@misc{MulderBoitBonkowskietal.2011, author = {Mulder, Christian and Boit, Alice and Bonkowski, Michael and De Ruiter, Peter C. and Mancinelli, Giorgio and Van der Heijden, Marcel G. A. and Van Wijnen, Harm J. and Vonk, J. Arie and Rutgers, Michiel}, title = {A belowground perspective on dutch agroecosystems how soil organisms interact to support ecosystem services}, series = {Advances in ecological research}, volume = {44}, journal = {Advances in ecological research}, number = {2}, editor = {Woodward, G}, publisher = {Elsevier}, address = {San Diego}, isbn = {978-0-12-374794-5}, issn = {0065-2504}, doi = {10.1016/B978-0-12-374794-5.00005-5}, pages = {277 -- 357}, year = {2011}, abstract = {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.}, language = {en} } @article{SamuelHornDoeringetal.2011, author = {Samuel, Prinson P. and Horn, Sebastian and D{\"o}ring, Alexander and Havelius, Kajsa G. V. and Reschke, Stefan and Leimk{\"u}hler, Silke and Haumann, Michael and Schulzke, Carola}, title = {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}, series = {European journal of inorganic chemistry : a journal of ChemPubSoc Europe}, journal = {European journal of inorganic chemistry : a journal of ChemPubSoc Europe}, number = {28}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1434-1948}, doi = {10.1002/ejic.201100331}, pages = {4387 -- 4399}, year = {2011}, abstract = {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.}, language = {en} } @article{SchwarteTiedemann2011, author = {Schwarte, Sandra and Tiedemann, Ralph}, title = {A Gene Duplication/Loss Event in the Ribulose-1,5-Bisphosphate-Carboxylase/Oxygenase (Rubisco) Small Subunit Gene Family among Accessions of Arabidopsis thaliana}, series = {Molecular biology and evolution}, volume = {28}, journal = {Molecular biology and evolution}, number = {6}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0737-4038}, doi = {10.1093/molbev/msr008}, pages = {1861 -- 1876}, year = {2011}, abstract = {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.}, language = {en} } @article{WulfRujner2011, author = {Wulf, Monika and Rujner, Hendrik}, title = {A GIS-based method for the reconstruction of the late eighteenth century forest vegetation in the Prignitz region (NE Germany)}, series = {Landscape ecology}, volume = {26}, journal = {Landscape ecology}, number = {2}, publisher = {Springer}, address = {Dordrecht}, issn = {0921-2973}, doi = {10.1007/s10980-010-9555-1}, pages = {153 -- 168}, year = {2011}, abstract = {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.}, language = {en} } @article{ArvidssonPerezRodriguezMuellerRoeber2011, author = {Arvidsson, Samuel Janne and Perez-Rodriguez, Paulino and M{\"u}ller-R{\"o}ber, Bernd}, title = {A growth phenotyping pipeline for Arabidopsis thaliana integrating image analysis and rosette area modeling for robust quantification of genotype effects}, series = {New phytologist : international journal of plant science}, volume = {191}, journal = {New phytologist : international journal of plant science}, number = {3}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0028-646X}, doi = {10.1111/j.1469-8137.2011.03756.x}, pages = {895 -- 907}, year = {2011}, abstract = {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.}, language = {en} } @inproceedings{TikhonenkoMagidsonGraefetal.2011, author = {Tikhonenko, I. and Magidson, V. and Gr{\"a}f, Ralph and Khodjakov, A. and Koonce, M.}, title = {A kinesin-mediated linkage between centrosomes and the nuclear envelope}, series = {Molecular biology of the cell : the official publication of the American Society for Cell Biology}, volume = {22}, booktitle = {Molecular biology of the cell : the official publication of the American Society for Cell Biology}, number = {1}, publisher = {American Society for Cell Biology}, address = {Bethesda}, issn = {1059-1524}, pages = {1}, year = {2011}, language = {en} } @article{DeFrenneKolbGraaeetal.2011, author = {De Frenne, P. and Kolb, Annette and Graae, Benete Jessen and Decocq, Guillaume and Baltora, S. and De Schrijver, A. and Brunet, J. and Chabrerie, Olivier and Cousins, Sara A. O. and Dhondt, Rob and Diekmann, Martin and Gruwez, R. and Heinken, Thilo and Hermy, Martin and Liira, J. and Saguez, R. and Shevtsova, Anna and Baskin, Carol C. and Verheyen, Kris}, title = {A latitudinal gradient in seed nutrients of the forest herb Anemone nemorosa}, series = {Plant biology}, volume = {13}, journal = {Plant biology}, number = {3}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {1435-8603}, doi = {10.1111/j.1438-8677.2010.00404.x}, pages = {493 -- 501}, year = {2011}, abstract = {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.}, language = {en} } @article{EbenhoehHouwaartLoksteinetal.2011, author = {Ebenhoeh, Oliver and Houwaart, Torsten and Lokstein, Heiko and Schlede, Stephanie and Tirok, Katrin}, title = {A minimal mathematical model of nonphotochemical quenching of chlorophyll fluorescence}, series = {Biosystems : journal of biological and information processing sciences}, volume = {103}, journal = {Biosystems : journal of biological and information processing sciences}, number = {2}, publisher = {Elsevier}, address = {Oxford}, issn = {0303-2647}, doi = {10.1016/j.biosystems.2010.10.011}, pages = {196 -- 204}, year = {2011}, abstract = {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.}, language = {en} } @article{AksuFrascaWollenbergeretal.2011, author = {Aksu, Yilmaz and Frasca, Stefano and Wollenberger, Ursula and Driess, Matthias and Thomas, Arne}, title = {A molecular precursor approach to tunable porous tin-rich indium tin oxide with durable high electrical conductivity for bioelectronic devices}, series = {Chemistry of materials : a publication of the American Chemical Society}, volume = {23}, journal = {Chemistry of materials : a publication of the American Chemical Society}, number = {7}, publisher = {American Chemical Society}, address = {Washington}, issn = {0897-4756}, doi = {10.1021/cm103087p}, pages = {1798 -- 1804}, year = {2011}, abstract = {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.}, language = {en} } @phdthesis{Schoenheit2011, author = {Sch{\"o}nheit, J{\"o}rg}, title = {A phagocyte-specific Irf8 gene enhancer establishes early conventional dendritic cell commitment}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-55482}, school = {Universit{\"a}t Potsdam}, year = {2011}, abstract = {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.}, language = {en} }