@misc{MeierMeschenmoser2009, author = {Meier, Bernd and Meschenmoser, Helmut}, title = {Zwischen Kundenwunsch und didaktischem Konzept : Sch{\"u}lerfirmen als integratives Lernarrangement arbeitsorientierter Bildung}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-46160}, year = {2009}, abstract = {Sch{\"u}lerfirmen haben im Bereich Arbeitslehre in j{\"u}ngster Zeit an Bedeutung gewonnen. Die Autoren stellen im Basisartikel des vorliegenden Heftes Lernen. Gewinn verschiedene Formen von Sch{\"u}lerfirmen vor und erl{\"a}utern Probleme bei der Sicherung der Lernqualit{\"a}t. Diese beziehen sich einerseits auf die optimale F{\"o}rderung arbeitsrelevanter Basiskompetenzen der Sch{\"u}ler und andererseits auf das Erreichen der curricularen Ziele der Arbeitslehre, insbesondere hinsichtlich der technischen und {\"o}konomischen Bildung sowie der Berufsorientierung. Zur Optimierung sind Lehrplankorrekturen, weitere Erfahrungen mit Sch{\"u}lerfirmen und die Unterst{\"u}tzung der Fachdidaktik notwendig. Wichtig sind zudem eine kollegiale Kooperation und Vernetzung an den Lernorten. Die Verfasser f{\"u}hren dar{\"u}ber hinaus in die Beitr{\"a}ge des vorliegenden Heftes ein.}, language = {de} } @misc{Bircken2009, author = {Bircken, Margrid}, title = {Wilhelm Fraenger (1890 bis 1964) und Anna Seghers (1900 bis 1983)}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44546}, year = {2009}, language = {de} } @misc{Tristram2009, author = {Tristram, Hildegard L.C.}, title = {Wie weit sind die inselkeltischen Sprachen (und das Englische) analytisiert?}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41251}, year = {2009}, abstract = {Der gemeinsame Wandel der inselkeltischen Sprachen wie auch des Englischen vom vorwiegend synthetischen Typus zum vorwiegend analytischen Typus l{\"a}ßt sich vermutlich auf einen ca. 1500 Jahre dauernden intensiven Sprachenkontakt zwischen diesen Sprachen zur{\"u}ckf{\"u}hren. Heute ist das Englische die analytischste Sprache der Britischen Inseln und Irlands, gefolgt vom Walisischen, Bretonischen und Irischen. Letzteres ist von den genannten Sprachen noch am weitesten morphologisch komplex.}, language = {de} } @misc{VossBlenauWalzetal.2009, author = {Voss, Martin and Blenau, Wolfgang and Walz, Bernd and Baumann, Otto}, title = {V-ATPase deactivation in blowfly salivary glands is mediated by protein phosphatase 2C}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44360}, year = {2009}, abstract = {The activity of vacuolar H+-ATPase (V-ATPase) in the apical membrane of blowfly (Calliphora vicina) salivary glands is regulated by the neurohormone serotonin (5-HT). 5-HT induces, via protein kinase A, the phosphorylation of V-ATPase subunit C and the assembly of V-ATPase holoenzymes. The protein phosphatase responsible for the dephosphorylation of subunit C and V-ATPase inactivation is not as yet known. We show here that inhibitors of protein phosphatases PP1 and PP2A (tautomycin, ocadaic acid) and PP2B (cyclosporin A, FK-506) do not prevent V-ATPase deactivation and dephosphorylation of subunit C. A decrease in the intracellular Mg2+ level caused by loading secretory cells with EDTA-AM leads to the activation of proton pumping in the absence of 5-HT, prolongs the 5-HT-induced response in proton pumping, and inhibits the dephosphorylation of subunit C. Thus, the deactivation of V-ATPase is most probably mediated by a protein phosphatase that is insensitive to okadaic acid and that requires Mg2+, namely, a member of the PP2C protein family. By molecular biological techniques, we demonstrate the expression of at least two PP2C protein family members in blowfly salivary glands. © 2009 Wiley Periodicals, Inc.}, language = {en} } @misc{BlumeZeheBronstert2009, author = {Blume, Theresa and Zehe, Erwin and Bronstert, Axel}, title = {Use of soil moisture dynamics and patterns at different spatio-temporal scales for the investigation of subsurface flow processes}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44924}, year = {2009}, abstract = {Spatial patterns as well as temporal dynamics of soil moisture have a major influence on runoff generation. The investigation of these dynamics and patterns can thus yield valuable information on hydrological processes, especially in data scarce or previously ungauged catchments. The combination of spatially scarce but temporally high resolution soil moisture profiles with episodic and thus temporally scarce moisture profiles at additional locations provides information on spatial as well as temporal patterns of soil moisture at the hillslope transect scale. This approach is better suited to difficult terrain (dense forest, steep slopes) than geophysical techniques and at the same time less cost-intensive than a high resolution grid of continuously measuring sensors. Rainfall simulation experiments with dye tracers while continuously monitoring soil moisture response allows for visualization of flow processes in the unsaturated zone at these locations. Data was analyzed at different spacio-temporal scales using various graphical methods, such as space-time colour maps (for the event and plot scale) and binary indicator maps (for the long-term and hillslope scale). Annual dynamics of soil moisture and decimeterscale variability were also investigated. The proposed approach proved to be successful in the investigation of flow processes in the unsaturated zone and showed the importance of preferential flow in the Malalcahuello Catchment, a datascarce catchment in the Andes of Southern Chile. Fast response times of stream flow indicate that preferential flow observed at the plot scale might also be of importance at the hillslope or catchment scale. Flow patterns were highly variable in space but persistent in time. The most likely explanation for preferential flow in this catchment is a combination of hydrophobicity, small scale heterogeneity in rainfall due to redistribution in the canopy and strong gradients in unsaturated conductivities leading to self-reinforcing flow paths.}, language = {en} } @misc{Eckstein2009, author = {Eckstein, Lars}, title = {Transatlantic slavery and the literary imagination}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-59201}, year = {2009}, abstract = {Transatlantic slavery and the literary imagination The challenges of turning transatlantic slavery into literature A polyphony of historical voices: Caryl Phillips's dialogic imagination Literary imagination and the Zong Massacre: Fred D'Aguiar and David Dabydeen Perspectives}, language = {en} } @misc{Eckstein2009, author = {Eckstein, Lars}, title = {Torpedoing the authorship of popular music : a reading of Gorillaz' 'Feel Good Inc.'}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-59116}, year = {2009}, abstract = {This article addresses problems of authorship and creative authority in popular music, in particular in view of a pervasive split between modes of aesthetic production (involving modernist assemblage, multiple authorship, and the late capitalist logic of major label policies) and modes of aesthetic reception (which tend to take popular music as the organic output of individual performers). While rock musicians have attempted to come to terms with this phenomenon by either performing a 'Romantic' sense of authenticity (basically by importing folk values to the production process) or 'Modernist authenticity' (by highlighting experimen- tation and alienation), Damon Albarn and Jamie Hewlett, creators of Gorillaz, found a third way which ingeniously allows them to do both. By creating a virtual rock band, and by hiding their own media personalities behind those of their virtual alter egos, they brought themselves into a position which allows them to produce 'sincere' popular music which 'playfully' stages the absurdities of major label music business while very successfully operating within its very confines.}, language = {en} } @misc{KoseskaZaikinKurthsetal.2009, author = {Koseska, Aneta and Zaikin, Alexey and Kurths, J{\"u}rgen and Garc{\´i}a-Ojalvo, Jordi}, title = {Timing cellular decision making under noise via cell-cell communication}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45260}, year = {2009}, abstract = {Many cellular processes require decision making mechanisms, which must act reliably even in the unavoidable presence of substantial amounts of noise. However, the multistable genetic switches that underlie most decision-making processes are dominated by fluctuations that can induce random jumps between alternative cellular states. Here we show, via theoretical modeling of a population of noise-driven bistable genetic switches, that reliable timing of decision-making processes can be accomplished for large enough population sizes, as long as cells are globally coupled by chemical means. In the light of these results, we conjecture that cell proliferation, in the presence of cell-cell communication, could provide a mechanism for reliable decision making in the presence of noise, by triggering cellular transitions only when the whole cell population reaches a certain size. In other words , the summation performed by the cell population would average out the noise and reduce its detrimental impact.}, language = {en} } @misc{SchroederLissoLangeetal.2009, author = {Schr{\"o}der, Florian and Lisso, Janina and Lange, Peggy and M{\"u}ssig, Carsten}, title = {The extracellular EXO protein mediates cell expansion in Arabidopsis leaves}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45107}, year = {2009}, abstract = {Background: The EXO (EXORDIUM) gene was identified as a potential mediator of brassinosteroid (BR)-promoted growth. It is part of a gene family with eight members in Arabidopsis. EXO gene expression is under control of BR, and EXO overexpression promotes shoot and root growth. In this study, the consequences of loss of EXO function are described. Results: The exo loss of function mutant showed diminished leaf and root growth and reduced biomass production. Light and scanning electron microscopy analyses revealed that impaired leaf growth is due to reduced cell expansion. Epidermis, palisade, and spongy parenchyma cells were smaller in comparison to the wild-type. The exo mutant showed reduced brassinolide-induced cotyledon and hypocotyl growth. In contrast, exo roots were significantly more sensitive to the inhibitory effect of synthetic brassinolide. Apart from reduced growth, exo did not show severe morphological abnormalities. Gene expression analyses of leaf material identified genes that showed robust EXO-dependent expression. Growth-related genes such as WAK1, EXP5, and KCS1, and genes involved in primary and secondary metabolism showed weaker expression in exo than in wild-type plants. However, the vast majority of BR-regulated genes were normally expressed in exo. HA- and GFP-tagged EXO proteins were targeted to the apoplast. Conclusion: The EXO gene is essential for cell expansion in leaves. Gene expression patterns and growth assays suggest that EXO mediates BR-induced leaf growth. However, EXO does not control BR-levels or BR-sensitivity in the shoot. EXO presumably is involved in a signalling process which coordinates BR-responses with environmental or developmental signals. The hypersensitivity of exo roots to BR suggests that EXO plays a diverse role in the control of BR responses in the root.}, language = {en} } @misc{SzymanskiJozefczukNikoloskietal.2009, author = {Szymanski, Jedrzej and Jozefczuk, Szymon and Nikoloski, Zoran and Selbig, Joachim and Nikiforova, Victoria and Catchpole, Gareth and Willmitzer, Lothar}, title = {Stability of metabolic correlations under changing environmental conditions in Escherichia coli : a systems approach}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45253}, year = {2009}, abstract = {Background: Biological systems adapt to changing environments by reorganizing their cellula r and physiological program with metabolites representing one important response level. Different stresses lead to both conserved and specific responses on the metabolite level which should be reflected in the underl ying metabolic network. Methodology/Principal Findings: Starting from experimental data obtained by a GC-MS based high-throughput metabolic profiling technology we here develop an approach that: (1) extracts network representations from metabolic conditiondependent data by using pairwise correlations, (2) determines the sets of stable and condition-dependent correlations based on a combination of statistical significance and homogeneity tests, and (3) can identify metabolites related to the stress response, which goes beyond simple ob servation s about the changes of metabolic concentrations. The approach was tested with Escherichia colias a model organism observed under four different environmental stress conditions (cold stress, heat stress, oxidative stress, lactose diau xie) and control unperturbed conditions. By constructing the stable network component, which displays a scale free topology and small-world characteristics, we demonstrated that: (1) metabolite hubs in this reconstructed correlation networks are significantly enriched for those contained in biochemical networks such as EcoCyc, (2) particular components of the stable network are enriched for functionally related biochemical path ways, and (3) ind ependently of the response scale, based on their importance in the reorganization of the cor relation network a set of metabolites can be identified which represent hypothetical candidates for adjusting to a stress-specific response. Conclusions/Significance: Network-based tools allowed the identification of stress-dependent and general metabolic correlation networks. This correlation-network-ba sed approach does not rely on major changes in concentration to identify metabolites important for st ress adaptation, but rather on the changes in network properties with respect to metabolites. This should represent a useful complementary technique in addition to more classical approaches.}, language = {en} } @misc{BlenauRotteWitteetal.2009, author = {Blenau, Wolfgang and Rotte, Cathleen and Witte, Jeannine and Baumann, Otto and Walz, Bernd}, title = {Source, topography and excitatory effects of GABAergic innervation in cockroach salivary glands}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44353}, year = {2009}, abstract = {Cockroach salivary glands are innervated by dopaminergic and serotonergic neurons. Both transmitters elicit saliva secretion. We studied the distribution pattern of neurons containing gamma-aminobutyric acid ( GABA) and their physiological role. Immunofluorescence revealed a GABA-immunoreactive axon that originates within the subesophageal ganglion at the salivary neuron 2 (SN2) and this extends within the salivary duct nerve towards the salivary gland. GABA-positive fibers form a network on most acinar lobules and a dense plexus in the interior of a minor fraction of acinar lobules. Co-staining with anti-synapsin revealed that some putative GABAergic terminals seem to make pre-synaptic contacts with GABA-negative release sites. Many putative GABAergic release sites are at some distance from other synapses and at distance from the acinar tissue. Intracellular recordings from isolated salivary glands have revealed that GABA does not affect the basolateral membrane potential of the acinar cells directly. When applied during salivary duct nerve stimulation, GABA enhances the electrical response of the acinar cells and increases the rates of fluid and protein secretion. The effect on electrical cell responses is mimicked by the GABA(B) receptor agonists baclofen and SKF97541, and blocked by the GABAB receptor antagonists CGP52432 and CGP54626. These findings indicate that GABA has a modulatory role in the control of salivation, acting presynaptically on serotonergic and/or dopaminergic neurotransmission.}, language = {en} } @misc{SchumannTeraoGarattinietal.2009, author = {Schumann, Silvia and Terao, Mineko and Garattini, Enrico and Saggu, Miguel and Lendzian, Friedhelm and Hildebrandt, Peter and Leimk{\"u}hler, Silke}, title = {Site directed mutagenesis of amino acid residues at the active site of mouse aldehyde oxidase AOX1}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45030}, year = {2009}, abstract = {Mouse aldehyde oxidase (mAOX1) forms a homodimer and belongs to the xanthine oxidase family of molybdoenzymes which are characterized by an essential equatorial sulfur ligand coordinated to the molybdenum atom. In general, mammalian AOs are characterized by broad substrate specificity and an yet obscure physiological function. To define the physiological substrates and the enzymatic characteristics of mAOX1, we established a system for the heterologous expression of the enzyme in Eschericia coli. The recombinant protein showed spectral features and a range of substrate specificity similar to the native protein purified from mouse liver. The EPR data of recombinant mAOX1 were similar to those of AO from rabbit liver, but differed from the homologous xanthine oxidoreductase enzymes. Site-directed mutagenesis of amino acids Val806, Met884 and Glu1265 at the active site resulted in a drastic decrease in the oxidation of aldehydes with no increase in the oxidation of purine substrates. The double mutant V806E/M884R and the single mutant E1265Q were catalytically inactive enzymes regardless of the aldehyde or purine substrates tested. Our results show that only Glu1265 is essential for the catalytic activity by initiating the base-catalyzed mechanism of substrate oxidation. In addition, it is concluded that the substrate specificity of molybdo-flavoenzymes is more complex and not only defined by the three characterized amino acids in the active site.}, language = {en} } @misc{Bircken2009, author = {Bircken, Margrid}, title = {Sehend werden}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44564}, year = {2009}, language = {de} } @misc{MeierMeschenmoser2009, author = {Meier, Bernd and Meschenmoser, Helmut}, title = {Sch{\"u}lerfirma Pausenschmaus arbeitet mit Erfolg}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-46177}, year = {2009}, abstract = {Mit Firma Pausenschmaus auf Erfolgskurs In diesem Material wird die Sch{\"u}lerfirma Pausenschmaus vorgestellt. Die Mitarbeiter der Firma Pausenschmaus sind schon gut vorangekommen. Sie haben mehrere Abteilungen gegr{\"u}ndet und gute Kunden gewonnen.}, language = {de} } @misc{KuglerKoehlerPalmeetal.2009, author = {Kugler, Annette and K{\"o}hler, Barbara and Palme, Klaus and Wolff, Patricia and Dietrich, Petra}, title = {Salt-dependent regulation of a CNG channel subfamily in Arabidopsis}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45019}, year = {2009}, abstract = {Background: In Arabidopsis thaliana, the family of cyclic nucleotide-gated channels (CNGCs) is composed of 20 members. Previous studies indicate that plant CNGCs are involved in the control of growth processes and responses to abiotic and biotic stresses. According to their proposed function as cation entry pathways these channels contribute to cellular cation homeostasis, including calcium and sodium, as well as to stress-related signal transduction. Here, we studied the expression patterns and regulation of CNGC19 and CNGC20, which constitute one of the five CNGC subfamilies. Results: GUS, GFP and luciferase reporter assays were used to study the expression of CNGC19 and CNGC20 genes from Arabidopsis thaliana in response to developmental cues and salt stress. CNGC19 and CNGC20 were differentially expressed in roots and shoots. The CNGC19 gene was predominantly active in roots already at early growth stages. Major expression was observed in the phloem. CNGC20 showed highest promoter activity in mesophyll cells surrounding the veins. Its expression increased during development and was maximal in mature and senescent leaves. Both genes were upregulated in the shoot in response to elevated NaCl but not mannitol concentrations. While in the root, CNGC19 did not respond to changes in the salt concentration, in the shoot it was strongly upregulated in the observed time frame (6-72 hours). Salt-induction of CNGC20 was also observed in the shoot, starting already one hour after stress treatment. It occurred with similar kinetics, irrespective of whether NaCl was applied to roots of intact plants or to the petiole of detached leaves. No differences in K and Na contents of the shoots were measured in homozygous T-DNA insertion lines for CNGC19 and CNGC20, respectively, which developed a growth phenotype in the presence of up to 75 mM NaCl similar to that of the wild type. Conclusion: Together, the results strongly suggest that both channels are involved in the salinity response of different cell types in the shoot. Upon salinity both genes are upregulated within hours. CNGC19 and CNGC20 could assist the plant to cope with toxic effects caused by salt stress, probably by contributing to a re-allocation of sodium within the plant.}, language = {en} } @misc{deCastroGaedkeBoenigk2009, author = {de Castro, Francisco and Gaedke, Ursula and Boenigk, Jens}, title = {Reverse evolution : driving forces behind the loss of acquired photosynthetic traits}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44968}, year = {2009}, abstract = {Background: The loss of photosynthesis has occurred often in eukaryotic evolution, even more than its acquisition, which occurred at least nine times independently and which generated the evolution of the supergroups Archaeplastida, Rhizaria, Chromalveolata and Excavata. This secondary loss of autotrophic capability is essential to explain the evolution of eukaryotes and the high diversity of protists, which has been severely underestimated until recently. However, the ecological and evolutionary scenarios behind this evolutionary ''step back'' are still largely unknown. Methodology/Principal Findings: Using a dynamic model of heterotrophic and mixotrophic flagellates and two types of prey, large bacteria and ultramicrobacteria, we examine the influence of DOC concentration, mixotroph's photosynthetic growth rate, and external limitations of photosynthesis on the coexistence of both types of flagellates. Our key premises are: large bacteria grow faster than small ones at high DOC concentrations, and vice versa; and heterotrophic flagellates are more efficient than the mixotrophs grazing small bacteria (both empirically supported). We show that differential efficiency in bacteria grazing, which strongly depends on cell size, is a key factor to explain the loss of photosynthesis in mixotrophs (which combine photosynthesis and bacterivory) leading to purely heterotrophic lineages. Further, we show in what conditions an heterotroph mutant can coexist, or even out-compete, its mixotrophic ancestor, suggesting that bacterivory and cell size reduction may have been major triggers for the diversification of eukaryotes. Conclusions/Significance: Our results suggest that, provided the mixotroph's photosynthetic advantage is not too large, the (small) heterotroph will also dominate in nutrient-poor environments and will readily invade a community of mixotrophs and bacteria, due to its higher efficiency exploiting the ultramicrobacteria. As carbon-limited conditions were presumably widespread throughout Earth history, such a scenario may explain the numerous transitions from phototrophy to mixotrophy and further to heterotrophy within virtually all major algal lineages. We challenge prevailing concepts that affiliated the evolution of phagotrophy with eutrophic or strongly light-limited environments only.}, language = {en} } @misc{MeierMeschenmoser2009, author = {Meier, Bernd and Meschenmoser, Helmut}, title = {Qualit{\"a}tssicherung in Sch{\"u}lerfirmen : indikatorengest{\"u}tztes Qualit{\"a}tsraster zum Lehren und Lernen in einem arbeitsorientierten Lernarrangement}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-46186}, year = {2009}, abstract = {Sch{\"u}lerfirmen zeugen von der Innovationsf{\"a}higkeit der Schulen. Sie lassen auf Ver{\"a}nderungen des Unterrichts und des Selbstverst{\"a}ndnisses von Schule und Kollegien schließen, denn sie stehen im Kontrast zum traditionellen Fachunterricht. Ihre Existenz sagt allerdings relativ wenig {\"u}ber die damit verbundene Qualit{\"a}t aus. So ist zu kl{\"a}ren, welche Intentionen mit Qualit{\"a}tssicherung verbunden sind. Dar{\"u}ber hinaus wird ein Qualit{\"a}tsraster mit Indikatoren zur Analyse der Entwicklungsprozesse f{\"u}r Sch{\"u}lerfirmen zur Diskussion gestellt.}, language = {de} } @misc{MeyerKustererLisecetal.2009, author = {Meyer, Rhonda Christiane and Kusterer, Barbara and Lisec, Jan and Steinfath, Matthias and Becher, Martina and Scharr, Hanno and Melchinger, Albrecht E. and Selbig, Joachim and Schurr, Ulrich and Willmitzer, Lothar and Altmann, Thomas}, title = {QTL analysis of early stage heterosis for biomass in Arabidopsis}, series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1330}, issn = {1866-8372}, doi = {10.25932/publishup-43127}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431272}, pages = {11}, year = {2009}, abstract = {The main objective of this study was to identify genomic regions involved in biomass heterosis using QTL, generation means, and mode-of-inheritance classification analyses. In a modified North Carolina Design III we backcrossed 429 recombinant inbred line and 140 introgression line populations to the two parental accessions, C24 and Col-0, whose F 1 hybrid exhibited 44\% heterosis for biomass. Mid-parent heterosis in the RILs ranged from -31 to 99\% for dry weight and from -58 to 143\% for leaf area. We detected ten genomic positions involved in biomass heterosis at an early developmental stage, individually explaining between 2.4 and 15.7\% of the phenotypic variation. While overdominant gene action was prevalent in heterotic QTL, our results suggest that a combination of dominance, overdominance and epistasis is involved in biomass heterosis in this Arabidopsis cross.}, language = {en} } @misc{SteinfathGaertnerLisecetal.2009, author = {Steinfath, Matthias and G{\"a}rtner, Tanja and Lisec, Jan and Meyer, Rhonda C. and Altmann, Thomas and Willmitzer, Lothar and Selbig, Joachim}, title = {Prediction of hybrid biomass in Arabidopsis thaliana by selected parental SNP and metabolic markers}, series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1324}, issn = {1866-8372}, doi = {10.25932/publishup-43111}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431115}, pages = {9}, year = {2009}, abstract = {A recombinant inbred line (RIL) population, derived from two Arabidopsis thaliana accessions, and the corresponding testcrosses with these two original accessions were used for the development and validation of machine learning models to predict the biomass of hybrids. Genetic and metabolic information of the RILs served as predictors. Feature selection reduced the number of variables (genetic and metabolic markers) in the models by more than 80\% without impairing the predictive power. Thus, potential biomarkers have been revealed. Metabolites were shown to bear information on inherited macroscopic phenotypes. This proof of concept could be interesting for breeders. The example population exhibits substantial mid-parent biomass heterosis. The results of feature selection could therefore be used to shed light on the origin of heterosis. In this respect, mainly dominance effects were detected.}, language = {en} } @misc{Bircken2009, author = {Bircken, Margrid}, title = {Pergande, Ingrid ; Kaufmann, Ulrich (Hrsg.): Gegen das große Umsonst : vierzig Jahre mit dem Dichter Volker Braun / [rezensiert von] Margrid Bircken}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44530}, year = {2009}, abstract = {rezensiertes Werk: Gegen das große Umsonst : vierzig Jahre mit dem Dichter Volker Braun / Ingrid Pergande ... (Hrsg.). - Berlin [u.a.] : Pergande und Kaufmann, 2009. - 335 S. : Ill. ISBN 978-3-00-027239-4}, language = {de} } @misc{BleidornPodsiadlowskiZhongetal.2009, author = {Bleidorn, Christoph and Podsiadlowski, Lars and Zhong, Min and Eeckhaut, Igor and Hartmann, Stefanie and Halanych, Kenneth M. and Tiedemann, Ralph}, title = {On the phylogenetic position of Myzostomida : can 77 genes get it wrong?}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44893}, year = {2009}, abstract = {Background: Phylogenomic analyses recently became popular to address questions about deep metazoan phylogeny. Ribosomal proteins (RP) dominate many of these analyses or are, in some cases, the only genes included. Despite initial hopes, hylogenomic analyses including tens to hundreds of genes still fail to robustly place many bilaterian taxa. Results: Using the phylogenetic position of myzostomids as an example, we show that phylogenies derived from RP genes and mitochondrial genes produce incongruent results. Whereas the former support a position within a clade of platyzoan taxa, mitochondrial data recovers an annelid affinity, which is strongly supported by the gene order data and is congruent with morphology. Using hypothesis testing, our RP data significantly rejects the annelids affinity, whereas a platyzoan relationship is significantly rejected by the mitochondrial data. Conclusion: We conclude (i) that reliance of a set of markers belonging to a single class of macromolecular complexes might bias the analysis, and (ii) that concatenation of all available data might introduce conflicting signal into phylogenetic analyses. We therefore strongly recommend testing for data incongruence in phylogenomic analyses. Furthermore, judging all available data, we consider the annelid affinity hypothesis more plausible than a possible platyzoan affinity for myzostomids, and suspect long branch attraction is influencing the RP data. However, this hypothesis needs further confirmation by future analyses.}, language = {en} } @misc{HeinkenWinkler2009, author = {Heinken, Thilo and Winkler, Eckart}, title = {Non-random dispersal by ants : long-term field data versus model predictions of population spread of a forest herb}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-46482}, year = {2009}, abstract = {Myrmecochory, i.e. dispersal of seeds by ants towards and around their nests, plays an important role in temperate forests. Yet hardly any study has examined plant population spread over several years and the underlying joint contribution of a hierarchy of dispersal modes and plant demography. We used a seed-sowing approach with three replicates to examine colonization patterns of Melampyrum pratense, an annual myrmecochorous herb, in a mixed Scots pine forest in northeastern Germany. Using a spatially explicit individualbased (SEIB) model population patterns over 4 years were explained by short-distance transport of seeds by small ant species with high nest densities, resulting in random spread. However, plant distributions in the field after another 4 years were clearly deviating from model predictions. Mean annual spread rate increased from 0.9 m to 5.1 m per year, with a clear inhomogeneous component. Obviously, after a lag-phase of several years, non-random seed dispersal by large red wood ants (Formica rufa) was determining the species' spread, thus resulting in stratified dispersal due to interactions with different-sized ant species. Hypotheses on stratified dispersal, on dispersal lag, and on non-random dispersal were verified using an extended SEIB model, by comparison of model outputs with field patterns (individual numbers, population areas, and maximum distances). Dispersal towards red wood ant nests together with seed loss during transport and redistribution around nests were essential features of the model extension. The observed lag-phase in the initiation of non-random, medium-distance transport was probably due to a change of ant behaviour towards a new food source of increasing importance, being a meaningful example for a lag-phase in local plant species invasion. The results demonstrate that field studies should check model predictions wherever possible. Future research will show whether or not the M. pratense-ant system is representative for migration patterns of similar animal dispersal systems after having crossed range edges by long-distance dispersal events.}, language = {en} } @misc{BlenauRotteKrachetal.2009, author = {Blenau, Wolfgang and Rotte, Cathleen and Krach, Christian and Balfanz, Sabine and Baumann, Arnd and Walz, Bernd}, title = {Molecular characterization and localization of the first tyramine receptor of the American cockroach (Periplaneta americana)}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44335}, year = {2009}, abstract = {The phenolamines octopamine and tyramine control, regulate, and modulate many physiological and behavioral processes in invertebrates. Vertebrates possess only small amounts of both substances, and thus, octopamine and tyramine, together with other biogenic amines, are referred to as "trace amines." Biogenic amines evoke cellular responses by activating G-protein-coupled receptors. We have isolated a complementary DNA (cDNA) that encodes a biogenic amine receptor from the American cockroach Periplaneta americana, viz., Peatyr1, which shares high sequence similarity to members of the invertebrate tyramine-receptor family. The PeaTYR1 receptor was stably expressed in human embryonic kidney (HEK) 293 cells, and its ligand response has been examined. Receptor activation with tyramine reduces adenylyl cyclase activity in a dose-dependent manner (EC50 350 nM). The inhibitory effect of tyramine is abolished by co-incubation with either yohimbine or chlorpromazine. Receptor expression has been investigated by reverse transcription polymerase chain reaction and immunocytochemistry. The mRNA is present in various tissues including brain, salivary glands, midgut, Malpighian tubules, and leg muscles. The effect of tyramine on salivary gland acinar cells has been investigated by intracellular recordings, which have revealed excitatory presynaptic actions of tyramine. This study marks the first comprehensive molecular, pharmacological, and functional characterization of a tyramine receptor in the cockroach.}, language = {en} } @misc{MwinyiMeyerBleidornetal.2009, author = {Mwinyi, Adina and Meyer, Achim and Bleidorn, Christoph and Lieb, Bernhard and Bartolomaeus, Thomas and Podsiadlowski, Lars}, title = {Mitochondrial genome sequence and gene order of Sipunculus nudus give additional support for an inclusion of Sipuncula into Annelida}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44916}, year = {2009}, abstract = {Background: Mitochondrial genomes are a valuable source of data for analysing phylogenetic relationships. Besides sequence information, mitochondrial gene order may add phylogenetically useful information, too. Sipuncula are unsegmented marine worms, traditionally placed in their own phylum. Recent molecular and morphological findings suggest a close affinity to the segmented Annelida. Results: The first complete mitochondrial genome of a member of Sipuncula, Sipunculus nudus, is presented. All 37 genes characteristic for metazoan mtDNA were detected and are encoded on the same strand. The mitochondrial gene order (protein-coding and ribosomal RNA genes) resembles that of annelids, but shows several derivations so far found only in Sipuncula. Sequence based phylogenetic analysis of mitochondrial protein-coding genes results in significant bootstrap support for Annelida sensu lato, combining Annelida together with Sipuncula, Echiura, Pogonophora and Myzostomida. Conclusion: The mitochondrial sequence data support a close relationship of Annelida and Sipuncula. Also the most parsimonious explanation of changes in gene order favours a derivation from the annelid gene order. These results complement findings from recent phylogenetic analyses of nuclear encoded genes as well as a report of a segmental neural patterning in Sipuncula.}, language = {en} } @misc{DevchandNuytsWeingart2009, author = {Devchand, Chandrashekar and Nuyts, Jean and Weingart, Gregor}, title = {Matryoshka of special democratic forms}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {841}, issn = {1866-8372}, doi = {10.25932/publishup-42900}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-429002}, pages = {545 -- 562}, year = {2009}, abstract = {Special p-forms are forms which have components fµ1…µp equal to +1, -1 or 0 in some orthonormal basis. A p-form ϕ ∈ � pRd is called democratic if the set of nonzero components {ϕμ1...μp} is symmetric under the transitive action of a subgroup of O(d,Z) on the indices {1, . . . , d}. Knowledge of these symmetry groups allows us to define mappings of special democratic p-forms in d dimensions to special democratic P-forms in D dimensions for successively higher P = p and D = d. In particular, we display a remarkable nested structure of special forms including a U(3)-invariant 2-form in six dimensions, a G2-invariant 3-form in seven dimensions, a Spin(7)-invariant 4-form in eight dimensions and a special democratic 6-form O in ten dimensions. The latter has the remarkable property that its contraction with one of five distinct bivectors, yields, in the orthogonal eight dimensions, the Spin(7)-invariant 4-form. We discuss various properties of this ten dimensional form.}, language = {en} } @misc{KroellerWarschburger2009, author = {Kr{\"o}ller, Katja and Warschburger, Petra}, title = {Maternal feeding strategies and child's food intake : considering weight and demographic influences using structural equation modeling}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45023}, year = {2009}, abstract = {Background: Research concerning child's food intake have considered various influencing factors, for example parental feeding strategies, demographic and weight factors. At this time, however, there are few findings that explore these factors simultaneously. Accordingly, the aim of this study was to test a structural equation model regarding the associations between maternal feeding strategies and child's food intake. Methods: 556 mothers and their children between 1 and 10 years of age participated in this crosssectional study. Besides socio-demographic and weight data, the mothers were asked about their feeding strategies as well as their child's food intake. Results: The well-fitting model explained 73\% of the variance in the child's consumption of healthy and 34\% of unhealthy food. In addition to the effect of the mother's social status and the child's age, a rewarding and modeling feeding behavior significantly influenced the child's food intake. Conclusion: The results highlight the relevance of maternal feeding behavior on the child's food intake. In terms of preventing eating- or weight-related problems, the findings indicate the usefulness of training parents in explicit modeling behavior and avoiding food as a reward.}, language = {en} } @misc{MeierMeschenmoser2009, author = {Meier, Bernd and Meschenmoser, Helmut}, title = {Mal sehen, wie Tabea, Ali und ... in der Sch{\"u}lerfirma arbeiten : Lernen am und mit Modell}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-46153}, year = {2009}, abstract = {Die in den Materialien thematisierte Sch{\"u}lerfirma Pausenschmaus wurde als Prototyp f{\"u}r Lehr- und Lernzwecke modelliert. Die didaktische Modellvorstellung beruht auf Analysen existierender Sch{\"u}lerfirmen und bezieht sich auf die Forumsbeitr{\"a}ge zur Qualit{\"a}tssicherung in diesem Heft. Das Material gibt einerseits f{\"u}r den Unterricht wie f{\"u}r Lehrerfortbildung einen exemplarischen Orientierungsrahmen zur Gestaltung eigener Sch{\"u}lerfirmen, anderseits ist es Grundlage f{\"u}r komplexe Aufgabenstellungen zur arbeitsorientierten Bildung, wie sie im gesonderten Beitrag am Beispiel eines konkreten unternehmerischen Problems ausgef{\"u}hrt werden. Die Darstellungen im Material sind situativ angelegt, um somit Sch{\"u}lerinnen und Sch{\"u}ler an Prozesse und Strukturen von Unternehmen und damit befassten betrieblichen Funktionen heranzuf{\"u}hren. Das Modellunternehmen hat einen Schwerpunkt im Catering.}, language = {de} } @misc{MinchevChambodutHolschneideretal.2009, author = {Minchev, Borislav and Chambodut, Aude and Holschneider, Matthias and Panet, Isabelle and Sch{\"o}ll, Eckehard and Mandea, Mioara and Ramillien, Guillaume}, title = {Local multi-polar expansions in potential field modeling}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {845}, issn = {1866-8372}, doi = {10.25932/publishup-42899}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-428990}, pages = {1127 -- 1141}, year = {2009}, abstract = {The satellite era brings new challenges in the development and the implementation of potential field models. Major aspects are, therefore, the exploitation of existing space- and ground-based gravity and magnetic data for the long-term. Moreover, a continuous and near real-time global monitoring of the Earth system, allows for a consistent integration and assimilation of these data into complex models of the Earth's gravity and magnetic fields, which have to consider the constantly increasing amount of available data. In this paper we propose how to speed up the computation of the normal equation in potential filed modeling by using local multi-polar approximations of the modeling functions. The basic idea is to take advantage of the rather smooth behavior of the internal fields at the satellite altitude and to replace the full available gravity or magnetic data by a collection of local moments. We also investigate what are the optimal values for the free parameters of our method. Results from numerical experiments with spherical harmonic models based on both scalar gravity potential and magnetic vector data are presented and discussed. The new developed method clearly shows that very large datasets can be used in potential field modeling in a fast and more economic manner.}, language = {en} } @misc{ScholtkaKuehnelTaugneretal.2009, author = {Scholtka, Bettina and K{\"u}hnel, Dana and Taugner, Felicitas and Steinberg, Pablo}, title = {Inflammation does not precede or accompany the induction of perneoplastic lesions in the colon of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine-fed rats}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44570}, year = {2009}, abstract = {Heterocyclic aromatic amines (HCAs) are formed in meat cooked at high temperatures for a long time or over an open flame. In this context 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), the most abundant HCA in cooked meat, has been suggested to be involved in colon and prostate carcinogenesis. In the latter case it has been reported that: (1) roughly 50\% of Fischer F344 male rats treated with PhIP develop carcinomas in the ventral prostate lobe at 1 year of age; (2) inflammation precedes prostatic intraepithelial neoplasia in PhIP-fed rats; (3) inflammation specifically occurs in the ventral prostate lobe of PhIP-fed rats. To test whether PhIP by itself leads to inflammation in the colon and whether a human-relevant concentration of PhIP is able to induce preneoplastic lesions in the colon, male F344 rats were fed 0.1 or 100 ppm PhIP for up to 10 months and thereafter the colon tissue was analyzed histochemically. In none of the experimental groups signs of acute or chronic colonic inflammation were observed. 0.1 ppm PhIP leads to the development of hyperplastic and dysplastic lesions in the colon of single animals, but the incidence of these lesions does not reach a statistical significance. In contrast, in rats fed 100 ppm PhIP for 10 months hyperplastic and dysplastic colonic lesions were induced in a statistically significant number of animals. It is concluded that: (1) the induction of preneoplastic lesions in rat colon by PhIP is not preceded or accompanied by an inflammatory process; (2) a human-relevant concentration of PhIP alone is not sufficient to initiate colon carcinogenesis in rats.}, language = {en} } @misc{GaertnerSteinfathAndorfetal.2009, author = {G{\"a}rtner, Tanja and Steinfath, Matthias and Andorf, Sandra and Lisec, Jan and Meyer, Rhonda C. and Altmann, Thomas and Willmitzer, Lothar and Selbig, Joachim}, title = {Improved heterosis prediction by combining information on DNA- and metabolic markers}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45132}, year = {2009}, abstract = {Background: Hybrids represent a cornerstone in the success story of breeding programs. The fundamental principle underlying this success is the phenomenon of hybrid vigour, or heterosis. It describes an advantage of the offspring as compared to the two parental lines with respect to parameters such as growth and resistance against abiotic or biotic stress. Dominance, overdominance or epistasis based models are commonly used explanations. Conclusion/Significance: The heterosis level is clearly a function of the combination of the parents used for offspring production. This results in a major challenge for plant breeders, as usually several thousand combinations of parents have to be tested for identifying the best combinations. Thus, any approach to reliably predict heterosis levels based on properties of the parental lines would be highly beneficial for plant breeding. Methodology/Principal Findings: Recently, genetic data have been used to predict heterosis. Here we show that a combination of parental genetic and metabolic markers, identified via feature selection and minimum-description-length based regression methods, significantly improves the prediction of biomass heterosis in resulting offspring. These findings will help furthering our understanding of the molecular basis of heterosis, revealing, for instance, the presence of nonlinear genotype-phenotype relationships. In addition, we describe a possible approach for accelerated selection in plant breeding.}, language = {en} } @misc{ChildsNikoloskiMayetal.2009, author = {Childs, Liam H. and Nikoloski, Zoran and May, Patrick and Walther, Dirk}, title = {Identification and classification of ncRNA molecules using graph properties}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45192}, year = {2009}, abstract = {The study of non-coding RNA genes has received increased attention in recent years fuelled by accumulating evidence that larger portions of genomes than previously acknowledged are transcribed into RNA molecules of mostly unknown function, as well as the discovery of novel non-coding RNA types and functional RNA elements. Here, we demonstrate that specific properties of graphs that represent the predicted RNA secondary structure reflect functional information. We introduce a computational algorithm and an associated web-based tool (GraPPLE) for classifying non-coding RNA molecules as functional and, furthermore, into Rfam families based on their graph properties. Unlike sequence-similarity-based methods and covariance models, GraPPLE is demonstrated to be more robust with regard to increasing sequence divergence, and when combined with existing methods, leads to a significant improvement of prediction accuracy. Furthermore, graph properties identified as most informative are shown to provide an understanding as to what particular structural features render RNA molecules functional. Thus, GraPPLE may offer a valuable computational filtering tool to identify potentially interesting RNA molecules among large candidate datasets.}, language = {en} } @misc{Bircken2009, author = {Bircken, Margrid}, title = {H{\"o}rnigk, Therese (Hrsg.): Sich aussetzen : das Wort ergreifen ; Texte und Bilder zum 80.Geburtstag von Christa Wolf / [rezensiert von] Margrid Bircken}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44550}, year = {2009}, abstract = {rezensiertes Werk: Sich aussetzen : das Wort ergreifen ; Texte und Bilder zum 80. Geburtstag von Christa Wolf / hrsg. von Therese H{\"o}rnigk im Auftr. des Literaturforums im Brecht-Haus und in Zusammenarbeit mit der Stiftung Preußische Seehandlung. - G{\"o}ttingen : Wallstein-Verl., 2009. - 192 S. : Ill. ISBN 978-3-8353-0481-9}, language = {de} } @misc{Bircken2009, author = {Bircken, Margrid}, title = {Gr{\"u}nzweig, Walter ; Seeber, Ursula (Hrsg.): Fred Wander : Leben und Werk / [rezensiert von] Margrid Bircken}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44593}, year = {2009}, abstract = {rezensiertes Werk: Fred Wander : Leben und Werk / Walter Gr{\"u}nzweig und Ursula Seeber (Hrsg.). - Bonn : Weidle, c 2005. - 256 S. ISBN 3-931135-88-8}, language = {de} } @misc{KartalEbenhoeh2009, author = {Kartal, {\"O}nder and Ebenh{\"o}h, Oliver}, title = {Ground state robustness as an evolutionary design principle in signaling networks}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44982}, year = {2009}, abstract = {The ability of an organism to survive depends on its capability to adapt to external conditions. In addition to metabolic versatility and efficient replication, reliable signal transduction is essential. As signaling systems are under permanent evolutionary pressure one may assume that their structure reflects certain functional properties. However, despite promising theoretical studies in recent years, the selective forces which shape signaling network topologies in general remain unclear. Here, we propose prevention of autoactivation as one possible evolutionary design principle. A generic framework for continuous kinetic models is used to derive topological implications of demanding a dynamically stable ground state in signaling systems. To this end graph theoretical methods are applied. The index of the underlying digraph is shown to be a key topological property which determines the so-called kinetic ground state (or off-state) robustness. The kinetic robustness depends solely on the composition of the subdigraph with the strongly connected components, which comprise all positive feedbacks in the network. The component with the highest index in the feedback family is shown to dominate the kinetic robustness of the whole network, whereas relative size and girth of these motifs are emphasized as important determinants of the component index. Moreover, depending on topological features, the maintenance of robustness differs when networks are faced with structural perturbations. This structural off-state robustness, defined as the average kinetic robustness of a network's neighborhood, turns out to be useful since some structural features are neutral towards kinetic robustness, but show up to be supporting against structural perturbations. Among these are a low connectivity, a high divergence and a low path sum. All results are tested against real signaling networks obtained from databases. The analysis suggests that ground state robustness may serve as a rationale for some structural peculiarities found in intracellular signaling networks.}, language = {en} } @misc{ZhangIgnatova2009, author = {Zhang, Gong and Ignatova, Zoya}, title = {Generic algorithm to predict the speed of translational elongation : implications for protein biogenesis}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45007}, year = {2009}, abstract = {Synonymous codon usage and variations in the level of isoaccepting tRNAs exert a powerful selective force on translation fidelity. We have developed an algorithm to evaluate the relative rate of translation which allows large-scale comparisons of the non-uniform translation rate on the protein biogenesis. Using the complete genomes of Escherichia coli and Bacillus subtilis we show that stretches of codons pairing to minor tRNAs form putative sites to locally attenuate translation; thereby the tendency is to cluster in near proximity whereas long contiguous stretches of slow-translating triplets are avoided. The presence of slow-translating segments positively correlates with the protein length irrespective of the protein abundance. The slow-translating clusters are predominantly located down-stream of the domain boundaries presumably to fine-tune translational accuracy with the folding fidelity of multidomain proteins. Translation attenuation patterns at highly structurally and functionally conserved domains are preserved across the species suggesting a concerted selective pressure on the codon selection and species-specific tRNA abundance in these regions.}, language = {en} } @misc{SzarzynskaSobkowiakPantetal.2009, author = {Szarzynska, Bogna and Sobkowiak, Lukasz and Pant, Bikram Datt and Balazadeh, Salma and Scheible, Wolf-R{\"u}diger and M{\"u}ller-R{\"o}ber, Bernd and Jarmolowski, Artur and Szweykowska-Kulinska, Zofia}, title = {Gene structures and processing of Arabidopsis thaliana HYL1-dependent pri-miRNAs}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45085}, year = {2009}, abstract = {Arabidopsis thaliana HYL1 is a nuclear doublestranded RNA-binding protein involved in the maturation of pri-miRNAs. A quantitative real-time PCR platform for parallel quantification of 176 primiRNAs was used to reveal strong accumulation of 57 miRNA precursors in the hyl1 mutant that completely lacks HYL1 protein. This approach enabled us for the first time to pinpoint particular members of MIRNA family genes that require HYL1 activity for efficient maturation of their precursors. Moreover, the accumulation of miRNA precursors in the hyl1 mutant gave us the opportunity to carry out 3' and 5' RACE experiments which revealed that some of these precursors are of unexpected length. The alignment of HYL1- dependent miRNA precursors to A. thaliana genomic sequences indicated the presence of introns in 12 out of 20 genes studied. Some of the characterized intron-containing pri-miRNAs undergo alternative splicing such as exon skipping or usage of alternative 5' splice sites suggesting that this process plays a role in the regulation of miRNA biogenesis. In the hyl1 mutant intron-containing pri-miRNAs accumulate alongside spliced primiRNAs suggesting the recruitment of HYL1 into the miRNA precursor maturation pathway before their splicing occurs.}, language = {en} } @misc{RianoPachonNagelNeigenfindetal.2009, author = {Riano-Pachon, Diego Mauricio and Nagel, Axel and Neigenfind, Jost and Wagner, Robert and Basekow, Rico and Weber, Elke and M{\"u}ller-R{\"o}ber, Bernd and Diehl, Svenja and Kersten, Birgit}, title = {GabiPD : the GABI primary database - a plant integrative "omics" database}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45075}, year = {2009}, abstract = {The GABI Primary Database, GabiPD (http:// www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyze and visualize primary information from GABI projects. GabiPD constitutes a repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species. Data from different 'omics' fronts are incorporated (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for textbased retrieval of all data types in GabiPD (e.g. clones, genes, mutant lines). All data types point to a central Gene GreenCard, where gene information is integrated from genome projects or NCBI UniGene sets. The centralized Gene GreenCard allows visualizing ESTs aligned to annotated transcripts as well as displaying identified protein domains and gene structure. Moreover, GabiPD makes available interactive genetic maps from potato and barley, and protein 2DE gels from Arabidopsis thaliana and Brassica napus. Gene expression and metabolic-profiling data can be visualized through MapManWeb. By the integration of complex data in a framework of existing knowledge, GabiPD provides new insights and allows for new interpretations of the data.}, language = {en} } @misc{EbenhoehHandorf2009, author = {Ebenh{\"o}h, Oliver and Handorf, Thomas}, title = {Functional classification of genome-scale metabolic networks}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44975}, year = {2009}, abstract = {We propose two strategies to characterize organisms with respect to their metabolic capabilities. The first, investigative, strategy describes metabolic networks in terms of their capability to utilize different carbon sources, resulting in the concept of carbon utilization spectra. In the second, predictive, approach minimal nutrient combinations are predicted from the structure of the metabolic networks, resulting in a characteristic nutrient profile. Both strategies allow for a quantification of functional properties of metabolic networks, allowing to identify groups of organisms with similar functions. We investigate whether the functional description reflects the typical environments of the corresponding organisms by dividing all species into disjoint groups based on whether they are aerotolerant and/or photosynthetic. Despite differences in the underlying concepts, both measures display some common features. Closely related organisms often display a similar functional behavior and in both cases the functional measures appear to correlate with the considered classes of environments. Carbon utilization spectra and nutrient profiles are complementary approaches toward a functional classification of organism-wide metabolic networks. Both approaches contain different information and thus yield different clusterings, which are both different from the classical taxonomy of organisms. Our results indicate that a sophisticated combination of our approaches will allow for a quantitative description reflecting the lifestyles of organisms.}, language = {en} } @misc{KienelWulfBowenByrneetal.2009, author = {Kienel, Ulrike and Wulf Bowen, Sabine and Byrne, Roger and Park, Jungjae and B{\"o}hnel, Harald and Dulski, Peter and Luhr, James F. and Siebert, Lee and Haug, Gerald H. and Negendank, J{\"o}rg F. W.}, title = {First lacustrine varve chronologies from Mexico}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {860}, issn = {1866-8372}, doi = {10.25932/publishup-43279}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-432794}, pages = {587 -- 609}, year = {2009}, abstract = {We present varve chronologies for sediments from two maar lakes in the Valle de Santiago region (Central Mexico): Hoya La Alberca (AD 1852-1973) and Hoya Rincn de Parangueo (AD 1839-1943). These are the first varve chronologies for Mexican lakes. The varved sections were anchored with tephras from Colima (1913) and Paricutin (1943/1944) and (210)Pb ages. We compare the sequences using the thickness of seasonal laminae and element counts (Al, Si, S, Cl, K, Ti, Mn, Fe, and Sr) determined by micro X-ray fluorescence spectrometry. The formation of the varve sublaminae is attributed to the strongly seasonal climate regime. Limited rainfall and high evaporation rates in winter and spring induce precipitation of carbonates (high Ca, Sr) enriched in (13)C and (18)O, whereas rainfall in summer increases organic and clastic input (plagioclase, quartz) with high counts of lithogenic elements (K, Al, Ti, and Si). Eolian input of Ti occurs also in the dry season. Moving correlations (5-yr windows) of the Ca and Ti counts show similar development in both sequences until the 1930s. Positive correlations indicate mixing of allochthonous Ti and autochthonous Ca, while negative correlations indicate their separation in sublaminae. Negative excursions in the correlations correspond with historic and reconstructed droughts, El Nio events, and positive SST anomalies. Based on our data, droughts (3-7 year duration) were severe and centred around the following years: the early 1850s, 1865, 1880, 1895, 1905, 1915 and the late 1920s with continuation into the 1930s. The latter dry period brought both lake systems into a critical state making them susceptible to further drying. Groundwater overexploitation due to the expansion of irrigation agriculture in the region after 1940 induced the transition from calcite to aragonite precipitation in Alberca and halite infiltration in Rincn. The proxy data indicate a faster response to increased evaporation for Rincn, the lake with the larger maar dimensions, solar radiation receipt and higher conductivity, whereas the smaller, steeper Alberca maar responded rapidly to increased precipitation.}, language = {en} } @misc{DambacherRolfsGoellneretal.2009, author = {Dambacher, Michael and Rolfs, Martin and G{\"o}llner, Kristin and Kliegl, Reinhold and Jacobs, Arthur M.}, title = {Event-related potentials reveal rapid verification of predicted visual input}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44953}, year = {2009}, abstract = {Human information processing depends critically on continuous predictions about upcoming events, but the temporal convergence of expectancy-based top-down and input-driven bottom-up streams is poorly understood. We show that, during reading, event-related potentials differ between exposure to highly predictable and unpredictable words no later than 90 ms after visual input. This result suggests an extremely rapid comparison of expected and incoming visual information and gives an upper temporal bound for theories of top-down and bottom-up interactions in object recognition.}, language = {en} } @misc{SpricigoDronovLisdatetal.2009, author = {Spricigo, Roberto and Dronov, Roman and Lisdat, Fred and Leimk{\"u}hler, Silke and Scheller, Frieder W. and Wollenberger, Ursula}, title = {Electrocatalytic sulfite biosensor with human sulfite oxidase co-immobilized with cytochrome c in a polyelectrolyte-containing multilayer}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {945}, issn = {1866-8372}, doi = {10.25932/publishup-43117}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431176}, pages = {225 -- 233}, year = {2009}, abstract = {An efficient electrocatalytic biosensor for sulfite detection was developed by co-immobilizing sulfite oxidase and cytochrome c with polyaniline sulfonic acid in a layer-by-layer assembly. QCM, UV-Vis spectroscopy and cyclic voltammetry revealed increasing loading of electrochemically active protein with the formation of multilayers. The sensor operates reagentless at low working potential. A catalytic oxidation current was detected in the presence of sulfite at the modified gold electrode, polarized at +0.1 V ( vs. Ag/AgCl 1 M KCl). The stability of the biosensor performance was characterized and optimized. A 17-bilayer electrode has a linear range between 1 and 60 mu M sulfite with a sensitivity of 2.19 mA M-1 sulfite and a response time of 2 min. The electrode retained a stable response for 3 days with a serial reproducibility of 3.8\% and lost 20\% of sensitivity after 5 days of operation. It is possible to store the sensor in a dry state for more than 2 months. The multilayer electrode was used for determination of sulfite in unspiked and spiked samples of red and white wine. The recovery and the specificity of the signals were evaluated for each sample.}, language = {en} } @misc{Buerger2009, author = {B{\"u}rger, Gerd}, title = {Dynamically vs. empirically downscaled medium-range precipitation forecasts}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44939}, year = {2009}, abstract = {For three small, mountainous catchments in Germany two medium-range forecast systems are compared that predict precipitation for up to 5 days in advance. One system is composed of the global German weather service (DWD) model, GME, which is dynamically downscaled using the COSMO-EU regional model. The other system is an empirical (expanded) downscaling of the ECMWF model IFS. Forecasts are verified against multi-year daily observations, by applying standard skill scores to events of specified intensity. All event classes are skillfully predicted by the empirical system for up to five days lead time. For the available prediction range of one to two days it is superior to the dynamical system.}, language = {en} } @misc{DurekSchudomaWeckwerthetal.2009, author = {Durek, Pawel and Schudoma, Christian and Weckwerth, Wolfram and Selbig, Joachim and Walther, Dirk}, title = {Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45129}, year = {2009}, abstract = {Background: Phosphorylation of proteins plays a crucial role in the regulation and activation of metabolic and signaling pathways and constitutes an important target for pharmaceutical intervention. Central to the phosphorylation process is the recognition of specific target sites by protein kinases followed by the covalent attachment of phosphate groups to the amino acids serine, threonine, or tyrosine. The experimental identification as well as computational prediction of phosphorylation sites (P-sites) has proved to be a challenging problem. Computational methods have focused primarily on extracting predictive features from the local, one-dimensional sequence information surrounding phosphorylation sites. Results: We characterized the spatial context of phosphorylation sites and assessed its usability for improved phosphorylation site predictions. We identified 750 non-redundant, experimentally verified sites with three-dimensional (3D) structural information available in the protein data bank (PDB) and grouped them according to their respective kinase family. We studied the spatial distribution of amino acids around phosphorserines, phosphothreonines, and phosphotyrosines to extract signature 3D-profiles. Characteristic spatial distributions of amino acid residue types around phosphorylation sites were indeed discernable, especially when kinase-family-specific target sites were analyzed. To test the added value of using spatial information for the computational prediction of phosphorylation sites, Support Vector Machines were applied using both sequence as well as structural information. When compared to sequence-only based prediction methods, a small but consistent performance improvement was obtained when the prediction was informed by 3D-context information. Conclusion: While local one-dimensional amino acid sequence information was observed to harbor most of the discriminatory power, spatial context information was identified as relevant for the recognition of kinases and their cognate target sites and can be used for an improved prediction of phosphorylation sites. A web-based service (Phos3D) implementing the developed structurebased P-site prediction method has been made available at http://phos3d.mpimp-golm.mpg.de.}, language = {en} } @misc{Buerkner2009, author = {B{\"u}rkner, Hans-Joachim}, title = {Der lokale Staat als Akteur im Feld kreativer Nischen{\"o}konomien}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {812}, issn = {1866-8372}, doi = {10.25932/publishup-41988}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-419889}, pages = {16}, year = {2009}, language = {de} } @misc{MayChristianKempaetal.2009, author = {May, Patrick and Christian, Jan-Ole and Kempa, Stefan and Walther, Dirk}, title = {ChlamyCyc : an integrative systems biology database and web-portal for Chlamydomonas reinhardtii}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44947}, year = {2009}, abstract = {Background: The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern highthroughput technologies there is an imperative need to integrate large-scale data sets from highthroughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. Results: In the framework of the German Systems Biology initiative GoFORSYS, a pathway database and web-portal for Chlamydomonas (ChlamyCyc) was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification. Conclusion: ChlamyCyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de.}, language = {en} } @misc{LiTaubert2009, author = {Li, Zhonghao and Taubert, Andreas}, title = {Cellulose/gold nanocrystal hybrids via an ionic liquid/aqueous precipitation route}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45046}, year = {2009}, abstract = {Injection of a mixture of HAuCl4 and cellulose dissolved in the ionic liquid (IL) 1-butyl-3-methylimidazolium chloride [Bmim]Cl into aqueous NaBH4 leads to colloidal gold nanoparticle/cellulose hybrid precipitates. This process is a model example for a very simple and generic approach towards (noble) metal/cellulose hybrids, which could find applications in sensing, sterile filtration, or as biomaterials.}, language = {en} } @misc{LamprechtMargariaSteffen2009, author = {Lamprecht, Anna-Lena and Margaria, Tiziana and Steffen, Bernhard}, title = {Bio-jETI : a framework for semantics-based service composition}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45066}, year = {2009}, abstract = {Background: The development of bioinformatics databases, algorithms, and tools throughout the last years has lead to a highly distributedworld of bioinformatics services. Without adequatemanagement and development support, in silico researchers are hardly able to exploit the potential of building complex, specialized analysis processes from these services. The Semantic Web aims at thoroughly equipping individual data and services with machine-processable meta-information, while workflow systems support the construction of service compositions. However, even in this combination, in silico researchers currently would have to deal manually with the service interfaces, the adequacy of the semantic annotations, type incompatibilities, and the consistency of service compositions. Results: In this paper, we demonstrate by means of two examples how Semantic Web technology together with an adequate domain modelling frees in silico researchers from dealing with interfaces, types, and inconsistencies. In Bio-jETI, bioinformatics services can be graphically combined to complex services without worrying about details of their interfaces or about type mismatches of the composition. These issues are taken care of at the semantic level by Bio-jETI's model checking and synthesis features. Whenever possible, they automatically resolve type mismatches in the considered service setting. Otherwise, they graphically indicate impossible/incorrect service combinations. In the latter case, the workflow developermay either modify his service composition using semantically similar services, or ask for help in developing the missing mediator that correctly bridges the detected type gap. Newly developed mediators should then be adequately annotated semantically, and added to the service library for later reuse in similar situations. Conclusion: We show the power of semantic annotations in an adequately modelled and semantically enabled domain setting. Using model checking and synthesis methods, users may orchestrate complex processes from a wealth of heterogeneous services without worrying about interfaces and (type) consistency. The success of this method strongly depends on a careful semantic annotation of the provided services and on its consequent exploitation for analysis, validation, and synthesis. We are convinced that these annotations will become standard, as they will become preconditions for the success and widespread use of (preferred) services in the Semantic Web}, language = {en} } @misc{ZiegeMahlowHennigeSulzetal.2009, author = {Ziege, Madlen and Mahlow, Kristin and Hennige-Sulz, Carmen and Kronmarck, Claudia and Tiedemann, Ralph and Streit, Bruno and Plath, Martin}, title = {Audience effects in the Atlantic molly (Poecilia mexicana) : prudent male mate choice in response to perceived sperm competition risk?}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45171}, year = {2009}, abstract = {Background: Multidirectional interactions in social networks can have a profound effect on mate choice behavior; e.g., Poecilia mexicana males show weaker expression of mating preferences when being observed by a rival. This may be an adaptation to reduce sperm competition risk, which arises because commonly preferred female phenotypes will receive attention also from surrounding males, and/or because other males can copy the focal male's mate choice. Do P. mexicana males indeed respond to perceived sperm competition risk? We gave males a choice between two females and repeated the tests under one of the following conditions: (1) an empty transparent cylinder was presented (control); (2) another ("audience") male inside the cylinder observed the focal male throughout the 2nd part, or (3) the audience male was presented only before the tests, but could not eavesdrop during the actual choice tests (non-specific sperm competition risk treatments); (4) the focal male could see a rival male interact sexually with the previously preferred, or (5) with the non-preferred female before the 2nd part of the tests (specific sperm competition risk treatments). Results: The strength of individual male preferences declined slightly also during the control treatment (1). However, this decrease was more than two-fold stronger in audience treatment (2), i.e., with non-specific sperm competition risk including the possibility for visual eavesdropping by the audience male. No audience effect was found in treatments (3) and (5), but a weak effect was also observed when the focal male had seen the previously preferred female sexually interact with a rival male (treatment 4; specific sperm competition risk). Conclusion: When comparing the two 'non-specific sperm competition risk' treatments, a very strong effect was found only when the audience male could actually observe the focal male during mate choice [treatment (2)]. This suggests that focal males indeed attempt to conceal their mating preferences so as to prevent surrounding males from copying their mate choice. When there is no potential for eavesdropping [treatment (3)], non-specific specific sperm competition risk seems to play a minor or no role. Our results also show that P. mexicana males tend to share their mating effort more equally among females when the resource value of their previously preferred mate decreases after mating with a rival male (perceived specific sperm competition risk), but this effect is comparatively weak.}, language = {en} } @misc{WienhoeferGermerLindenmaieretal.2009, author = {Wienh{\"o}fer, Jan and Germer, Kai and Lindenmaier, Falk and F{\"a}rber, Arne and Zehe, Erwin}, title = {Applied tracers for the observation of subsurface stormflow at the hillslope scale}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45246}, year = {2009}, abstract = {Rain fall-runoff response in temperate humid headwater catchments is mainly controlled by hydrolo gical processes at the hillslope scale. Applied tracer experiments with fluore scent dye and salt tracers are well known tools in groundwater studies at the large scale and vadose zone studies at the plot scale, where they provide a means to characterise subsurface flow. We extend this approach to the hillslope scale to investigate saturated and unsaturated flow path s concertedly at a forested hill slope in the Austrian Alps. Dye staining experiments at the plot scale revealed that crack s and soil pipe s function as preferential flow path s in the fine-textured soils of the study area, and these preferenti al flow structures were active in fast subsurface transport of tracers at the hillslope scale. Breakthrough curves obtained under steady flow conditions could be fitted well to a one-dimensional convection-dispersion model. Under natural rain fall a positive correlation of tracer concentrations to the transient flows was observed. The results of this study demon strate qualitative and quantitative effects of preferential flow feature s on subsurface stormflow in a temperate humid headwater catchment. It turn s out that , at the hill slope scale, the interaction s of structures and processes are intrinsically complex, which implies that attempts to model such a hillslope satisfactorily require detailed investigation s of effective structures and parameters at the scale of interest.}, language = {en} } @misc{PeterMuivaYenesewetal.2009, author = {Peter, Martin G. and Muiva, Lois M. and Yenesew, Abiy and Derese, Solomon and Heydenreich, Matthias and Akala, Hoseah M. and Eyase, Fredrick and Waters, Norman C. and Mutai, Charles and Keriko, Joseph M. and Walsh, Douglas S.}, title = {Antiplasmodial β-hydroxydihydrochalcone from seedpods of Tephrosia elata}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44437}, year = {2009}, abstract = {From the seedpods of Tephrosia elata, a new β-hydroxydihydrochalcone named (S)-elatadihydrochalcone was isolated. In addition, the known flavonoids obovatachalcone, obovatin, obovatin methyl ether and deguelin were identified. The structures were determined on the basis of spectroscopic evidence. The crude extract and the flavonoids obtained from the seedpods of this plant showed antiplasmodial activities. The literature NMR data on β-hydroxydihydrochalcones is reviewed and the identity of some of the compounds assigned β-hydroxydihydrochalcone skeleton is questioned.}, language = {en} }