TY - JOUR A1 - Mulder, Christian A1 - Boit, Alice A1 - Bonkowski, Michael A1 - De Ruiter, Peter C. A1 - Mancinelli, Giorgio A1 - Van der Heijden, Marcel G. A. A1 - Van Wijnen, Harm J. A1 - Vonk, J. Arie A1 - Rutgers, Michiel ED - Woodward, G T1 - A belowground perspective on dutch agroecosystems how soil organisms interact to support ecosystem services JF - Advances in ecological research JF - Advances in Ecological Research N2 - 1. New patterns and trends in land use are becoming increasingly evident in Europe's heavily modified landscape and else whereas sustainable agriculture and nature restoration are developed as viable long-term alternatives to intensively farmed arable land. The success of these changes depends on how soil biodiversity and processes respond to changes in management. To improve our understanding of the community structure and ecosystem functioning of the soil biota, we analyzed abiotic variables across 200 sites, and biological variables across 170 sites in The Netherlands, one of the most intensively farmed countries. The data were derived from the Dutch Soil Quality Network (DSQN), a long-term monitoring framework designed to obtain ecological insight into soil types (STs) and ecosystem types (ETs). 2. At the outset we describe STs and biota, and we estimate the contribution of various groups to the provision of ecosystem services. We focused on interactive effects of soil properties on community patterns and ecosystem functioning using food web models. Ecologists analyze soil food webs by means of mechanistic and statistical modelling, linking network structure to energy flow and elemental dynamics commonly based on allometric scaling. 3. We also explored how predatory and metabolic processes are constrained by body size, diet and metabolic type, and how these constraints govern the interactions within and between trophic groups. In particular, we focused on how elemental fluxes determine the strengths of ecological interactions, and the resulting ecosystem services, in terms of sustenance of soil fertility. 4. We discuss data mining, food web visualizations, and an appropriate categorical way to capture subtle interrelationships within the DSQN dataset. Sampled metazoans were used to provide an overview of below-ground processes and influences of land use. Unlike most studies to date we used data from the entire size spectrum, across 15 orders of magnitude, using body size as a continuous trait crucial for understanding ecological services. 5. Multimodality in the frequency distributions of body size represents a performance filter that acts as a buffer to environmental change. Large differences in the body-size distributions across ETs and STs were evident. Most observed trends support the hypothesis that the direct influence of ecological stoichiometry on the soil biota as an independent predictor (e.g. in the form of nutrient to carbon ratios), and consequently on the allometric scaling, is more dominant than either ET or ST. This provides opportunities to develop a mechanistic and physiologically oriented model for the distribution of species' body sizes, where responses of invertebrates can be predicted. 6. Our results highlight the different roles that organisms play in a number of key ecosystem services. Such a trait-based research has unique strengths in its rigorous formulation of fundamental scaling rules, as well as in its verifiability by empirical data. Nonetheless, it still has weaknesses that remain to be addressed, like the consequences of intraspecific size variation, the high degree of omnivory, and a possibly inaccurate assignment to trophic groups. 7. Studying the extent to which nutrient levels influence multitrophic interactions and how different land-use regimes affect soil biodiversity is clearly a fruitful area for future research to develop predictive models for soil ecosystem services under different management regimes. No similar efforts have been attempted previously for soil food webs, and our dataset has the potential to test and further verify its usefulness at an unprecedented space scale. Y1 - 2011 SN - 978-0-12-374794-5 U6 - https://doi.org/10.1016/B978-0-12-374794-5.00005-5 SN - 0065-2504 VL - 44 IS - 2 SP - 277 EP - 357 PB - Elsevier CY - San Diego ER - TY - JOUR A1 - Samuel, Prinson P. A1 - Horn, Sebastian A1 - Döring, Alexander A1 - Havelius, Kajsa G. V. A1 - Reschke, Stefan A1 - Leimkühler, Silke A1 - Haumann, Michael A1 - Schulzke, Carola T1 - A Crystallographic and Mo K-Edge XAS Study of Molybdenum Oxo Bis-,Mono-, and Non-Dithiolene Complexes - First-Sphere Coordination Geometry and Noninnocence of Ligands JF - European journal of inorganic chemistry : a journal of ChemPubSoc Europe N2 - Ten square-based pyramidal molybdenum complexes with different sulfur donor ligands, that is, a variety of dithiolenes and sulfides, were prepared, which mimic coordination motifs of the molybdenum cofactors of molybdenum-dependent oxidoreductases. The model compounds were investigated by Mo K-edge X-ray absorption spectroscopy (XAS) and (with one exception) their molecular structures were analyzed by X-ray diffraction to derive detailed information on bond lengths and geometries of the first coordination shell of molybdenum. Only small variations in Mo=O and Mo-S bond lengths and their respective coordination angles were observed for all complexes including those containing Mo(CO)(2) or Mo(mu-S)(2)Mo motifs. XAS analysis (edge energy) revealed higher relative oxidation levels in the molybdenum ion in compounds with innocent sulfur-based ligands relative to those in dithiolene complexes, which are known to exhibit noninnocence, that is, donation of substantial electron density from ligand to metal. In addition, longer average Mo-S and Mo=O bonds and consequently lower.(Mo=O) stretching frequencies in the IR spectra were observed for complexes with dithiolene-derived ligands. The results emphasize that the noninnocent character of the dithiolene ligand influences the electronic structure of the model compounds, but does not significantly affect their metal coordination geometry, which is largely determined by the Mo(IV) or (V) ion itself. The latter conclusion also holds for the molybdenum site geometries in the oxidized Mo-VI cofactor of DMSO reductase and the reduced Mo-IV cofactor of arsenite oxidase. The innocent behavior of the dithiolene molybdopterin ligands observed in the enzymes is likely to be related to cofactor-protein interactions. KW - Molybdenum KW - Enzyme models KW - X-ray absorption spectroscopy KW - Noninnocence KW - Bioinorganic chemistry Y1 - 2011 U6 - https://doi.org/10.1002/ejic.201100331 SN - 1434-1948 IS - 28 SP - 4387 EP - 4399 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Schwarte, Sandra A1 - Tiedemann, Ralph T1 - A Gene Duplication/Loss Event in the Ribulose-1,5-Bisphosphate-Carboxylase/Oxygenase (Rubisco) Small Subunit Gene Family among Accessions of Arabidopsis thaliana JF - Molecular biology and evolution N2 - Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39), the most abundant protein in nature, catalyzes the assimilation of CO(2) (worldwide about 10(11) t each year) by carboxylation of ribulose-1,5-bisphosphate. It is a hexadecamer consisting of eight large and eight small subunits. Although the Rubisco large subunit (rbcL) is encoded by a single gene on the multicopy chloroplast genome, the Rubisco small subunits (rbcS) are encoded by a family of nuclear genes. In Arabidopsis thaliana, the rbcS gene family comprises four members, that is, rbcS-1a, rbcS-1b, rbcS-2b, and rbcS-3b. We sequenced all Rubisco genes in 26 worldwide distributed A. thaliana accessions. In three of these accessions, we detected a gene duplication/loss event, where rbcS-1b was lost and substituted by a duplicate of rbcS-2b (called rbcS-2b*). By screening 74 additional accessions using a specific polymerase chain reaction assay, we detected five additional accessions with this duplication/loss event. In summary, we found the gene duplication/loss in 8 of 100 A. thaliana accessions, namely, Bch, Bu, Bur, Cvi, Fei, Lm, Sha, and Sorbo. We sequenced an about 1-kb promoter region for all Rubisco genes as well. This analysis revealed that the gene duplication/loss event was associated with promoter alterations (two insertions of 450 and 850 bp, one deletion of 730 bp) in rbcS-2b and a promoter deletion (2.3 kb) in rbcS-2b* in all eight affected accessions. The substitution of rbcS-1b by a duplicate of rbcS-2b (i.e., rbcS-2b*) might be caused by gene conversion. All four Rubisco genes evolve under purifying selection, as expected for central genes of the highly conserved photosystem of green plants. We inferred a single positive selected site, a tyrosine to aspartic acid substitution at position 72 in rbcS-1b. Exactly the same substitution compromises carboxylase activity in the cyanobacterium Anacystis nidulans. In A. thaliana, this substitution is associated with an inferred recombination. Functional implications of the substitution remain to be evaluated. KW - Arabidopsis thaliana KW - Arabidopsis lyrata KW - Rubisco KW - gene duplication KW - positive selection Y1 - 2011 U6 - https://doi.org/10.1093/molbev/msr008 SN - 0737-4038 VL - 28 IS - 6 SP - 1861 EP - 1876 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Wulf, Monika A1 - Rujner, Hendrik T1 - A GIS-based method for the reconstruction of the late eighteenth century forest vegetation in the Prignitz region (NE Germany) JF - Landscape ecology N2 - Our goal was to reconstruct the late eighteenth century forest vegetation of the Prignitz region (NE Germany) at a scale of 1:50,000. We also wanted to relate the historical forest vegetation to the actual and potential natural vegetation. For these purposes, we selected 15 woody species and transferred relevant data found in historical records from various sources together with the recent localities of (very) old individuals belonging to these woody species into ArcView GIS. Following multi-step data processing including the generation of a point density layer using a moving window with kernel estimation and derivation of vegetation units applying Boolean algebra rules together with information on site conditions, we derived 17 forest communities corresponding to the potential natural vegetation. We were able to reconstruct the historical forest vegetation for 90% of the forest area ca. 1780. Only two of the 17 forest communities covered large parts of the forested area. The oak forest with Agrostis capillaris covered about 44% of the total forest area, and alder forests on fenland made up about 37%. Oak-hornbeam forests with Stellaria holostea comprised slightly less than 6% of the forest area, while all other forest communities comprised less than 1%. The historical forest vegetation is more similar to the potential forest vegetation and quite different from the actual forest vegetation because coniferous tree species currently cover approximately two-thirds of the actual forest area. The most beneficial result of this study is the map of high-resolution historical vegetation units that may serve as the basis for various further studies, e.g., modelling long-term changes in biodiversity at the landscape scale. KW - Boolean algebra KW - Historical ecology KW - Kernel estimation KW - Moving window KW - Point density KW - Potential natural vegetation KW - Schmettau map KW - Toponymy KW - Vegetation map Y1 - 2011 U6 - https://doi.org/10.1007/s10980-010-9555-1 SN - 0921-2973 VL - 26 IS - 2 SP - 153 EP - 168 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Arvidsson, Samuel Janne A1 - Perez-Rodriguez, Paulino A1 - Müller-Röber, Bernd T1 - A growth phenotyping pipeline for Arabidopsis thaliana integrating image analysis and rosette area modeling for robust quantification of genotype effects JF - New phytologist : international journal of plant science N2 - To gain a deeper understanding of the mechanisms behind biomass accumulation, it is important to study plant growth behavior. Manually phenotyping large sets of plants requires important human resources and expertise and is typically not feasible for detection of weak growth phenotypes. Here, we established an automated growth phenotyping pipeline for Arabidopsis thaliana to aid researchers in comparing growth behaviors of different genotypes. The analysis pipeline includes automated image analysis of two-dimensional digital plant images and evaluation of manually annotated information of growth stages. It employs linear mixed-effects models to quantify genotype effects on total rosette area and relative leaf growth rate (RLGR) and ANOVAs to quantify effects on developmental times. Using the system, a single researcher can phenotype up to 7000 plants d(-1). Technical variance is very low (typically < 2%). We show quantitative results for the growth-impaired starch-excessmutant sex4-3 and the growth-enhancedmutant grf9. We show that recordings of environmental and developmental variables reduce noise levels in the phenotyping datasets significantly and that careful examination of predictor variables (such as d after sowing or germination) is crucial to avoid exaggerations of recorded phenotypes and thus biased conclusions. KW - development KW - growth KW - leaf area KW - modeling KW - phenotyping Y1 - 2011 U6 - https://doi.org/10.1111/j.1469-8137.2011.03756.x SN - 0028-646X VL - 191 IS - 3 SP - 895 EP - 907 PB - Wiley-Blackwell CY - Malden ER - TY - CHAP A1 - Tikhonenko, I. A1 - Magidson, V. A1 - Gräf, Ralph A1 - Khodjakov, A. A1 - Koonce, M. T1 - A kinesin-mediated linkage between centrosomes and the nuclear envelope T2 - Molecular biology of the cell : the official publication of the American Society for Cell Biology Y1 - 2011 SN - 1059-1524 VL - 22 IS - 1 PB - American Society for Cell Biology CY - Bethesda ER - TY - JOUR A1 - De Frenne, P. A1 - Kolb, Annette A1 - Graae, Benete Jessen A1 - Decocq, Guillaume A1 - Baltora, S. A1 - De Schrijver, A. A1 - Brunet, J. A1 - Chabrerie, Olivier A1 - Cousins, Sara A. O. A1 - Dhondt, Rob A1 - Diekmann, Martin A1 - Gruwez, R. A1 - Heinken, Thilo A1 - Hermy, Martin A1 - Liira, J. A1 - Saguez, R. A1 - Shevtsova, Anna A1 - Baskin, Carol C. A1 - Verheyen, Kris T1 - A latitudinal gradient in seed nutrients of the forest herb Anemone nemorosa JF - Plant biology N2 - The nutrient concentration in seeds determines many aspects of potential success of the sexual reproductive phase of plants, including the seed predation probability, efficiency of seed dispersal and seedling performance. Despite considerable research interest in latitudinal gradients of foliar nutrients, a similar gradient for seeds remains unexplored. We investigated a potential latitudinal gradient in seed nutrient concentrations within the widespread European understorey forest herb Anemone nemorosa L. We sampled seeds of A. nemorosa in 15 populations along a 1900-km long latitudinal gradient at three to seven seed collection dates post-anthesis and investigated the relative effects of growing degree-hours > 5 degrees C, soil characteristics and latitude on seed nutrient concentrations. Seed nitrogen, nitrogen:phosphorus ratio and calcium concentration decreased towards northern latitudes, while carbon:nitrogen ratios increased. When taking differences in growing degree-hours and measured soil characteristics into account and only considering the most mature seeds, the latitudinal decline remained particularly significant for seed nitrogen concentration. We argue that the decline in seed nitrogen concentration can be attributed to northward decreasing seed provisioning due to lower soil nitrogen availability or greater investment in clonal reproduction. This pattern may have large implications for the reproductive performance of this forest herb as the degree of seed provisioning ultimately co-determines seedling survival and reproductive success. KW - Collection date KW - latitude KW - nutrient stoichiometry KW - seed nitrogen KW - seed predation KW - seed provisioning KW - sexual reproduction KW - wood anemone Y1 - 2011 U6 - https://doi.org/10.1111/j.1438-8677.2010.00404.x SN - 1435-8603 VL - 13 IS - 3 SP - 493 EP - 501 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Ebenhoeh, Oliver A1 - Houwaart, Torsten A1 - Lokstein, Heiko A1 - Schlede, Stephanie A1 - Tirok, Katrin T1 - A minimal mathematical model of nonphotochemical quenching of chlorophyll fluorescence JF - Biosystems : journal of biological and information processing sciences N2 - Under natural conditions, plants are exposed to rapidly changing light intensities. To acclimate to such fluctuations, plants have evolved adaptive mechanisms that optimally exploit available light energy and simultaneously minimise damage of the photosynthetic apparatus through excess light. An important mechanism is the dissipation of excess excitation energy as heat which can be measured as nonphotochemical quenching of chlorophyll fluorescence (NPQ). In this paper, we present a highly simplified mathematical model that captures essential experimentally observed features of the short term adaptive quenching dynamics. We investigate the stationary and dynamic behaviour of the model and systematically analyse the dependence of characteristic system properties on key parameters such as rate constants and pool sizes. Comparing simulations with experimental data allows to derive conclusions about the validity of the simplifying assumptions and we further propose hypotheses regarding the role of the xanthophyll cycle in NPQ. We envisage that the presented theoretical description of the light reactions in conjunction with short term adaptive processes serves as a basis for the development of more detailed mechanistic models by which the molecular mechanisms of NPQ can be theoretically studied. KW - Photosynthesis KW - Light reactions KW - Nonphotochemical quenching of chlorophyll fluorescence KW - Chlorophyll fluorescence KW - Mathematical model Y1 - 2011 U6 - https://doi.org/10.1016/j.biosystems.2010.10.011 SN - 0303-2647 VL - 103 IS - 2 SP - 196 EP - 204 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Aksu, Yilmaz A1 - Frasca, Stefano A1 - Wollenberger, Ursula A1 - Driess, Matthias A1 - Thomas, Arne T1 - A molecular precursor approach to tunable porous tin-rich indium tin oxide with durable high electrical conductivity for bioelectronic devices JF - Chemistry of materials : a publication of the American Chemical Society N2 - The preparation of porous, i.e., high surface area electrodes from transparent conducting oxides, is a valuable goal in materials chemistry as such electrodes can enable further development of optoelectronic, electrocatalytic, or bioelectronic devices. In this work the first tin-rich mesoporous indium tin oxide is prepared using the molecular heterobimetallic single-source precursor, indium tin tris-tert-butoxide, together with an appropriate structure-directing template, yielding materials with high surface areas and tailorable pore size. The resulting mesoporous tin-rich ITO films show a high and durable electrical conductivity and transparency, making them interesting materials for hosting electroactive biomolecules such as proteins. In fact, its unique performance in bioelectronic applications has been demonstrated by immobilization of high amounts of cytochrome c into the mesoporous film which undergo redox processes directly with the conductive electrode material. KW - indium tin oxide ITO KW - electrode KW - bioelectrochemistry KW - device KW - cytochrome c Y1 - 2011 U6 - https://doi.org/10.1021/cm103087p SN - 0897-4756 VL - 23 IS - 7 SP - 1798 EP - 1804 PB - American Chemical Society CY - Washington ER - TY - THES A1 - Schönheit, Jörg T1 - A phagocyte-specific Irf8 gene enhancer establishes early conventional dendritic cell commitment T1 - Ein Phagozyten spezifischer Enhancer des Irf8 Gens steuert die Entwicklung konventioneller dendritischer Zellen N2 - Haematopoietic development is a complex process that is strictly hierarchically organized. Here, the phagocyte lineages are a very heterogeneous cell compartment with specialized functions in innate immunity and induction of adaptive immune responses. Their generation from a common precursor must be tightly controlled. Interference within lineage formation programs for example by mutation or change in expression levels of transcription factors (TF) is causative to leukaemia. However, the molecular mechanisms driving specification into distinct phagocytes remain poorly understood. In the present study I identify the transcription factor Interferon Regulatory Factor 8 (IRF8) as the specification factor of dendritic cell (DC) commitment in early phagocyte precursors. Employing an IRF8 reporter mouse, I showed the distinct Irf8 expression in haematopoietic lineage diversification and isolated a novel bone marrow resident progenitor which selectively differentiates into CD8α+ conventional dendritic cells (cDCs) in vivo. This progenitor strictly depends on Irf8 expression to properly establish its transcriptional DC program while suppressing a lineage-inappropriate neutrophile program. Moreover, I demonstrated that Irf8 expression during this cDC commitment-step depends on a newly discovered myeloid-specific cis-enhancer which is controlled by the haematopoietic transcription factors PU.1 and RUNX1. Interference with their binding leads to abrogation of Irf8 expression, subsequently to disturbed cell fate decisions, demonstrating the importance of these factors for proper phagocyte cell development. Collectively, these data delineate a transcriptional program establishing cDC fate choice with IRF8 in its center. N2 - Die Differenzierung von hämatopoietischen Zellen ist ein komplexer Prozess, der strikt hierarchisch organisiert ist. Dabei stellen die Phagozyten eine sehr heterogene Zellpopulation dar, mit hochspezialisierten Funktionen im angeborenen Immunsystem sowie während der Initialisierung der adaptiven Immunreaktion. Ihre Entwicklung, ausgehend von einer gemeinsamen Vorläuferzelle, unterliegt einer strikten Kontrolle. Die Beeinträchtigung dieser Linienentscheidungsprogramme, z.B. durch Mutationen oder Änderungen der Expressionslevel von Transkriptionsfaktoren kann Leukämie auslösen. Die molekularen Mechanismen, welche die linienspezifische Entwicklung steuern, sind allerdings noch nicht im Detail bekannt. In dieser Arbeit zeige ich den maßgeblichen Einfluss des Transkriptionsfaktors Interferon Regulierender Faktor 8 (IRF8) auf die Entwicklung von dendritischen Zellen (DC) innerhalb der Phagozyten. Mittels einer IRF8-Reporter Maus stellte ich die sehr differenziellen Expressionsmuster von Irf8 in der hämatopoietischen Entwicklung dar. Dabei konnte ich eine neue, im Knochenmark lokalisierte, Vorläuferpopulation isolieren, die in vivo spezifisch Differenzierung in CD8α+ konventionelle dendritische Zellen (cDC) steuert. Dieser Vorläufer ist dabei absolut von der Expression von Irf8 abhängig und etabliert auf transkriptioneller Ebene die dendritische Zellentwicklung, während gleichzeitig die Entwicklung neutrophiler Zellen unterdrückt wird. Darüber hinaus zeigte ich, dass Irf8 Expression während der cDC Entwicklung von einem neu charakterisierten cis-regulatorischen Enhancer abhängt, der spezifisch in myeloiden Zellen agiert. Ich konnte zeigen, dass die hämatopoietischen Transkriptionfaktoren PU.1 und RUNX1 mittels dieses Enhancers die Irf8 Expression steuern. Können diese beiden Faktoren nicht mit dem Enhancer interagieren, führt das zu stark verminderter Irf8 Expression, damit zu Veränderungen in den Differnzierungsprogrammen der Zellen, was die Bedeutung dieses regulatorischen Mechanismus unterstreicht. Zusammengefasst beschreiben diese Daten die Etablierung der frühen cDC Entwicklung, in der IRF8 die zentrale Rolle spielt. KW - Hämatopoiese KW - dendritische Zelle KW - Immunologie KW - Transkiptionsfaktor KW - Genregulation KW - haematopoiesis KW - dendritic cell KW - immunology KW - transcription factor KW - gene regulation Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-55482 ER - TY - JOUR A1 - Liaimer, Anton A1 - Jenke-Kodama, Holger A1 - Ishida, Keishi A1 - Hinrichs, Katrin A1 - Stangeland, Janne A1 - Hertweck, Christian A1 - Dittmann-Thünemann, Elke T1 - A polyketide interferes with cellular differentiation in the symbiotic cyanobacterium Nostoc punctiforme JF - Environmental microbiology reports N2 - Nostoc punctiforme is a filamentous cyanobacterium capable of forming symbiotic associations with a wide range of plants. The strain exhibits extensive phenotypic characteristics and can differentiate three mutually exclusive cell types: nitrogen-fixing heterocysts, motile hormogonia and spore-like akinetes. Here, we provide evidence for a crucial role of an extracellular metabolite in balancing cellular differentiation. Insertional mutagenesis of a gene of the polyketide synthase gene cluster pks2 led to the accumulation of short filaments carrying mostly terminal heterocysts under diazotrophic conditions. The mutant has a strong tendency to form biofilms on solid surfaces as well as in liquid culture. The pks2-strain keeps forming hormogonia over the entire growth curve and shows an early onset of akinete formation. We could isolate two fractions of the wildtype supernatant that could restore the capability to form long filaments with intercalary heterocysts. Growth of the mutant cells in the neighbourhood of wild-type cells on plates led to a reciprocal influence and a partial reconstruction of wild-type and mutant phenotype respectively. We postulate that extracellular metabolites of Nostoc punctiforme act as life cycle governing factors (LCGFs) and that the ratio between distinct factors may guide the differentiation into different life stages. Y1 - 2011 U6 - https://doi.org/10.1111/j.1758-2229.2011.00258.x SN - 1758-2229 VL - 3 IS - 5 SP - 550 EP - 558 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Arnold, Anne A1 - Nikoloski, Zoran T1 - A quantitative comparison of Calvin-Benson cycle models JF - Trends in plant science N2 - The Calvin-Benson cycle (CBC) provides the precursors for biomass synthesis necessary for plant growth. The dynamic behavior and yield of the CBC depend on the environmental conditions and regulation of the cellular state. Accurate quantitative models hold the promise of identifying the key determinants of the tightly regulated CBC function and their effects on the responses in future climates. We provide an integrative analysis of the largest compendium of existing models for photosynthetic processes. Based on the proposed ranking, our framework facilitates the discovery of best-performing models with regard to metabolomics data and of candidates for metabolic engineering. Y1 - 2011 U6 - https://doi.org/10.1016/j.tplants.2011.09.004 SN - 1360-1385 VL - 16 IS - 12 SP - 676 EP - 683 PB - Elsevier CY - London ER - TY - THES A1 - Andorf, Sandra T1 - A systems biological approach towards the molecular basis of heterosis in Arabidopsis thaliana T1 - Ein systembiologischer Ansatz für das Verständnis der molekularen Grundlagen von Heterosis in Arabidopsis thaliana N2 - Heterosis is defined as the superiority in performance of heterozygous genotypes compared to their corresponding genetically different homozygous parents. This phenomenon is already known since the beginning of the last century and it has been widely used in plant breeding, but the underlying genetic and molecular mechanisms are not well understood. In this work, a systems biological approach based on molecular network structures is proposed to contribute to the understanding of heterosis. Hybrids are likely to contain additional regulatory possibilities compared to their homozygous parents and, therefore, they may be able to correctly respond to a higher number of environmental challenges, which leads to a higher adaptability and, thus, the heterosis phenomenon. In the network hypothesis for heterosis, presented in this work, more regulatory interactions are expected in the molecular networks of the hybrids compared to the homozygous parents. Partial correlations were used to assess this difference in the global interaction structure of regulatory networks between the hybrids and the homozygous genotypes. This network hypothesis for heterosis was tested on metabolite profiles as well as gene expression data of the two parental Arabidopsis thaliana accessions C24 and Col-0 and their reciprocal crosses. These plants are known to show a heterosis effect in their biomass phenotype. The hypothesis was confirmed for mid-parent and best-parent heterosis for either hybrid of our experimental metabolite as well as gene expression data. It was shown that this result is influenced by the used cutoffs during the analyses. Too strict filtering resulted in sets of metabolites and genes for which the network hypothesis for heterosis does not hold true for either hybrid regarding mid-parent as well as best-parent heterosis. In an over-representation analysis, the genes that show the largest heterosis effects according to our network hypothesis were compared to genes of heterotic quantitative trait loci (QTL) regions. Separately for either hybrid regarding mid-parent as well as best-parent heterosis, a significantly larger overlap between the resulting gene lists of the two different approaches towards biomass heterosis was detected than expected by chance. This suggests that each heterotic QTL region contains many genes influencing biomass heterosis in the early development of Arabidopsis thaliana. Furthermore, this integrative analysis led to a confinement and an increased confidence in the group of candidate genes for biomass heterosis in Arabidopsis thaliana identified by both approaches. N2 - Als Heterosis-Effekt wird die Überlegenheit in einem oder mehreren Leistungsmerkmalen (z.B. Blattgröße von Pflanzen) von heterozygoten (mischerbigen) Nachkommen über deren unterschiedlich homozygoten (reinerbigen) Eltern bezeichnet. Dieses Phänomen ist schon seit Beginn des letzten Jahrhunderts bekannt und wird weit verbreitet in der Pflanzenzucht genutzt. Trotzdem sind die genetischen und molekularen Grundlagen von Heterosis noch weitestgehend unbekannt. Es wird angenommen, dass heterozygote Individuen mehr regulatorische Möglichkeiten aufweisen als ihre homozygoten Eltern und sie somit auf eine größere Anzahl an wechselnden Umweltbedingungen richtig reagieren können. Diese erhöhte Anpassungsfähigkeit führt zum Heterosis-Effekt. In dieser Arbeit wird ein systembiologischer Ansatz, basierend auf molekularen Netzwerkstrukturen verfolgt, um zu einem besseren Verständnis von Heterosis beizutragen. Dazu wird eine Netzwerkhypothese für Heterosis vorgestellt, die vorhersagt, dass die heterozygoten Individuen, die Heterosis zeigen, mehr regulatorische Interaktionen in ihren molekularen Netzwerken aufweisen als die homozygoten Eltern. Partielle Korrelationen wurden verwendet, um diesen Unterschied in den globalen Interaktionsstrukturen zwischen den Heterozygoten und ihren homozygoten Eltern zu untersuchen. Die Netzwerkhypothese wurde anhand von Metabolit- und Genexpressionsdaten der beiden homozygoten Arabidopsis thaliana Pflanzenlinien C24 und Col-0 und deren wechselseitigen Kreuzungen getestet. Arabidopsis thaliana Pflanzen sind bekannt dafür, dass sie einen Heterosis-Effekt im Bezug auf ihre Biomasse zeigen. Die heterozygoten Pflanzen weisen bei gleichem Alter eine höhere Biomasse auf als die homozygoten Pflanzen. Die Netzwerkhypothese für Heterosis konnte sowohl im Bezug auf mid-parent Heterosis (Unterschied in der Leistung des Heterozygoten im Vergleich zum Mittelwert der Eltern) als auch auf best-parent Heterosis (Unterschied in der Leistung des Heterozygoten im Vergleich zum Besseren der Eltern) für beide Kreuzungen für die Metabolit- und Genexpressionsdaten bestätigt werden. In einer Überrepräsentations-Analyse wurden die Gene, für die die größte Veränderung in der Anzahl der regulatorischen Interaktionen, an denen sie vermutlich beteiligt sind, festgestellt wurde, mit den Genen aus einer quantitativ genetischen (QTL) Analyse von Biomasse-Heterosis in Arabidopsis thaliana verglichen. Die ermittelten Gene aus beiden Studien zeigen eine größere Überschneidung als durch Zufall erwartet. Das deutet darauf hin, dass jede identifizierte QTL-Region viele Gene, die den Biomasse-Heterosis-Effekt in Arabidopsis thaliana beeinflussen, enthält. Die Gene, die in den Ergebnislisten beider Analyseverfahren überlappen, können mit größerer Zuversicht als Kandidatengene für Biomasse-Heterosis in Arabidopsis thaliana betrachtet werden als die Ergebnisse von nur einer Studie. KW - Systembiologie KW - Heterosis KW - Molekulare Profildaten KW - Integrative Analyse KW - Systems biology KW - Heterosis KW - Molecular profile data KW - Integrative analysis Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-51173 ER - TY - JOUR A1 - Mutig, Kerim A1 - Kahl, Thomas A1 - Saritas, Turgay A1 - Godes, Michael A1 - Persson, Pontus A1 - Bates, James A1 - Raffi, Hajamohideen A1 - Rampoldi, Luca A1 - Uchida, Shinichi A1 - Hille, Carsten A1 - Dosche, Carsten A1 - Kumar, Satish A1 - Castaneda-Bueno, Maria A1 - Gamba, Gerardo A1 - Bachmann, Sebastian T1 - Activation of the Bumetanide-sensitive Na+, K+,2Cl(-) Cotransporter (NKCC2) Is Facilitated by Tamm-Horsfall Protein in a Chloride-sensitive Manner JF - The journal of biological chemistry N2 - Active transport of NaCl across thick ascending limb (TAL) epithelium is accomplished by Na+, K+,2Cl(-) cotransporter (NKCC2). The activity of NKCC2 is determined by vasopressin (AVP) or intracellular chloride concentration and includes its amino-terminal phosphorylation. Co-expressed Tamm-Horsfall protein (THP) has been proposed to interact with NKCC2. We hypothesized that THP modulates NKCC2 activity in TAL. THP-deficient mice (THP-/-) showed an increased abundance of intracellular NKCC2 located in subapical vesicles (+47% compared with wild type (WT) mice), whereas base-line phosphorylation of NKCC2 was significantly decreased (-49% compared with WT mice), suggesting reduced activity of the transporter in the absence of THP. Cultured TAL cells with low endogenous THP levels and low base-line phosphorylation of NKCC2 displayed sharp increases in NKCC2 phosphorylation (+38%) along with a significant change of intracellular chloride concentration upon transfection with THP. In NKCC2-expressing frog oocytes, co-injection with THP cRNA significantly enhanced the activation of NKCC2 under low chloride hypotonic stress (+112% versus +235%). Short term (30 min) stimulation of the vasopressin V2 receptor pathway by V2 receptor agonist (deamino-cis-D-Arg vasopressin) resulted in enhanced NKCC2 phosphorylation in WT mice and cultured TAL cells transfected with THP, whereas in the absence of THP, NKCC2 phosphorylation upon deamino-cis-D-Arg vasopressin was blunted in both systems. Attenuated effects of furosemide along with functional and structural adaptation of the distal convoluted tubule in THP-/- mice supported the notion that NaCl reabsorption was impaired in TAL lacking THP. In summary, these results are compatible with a permissive role for THP in the modulation of NKCC2-dependent TAL salt reabsorptive function. Y1 - 2011 U6 - https://doi.org/10.1074/jbc.M111.222968 SN - 0021-9258 VL - 286 IS - 34 SP - 30200 EP - 30210 PB - American Society for Biochemistry and Molecular Biology CY - Bethesda ER - TY - JOUR A1 - Tiedemann, Ralph A1 - Paulus, Kirsten B. A1 - Havenstein, Katja A1 - Thorstensen, Sverrir A1 - Petersen, Aevar A1 - Lyngs, Peter A1 - Milinkovitch, Michel C. T1 - Alien eggs in duck nests brood parasitism or a help from Grandma? JF - Molecular ecology N2 - Intraspecific brood parasitism (IBP) is a remarkable phenomenon by which parasitic females can increase their reproductive output by laying eggs in conspecific females' nests in addition to incubating eggs in their own nest. Kin selection could explain the tolerance, or even the selective advantage, of IBP, but different models of IBP based on game theory yield contradicting predictions. Our analyses of seven polymorphic autosomal microsatellites in two eider duck colonies indicate that relatedness between host and parasitizing females is significantly higher than the background relatedness within the colony. This result is unlikely to be a by-product of relatives nesting in close vicinity, as nest distance and genetic identity are not correlated. For eider females that had been ring-marked during the decades prior to our study, our analyses indicate that (i) the average age of parasitized females is higher than the age of nonparasitized females, (ii) the percentage of nests with alien eggs increases with the age of nesting females, (iii) the level of IBP increases with the host females' age, and (iv) the number of own eggs in the nest of parasitized females significantly decreases with age. IBP may allow those older females unable to produce as many eggs as they can incubate to gain indirect fitness without impairing their direct fitness: genetically related females specialize in their energy allocation, with young females producing more eggs than they can incubate and entrusting these to their older relatives. Intraspecific brood parasitism in ducks may constitute cooperation among generations of closely related females. KW - eider duck KW - indirect fitness KW - intraspecific brood parasitism KW - microsatellites KW - relatedness KW - Somateria mollissima Y1 - 2011 U6 - https://doi.org/10.1111/j.1365-294X.2011.05158.x SN - 0962-1083 VL - 20 IS - 15 SP - 3237 EP - 3250 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Khuroo, Anzar A. A1 - Weber, Ewald A1 - Malik, A. H. A1 - Reshi, Zafar A. A1 - Dar, G. H. T1 - Altitudinal distribution patterns of the native and alien woody flora in Kashmir Himalaya, India JF - Environmental research N2 - Background: Many studies have shown that alien species richness pattern follows that of native species richness patterns along environmental gradients, without taking the specific composition of the two groups into account. Objectives: To compare species richness patterns of native and alien woody plants along an altitudinal gradient in Kashmir Himalaya, India, and to analyse the specific composition, e.g. proportion of life forms. Methods: Analysis of secondary data from published floristic inventories. The gradient (500-4800 m asl) was split into 100 m bands and presence/absence data for each species were obtained, for each band. Results: Species richness of both native and alien species followed a hump-shaped distribution. Alien species richness dropped faster above 2000 m asl than the native did. The ratio of trees to shrubs decreased monotonically along the gradient in native species, but showed a peak at c. 2500 m asl in alien species. Alien species flowered in average earlier than native species. Conclusions: The change of species richness of native and alien species along altitude is similar, but the proportion of life forms is not. Most likely both climatic and socio-economic factors affect alien species richness and its specific composition in the Kashmir Himalaya. KW - Alien species KW - Elevation KW - Floristics KW - Plant invasions KW - Species richness Y1 - 2011 U6 - https://doi.org/10.1016/j.envres.2011.05.006 SN - 0013-9351 VL - 111 IS - 7 SP - 967 EP - 977 PB - Elsevier CY - San Diego ER - TY - JOUR A1 - Buchmann, Carsten M. A1 - Schurr, Frank Martin A1 - Nathan, Ran A1 - Jeltsch, Florian T1 - An allometric model of home range formation explains the structuring of animal communities exploiting heterogeneous resources JF - Oikos N2 - Understanding and predicting the composition and spatial structure of communities is a central challenge in ecology. An important structural property of animal communities is the distribution of individual home ranges. Home range formation is controlled by resource heterogeneity, the physiology and behaviour of individual animals, and their intra- and interspecific interactions. However, a quantitative mechanistic understanding of how home range formation influences community composition is still lacking. To explore the link between home range formation and community composition in heterogeneous landscapes we combine allometric relationships for physiological properties with an algorithm that selects optimal home ranges given locomotion costs, resource depletion and competition in a spatially-explicit individual-based modelling framework. From a spatial distribution of resources and an input distribution of animal body mass, our model predicts the size and location of individual home ranges as well as the individual size distribution (ISD) in an animal community. For a broad range of body mass input distributions, including empirical body mass distributions of North American and Australian mammals, our model predictions agree with independent data on the body mass scaling of home range size and individual abundance in terrestrial mammals. Model predictions are also robust against variation in habitat productivity and landscape heterogeneity. The combination of allometric relationships for locomotion costs and resource needs with resource competition in an optimal foraging framework enables us to scale from individual properties to the structure of animal communities in heterogeneous landscapes. The proposed spatially-explicit modelling concept not only allows for detailed investigation of landscape effects on animal communities, but also provides novel insights into the mechanisms by which resource competition in space shapes animal communities. Y1 - 2011 U6 - https://doi.org/10.1111/j.1600-0706.2010.18556.x SN - 0030-1299 VL - 120 IS - 1 SP - 106 EP - 118 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - De Frenne, Pieter A1 - Graae, Bente J. A1 - Kolb, Annette A1 - Shevtsova, Anna A1 - Baeten, Lander A1 - Brunet, Jörg A1 - Chabrerie, Olivier A1 - Cousins, Sara A. O. A1 - Decocq, Guillaume A1 - Dhondt, Rob A1 - Diekmann, Martin A1 - Gruwez, Robert A1 - Heinken, Thilo A1 - Hermy, Martin A1 - Oster, Mathias A1 - Saguez, Robert A1 - Stanton, Sharon A1 - Tack, Wesley A1 - Vanhellemont, Margot A1 - Verheyen, Kris T1 - An intraspecific application of the leaf-height-seed ecology strategy scheme to forest herbs along a latitudinal gradient JF - Ecography : pattern and diversity in ecology ; research papers forum N2 - We measured LHS traits in 41 Anemone nemorosa and 44 Milium effusum populations along a 1900-2300 km latitudinal gradient from N France to N Sweden. We then applied multilevel models to identify the effects of regional (temperature, latitude) and local (soil fertility and acidity, overstorey canopy cover) environmental factors on LHS traits. Both species displayed a significant 4% increase in plant height with every degree northward shift (almost a two-fold plant height difference between the southernmost and northernmost populations). Neither seed mass nor SLA showed a significant latitudinal cline. Temperature had a large effect on the three LHS traits of Anemone. Latitude, canopy cover and soil nutrients were related to the SLA and plant height of Milium. None of the investigated variables appeared to be related to the seed mass of Milium. The variation in LHS traits indicates that the ecological strategy determined by the position of each population in this three-factor triangle is not constant along the latitudinal gradient. The significant increase in plant height suggests greater competitive abilities for both species in the northernmost populations. We also found that the studied environmental factors affected the LHS traits of the two species on various scales: spring-flowering Anemone was affected more by temperature, whereas early-summer flowering Milium was affected more by local and other latitude-related factors. Finally, previously reported cross-species correlations between LHS traits and latitude were generally unsupported by our within-species approach. Y1 - 2011 U6 - https://doi.org/10.1111/j.1600-0587.2010.06399.x SN - 0906-7590 VL - 34 IS - 1 SP - 132 EP - 140 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Winck, Flavia Vischi A1 - Kwasniewski, Miroslaw A1 - Wienkoop, Stefanie A1 - Müller-Röber, Bernd T1 - An optimized method for the isolation of nuclei from chlamydomas Reinhardtii (Chlorophyceae) JF - Journal of phycology N2 - The cell nucleus harbors a large number of proteins involved in transcription, RNA processing, chromatin remodeling, nuclear signaling, and ribosome assembly. The nuclear genome of the model alga Chlamydomonas reinhardtii P. A. Dang. was recently sequenced, and many genes encoding nuclear proteins, including transcription factors and transcription regulators, have been identified through computational discovery tools. However, elucidating the specific biological roles of nuclear proteins will require support from biochemical and proteomics data. Cellular preparations with enriched nuclei are important to assist in such analyses. Here, we describe a simple protocol for the isolation of nuclei from Chlamydomonas, based on a commercially available kit. The modifications done in the original protocol mainly include alterations of the differential centrifugation parameters and detergent-based cell lysis. The nuclei-enriched fractions obtained with the optimized protocol show low contamination with mitochondrial and plastid proteins. The protocol can be concluded within only 3 h, and the proteins extracted can be used for gel-based and non-gel-based proteomic approaches. KW - 2D gel electrophoresis KW - algae KW - Chlamydomonas KW - nuclear proteins KW - nucleus KW - proteomics Y1 - 2011 U6 - https://doi.org/10.1111/j.1529-8817.2011.00967.x SN - 0022-3646 VL - 47 IS - 2 SP - 333 EP - 340 PB - Wiley-Blackwell CY - Malden ER - TY - THES A1 - Fettke, Jörg T1 - Analysen Stärke-bezogener Kohlenstoffflüsse Y1 - 2011 CY - Potsdam ER - TY - JOUR A1 - Samereier, Matthias A1 - Baumann, Otto A1 - Meyer, Irene A1 - Gräf, Ralph T1 - Analysis of dictyostelium TACC reveals differential interactions with CP224 and unusual dynamics of dictyostelium microtubules JF - Cellular and molecular life sciences N2 - We have localized TACC to the microtubule-nucleating centrosomal corona and to microtubule plus ends. Using RNAi we proved that Dictyostelium TACC promotes microtubule growth during interphase and mitosis. For the first time we show in vivo that both TACC and XMAP215 family proteins can be differentially localized to microtubule plus ends during interphase and mitosis and that TACC is mainly required for recruitment of an XMAP215-family protein to interphase microtubule plus ends but not for recruitment to centrosomes and kinetochores. Moreover, we have now a marker to study dynamics and behavior of microtubule plus ends in living Dictyostelium cells. In a combination of live cell imaging of microtubule plus ends and fluorescence recovery after photobleaching (FRAP) experiments of GFP-alpha-tubulin cells we show that Dictyostelium microtubules are dynamic only in the cell periphery, while they remain stable at the centrosome, which also appears to harbor a dynamic pool of tubulin dimers. KW - Dictyostelium KW - TACC KW - DdCP224 KW - XMAP215 KW - Microtubules KW - Centrosome Y1 - 2011 U6 - https://doi.org/10.1007/s00018-010-0453-0 SN - 1420-682X VL - 68 IS - 2 SP - 275 EP - 287 PB - Springer CY - Basel ER - TY - JOUR A1 - Kayler, Z. E. A1 - Kaiser, Michael A1 - Gessler, A. A1 - Ellerbrock, Ruth H. A1 - Sommer, Michael T1 - Application of delta C-13 and delta N-15 isotopic signatures of organic matter fractions sequentially separated from adjacent arable and forest soils to identify carbon stabilization mechanisms JF - Biogeosciences N2 - Identifying the chemical mechanisms behind soil carbon bound in organo-mineral complexes is necessary to determine the degree to which soil organic carbon is stabilized belowground. Analysis of delta C-13 and delta N-15 isotopic signatures of stabilized OM fractions along with soil mineral characteristics may yield important information about OM-mineral associations and their processing history. We anlayzed the delta C-13 and delta N-15 isotopic signatures from two organic matter (OM) fractions along with soil mineral proxies to identify the likely binding mechanisms involved. We analyzed OM fractions hypothesized to contain carbon stabilized through organo-mineral complexes: (1) OM separated chemically with sodium pyrophosphate (OM(PY)) and (2) OM occluded in micro-structures found in the chemical extraction residue (OM(ER)). Because the OM fractions were separated from five different soils with paired forest and arable land use histories, we could address the impact of land use change on carbon binding and processing mechanisms. We used partial least squares regression to analyze patterns in the isotopic signature of OM with established mineral and chemical proxies indicative for certain binding mechanisms. We found different mechanisms predominate in each land use type. For arable soils, the formation of OM(PY)-Ca-mineral associations was identified as an important OM binding mechanism. Therefore, we hypothesize an increased stabilization of microbial processed OM(PY) through Ca2+ interactions. In general, we found the forest soils to contain on average 10% more stabilized carbon relative to total carbon stocks, than the agricultural counter part. In forest soils, we found a positive relationship between isotopic signatures of OM(PY) and the ratio of soil organic carbon content to soil surface area (SOC/SSA). This indicates that the OM(PY) fractions of forest soils represent layers of slower exchange not directly attached to mineral surfaces. From the isotopic composition of the OM(ER) fraction, we conclude that the OM in this fraction from both land use types have undergone a different pathway to stabilization that does not involve microbial processing, which may include OM which is highly protected within soil micro-structures. Y1 - 2011 U6 - https://doi.org/10.5194/bg-8-2895-2011 SN - 1726-4170 VL - 8 IS - 10 SP - 2895 EP - 2906 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - Scheffler, Ingo T1 - Artenspektren und Wirtsbindung von Ektoparasiten der Fledermäuse aus Nordbulgarien : Bewertung des Zusammenhangs von Körperkondition und Ektoparasitenlast N2 - Waehrend der herbstlichen Schwaermpase wurden im Norden Bulgariens die Ektoparasiten von neun Fledermausarten untersucht. Die hoechsten Abundanzen erreichten Fledermausfliegen, von denen 6 verschiedene Arten determiniert wurden. In geringeren Dichten besiedelten auch Flughautmilben (6 Arten) sowie Macronyssidae und Ixodidae (jeweils eine Art) die Fledermaeuse. Die Bindung an den Wirt und die Verbreitung aller Ektoparasiten sind kurz zusammengefasst. Fuer die Berechnung der Parasitenlast wird ein neues Modell vorgeschlagen, dass unter Beruecksichtigung von Groessenrealtionen und Abundanzen vergleichbare Daten bei unterschiedlichen Befallsszenarien ermoeglicht. Parasitenkombinationen traten im Norden Bulgariens seltener auf, als erwartet. Mit den Werten der haeufigsten Fledermausarten wurde ueberprueft, ob es einen Zusammenhang zwischen Masse, Unterarmlaenge und Parasitierung gibt. In keinem Fall konnte eine sichere Korrelation zwischen diesen Faktoren ermittelt werden. Unter Verwendung eines adaptierten Body-Mass-Index (BMI) oder eines Body- Condition-Index (BCI) ergab sich ebenfalls kein Zusammenhang zwischen der Koerperkondition und der Parasitenlast. Im Verlaufe der Untersuchung kam es in einer Hoehle zu einer unerwarteten Zunahme der Abundanzen von Flughautmilben. Dieses Phaenomen koennte ein interessanter Ansatz weiterer Studien sein. Im Vergleich zu herbstlichen Untersuchungen in Deutschland waren die Fledermaeuse im Norden Bulgariens deutlich staerker parasitiert. Y1 - 2011 ER - TY - JOUR A1 - Maitrejean, Marie A1 - Wudick, Michael M. A1 - Völker, Camilla A1 - Prinsi, Bhakti A1 - Müller-Röber, Bernd A1 - Czempinski, Katrin A1 - Pedrazzini, Emanuela A1 - Vitale, Alessandro T1 - Assembly and sorting of the tonoplast potassium channel AtTPK1 and its turnover by internalization into the Vacuole JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - The assembly, sorting signals, and turnover of the tonoplast potassium channel AtTPK1 of Arabidopsis (Arabidopsis thaliana) were studied. We used transgenic Arabidopsis expressing a TPK1-green fluorescent protein (GFP) fusion or protoplasts transiently transformed with chimeric constructs based on domain exchange between TPK1 and TPK4, the only TPK family member not located at the tonoplast. The results show that TPK1-GFP is a dimer and that the newly synthesized polypeptides transiently interact with a thus-far unidentified 20-kD polypeptide. A subset of the TPK1-TPK4 chimeras were unable to assemble correctly and these remained located in the endoplasmic reticulum where they interacted with the binding protein chaperone. Therefore, TPK1 must assemble correctly to pass endoplasmic reticulum quality control. Substitution of the cytosolic C terminus of TPK4 with the corresponding domain of TPK1 was sufficient to allow tonoplast delivery, indicating that this domain contains tonoplast sorting information. Pulse-chase labeling indicated that TPK1-GFP has a half-life of at least 24 h. Turnover of the fusion protein involves internalization into the vacuole where the GFP domain is released. This indicates a possible mechanism for the turnover of tonoplast proteins. Y1 - 2011 U6 - https://doi.org/10.1104/pp.111.177816 SN - 0032-0889 VL - 156 IS - 4 SP - 1783 EP - 1796 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Feher, Kristen A1 - Whelan, James A1 - Müller, Samuel T1 - Assessing modularity using a random matrix theory approach JF - Statistical applications in genetics and molecular biology N2 - Random matrix theory (RMT) is well suited to describing the emergent properties of systems with complex interactions amongst their constituents through their eigenvalue spectrums. Some RMT results are applied to the problem of clustering high dimensional biological data with complex dependence structure amongst the variables. It will be shown that a gene relevance or correlation network can be constructed by choosing a correlation threshold in a principled way, such that it corresponds to a block diagonal structure in the correlation matrix, if such a structure exists. The structure is then found using community detection algorithms, but with parameter choice guided by RMT predictions. The resulting clustering is compared to a variety of hierarchical clustering outputs and is found to the most generalised result, in that it captures all the features found by the other considered methods. KW - random matrix theory KW - clustering KW - modularity Y1 - 2011 U6 - https://doi.org/10.2202/1544-6115.1667 SN - 2194-6302 SN - 1544-6115 VL - 10 IS - 1 PB - De Gruyter CY - Berlin ER - TY - CHAP A1 - Rietsch, Katrin A1 - Scheffler, Christiane T1 - Association between skeletal robustness and physical activity in schoolchildren - First results T2 - Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft für Anthropologie Y1 - 2011 SN - 0003-5548 VL - 68 IS - 4 SP - 516 EP - 516 PB - Schweizerbart CY - Stuttgart ER - TY - THES A1 - Siewert, Katharina T1 - Autoaggressive human t cell receptorrs and their antigen specificities Y1 - 2011 CY - Potsdam ER - TY - JOUR A1 - Paasche, Hendrik A1 - Eberle, Detlef T1 - Automated compilation of pseudo-lithology maps from geophysical data sets a comparison of Gustafson-Kessel and fuzzy c-means cluster algorithms JF - Exploration geophysics : the bulletin of the Australian Society of Exploration Geophysicists N2 - The fuzzy partitioning Gustafson-Kessel cluster algorithm is employed for rapid and objective integration of multi-parameter Earth-science related databases. We begin by evaluating the Gustafson-Kessel algorithm using the example of a synthetic study and compare the results to those obtained from the more widely employed fuzzy c-means algorithm. Since the Gustafson-Kessel algorithm goes beyond the potential of the fuzzy c-means algorithm by adapting the shape of the clusters to be detected and enabling a manual control of the cluster volume, we believe the results obtained from Gustafson-Kessel algorithm to be superior. Accordingly, a field database comprising airborne and ground-based geophysical data sets is analysed, which has previously been classified by means of the fuzzy c-means algorithm. This database is integrated using the Gustafson-Kessel algorithm thus minimising the amount of empirical data processing required before and after fuzzy c-means clustering. The resultant zonal geophysical map is more evenly clustered matching regional geology information available from the survey area. Even additional information about linear structures, e. g. as typically caused by the presence of dolerite dykes or faults, is visible in the zonal map obtained from Gustafson-Kessel cluster analysis. KW - cluster analysis KW - data integration KW - airborne KW - South Africa KW - Gustafson-Kessel KW - fuzzy c-means Y1 - 2011 U6 - https://doi.org/10.1071/EG11014 SN - 0812-3985 VL - 42 IS - 4 SP - 275 EP - 285 PB - CSIRO CY - Collingwood ER - TY - THES A1 - Lehmann, Martin T1 - Back to the roots : regulation of arabidopsis root metabolism during oxidative stress Y1 - 2011 CY - Potsdam ER - TY - THES A1 - Schudoma, Christian T1 - Bioinformatic approaches to sequence-structure relationships in RNA loops Y1 - 2011 CY - Potsdam ER - TY - GEN A1 - Eccard, Jana A1 - Fey, Karen A1 - Caspers, Barbara A. A1 - Ylönen, Hannu T1 - Breeding state and season affect interspecific interaction types BT - indirect resource competition and direct interference T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Indirect resource competition and interference are widely occurring mechanisms of interspecific interactions. We have studied the seasonal expression of these two interaction types within a two-species, boreal small mammal system. Seasons differ by resource availability, individual breeding state and intraspecific social system. Live-trapping methods were used to monitor space use and reproduction in 14 experimental populations of bank voles Myodes glareolus in large outdoor enclosures with and without a dominant competitor, the field vole Microtus agrestis. We further compared vole behaviour using staged dyadic encounters in neutral arenas in both seasons. Survival of the non-breeding overwintering bank voles was not affected by competition. In the spring, the numbers of male bank voles, but not of females, were reduced significantly in the competition populations. Bank vole home ranges expanded with vole density in the presence of competitors, indicating food limitation. A comparison of behaviour between seasons based on an analysis of similarity revealed an avoidance of costly aggression against opponents, independent of species. Interactions were more aggressive during the summer than during the winter, and heterospecific encounters were more aggressive than conspecific encounters. Based on these results, we suggest that interaction types and their respective mechanisms are not either–or categories and may change over the seasons. During the winter, energy constraints and thermoregulatory needs decrease direct aggression, but food constraints increase indirect resource competition. Direct interference appears in the summer, probably triggered by each individual’s reproductive and hormonal state and the defence of offspring against conspecific and heterospecific intruders. Both interaction forms overlap in the spring, possibly contributing to spring declines in the numbers of subordinate species. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 729 KW - rodents KW - aggression KW - seasonality KW - space use KW - winter biology Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-429398 SN - 1866-8372 IS - 729 SP - 623 EP - 633 ER - TY - JOUR A1 - Eccard, Jana A1 - Fey, Karen A1 - Caspers, Barbara A. A1 - Ylönen, Hannu T1 - Breeding state and season affect interspecific interaction types indirect resource competition and direct interference JF - Oecologia N2 - Indirect resource competition and interference are widely occurring mechanisms of interspecific interactions. We have studied the seasonal expression of these two interaction types within a two-species, boreal small mammal system. Seasons differ by resource availability, individual breeding state and intraspecific social system. Live-trapping methods were used to monitor space use and reproduction in 14 experimental populations of bank voles Myodes glareolus in large outdoor enclosures with and without a dominant competitor, the field vole Microtus agrestis. We further compared vole behaviour using staged dyadic encounters in neutral arenas in both seasons. Survival of the non-breeding overwintering bank voles was not affected by competition. In the spring, the numbers of male bank voles, but not of females, were reduced significantly in the competition populations. Bank vole home ranges expanded with vole density in the presence of competitors, indicating food limitation. A comparison of behaviour between seasons based on an analysis of similarity revealed an avoidance of costly aggression against opponents, independent of species. Interactions were more aggressive during the summer than during the winter, and heterospecific encounters were more aggressive than conspecific encounters. Based on these results, we suggest that interaction types and their respective mechanisms are not either-or categories and may change over the seasons. During the winter, energy constraints and thermoregulatory needs decrease direct aggression, but food constraints increase indirect resource competition. Direct interference appears in the summer, probably triggered by each individual's reproductive and hormonal state and the defence of offspring against conspecific and heterospecific intruders. Both interaction forms overlap in the spring, possibly contributing to spring declines in the numbers of subordinate species. KW - Rodents KW - Aggression KW - Seasonality KW - Space use KW - Winter biology Y1 - 2011 U6 - https://doi.org/10.1007/s00442-011-2008-y SN - 0029-8549 SN - 1432-1939 VL - 167 IS - 3 SP - 623 EP - 633 PB - Springer CY - New York ER - TY - JOUR A1 - Pauliuk, Franziska A1 - Müller, Jörg A1 - Heinken, Thilo T1 - Bryophyte dispersal by sheep on dry grassland JF - Nova Hedwigia : Zeitschrift für Kryptogamenkunde N2 - Many bryophytes may depend on epizoochorous dispersal by large mammals for maintaining their populations and colonizing new habitats. On dry grassland we investigated the transport of bryophyte diaspores by sheep, which are known to be effective epizoochorous dispersal vectors of seed plants. Twelve sheep of two breeds were examined by collecting gametophyte fragments from their fleece and hooves. Furthermore, microscopic diaspores from the soil adhering to the hooves were grown in a greenhouse. Species frequency and composition were compared to bryophyte vegetation on the pasture. Considerable amounts of unspecialized gametophyte fragments from 16 moss species, 40% of the species growing on the pasture, were transported by sheep, especially on the belly and the tail. Additionally, we provide first evidence of epizoochorous dispersal of thallus fragments from fruticose lichens. Sheep breeds differed in species spectrum and frequency, i.e. sheep with dense, curly fleece carried more fragments and larger species than those with smooth and fine hair. Among the dispersed bryophytes pleurocarps, certain taxa, sizes (small species) and life forms (mats) were overrepresented compared to the vegetation of the pasture, while large species, acrocarps, wefts and turfs were underrepresented, reflecting fragmentation and adhesion features of the species. In the hooves mostly acrocarpous colonist species were transported. We conclude that sheep are important dispersal vectors with the potential of long-range dispersal for bryophytes, especially for species without sexual reproduction, and that epizoochorous dispersal of microscopic diaspores might be underestimated in its importance so far. KW - Calcareous grassland KW - dispersal of cryptogams KW - epizoochory KW - shoot fragments KW - life history attributes KW - vegetative reproduction Y1 - 2011 U6 - https://doi.org/10.1127/0029-5035/2011/0092-0327 SN - 0029-5035 VL - 92 IS - 3-4 SP - 327 EP - 341 PB - Cramer CY - Stuttgart ER - TY - JOUR A1 - Fayzrakhmanova, Irina S. A1 - Straube, Arthur V. A1 - Shklyaev, Sergey T1 - Bubble dynamics atop an oscillating substrate: Interplay of compressibility and contact angle hysteresis JF - Physics of fluids N2 - We consider a sessile hemispherical bubble sitting on the transversally oscillating bottom of a deep liquid layer and focus on the interplay of the compressibility of the bubble and the contact angle hysteresis. In the presence of contact angle hysteresis, the compressible bubble exhibits two kinds of terminal oscillations: either with the stick-slip motion of the contact line or with the completely immobile contact line. For the stick-slip oscillations, we detect a double resonance, when the external frequency is close to eigenfrequencies of both the breathing mode and shape oscillations. For the regimes evolving to terminal oscillations with the fixed contact line, we find an unusual transient resembling modulated oscillations. Y1 - 2011 U6 - https://doi.org/10.1063/1.3650280 SN - 1070-6631 VL - 23 IS - 10 PB - American Institute of Physics CY - Melville ER - TY - JOUR A1 - Held, Katrin A1 - Pascaud, Francois A1 - Eckert, Christian A1 - Gajdanowicz, Pawel A1 - Hashimoto, Kenji A1 - Corratge-Faillie, Claire A1 - Offenborn, Jan Niklas A1 - Lacombe, Benoit A1 - Dreyer, Ingo A1 - Thibaud, Jean-Baptiste A1 - Kudla, Jörg T1 - Calcium-dependent modulation and plasma membrane targeting of the AKT2 potassium channel by the CBL4/CIPK6 calcium sensor/protein kinase complex JF - Cell research N2 - Potassium (K(+)) channel function is fundamental to many physiological processes. However, components and mechanisms regulating the activity of plant K(+) channels remain poorly understood. Here, we show that the calcium (Ca(2+)) sensor CBL4 together with the interacting protein kinase CIPK6 modulates the activity and plasma membrane (PM) targeting of the K(+) channel AKT2 from Arabidopsis thaliana by mediating translocation of AKT2 to the PM in plant cells and enhancing AKT2 activity in oocytes. Accordingly, akt2, cbl4 and cipk6 mutants share similar developmental and delayed flowering phenotypes. Moreover, the isolated regulatory C-terminal domain of CIPK6 is sufficient for mediating CBL4- and Ca(2+)-dependent channel translocation from the endoplasmic reticulum membrane to the PM by a novel targeting pathway that is dependent on dual lipid modifications of CBL4 by myristoylation and palmitoylation. Thus, we describe a critical mechanism of ion-channel regulation where a Ca(2+) sensor modulates K(+) channel activity by promoting a kinase interaction-dependent but phosphorylation-independent translocation of the channel to the PM. KW - calcium sensor KW - protein kinase KW - potassium channel KW - signal transduction Y1 - 2011 U6 - https://doi.org/10.1038/cr.2011.50 SN - 1001-0602 VL - 21 IS - 7 SP - 1116 EP - 1130 PB - Nature Publ. Group CY - Shanghai ER - TY - JOUR A1 - Kartal, Oender A1 - Mahlow, Sebastian A1 - Skupin, Alexander A1 - Ebenhoeh, Oliver T1 - Carbohydrate-active enzymes exemplify entropic principles in metabolism JF - Molecular systems biology N2 - Glycans comprise ubiquitous and essential biopolymers, which usually occur as highly diverse mixtures. The myriad different structures are generated by a limited number of carbohydrate-active enzymes (CAZymes), which are unusual in that they catalyze multiple reactions by being relatively unspecific with respect to substrate size. Existing experimental and theoretical descriptions of CAZyme-mediated reaction systems neither comprehensively explain observed action patterns nor suggest biological functions of polydisperse pools in metabolism. Here, we overcome these limitations with a novel theoretical description of this important class of biological systems in which the mixing entropy of polydisperse pools emerges as an important system variable. In vitro assays of three CAZymes essential for central carbon metabolism confirm the power of our approach to predict equilibrium distributions and non-equilibrium dynamics. A computational study of the turnover of the soluble heteroglycan pool exemplifies how entropy-driven reactions establish a metabolic buffer in vivo that attenuates fluctuations in carbohydrate availability. We argue that this interplay between energy- and entropy-driven processes represents an important regulatory design principle of metabolic systems. KW - energy metabolism KW - entropic enzymes KW - glycobiology KW - metabolic regulation Y1 - 2011 U6 - https://doi.org/10.1038/msb.2011.76 SN - 1744-4292 VL - 7 IS - 10 PB - Nature Publ. Group CY - New York ER - TY - JOUR A1 - Kahmen, Ansgar A1 - Sachse, Dirk A1 - Arndt, Stefan K. A1 - Tu, Kevin P. A1 - Farrington, Heraldo A1 - Vitousek, Peter M. A1 - Dawson, Todd E. T1 - Cellulose delta O-18 is an index of leaf-to-air vapor pressure difference (VPD) in tropical plants JF - Proceedings of the National Academy of Sciences of the United States of America N2 - Cellulose in plants contains oxygen that derives in most cases from precipitation. Because the stable oxygen isotope composition, delta O-18, of precipitation is associated with environmental conditions, cellulose delta O-18 should be as well. However, plant physiological models using delta O-18 suggest that cellulose delta O-18 is influenced by a complex mix of both climatic and physiological drivers. This influence complicates the interpretation of cellulose delta O-18 values in a paleo-context. Here, we combined empirical data analyses with mechanistic model simulations to i) quantify the impacts that the primary climatic drivers humidity (e(a)) and air temperature (T-air) have on cellulose delta O-18 values in different tropical ecosystems and ii) determine which environmental signal is dominating cellulose delta O-18 values. Our results revealed that e(a) and T-air equally influence cellulose delta O-18 values and that distinguishing which of these factors dominates the delta O-18 values of cellulose cannot be accomplished in the absence of additional environmental information. However, the individual impacts of e(a) and T-air on the delta O-18 values of cellulose can be integrated into a single index of plant-experienced atmospheric vapor demand: the leaf-to-air vapor pressure difference (VPD). We found a robust relationship between VPD and cellulose delta O-18 values in both empirical and modeled data in all ecosystems that we investigated. Our analysis revealed therefore that delta O-18 values in plant cellulose can be used as a proxy for VPD in tropical ecosystems. As VPD is an essential variable that determines the biogeochemical dynamics of ecosystems, our study has applications in ecological-, climate-, or forensic-sciences. KW - stable isotopes KW - plant-water relations KW - paleoecology KW - climate change KW - Hawaii Y1 - 2011 U6 - https://doi.org/10.1073/pnas.1018906108 SN - 0027-8424 VL - 108 IS - 5 SP - 1981 EP - 1986 PB - National Acad. of Sciences CY - Washington ER - TY - JOUR A1 - Jersabek, Christian D. A1 - Weithoff, Guntram A1 - Weisse, Thomas T1 - Cephalodella acidophila n. sp (Monogononta: Notommatidae), a new rotifer species from highly acidic mining lakes JF - Zootaxa : an international journal of zootaxonomy ; a rapid international journal for animal taxonomists N2 - We describe a new species of Cephalodella, C. acidophila n. sp., from the plankton of two extremely acidic mining lakes (pH <3) in Austria and Germany. The species is morphologically closely related to Cephalodella delicata Wulfert. It shares with the latter an almost identical trophi morphology and anatomical organization, but differs clearly by form and length of its toes, larger body size, and ecology. Laboratory experiments revealed that the species is acidophilic, i.e. it thrives at low pH (<4) and does not survive at circumneutral conditions. The species occurs in man-made habitats at low to moderate abundance (usually 5-22 individuals l(-1)) and in stock cultures thrives on the green alga Chlamydomonas acidophila. The easily cultured species has previously been used in various experimental studies, but has only now been recognized as an undescribed species. KW - Rotifera KW - taxonomy KW - acidophily KW - new species Y1 - 2011 SN - 1175-5326 IS - 2939 SP - 50 EP - 58 PB - Magnolia Press CY - Auckland ER - TY - JOUR A1 - Mahro, Martin A1 - Coelho, Catarina A1 - Trincao, Jose A1 - Rodrigues, David A1 - Terao, Mineko A1 - Garattini, Enrico A1 - Saggu, Miguel A1 - Lendzian, Friedhelm A1 - Hildebrandt, Peter A1 - Romao, Maria Joao A1 - Leimkühler, Silke T1 - Characterization and crystallization of mouse aldehyde oxidase 3 - from mouse liver to escherichia coli heterologous protein expression JF - Drug metabolism and disposition : the biological fate of chemicals N2 - Aldehyde oxidase (AOX) is characterized by a broad substrate specificity, oxidizing aromatic azaheterocycles, such as N(1)-methylnicotinamide and N-methylphthalazinium, or aldehydes, such as benzaldehyde, retinal, and vanillin. In the past decade, AOX has been recognized increasingly to play an important role in the metabolism of drugs through its complex cofactor content, tissue distribution, and substrate recognition. In humans, only one AOX gene (AOX1) is present, but in mouse and other mammals different AOX homologs were identified. The multiple AOX isoforms are expressed tissue-specifically in different organisms, and it is believed that they recognize distinct substrates and carry out different physiological tasks. AOX is a dimer with a molecular mass of approximately 300 kDa, and each subunit of the homodimeric enzyme contains four different cofactors: the molybdenum cofactor, two distinct [2Fe-2S] clusters, and one FAD. We purified the AOX homolog from mouse liver (mAOX3) and established a system for the heterologous expression of mAOX3 in Escherichia coli. The purified enzymes were compared. Both proteins show the same characteristics and catalytic properties, with the difference that the recombinant protein was expressed and purified in a 30% active form, whereas the native protein is 100% active. Spectroscopic characterization showed that FeSII is not assembled completely in mAOX3. In addition, both proteins were crystallized. The best crystals were from native mAOX3 and diffracted beyond 2.9 angstrom. The crystals belong to space group P1, and two dimers are present in the unit cell. Y1 - 2011 U6 - https://doi.org/10.1124/dmd.111.040873 SN - 0090-9556 VL - 39 IS - 10 SP - 1939 EP - 1945 PB - American Society for Pharmacology and Experimental Therapeutics CY - Bethesda ER - TY - THES A1 - Ruprecht, Colin T1 - Characterization of genetic modules involved in cellulose synthesis in Arabidopsis thaliana Y1 - 2011 CY - Potsdam ER - TY - THES A1 - Andrade Linares, Diana Rocío T1 - Characterization of tomato root-endophytic fungi and analysis of their effects on plant development, on fruit yield and quality and on interaction with the pathogen Verticillium dahliae T1 - Charakterisierung wurzelendophytischer Pilze von Tomate und Analyse ihrer Effekte auf Pflanzenentwicklung, auf Ertrag und Fruchtqualität und auf die Wechselwirkung mit dem Pathogen Verticillium dahliae N2 - Non-mycorrhizal fungal endophytes are able to colonize internally roots without causing visible disease symptoms establishing neutral or mutualistic associations with plants. These fungi known as non-clavicipitaceous endophytes have a broad host range of monocot and eudicot plants and are highly diverse. Some of them promote plant growth and confer increased abiotic-stress tolerance and disease resistance. According to such possible effects on host plants, it was aimed to isolate and to characterize native fungal root endophytes from tomato (Lycopersicon esculentum Mill.) and to analyze their effects on plant development, plant resistance and fruit yield and quality together with the model endophyte Piriformospora indica. Fifty one new fungal strains were isolated from desinfected tomato roots of four different crop sites in Colombia. These isolates were roughly characterized and fourteen potential endophytes were further analyzed concerning their taxonomy, their root colonization capacity and their impact on plant growth. Sequencing of the ITS region from the ribosomal RNA gene cluster and in-depth morphological characterisation revealed that they correspond to different phylogenetic groups among the phylum Ascomycota. Nine different morphotypes were described including six dark septate endophytes (DSE) that did not correspond to the Phialocephala group. Detailed confocal microscopy analysis showed various colonization patterns of the endophytes inside the roots ranging from epidermal penetration to hyphal growth through the cortex. Tomato pot experiments under glass house conditions showed that they differentially affect plant growth depending on colonization time and inoculum concentration. Three new isolates (two unknown fungal endophyte DSE48, DSE49 and one identified as Leptodontidium orchidicola) with neutral or positiv effects were selected and tested in several experiments for their influence on vegetative growth, fruit yield and quality and their ability to diminish the impact of the pathogen Verticillium dahliae on tomato plants. Although plant growth promotion by all three fungi was observed in young plants, vegetative growth parameters were not affected after 22 weeks of cultivation except a reproducible increase of root diameter by the endophyte DSE49. Additionally, L. orchidicola increased biomass and glucose content of tomato fruits, but only at an early date of harvest and at a certain level of root colonization. Concerning bioprotective effects, the endophytes DSE49 and L. orchidicola decreased significantly disease symptoms caused by the pathogen V. dahliae, but only at a low dosis of the pathogen. In order to analyze, if the model root endophytic fungus Piriformospora indica could be suitable for application in production systems, its impact on tomato was evaluated. Similarly to the new fungal isolates, significant differences for vegetative growth parameters were only observable in young plants and, but protection against V. dahliae could be seen in one experiment also at high dosage of the pathogen. As the DSE L. orchidicola, P. indica increased the number and biomass of marketable tomatoes only at the beginning of fruit setting, but this did not lead to a significant higher total yield. If the effects on growth are due to a better nutrition of the plant with mineral element was analyzed in barley in comparison to the arbuscular mycorrhizal fungus Glomus mosseae. While the mycorrhizal fungus increased nitrogen and phosphate uptake of the plant, no such effect was observed for P. indica. In summary this work shows that many different fungal endophytes can be also isolated from roots of crops and, that these isolates can have positive effects on early plant development. This does, however, not lead to an increase in total yield or in improvement of fruit quality of tomatoes under greenhouse conditions. N2 - Endophyten, die nicht zu den Mykorrhizapilzen gehören, können das Innere von Wurzeln ohne sichtbare Krankheitssymptome besiedeln und bilden so mit der Pflanze neutrale oder mutualistische Wechselwirkungen. Diese Pilze, auch als nicht-clavicipetale Endophyten bekannt, haben ein breites Wirtsspektrum von mono- und dikotyledonen Pflanzen und weisen eine hohe Diversität auf. Einige von ihnen fördern Pflanzenwachstum und erhöhen Resistenz und Toleranz gegenüber biotischem und abiotischem Stress. Ausgehenden von diesen möglichen Effekten auf ihre Wirtspflanzen war das Ziel der vorliegenden Arbeit die Isolierung und Charakterisierung neuer pilzlicher Wurzelendophyten der Tomate (Lycopersicon esculentum Mill.) und die Analyse ihres Einflusses auf Pflanzenentwicklung und Pflanzenresistenz, sowie auf Ertrag und Fruchtqualität unter Einbeziehung des Modellendophyten Piriformospora indica. Aus vier verschiedenen Anbaugebieten in Kolumbien konnten 51 neue Pilzstämme von oberflächensterilisierten Tomatenwurzeln isoliert werden. Diese Isolate wurden vorcharakterisiert und 14 potentielle Endophyten bezüglich ihrer Taxonomie, ihrer Besiedlungsmuster und ihres Einfluss auf das Pflanzenwachstum näher untersucht. Sequenzierung der ITS Region des ribosomalen RNA Genclusters und genaue morphologische Charakterisierung zeigten, dass sie zu verschiedenen phylogenetischen Gruppen innerhalb der Ascomycota gehören. Neun Morphotypen ließen sich beschreiben, wobei sechs zu den ‚Dark Septate Endophytes’ (DSEs) gehören, aber nicht mit der bekannten Phialocephala Gruppe verwandt waren. Ausführliche konfokale mikroskopische Untersuchungen ergaben sehr verschiedene Besiedelungsmuster der Wurzelendophyten vom Endringen in die Epidermis bis zum Hyphenwachstum durch den Kortex. Topfexperimente unter Gewächshausbedingungen zeigten dass die Isolate in Abhängigkeit von der Inokulumkonzentration und der Zeit der Besiedlung das Wachstum der Tomaten sehr unterschiedlich beeinflussten. Drei neue Isolate (die beiden unbekannte pilzlichen Endophyten DSE48 und DSE49 und eines identifiziert als Leptodontidium orchidicola) mit neutralen oder positiven Effekten wurden für weitere Versuche ausgewählt. In mehreren Experimenten sollte ihr Einfluss auf das vegetative Wachstum, auf Ertrag und auf Fruchtqualität untersucht werden, sowie ihre Fähigkeit die Auswirkungen des Pathogens Verticillium dahliae auf Tomatenpflanzen zu vermindern. Obwohl wachstumsfördernde Effekte durch alle drei Pilze in jungen Pflanzen beobachtet wurden, waren vegetative Wachstumsparameter nach 22 Wochen der Besiedlung nicht mehr beeinflusst bis auf ein signifikante Erhöhung des Wurzeldurchmessers durch den Endophyten DSE49. L. orchidicola dagegen erhöhte die Biomasse und den Glukosegehalt der Früchte, aber nur zu frühen Ernteterminen und bei einer bestimmten Intensität der Wurzelbesiedelung. Hinsichtlich eines schützenden Effekts, konnten die Endophyten DSE49 und L. orchidicola die Krankheitssymptome, die durch V. dahliae verursacht wurden, vermindern, aber nur bei einem geringen Pathogendruck. Um zu überprüfen, ob der Modellendophyt P. indica in Produktionssytemen eingesetzt werden kann, wurde seine Auswirkungen auf Tomaten untersucht. Ähnlich wie die neuen pilzlichen Isolate, zeigte aber auch er seinen fördernden Einfluss nur auf das frühe vegetative Wachstum. Schützende Effekte gegen V. dahliae konnten ebenfalls nur bei niedrigem Pathogendruck konstant beobachtet werden. Wie L. orchidicola erhöhte P. indica die Biomasse an marktfähigen Tomaten am Anfang des Fruchtansatzes, was nicht zu einem insgesamt höheren Ertrag führte. Ob die beobachteten Effekte auf ein verbesserte Nährstoffversorgung der Pflanze zurückzuführen seien, wurde in Gerste im Vergleich mit dem arbuskulären Mykorrhizapilz Glomus mosseae untersucht. Während der Mykorrhizapilz sowohl Phosphat wie Stickstoffaufnehme der Pflanze erhöhte, konnte dies für P. indica nicht festgestellt werden. Zusammenfassend zeigt diese Arbeit, dass auch aus Wurzeln von Kulturpflanzen viele verschiedene pilzliche Endophyten isoliert werden können, und dass einige von diesen durchaus einen positiven Effekt auf die frühe Pflanzenentwicklung aufweisen. Zumindest für Tomate unter Gewächshausbedingungen führen diese Effekte aber nicht zu einer Erhöhung des Gesamtertrags oder einer nachhaltigen Verbesserung der Fruchtqualität. KW - Pilz-Endophyten KW - Ascomycota KW - Wurzelbesiedlung KW - Tomaten (Solanum lycopersicum) KW - Pflanze-Pilz-Interaktionen KW - Fungal endophyte KW - Ascomycota KW - root colonization KW - tomato (Solanum lycopersicum) KW - plant-fungal interactions Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-51375 ER - TY - JOUR A1 - Geyer, Juliane A1 - Kiefer, Iris A1 - Kreft, Stefan A1 - Chavez, Veronica A1 - Salafsky, Nick A1 - Jeltsch, Florian A1 - Ibisch, Pierre L. T1 - Classification of climate-change-induced stresses on biological diversity JF - Conservation biology : the journal of the Society for Conservation Biology N2 - Conservation actions need to account for and be adapted to address changes that will occur under global climate change. The identification of stresses on biological diversity (as defined in the Convention on Biological Diversity) is key in the process of adaptive conservation management. We considered any impact of climate change on biological diversity a stress because such an effect represents a change (negative or positive) in key ecological attributes of an ecosystem or parts of it. We applied a systemic approach and a hierarchical framework in a comprehensive classification of stresses to biological diversity that are caused directly by global climate change. Through analyses of 20 conservation sites in 7 countries and a review of the literature, we identified climate-change-induced stresses. We grouped the identified stresses according to 3 levels of biological diversity: stresses that affect individuals and populations, stresses that affect biological communities, and stresses that affect ecosystem structure and function. For each stress category, we differentiated 3 hierarchical levels of stress: stress class (thematic grouping with the coarsest resolution, 8); general stresses (thematic groups of specific stresses, 21); and specific stresses (most detailed definition of stresses, 90). We also compiled an overview of effects of climate change on ecosystem services using the categories of the Millennium Ecosystem Assessment and 2 additional categories. Our classification may be used to identify key climate-change-related stresses to biological diversity and may assist in the development of appropriate conservation strategies. The classification is in list format, but it accounts for relations among climate-change-induced stresses. KW - adaptation of conservation strategies KW - adaptive management KW - climate change KW - conservation planning KW - conservation targets KW - hierarchical framework KW - threats to biological diversity Y1 - 2011 U6 - https://doi.org/10.1111/j.1523-1739.2011.01676.x SN - 0888-8892 VL - 25 IS - 4 SP - 708 EP - 715 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Rohrmann, Johannes A1 - Tohge, Takayuki A1 - Alba, Rob A1 - Osorio, Sonia A1 - Caldana, Camila A1 - McQuinn, Ryan A1 - Arvidsson, Samuel Janne A1 - van der Merwe, Margaretha J. A1 - Riano-Pachon, Diego Mauricio A1 - Müller-Röber, Bernd A1 - Fei, Zhangjun A1 - Nesi, Adriano Nunes A1 - Giovannoni, James J. A1 - Fernie, Alisdair R. T1 - Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development JF - The plant journal N2 - Maturation of fleshy fruits such as tomato (Solanum lycopersicum) is subject to tight genetic control. Here we describe the development of a quantitative real-time PCR platform that allows accurate quantification of the expression level of approximately 1000 tomato transcription factors. In addition to utilizing this novel approach, we performed cDNA microarray analysis and metabolite profiling of primary and secondary metabolites using GC-MS and LC-MS, respectively. We applied these platforms to pericarp material harvested throughout fruit development, studying both wild-type Solanum lycopersicum cv. Ailsa Craig and the hp1 mutant. This mutant is functionally deficient in the tomato homologue of the negative regulator of the light signal transduction gene DDB1 from Arabidopsis, and is furthermore characterized by dramatically increased pigment and phenolic contents. We choose this particular mutant as it had previously been shown to have dramatic alterations in the content of several important fruit metabolites but relatively little impact on other ripening phenotypes. The combined dataset was mined in order to identify metabolites that were under the control of these transcription factors, and, where possible, the respective transcriptional regulation underlying this control. The results are discussed in terms of both programmed fruit ripening and development and the transcriptional and metabolic shifts that occur in parallel during these processes. KW - transcription factor KW - Solanum lycopersicum KW - quantitative RT-PCR KW - microarray KW - metabolomics KW - fleshy fruit ripening Y1 - 2011 U6 - https://doi.org/10.1111/j.1365-313X.2011.04750.x SN - 0960-7412 VL - 68 IS - 6 SP - 999 EP - 1013 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Vater, Marianne A1 - Koessl, Manfred T1 - Comparative aspects of cochlear functional organization in mammals JF - Hearing research N2 - This review addresses the functional organization of the mammalian cochlea under a comparative and evolutionary perspective. A comparison of the monotreme cochlea with that of marsupial and placental mammals highlights important evolutionary steps towards a hearing organ dedicated to process higher frequencies and a larger frequency range than found in non-mammalian vertebrates. Among placental mammals, there are numerous cochlear specializations which relate to hearing range in adaptation to specific habitats that are superimposed on a common basic design. These are illustrated by examples of specialist ears which evolved excellent high frequency hearing and echolocation (bats and dolphins) and by the example of subterranean rodents with ears devoted to processing low frequencies. Furthermore, structural functional correlations important for tonotopic cochlear organization and predictions of hearing capabilities are discussed. Y1 - 2011 U6 - https://doi.org/10.1016/j.heares.2010.05.018 SN - 0378-5955 VL - 273 IS - 1-2 SP - 89 EP - 99 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Juerchott, Kathrin A1 - Guo, Ke-Tai A1 - Catchpole, Gareth A1 - Feher, Kristen A1 - Willmitzer, Lothar A1 - Schichor, Christian A1 - Selbig, Joachim T1 - Comparison of metabolite profiles in U87 glioma cells and mesenchymal stem cells JF - Biosystems : journal of biological and information processing sciences N2 - Gas chromatography-mass spectrometry (GC-MS) profiles were generated from U87 glioma cells and human mesenchymal stem cells (hMSC). 37 metabolites representing glycolysis intermediates, TCA cycle metabolites, amino acids and lipids were selected for a detailed analysis. The concentrations of these. metabolites were compared and Pearson correlation coefficients were used to calculate the relationship between pairs of metabolites. Metabolite profiles and correlation patterns differ significantly between the two cell lines. These profiles can be considered as a signature of the underlying biochemical system and provide snap-shots of the metabolism in mesenchymal stem cells and tumor cells. KW - Metabolite profiles KW - Correlation networks KW - U87 glioma cells KW - Human mesenchymal stem cells Y1 - 2011 U6 - https://doi.org/10.1016/j.biosystems.2011.05.005 SN - 0303-2647 VL - 105 IS - 2 SP - 130 EP - 139 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Hagemann, Cornelia A1 - Vater, Marianne A1 - Koessl, Manfred T1 - Comparison of properties of cortical echo delay-tuning in the short-tailed fruit bat and the mustached bat JF - Journal of comparative physiology : A, Neuroethology, sensory, neural, and behavioral physiology N2 - Target-distance computation by cortical neurons sensitive to echo delay is an essential characteristic of the auditory system of insectivorous bats. To assess if functional requirements such as detection of small insects versus larger stationary surfaces of plants are reflected in cortical properties, we compare delay-tuned neurons in a frugivorous (C. perspicillata, CP) and an insectivorous (P. parnellii, PP) bat species that belong to related families within the superfamily of Noctilionoidea. The bandwidth and shape of delay-tuning curves and the range of characteristic delays are similar in both species and hence are not related to different echolocation strategies. Most units respond at 2-6 ms echo delay with most sensitive thresholds of 20-30 dB SPL. In CP, units tuned to delays > 12 ms are slightly more abundant and are more sensitive than in PP. All delay-tuned neurons in CP reliably respond to single pure-tone stimuli, whereas such responses are only observed in 49% of delay-tuned units in PP. The cortical representation of echo delay (chronotopy) covers a larger area in CP but is less precise than described in PP. Since chronotopy is absent in certain other insectivorous bat species, it is open if these differences in topography are related to echolocation behaviour. KW - Echolocation KW - Auditory cortex KW - Chronotopy KW - Carollia perspicillata KW - Pteronotus parnellii Y1 - 2011 U6 - https://doi.org/10.1007/s00359-010-0530-8 SN - 0340-7594 VL - 197 IS - 5 SP - 605 EP - 613 PB - Springer CY - New York ER - TY - JOUR A1 - Nikoloski, Zoran A1 - Grimbs, Sergio A1 - Klie, Sebastian A1 - Selbig, Joachim T1 - Complexity of automated gene annotation JF - Biosystems : journal of biological and information processing sciences N2 - Integration of high-throughput data with functional annotation by graph-theoretic methods has been postulated as promising way to unravel the function of unannotated genes. Here, we first review the existing graph-theoretic approaches for automated gene function annotation and classify them into two categories with respect to their relation to two instances of transductive learning on networks - with dynamic costs and with constant costs - depending on whether or not ontological relationship between functional terms is employed. The determined categories allow to characterize the computational complexity of the existing approaches and establish the relation to classical graph-theoretic problems, such as bisection and multiway cut. In addition, our results point out that the ontological form of the structured functional knowledge does not lower the complexity of the transductive learning with dynamic costs - one of the key problems in modern systems biology. The NP-hardness of automated gene annotation renders the development of heuristic or approximation algorithms a priority for additional research. KW - Complexity KW - Gene function prediction KW - External structural measures KW - Transductive learning Y1 - 2011 U6 - https://doi.org/10.1016/j.biosystems.2010.12.003 SN - 0303-2647 VL - 104 IS - 1 SP - 1 EP - 8 PB - Elsevier CY - Oxford ER - TY - THES A1 - Weiß, Julia T1 - Computer assisted proteomics in a systems biology context Y1 - 2011 CY - Potsdam ER - TY - JOUR A1 - Ensslin, Andreas A1 - Sandner, Tobias M. A1 - Matthies, Diethart T1 - Consequences of ex situ cultivation of plants genetic diversity, fitness and adaptation of the monocarpic Cynoglossum officinale L. in botanic gardens JF - : an international journal N2 - Ex situ collections in botanic gardens have great potential in contributing to the conservation of rare plants. However, little is known about the effects of cultivation on the genetic diversity and fitness of garden populations, about genetic changes due to unconscious selection and potential adaptation to the artificial conditions. We compared the genetic variability and fitness of the rare, short-lived perennial Cynoglossum officinale from 12 botanic gardens and five natural populations in Germany. Genetic variability was assessed with eight nuclear microsatellites. Plants were grown in a common garden and performance was measured over 2 years. Mean genetic diversity was very similar in botanic garden and natural populations. However, four of the garden populations exhibited no genetic variability at all. Moreover, the genetic diversity of garden populations decreased with increasing duration of cultivation, indicating genetic drift. Plant performance from natural and garden populations in terms of growth, flowering and seed production was similar and in garden populations only seed mass was strongly related to genetic diversity. Several lines of evidence indicated genetic changes in garden populations in response to cultivation. Seed dormancy was strongly reduced in garden populations, and in response to nutrient addition garden plants increased the size of their main inflorescence, while wild plants increased the number of inflorescences. These changes could be maladaptive in nature and reduce the suitability of garden populations as a source for reintroductions. We suggest that botanic gardens should pay more attention to the problem of potential genetic changes in their plant collections. KW - Boraginaceae KW - Genetic drift KW - Microsatellites KW - Seed dormancy KW - Unconscious selection Y1 - 2011 U6 - https://doi.org/10.1016/j.biocon.2010.09.001 SN - 0006-3207 VL - 144 IS - 1 SP - 272 EP - 278 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Wand, Inga A1 - Holzlöhner, Pamela A1 - Neupert, Steffi A1 - Micheel, Burkhard A1 - Heilmann, Katja T1 - Cooperation of dendritic cells with naive lymphocyte populations to induce the generation of antigen-specific antibodies in vitro JF - Journal of biotechnology N2 - The production of monoclonal antibodies by hybridoma technology is dependent on lymphocytes taken from vertebrates which have to be immunized against the corresponding antigen. We present here our first experiments which should allow the replacement of this in vivo immunization step by an in vitro immunization procedure. This work provides new possibilities for the specific activation of immune cells in order to use them for the generation of antibodies which are not of murine origin. Bone marrow-derived dendritic cells were loaded with antigen and co-cultured with naive T and B lymphocytes of non-immunized mice. The interaction and activation of the different cell types were investigated by measuring the expression of specific cell surface markers, the release of activation-dependent interleukins and the secretion of antigen-specific antibodies. We could demonstrate that dendritic cells process and present antigen fragments and activate T cells, that T cells proliferate and release activation-induced interleukins, and that B cells maturate under the influence of activated T cells and secrete antigen-specific antibodies. KW - In vitro immunization KW - Activation of dendritic cells KW - Interaction of T and B cells with antigen-presenting cells KW - Induction of antibody responses Y1 - 2011 U6 - https://doi.org/10.1016/j.jbiotec.2011.09.002 SN - 0168-1656 VL - 156 IS - 3 SP - 173 EP - 181 PB - Elsevier CY - Amsterdam ER -