leaves at night}, series = {The journal of biological chemistry}, volume = {288}, journal = {The journal of biological chemistry}, number = {40}, publisher = {American Society for Biochemistry and Molecular Biology}, address = {Bethesda}, issn = {0021-9258}, doi = {10.1074/jbc.M113.497867}, pages = {28581 -- 28598}, year = {2013}, abstract = {Controlled conversion of leaf starch to sucrose at night is essential for the normal growth of Arabidopsis. The conversion involves the cytosolic metabolism of maltose to hexose phosphates via an unusual, multidomain protein with 4-glucanotransferase activity, DPE2, believed to transfer glucosyl moieties to a complex heteroglycan prior to their conversion to hexose phosphate via a cytosolic phosphorylase. The significance of this complex pathway is unclear; conversion of maltose to hexose phosphate in bacteria proceeds via a more typical 4-glucanotransferase that does not require a heteroglycan acceptor. It has recently been suggested that DPE2 generates a heterogeneous series of terminal glucan chains on the heteroglycan that acts as a glucosyl buffer to ensure a constant rate of sucrose synthesis in the leaf at night. Alternatively, DPE2 and/or the heteroglycan may have specific properties important for their function in the plant. To distinguish between these ideas, we compared the properties of DPE2 with those of the Escherichia coli glucanotransferase MalQ. We found that MalQ cannot use the plant heteroglycan as an acceptor for glucosyl transfer. However, experimental and modeling approaches suggested that it can potentially generate a glucosyl buffer between maltose and hexose phosphate because, unlike DPE2, it can generate polydisperse malto-oligosaccharides from maltose. Consistent with this suggestion, MalQ is capable of restoring an essentially wild-type phenotype when expressed in mutant Arabidopsis plants lacking DPE2. In light of these findings, we discuss the possible evolutionary origins of the complex DPE2-heteroglycan pathway.}, language = {en} } @article{RuelensdeMaagdProostetal.2013, author = {Ruelens, Philip and de Maagd, Ruud A. and Proost, Sebastian and Theissen, G{\"u}nther and Geuten, Koen and Kaufmann, Kerstin}, title = {FLOWERING LOCUS C in monocots and the tandem origin of angiosperm-specific MADS-box genes}, series = {Nature Communications}, volume = {4}, journal = {Nature Communications}, number = {8}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/ncomms3280}, pages = {8}, year = {2013}, abstract = {MADS-domain transcription factors have been shown to act as key repressors or activators of the transition to flowering and as master regulators of reproductive organ identities. Despite their important roles in plant development, the origin of several MADS-box subfamilies has remained enigmatic so far. Here we demonstrate, through a combination of genome synteny and phylogenetic reconstructions, the origin of three major, apparently angiosperm-specific MADS-box gene clades: FLOWERING LOCUS C- (FLC-), SQUAMOSA- (SQUA-) and SEPALLATA- (SEP-) -like genes. We find that these lineages derive from a single ancestral tandem duplication in a common ancestor of extant seed plants. Contrary to common belief, we show that FLC- like genes are present in cereals where they can also act as floral repressors responsive to prolonged cold or vernalization. This opens a new perspective on the translation of findings from Arabidopsis to cereal crops, in which vernalization was originally described.}, language = {en} } @article{RietschGodinaScheffler2013, author = {Rietsch, Katrin and Godina, Elena and Scheffler, Christiane}, title = {Decreased external skeletal robustness in schoolchildren : a global trend? Ten year comparison of Russian and German data}, year = {2013}, language = {en} } @article{RietschGodinaScheffler2013, author = {Rietsch, Katrin and Godina, Elena and Scheffler, Christiane}, title = {Decreased External Skeletal Robustness in Schoolchildren - a Global Trend? ; Ten Year Comparison of Russian and German Data}, series = {PLoS one}, volume = {8}, journal = {PLoS one}, number = {7}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0068195}, pages = {7}, year = {2013}, abstract = {Objectives: Obesity and a reduced physical activity are global developments. Physical activity affects the external skeletal robustness which decreased in German children. It was assumed that the negative trend of decreased external skeletal robustness can be found in other countries. Therefore anthropometric data of Russian and German children from the years 2000 and 2010 were compared. Methods: Russian (2000/2010 n = 1023/268) and German (2000/2010 n = 2103/1750) children aged 6-10 years were investigated. Height, BMI and external skeletal robustness (Frame-Index) were examined and compared for the years and the countries. Statistical analysis was performed by Mann-Whitney-Test. Results: Comparison 2010 and 2000: In Russian children BMI was significantly higher; boys were significantly taller and exhibited a decreased Frame-Index (p = .002) in 2010. German boys showed significantly higher BMI in 2010. In both sexes Frame-Index (p = .001) was reduced in 2010. Comparison Russian and German children in 2000: BMI, height and Frame-Index were different between Russian and German children. German children were significantly taller but exhibited a lower Frame-Index (p<.001). Even German girls showed a significantly higher BMI. Comparison Russian and German children in 2010: BMI and Frame-Index were different. Russian children displayed a higher Frame-Index (p<.001) compared with Germans. Conclusions: In Russian children BMI has increased in recent years. Frame-Index is still higher in Russian children compared with Germans however in Russian boys Frame-Index is reduced. This trend and the physical activity should be observed in the future.}, language = {en} } @article{RietschEccardScheffler2013, author = {Rietsch, Katrin and Eccard, Jana and Scheffler, Christiane}, title = {Decreased external skeletal robustness due to reduced physical activity?}, series = {American journal of human biology : the official journal of the Human Biology Council}, volume = {25}, journal = {American journal of human biology : the official journal of the Human Biology Council}, number = {3}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1042-0533}, doi = {10.1002/ajhb.22389}, pages = {404 -- 410}, year = {2013}, abstract = {Objectives Childhood obesity is a global problem, e.g., due to physical inactivity. External skeletal robustness (Frame-Index) has decreased in German schoolchildren. An association between Frame-Index and physical activity was assumed. Further often body mass index (BMI) is analyzed without reference to bone structure. Therefore, we analyze relationships between Frame-Index, BMI, \% body fat, and physical activity. Methods In a cross-sectional study, 691 German children aged 610 years were investigated. BMI, \% body fat, Frame-Index, total steps p.w., sports club rate p.w., training time p.d., and TV-time p.d. were determined. Results Total steps (P<0.001), BMI (P<0.001), and \% body fat (P=0.024) are positively linked to Frame-Index. Total steps (P<0.001), sports club rate (P=0.001), and training time (P<0.001) are negatively associated with \% body fat. Total steps (P=0.017) are negatively linked to BMI. TV-time is positively related to BMI (P<0.001) and \% body fat (P<0.001). \% Body fat is affected by age (P<0.001), sex (P=0.028), and total steps (P=0.002). BMI is influenced by age (P<0.001), and Frame-Index by sex (P<0.001) and total steps (P=0.029). Principal component analysis indicates an association between BMI and TV-time and Frame-Index and total steps. Conclusions We demonstrate an association between external skeletal robustness and physical activity, which is not captured by in BMI measurements. Children should be physically active in order to maintain skeletal robustness. Am. J. Hum. Biol. 25:404410, 2013.}, language = {en} } @article{RietschEccardScheffler2013, author = {Rietsch, Katrin and Eccard, Jana and Scheffler, Christiane}, title = {Decreased external skeletal robustness due to reduced physical activity?}, year = {2013}, language = {en} } @phdthesis{Rietsch2013, author = {Rietsch, Katrin}, title = {Body composition especially external skeletal robustness in association with physical activity and recreation in pre-pubertal children : a national and international investigation}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-66913}, school = {Universit{\"a}t Potsdam}, year = {2013}, abstract = {In children the way of life, nutrition and recreation changed in recent years and as a consequence body composition shifted as well. It is established that overweight belongs to a global problem. In addition, German children exhibit a less robust skeleton than ten years ago. These developments may elevate the risk of cardiovascular diseases and skeletal modifications. Heredity and environmental factors as nutrition, socioeconomic status, physical activity and inactivity influence fat accumulation and the skeletal system. Based on these negative developments associations between type of body shape, skeletal measures and physical activity; relations between external skeletal robustness, physical activity and inactivity, BMI and body fat and also the progress of body composition especially external skeletal robustness in comparison in Russian and German children were investigated. In a cross-sectional study 691 German boys and girls aged 6 to 10 years were examined. Anthropometric measurements were taken and questionnaires about physical activity and inactivity were answered by parents. Additionally, pedometers were worn to determinate the physical activity in children. To compare the body composition in Russian and German children data from the years 2000 and 2010 were used. The study has shown that pyknomorphic individuals exhibit the highest external skeletal robustness and leptomorphic ones the lowest. Leptomorphic children may have a higher risk for bone diseases in adulthood. Pyknomorphic boys are more physically active by tendency. This is assessed as positive because pyknomorphic types display the highest BMI and body fat. Results showed that physical activity may reduce BMI and body fat. In contrast physical inactivity may lead to an increase of BMI and body fat and may rise with increasing age. Physical activity encourages additionally a robust skeleton. Furthermore external skeletal robustness is associated with BMI in order that BMI as a measure of overweight should be consider critically. The international 10-year comparison has shown an increase of BMI in Russian children and German boys. Currently, Russian children exhibit a higher external skeletal robustness than the Germans. However, in Russian boys skeleton is less robust than ten years ago. This trend should be observed in the future as well in other countries. All in all, several measures should be used to describe health situation in children and adults. Furthermore, in children it is essential to support physical activity in order to reduce the risk of obesity and to maintain a robust skeleton. In this way diseases are able to prevent in adulthood.}, language = {en} } @phdthesis{Riedelsberger2013, author = {Riedelsberger, Janin}, title = {Functional diversity of plant Shaker-like K+ channels and their regulation}, address = {Potsdam}, pages = {105 S.}, year = {2013}, language = {en} } @inproceedings{RichterFairhallHoffmannetal.2013, author = {Richter, M. and Fairhall, Emma A. and Hoffmann, S. A. and Fr{\"u}hwald, J. and Wright, Matthew C. and Zeilinger, Katrin}, title = {Dexamethasone induced hepatic differentiation of rat pancreatic progenitor cells (B-13) in a 3D multicompartment bioreactor system}, series = {Journal of hepatology}, volume = {58}, booktitle = {Journal of hepatology}, number = {1}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0168-8278}, pages = {S416 -- S416}, year = {2013}, language = {en} } @article{ReschkeSigfridssonKaufmannetal.2013, author = {Reschke, Stefan and Sigfridsson, Kajsa G. V. and Kaufmann, Paul and Leidel, Nils and Horn, Sebastian and Gast, Klaus and Schulzke, Carola and Haumann, Michael and Leimk{\"u}hler, Silke}, title = {Identification of a bis-molybdopterin intermediate in molybdenum cofactor biosynthesis in escherichia coli}, series = {The journal of biological chemistry}, volume = {288}, journal = {The journal of biological chemistry}, number = {41}, publisher = {American Society for Biochemistry and Molecular Biology}, address = {Bethesda}, issn = {0021-9258}, doi = {10.1074/jbc.M113.497453}, pages = {29736 -- 29745}, year = {2013}, abstract = {The molybdenum cofactor is an important cofactor, and its biosynthesis is essential for many organisms, including humans. Its basic form comprises a single molybdopterin (MPT) unit, which binds a molybdenum ion bearing three oxygen ligands via a dithiolene function, thus forming Mo-MPT. In bacteria, this form is modified to form the bis-MPT guanine dinucleotide cofactor with two MPT units coordinated at one molybdenum atom, which additionally contains GMPs bound to the terminal phosphate group of the MPTs (bis-MGD). The MobA protein catalyzes the nucleotide addition to MPT, but the mechanism of the biosynthesis of the bis-MGD cofactor has remained enigmatic. We have established an in vitro system for studying bis-MGD assembly using purified compounds. Quantification of the MPT/molybdenum and molybdenum/phosphorus ratios, time-dependent assays for MPT and MGD detection, and determination of the numbers and lengths of Mo-S and Mo-O bonds by X-ray absorption spectroscopy enabled identification of a novel bis-Mo-MPT intermediate on MobA prior to nucleotide attachment. The addition of Mg-GTP to MobA loaded with bis-Mo-MPT resulted in formation and release of the final bis-MGD product. This cofactor was fully functional and reconstituted the catalytic activity of apo-TMAO reductase (TorA). We propose a reaction sequence for bis-MGD formation, which involves 1) the formation of bis-Mo-MPT, 2) the addition of two GMP units to form bis-MGD on MobA, and 3) the release and transfer of the mature cofactor to the target protein TorA, in a reaction that is supported by the specific chaperone TorD, resulting in an active molybdoenzyme.}, language = {en} } @article{ReschkeNiksWilsonetal.2013, author = {Reschke, Stefan and Niks, Dimitri and Wilson, Heather and Sigfridsson, Kajsa G. V. and Haumann, Michael and Rajagopalan, K. V. and Hine, Russ and Leimk{\"u}hler, Silke}, title = {Effect of exchange of the cysteine molybdenum ligand with selenocysteine on the structure and function of the active site in human sulfite oxidase}, series = {Biochemistry}, volume = {52}, journal = {Biochemistry}, number = {46}, publisher = {American Chemical Society}, address = {Washington}, issn = {0006-2960}, doi = {10.1021/bi4008512}, pages = {8295 -- 8303}, year = {2013}, abstract = {Sulfite oxidase (SO) is an essential molybdoenzyme for humans, catalyzing the final step in the degradation of sulfur-containing amino acids and lipids, which is the oxidation of sulfite to sulfate. The catalytic site of SO consists of a molybdenum ion bound to the dithiolene sulfurs of one molybdopterin (MPT) molecule, carrying two oxygen ligands, and is further coordinated by the thiol sulfur of a conserved cysteine residue. We have exchanged four non-active site cysteines in the molybdenum cofactor (Moco) binding domain of human SO (SOMD) with serine using site-directed mutagenesis. This facilitated the specific replacement of the active site Cys207 with selenocysteine during protein expression in Escherichia coli. The sulfite oxidizing activity (k(cat)/K-M) of SeSOMD4Ser was increased at least 1.5-fold, and the pH optimum was shifted to a more acidic value compared to those of SOMD4Ser and SOMD4Cys(wt) X-ray absorption spectroscopy revealed a Mow Se bond length of 2.51 A, likely caused by the specific binding of Sec207 to the molybdenum, and otherwise rather similar square-pyramidal S/Se(Cys)(O2MoS2)-S-VI(MPT) site structures in the three constructs. The low-pH form of the Mo(V) electron paramagnetic resonance (EPR) signal of SeSOM4Ser was altered compared to those of SOMD4Ser and SOMD4cy,(,), with g, in particular shifted to a lower magnetic field, due to the Se ligation at the molybdenum. In contrast, the Mo(V) EPR signal of the high-pH form was unchanged. The substantially stronger effect of substituting selenocysteine for cysteine at low pH as compared to high pH is most likely due to the decreased covalency of the Mo Se bond.}, language = {en} } @phdthesis{Reschke2013, author = {Reschke, Stefan}, title = {Untersuchungen zur Bildung und Modifizierung des Molybd{\"a}ncofaktors und dessen Einbau in Molybdoenzyme}, address = {Potsdam}, pages = {133 S.}, year = {2013}, language = {de} } @inproceedings{RejibaFrelanHermannetal.2013, author = {Rejiba, Soukaina and Frelan, Megan and Hermann, Alex and Arndt, Katja Maren and Hajri, Amor}, title = {Interfering peptides targeting transcription factor AP1 for pancreatic cancer gene therapy}, series = {Molecular therapy : the journal of the American Society of Gene Therapy}, volume = {21}, booktitle = {Molecular therapy : the journal of the American Society of Gene Therapy}, number = {2}, publisher = {Nature Publ. Group}, address = {New York}, issn = {1525-0016}, pages = {S250 -- S250}, year = {2013}, language = {en} } @article{ReimThammRolkeetal.2013, author = {Reim, Tina and Thamm, Markus and Rolke, Daniel and Blenau, Wolfgang and Scheiner, Ricarda}, title = {Suitability of three common reference genes for quantitative real-time PCR in honey bees}, series = {Apidologie : a quality journal in bee science}, volume = {44}, journal = {Apidologie : a quality journal in bee science}, number = {3}, publisher = {Springer}, address = {Paris}, issn = {0044-8435}, doi = {10.1007/s13592-012-0184-3}, pages = {342 -- 350}, year = {2013}, abstract = {Honey bees are important model organisms for neurobiology, because they display a large array of behaviors. To link behavior with individual gene function, quantitative polymerase chain reaction is frequently used. Comparing gene expression of different individuals requires data normalization using adequate reference genes. These should ideally be expressed stably throughout lifetime. Unfortunately, this is frequently not the case. We studied how well three commonly used reference genes are suited for this purpose and measured gene expression in the brains of honey bees differing in age and social role. Although rpl32 is used most frequently, it only remains stable in expression between newly emerged bees, nurse-aged bees, and pollen foragers but shows a peak at the age of 12 days. The genes gapdh and ef1 alpha-f1, in contrast, are expressed stably in the brain throughout all age groups except newly emerged bees. According to stability software, gapdh was expressed most stably, followed by rpl32 and ef1 alpha-f1.}, language = {en} } @article{ReadKegelKluteetal.2013, author = {Read, Betsy A. and Kegel, Jessica and Klute, Mary J. and Kuo, Alan and Lefebvre, Stephane C. and Maumus, Florian and Mayer, Christoph and Miller, John and Monier, Adam and Salamov, Asaf and Young, Jeremy and Aguilar, Maria and Claverie, Jean-Michel and Frickenhaus, Stephan and Gonzalez, Karina and Herman, Emily K. and Lin, Yao-Cheng and Napier, Johnathan and Ogata, Hiroyuki and Sarno, Analissa F. and Shmutz, Jeremy and Schroeder, Declan and de Vargas, Colomban and Verret, Frederic and von Dassow, Peter and Valentin, Klaus and Van de Peer, Yves and Wheeler, Glen and Dacks, Joel B. and Delwiche, Charles F. and Dyhrman, Sonya T. and Gl{\"o}ckner, Gernot and John, Uwe and Richards, Thomas and Worden, Alexandra Z. and Zhang, Xiaoyu and Grigoriev, Igor V. and Allen, Andrew E. and Bidle, Kay and Borodovsky, M. and Bowler, C. and Brownlee, Colin and Cock, J. Mark and Elias, Marek and Gladyshev, Vadim N. and Groth, Marco and Guda, Chittibabu and Hadaegh, Ahmad and Iglesias-Rodriguez, Maria Debora and Jenkins, J. and Jones, Bethan M. and Lawson, Tracy and Leese, Florian and Lindquist, Erika and Lobanov, Alexei and Lomsadze, Alexandre and Malik, Shehre-Banoo and Marsh, Mary E. and Mackinder, Luke and Mock, Thomas and M{\"u}ller-R{\"o}ber, Bernd and Pagarete, Antonio and Parker, Micaela and Probert, Ian and Quesneville, Hadi and Raines, Christine and Rensing, Stefan A. and Riano-Pachon, Diego Mauricio and Richier, Sophie and Rokitta, Sebastian and Shiraiwa, Yoshihiro and Soanes, Darren M. and van der Giezen, Mark and Wahlund, Thomas M. and Williams, Bryony and Wilson, Willie and Wolfe, Gordon and Wurch, Louie L.}, title = {Pan genome of the phytoplankton Emiliania underpins its global distribution}, series = {Nature : the international weekly journal of science}, volume = {499}, journal = {Nature : the international weekly journal of science}, number = {7457}, publisher = {Nature Publ. Group}, address = {London}, organization = {Emiliania Huxleyi Annotation}, issn = {0028-0836}, doi = {10.1038/nature12221}, pages = {209 -- 213}, year = {2013}, abstract = {Coccolithophores have influenced the global climate for over 200 million years(1). These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems(2). They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space(3). Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean(4). Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.}, language = {en} } @phdthesis{Razzaq2013, author = {Razzaq, Muhammad Yasar}, title = {Shape-memory investigations of magneto-sensitive polymer nanocomposites}, address = {Potsdam}, pages = {140 S.}, year = {2013}, language = {en} } @article{RaufArifFisahnetal.2013, author = {Rauf, Mamoona and Arif, Muhammad and Fisahn, Joachim and Xue, Gang-Ping and Balazadeh, Salma and M{\"u}ller-R{\"o}ber, Bernd}, title = {NAC transcription factor speedy hyponastic growth regulates flooding-induced leaf movement in arabidopsis}, series = {The plant cell}, volume = {25}, journal = {The plant cell}, number = {12}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {1040-4651}, doi = {10.1105/tpc.113.117861}, pages = {4941 -- 4955}, year = {2013}, abstract = {In rosette plants, root flooding (waterlogging) triggers rapid upward (hyponastic) leaf movement representing an important architectural stress response that critically determines plant performance in natural habitats. The directional growth is based on localized longitudinal cell expansion at the lower (abaxial) side of the leaf petiole and involves the volatile phytohormone ethylene (ET). We report the existence of a transcriptional core unit underlying directional petiole growth in Arabidopsis thaliana, governed by the NAC transcription factor SPEEDY HYPONASTIC GROWTH (SHYG). Overexpression of SHYG in transgenic Arabidopsis thaliana enhances waterlogging-triggered hyponastic leaf movement and cell expansion in abaxial cells of the basal petiole region, while both responses are largely diminished in shyg knockout mutants. Expression of several EXPANSIN and XYLOGLUCAN ENDOTRANSGLYCOSYLASE/HYDROLASE genes encoding cell wall-loosening proteins was enhanced in SHYG overexpressors but lowered in shyg. We identified ACC OXIDASE5 (ACO5), encoding a key enzyme of ET biosynthesis, as a direct transcriptional output gene of SHYG and found a significantly reduced leaf movement in response to root flooding in aco5 T-DNA insertion mutants. Expression of SHYG in shoot tissue is triggered by root flooding and treatment with ET, constituting an intrinsic ET-SHYG-ACO5 activator loop for rapid petiole cell expansion upon waterlogging.}, language = {en} } @article{RaufArifDortayetal.2013, author = {Rauf, Mamoona and Arif, Muhammad and Dortay, Hakan and Matallana-Ramirez, Lilian P. and Waters, Mark T. and Nam, Hong Gil and Lim, Pyung-Ok and M{\"u}ller-R{\"o}ber, Bernd and Balazadeh, Salma}, title = {ORE1 balances leaf senescence against maintenance by antagonizing G2-like-mediated transcription}, series = {EMBO reports}, volume = {14}, journal = {EMBO reports}, number = {4}, publisher = {Nature Publ. Group}, address = {London}, issn = {1469-221X}, doi = {10.1038/embor.2013.24}, pages = {382 -- 388}, year = {2013}, abstract = {Leaf senescence is a key physiological process in all plants. Its onset is tightly controlled by transcription factors, of which NAC factor ORE1 (ANAC092) is crucial in Arabidopsis thaliana. Enhanced expression of ORE1 triggers early senescence by controlling a downstream gene network that includes various senescence-associated genes. Here, we report that unexpectedly ORE1 interacts with the G2-like transcription factors GLK1 and GLK2, which are important for chloroplast development and maintenance, and thereby for leaf maintenance. ORE1 antagonizes GLK transcriptional activity, shifting the balance from chloroplast maintenance towards deterioration. Our finding identifies a new mechanism important for the control of senescence by ORE1.}, language = {en} } @article{RadchukJohstGroeneveldetal.2013, author = {Radchuk, Viktoriia and Johst, Karin and Gr{\"o}neveld, Juergen and Grimm, Volker and Schtickzelle, Nicolas}, title = {Behind the scenes of population viability modeling predicting butterfly metapopulation dynamics under climate change}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {259}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, number = {2}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2013.03.014}, pages = {62 -- 73}, year = {2013}, abstract = {Studies explaining the choice of model structure for population viability analysis (PVA) are rare and no such study exists for butterfly species, a focal group for conservation. Here, we describe in detail the development of a model to predict population viability of a glacial relict butterfly species, Boloria eunomia, under climate change. We compared four alternative formulations of an individual-based model, differing in the environmental factors acting on the survival of immature life stages: temperature (only temperature impact), weather (temperature, precipitation, and sunshine), temperature and parasitism, and weather and parasitism. Following pattern-oriented modeling, four observed patterns were used to contrast these models: one qualitative (response of population size to habitat parameters) and three quantitative ones describing population dynamics during eight years (mean and variability of population size, and magnitude of the temporal autocorrelation in yearly population growth rates). The four model formulations were not equally able to depict population dynamics under current environmental conditions; the model including only temperature was selected as the most parsimonious model sufficiently well reproducing the empirical patterns. We used all four model formulations to test a range of climate change scenarios that were characterized by changes in both mean and variability of the weather variables. All models predicted adverse effects of climate change and resulted in the same ranking of mean climate change scenarios. However, models differed in their absolute values of population viability measures, underlining the need to explicitly choose the most appropriate model formulation and avoid arbitrary usage of environmental drivers in a model. We conclude that further applications of pattern-oriented modeling to butterfly and other species are likely to help in identifying the key factors impacting the viability of certain taxa, which, ultimately, will aid and speed up informed management decisions for endangered species under climate change.}, language = {en} } @article{PlueDeFrenneAcharyaetal.2013, author = {Plue, Jan and De Frenne, Pieter and Acharya, Kamal P. and Brunet, Jorg and Chabrerie, Olivier and Decocq, Guillaume and Diekmann, Martin and Graae, Bente J. and Heinken, Thilo and Hermy, Martin and Kolb, Annette and Lemke, Isgard and Liira, Jaan and Naaf, Tobias and Shevtsova, Anna and Verheyen, Kris and Wulf, Monika and Cousins, Sara A. O.}, title = {Climatic control of forest herb seed banks along a latitudinal gradient}, series = {Global ecology and biogeography : a journal of macroecology}, volume = {22}, journal = {Global ecology and biogeography : a journal of macroecology}, number = {10}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1466-822X}, doi = {10.1111/geb.12068}, pages = {1106 -- 1117}, year = {2013}, abstract = {Aim Seed banks are central to the regeneration strategy of many plant species. Any factor altering seed bank density thus affects plant regeneration and population dynamics. Although seed banks are dynamic entities controlled by multiple environmental drivers, climatic factors are the most comprehensive, but still poorly understood. This study investigates how climatic variation structures seed production and resulting seed bank patterns. Location Temperate forests along a 1900km latitudinal gradient in north-western (NW) Europe. Methods Seed production and seed bank density were quantified in 153 plots along the gradient for four forest herbs with different seed longevity: Geum urbanum, Milium effusum, Poa nemoralis and Stachys sylvatica. We tested the importance of climatic and local environmental factors in shaping seed production and seed bank density. Results Seed production was determined by population size, and not by climatic factors. G.urbanum and M.effusum seed bank density declined with decreasing temperature (growing degree days) and/or increasing temperature range (maximum-minimum temperature). P.nemoralis and S.sylvatica seed bank density were limited by population size and not by climatic variables. Seed bank density was also influenced by other, local environmental factors such as soil pH or light availability. Different seed bank patterns emerged due to differential seed longevities. Species with long-lived seeds maintained constant seed bank densities by counteracting the reduced chance of regular years with high seed production at colder northern latitudes. Main conclusions Seed bank patterns show clear interspecific variation in response to climate across the distribution range. Not all seed banking species may be as well equipped to buffer climate change via their seed bank, notably in short-term persistent species. Since the buffering capacity of seed banks is key to species persistence, these results provide crucial information to advance climatic change predictions on range shifts, community and biodiversity responses.}, language = {en} } @article{PlathPfenningerLerpetal.2013, author = {Plath, Martin and Pfenninger, Markus and Lerp, Hannes and Riesch, R{\"u}diger and Eschenbrenner, Christoph and Slattery, Patrick A. and Bierbach, David and Herrmann, Nina and Schulte, Matthias and Arias-Rodriguez, Lenin and Rimber Indy, Jeane and Passow, Courtney and Tobler, Michael}, title = {Genetic differentiation and selection against migrants in evolutionarily replicated extreme environments}, series = {Evolution}, volume = {67}, journal = {Evolution}, number = {9}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0014-3820}, doi = {10.1111/evo.12133}, pages = {2647 -- 2661}, year = {2013}, abstract = {We investigated mechanisms of reproductive isolation in livebearing fishes (genus Poecilia) inhabiting sulfidic and nonsulfidic habitats in three replicate river drainages. Although sulfide spring fish convergently evolved divergent phenotypes, it was unclear if mechanisms of reproductive isolation also evolved convergently. Using microsatellites, we found strongly reduced gene flow between adjacent populations from different habitat types, suggesting that local adaptation to sulfidic habitats repeatedly caused the emergence of reproductive isolation. Reciprocal translocation experiments indicate strong selection against immigrants into sulfidic waters, but also variation among drainages in the strength of selection against immigrants into nonsulfidic waters. Mate choice experiments revealed the evolution of assortative mating preferences in females from nonsulfidic but not from sulfidic habitats. The inferred strength of sexual selection against immigrants (RIs) was negatively correlated with the strength of natural selection (RIm), a pattern that could be attributed to reinforcement, whereby natural selection strengthens behavioral isolation due to reduced hybrid fitness. Overall, reproductive isolation and genetic differentiation appear to be replicated and direct consequences of local adaptation to sulfide spring environments, but the relative contributions of different mechanisms of reproductive isolation vary across these evolutionarily independent replicates, highlighting both convergent and nonconvergent evolutionary trajectories of populations in each drainage.}, language = {en} } @phdthesis{Picchi2013, author = {Picchi, Douglas Gatte}, title = {On the characterisation of biosynthetic pathways and functional metagenomic approaches of cyanobacterial peptides}, address = {Potsdam}, pages = {146 S}, year = {2013}, language = {en} } @article{PfestorfWeissMuelleretal.2013, author = {Pfestorf, H. and Weiss, L. and M{\"u}ller, J. and Boch, Steffen and Socher, S. A. and Prati, Daniel and Sch{\"o}ning, Ingo and Weisser, W. and Fischer, M. and Jeltsch, Florian}, title = {Community mean traits as additional indicators to monitor effects of land-use intensity On grassland plant diversity}, series = {Perspectives in plant ecology, evolution and systematics}, volume = {15}, journal = {Perspectives in plant ecology, evolution and systematics}, number = {1}, publisher = {Elsevier}, address = {Jena}, issn = {1433-8319}, doi = {10.1016/j.ppees.2012.10.003}, pages = {1 -- 11}, year = {2013}, abstract = {Semi-natural grasslands, biodiversity hotspots in Central-Europe, suffer from the cessation of traditional land-use. Amount and intensity of these changes challenge current monitoring frameworks typically based on classic indicators such as selected target species or diversity indices. Indicators based on plant functional traits provide an interesting extension since they reflect ecological strategies at individual and ecological processes at community levels. They typically show convergent responses to gradients of land-use intensity over scales and regions, are more directly related to environmental drivers than diversity components themselves and enable detecting directional changes in whole community dynamics. However, probably due to their labor- and cost intensive assessment in the field, they have been rarely applied as indicators so far. Here we suggest overcoming these limitations by calculating indicators with plant traits derived from online accessible databases. Aiming to provide a minimal trait set to monitor effects of land-use intensification on plant diversity we investigated relationships between 12 community mean traits, 2 diversity indices and 6 predictors of land-use intensity within grassland communities of 3 different regions in Germany (part of the German 'Biodiversity Exploratory' research network). By standardization of traits and diversity measures, use of null models and linear mixed models we confirmed (i) strong links between functional community composition and plant diversity, (ii) that traits are closely related to land-use intensity, and (iii) that functional indicators are equally, or even more sensitive to land-use intensity than traditional diversity indices. The deduced trait set consisted of 5 traits, i.e., specific leaf area (SLA), leaf dry matter content (LDMC), seed release height, leaf distribution, and onset of flowering. These database derived traits enable the early detection of changes in community structure indicative for future diversity loss. As an addition to current monitoring measures they allow to better link environmental drivers to processes controlling community dynamics.}, language = {en} } @article{PetrovSchippersBeninaetal.2013, author = {Petrov, Veselin and Schippers, Jos and Benina, Maria and Minkov, Ivan and M{\"u}ller-R{\"o}ber, Bernd and Gechev, Tsanko S.}, title = {In search for new players of the oxidative stress network by phenotyping an Arabidopsis T-DNA mutant collection on reactive oxygen species-eliciting chemicals}, series = {Plant omics}, volume = {6}, journal = {Plant omics}, number = {1}, publisher = {Southern Cross Publ.}, address = {Lismore}, issn = {1836-0661}, pages = {46 -- 54}, year = {2013}, abstract = {The ability of some chemical compounds to cause oxidative stress offers a fast and convenient way to study the responses of plants to reactive oxygen species (ROS). In order to unveil potential novel genetic players of the ROS-regulatory network, a population of similar to 2,000 randomly selected Arabidopsis thaliana T-DNA insertion mutants was screened for ROS sensitivity/resistance by growing seedlings on agar medium supplemented with stress-inducing concentrations of the superoxide-eliciting herbicide methyl viologen or the catalase inhibitor 3-amino-triazole. A semi-robotic setup was used to capture and analyze images of the chemically treated seedlings which helped interpret the screening results by providing quantitative information on seedling area and healthy-to-chlorotic tissue ratios for data verification. A ROS-related phenotype was confirmed in three of the initially selected 33 mutant candidates, which carry T-DNA insertions in genes encoding a Ring/Ubox superfamily protein, ABI5 binding protein 1 (AFP1), previously reported to be involved in ABA signaling, and a protein of unknown function, respectively. In addition, we identified six mutants, most of which have not been described yet, that are related to growth or chloroplast development and show defects in a ROS-independent manner. Thus, semi-automated image capturing and phenotyping applied on publically available T-DNA insertion collections adds a simple means for discovering novel mutants in complex physiological processes and identifying the genes involved.}, language = {en} } @article{PedersenWatthanaKocyanetal.2013, author = {Pedersen, Henrik AE. and Watthana, Santi and Kocyan, Alexander and Srimuang, Kanok-orn}, title = {Pollination biology of Luisia curtisii (Orchidaceae) indications of a deceptive system operated by beetles}, series = {Plant systematics and evolution}, volume = {299}, journal = {Plant systematics and evolution}, number = {1}, publisher = {Springer}, address = {Wien}, issn = {0378-2697}, doi = {10.1007/s00606-012-0713-6}, pages = {177 -- 185}, year = {2013}, abstract = {A population of Luisia curtisii (Orchidaceae: Aeridinae) in northern Thailand was studied with regard to pollination biology. Although a high level of self-compatibility was demonstrated experimentally, the very low natural fruit set (1.4-1.9 \%) clearly indicated that the species depends on external agents for pollination. Our observations suggest that L. curtisii is pollinated by beetles, as Lema unicolor (Chrysomelidae) and Clinteria ducalis (Scarabaeidae) were the only flower visitors observed to carry pollinaria of this species. The hypothesis of specialised cantharophily is further supported by 2-methylbutyric acid and caproic acid being striking components of the floral scent. Judging from the lack of nectar and the behaviour of visiting beetles, the pollination system seems to rely on food or brood site deception. Retention of the anther on the pollinarium for some time after pollinarium removal probably reduces the frequency of insect-mediated autogamy and geitonogamy in Luisia curtisii-a possibility that was supported by comparative data on (1) the anther retention time and inflorescence visitation time of Lema unicolor and (2) stigma and anther length in the orchid. Existing reports of specialised beetle pollination in orchids are reviewed, and we conclude that there is accumulating evidence that specialised cantharophily is more common in the Orchidaceae than previously assumed.}, language = {en} } @article{PavesiTiedemannDeMatthaeisetal.2013, author = {Pavesi, Laura and Tiedemann, Ralph and DeMatthaeis, Elvira and Ketmaier, Valerio}, title = {Genetic connectivity between land and sea: the case of the beachflea Orchestia montagui (Crustacea, Amphipoda, Talitridae) in the Mediterranean Sea}, issn = {1742-9994}, year = {2013}, language = {en} } @article{PavesiTiedemannDeMatthaeisetal.2013, author = {Pavesi, Laura and Tiedemann, Ralph and De Matthaeis, Elvira and Ketmaier, Valerio}, title = {Genetic connectivity between land and sea - the case of the beachflea Orchestia montagui (Crustacea, Amphipoda, Talitridae) in the Mediterranean Sea}, series = {Frontiers in zoology}, volume = {10}, journal = {Frontiers in zoology}, number = {4-5}, publisher = {BioMed Central}, address = {London}, issn = {1742-9994}, doi = {10.1186/1742-9994-10-21}, pages = {19}, year = {2013}, abstract = {Introduction: We examined patterns of genetic divergence in 26 Mediterranean populations of the semi-terrestrial beachflea Orchestia montagui using mitochondrial (cytochrome oxidase subunit I), microsatellite (eight loci) and allozymic data. The species typically forms large populations within heaps of dead seagrass leaves stranded on beaches at the waterfront. We adopted a hierarchical geographic sampling to unravel population structure in a species living at the sea-land transition and, hence, likely subjected to dramatically contrasting forces. Results: Mitochondrial DNA showed historical phylogeographic breaks among Adriatic, Ionian and the remaining basins (Tyrrhenian, Western and Eastern Mediterranean Sea) likely caused by the geological and climatic changes of the Pleistocene. Microsatellites (and to a lesser extent allozymes) detected a further subdivision between and within the Western Mediterranean and the Tyrrhenian Sea due to present-day processes. A pattern of isolation by distance was not detected in any of the analyzed data set. Conclusions: We conclude that the population structure of O. montagui is the result of the interplay of two contrasting forces that act on the species population genetic structure. On one hand, the species semi-terrestrial life style would tend to determine the onset of local differences. On the other hand, these differences are partially counter-balanced by passive movements of migrants via rafting on heaps of dead seagrass leaves across sites by sea surface currents. Approximate Bayesian Computations support dispersal at sea as prevalent over terrestrial regionalism.}, language = {en} } @misc{PavesiTiedemannDeMatthaeisetal.2013, author = {Pavesi, Laura and Tiedemann, Ralph and De Matthaeis, Elvira and Ketmaier, Valerio}, title = {Genetic connectivity between land and sea}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-401110}, pages = {19}, year = {2013}, abstract = {Introduction: We examined patterns of genetic divergence in 26 Mediterranean populations of the semi-terrestrial beachflea Orchestia montagui using mitochondrial (cytochrome oxidase subunit I), microsatellite (eight loci) and allozymic data. The species typically forms large populations within heaps of dead seagrass leaves stranded on beaches at the waterfront. We adopted a hierarchical geographic sampling to unravel population structure in a species living at the sea-land transition and, hence, likely subjected to dramatically contrasting forces. Results: Mitochondrial DNA showed historical phylogeographic breaks among Adriatic, Ionian and the remaining basins (Tyrrhenian, Western and Eastern Mediterranean Sea) likely caused by the geological and climatic changes of the Pleistocene. Microsatellites (and to a lesser extent allozymes) detected a further subdivision between and within the Western Mediterranean and the Tyrrhenian Sea due to present-day processes. A pattern of isolation by distance was not detected in any of the analyzed data set. Conclusions: We conclude that the population structure of O. montagui is the result of the interplay of two contrasting forces that act on the species population genetic structure. On one hand, the species semi-terrestrial life style would tend to determine the onset of local differences. On the other hand, these differences are partially counter-balanced by passive movements of migrants via rafting on heaps of dead seagrass leaves across sites by sea surface currents. Approximate Bayesian Computations support dispersal at sea as prevalent over terrestrial regionalism.}, language = {en} }