@misc{BreitensteinNielsenHoelzeletal.2011, author = {Breitenstein, Michael and Nielsen, Peter E. and H{\"o}lzel, Ralph and Bier, Frank Fabian}, title = {DNA-nanostructure-assembly by sequential spotting}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1027}, issn = {1866-8372}, doi = {10.25932/publishup-43110}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431108}, pages = {12}, year = {2011}, abstract = {Background: The ability to create nanostructures with biomolecules is one of the key elements in nanobiotechnology. One of the problems is the expensive and mostly custom made equipment which is needed for their development. We intended to reduce material costs and aimed at miniaturization of the necessary tools that are essential for nanofabrication. Thus we combined the capabilities of molecular ink lithography with DNA-self-assembling capabilities to arrange DNA in an independent array which allows addressing molecules in nanoscale dimensions. Results: For the construction of DNA based nanostructures a method is presented that allows an arrangement of DNA strands in such a way that they can form a grid that only depends on the spotted pattern of the anchor molecules. An atomic force microscope (AFM) has been used for molecular ink lithography to generate small spots. The sequential spotting process allows the immobilization of several different functional biomolecules with a single AFM-tip. This grid which delivers specific addresses for the prepared DNA-strand serves as a two-dimensional anchor to arrange the sequence according to the pattern. Once the DNA-nanoarray has been formed, it can be functionalized by PNA (peptide nucleic acid) to incorporate advanced structures. Conclusions: The production of DNA-nanoarrays is a promising task for nanobiotechnology. The described method allows convenient and low cost preparation of nanoarrays. PNA can be used for complex functionalization purposes as well as a structural element.}, language = {en} } @misc{BierbachSchulteHerrmannetal.2011, author = {Bierbach, David and Schulte, Matthias and Herrmann, Nina and Tobler, Michael and Stadler, Stefan and Jung, Christian T. and Kunkel, Benjamin and Riesch, R{\"u}diger and Klaus, Sebastian and Ziege, Madlen and Indy, Jeane Rimber and Arias-Rodriguez, Lenin and Plath, Martin}, title = {Predator-induced changes of female mating preferences}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {984}, issn = {1866-8372}, doi = {10.25932/publishup-43109}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431099}, pages = {12}, year = {2011}, abstract = {Background In many species males face a higher predation risk than females because males display elaborate traits that evolved under sexual selection, which may attract not only females but also predators. Females are, therefore, predicted to avoid such conspicuous males under predation risk. The present study was designed to investigate predator-induced changes of female mating preferences in Atlantic mollies (Poecilia mexicana). Males of this species show a pronounced polymorphism in body size and coloration, and females prefer large, colorful males in the absence of predators. Results In dichotomous choice tests predator-na{\"i}ve (lab-reared) females altered their initial preference for larger males in the presence of the cichlid Cichlasoma salvini, a natural predator of P. mexicana, and preferred small males instead. This effect was considerably weaker when females were confronted visually with the non-piscivorous cichlid Vieja bifasciata or the introduced non-piscivorous Nile tilapia (Oreochromis niloticus). In contrast, predator experienced (wild-caught) females did not respond to the same extent to the presence of a predator, most likely due to a learned ability to evaluate their predators' motivation to prey. Conclusions Our study highlights that (a) predatory fish can have a profound influence on the expression of mating preferences of their prey (thus potentially affecting the strength of sexual selection), and females may alter their mate choice behavior strategically to reduce their own exposure to predators. (b) Prey species can evolve visual predator recognition mechanisms and alter their mate choice only when a natural predator is present. (c) Finally, experiential effects can play an important role, and prey species may learn to evaluate the motivational state of their predators.}, language = {en} } @misc{EccardFeyCaspersetal.2011, author = {Eccard, Jana and Fey, Karen and Caspers, Barbara A. and Yl{\"o}nen, Hannu}, title = {Breeding state and season affect interspecific interaction types}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {729}, issn = {1866-8372}, doi = {10.25932/publishup-42939}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-429398}, pages = {623 -- 633}, year = {2011}, abstract = {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.}, language = {en} } @article{FeherWhelanMueller2011, author = {Feher, Kristen and Whelan, James and M{\"u}ller, Samuel}, title = {Assessing modularity using a random matrix theory approach}, series = {Statistical applications in genetics and molecular biology}, volume = {10}, journal = {Statistical applications in genetics and molecular biology}, number = {1}, publisher = {De Gruyter}, address = {Berlin}, issn = {2194-6302}, doi = {10.2202/1544-6115.1667}, pages = {36}, year = {2011}, abstract = {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.}, language = {en} } @article{SangoroIacobNaumovetal.2011, author = {Sangoro, J. R. and Iacob, C. and Naumov, S. and Valiullin, R. and Rexhausen, Hans and Hunger, J. and Buchner, R. and Strehmel, Veronika and Kaerger, J. and Kremer, F.}, title = {Diffusion in ionic liquids the interplay between molecular structure and dynamics}, series = {Soft matter}, volume = {7}, journal = {Soft matter}, number = {5}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1744-683X}, doi = {10.1039/c0sm01404d}, pages = {1678 -- 1681}, year = {2011}, abstract = {Diffusion in a series of ionic liquids is investigated by a combination of Broadband Dielectric Spectroscopy (BDS) and Pulsed Field Gradient Nuclear Magnetic Resonance (PFG NMR). It is demonstrated that the mean jump lengths increase with the molecular volumes determined from quantum-chemical calculations. This provides a direct means-via Einstein-Smoluchowski relation-to determine the diffusion coefficient by BDS over more than 8 decades unambiguously and in quantitative agreement with PFG NMR measurements. New possibilities in the study of charge transport and dynamic glass transition in ionic liquids are thus opened.}, language = {en} } @article{LilieBaerKettneretal.2011, author = {Lilie, Hauke and Baer, Dorit and Kettner, Karina and Weininger, Ulrich and Balbach, Jochen and Naumann, Manfred and Mueller, Eva-Christina and Otto, Albrecht and Gast, Klaus and Golbik, Ralph and Kriegel, Thomas}, title = {Yeast hexokinase isoenzyme ScHxk2 stability of a two-domain protein with discontinuous domains}, series = {Protein engineering design \& selection}, volume = {24}, journal = {Protein engineering design \& selection}, number = {1-2}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1741-0126}, doi = {10.1093/protein/gzq098}, pages = {79 -- 87}, year = {2011}, abstract = {The hexokinase isoenzyme 2 of Saccharomyces cerevisiae (ScHxk2) represents an archetype of a two-domain protein with the active site located in a cleft between the two domains. Binding of the substrate glucose results in a rigid body movement of the two domains leading to a cleft closure of the active site. Both domains of this enzyme are composed of discontinuous peptide sequences. This structural feature is reflected in the stability and folding of the ScHxk2 protein. Structural transitions induced by urea treatment resulted in the population of a thermodynamically stable folding intermediate, which, however, does not correspond to a molecule with one domain folded and the other unfolded. As demonstrated by different spectroscopic techniques, both domains are structurally affected by the partial denaturation. The intermediate possesses only 40\% of the native secondary structural content and a substantial increase in the Stokes radius as judged by circular dichroism and dynamic light scattering analyses. One-dimensional H-1 NMR data prove that all tryptophan residues are in a non-native environment in the intermediate, indicating substantial changes in the tertiary structure. Still, the intermediate possesses quite a high stability for a transition intermediate of about Delta G = -22 kJ mol(-1).}, language = {en} } @article{KlausKleinebeckerHoelzeletal.2011, author = {Klaus, Valentin H. and Kleinebecker, Till and Hoelzel, Norbert and Bluethgen, Nico and Boch, Steffen and M{\"u}ller, J{\"o}rg and Socher, Stephanie A. and Prati, Daniel and Fischer, Markus}, title = {Nutrient concentrations and fibre contents of plant community biomass reflect species richness patterns along a broad range of land-use intensities among agricultural grasslands}, series = {Perspectives in plant ecology, evolution and systematics}, volume = {13}, journal = {Perspectives in plant ecology, evolution and systematics}, number = {4}, publisher = {Elsevier}, address = {Jena}, issn = {1433-8319}, doi = {10.1016/j.ppees.2011.07.001}, pages = {287 -- 295}, year = {2011}, abstract = {Understanding changes in biodiversity in agricultural landscapes in relation to land-use type and intensity is a major issue in current ecological research. In this context nutrient enrichment has been identified as a key mechanism inducing species loss in Central European grassland ecosystems. At the same time, insights into the linkage between agricultural land use and plant nutrient status are largely missing. So far, studies on the relationship between chemical composition of plant community biomass and biodiversity have mainly been restricted to wetlands and all these studies neglected the effects of land use. Therefore, we analyzed aboveground biomass of 145 grassland plots covering a gradient of land-use intensities in three regions across Germany. In particular, we explored relationships between vascular plant species richness and nutrient concentrations as well as fibre contents (neutral and acid detergent fibre and lignin) in the aboveground community biomass. We found the concentrations of several nutrients in the biomass to be closely linked to plant species richness and land use. Whereas phosphorus concentrations increased with land-use intensity and decreased with plant species richness, nitrogen and potassium concentrations showed less clear patterns. Fibre fractions were negatively related to nutrient concentrations in biomass, but hardly to land-use measures and species richness. Only high lignin contents were positively associated with species richness of grasslands. The N:P ratio was strongly positively related to species richness and even more so to the number of endangered plant species, indicating a higher persistence of endangered species under P (co-)limited conditions. Therefore, we stress the importance of low P supply for species-rich grasslands and suggest the N:P ratio in community biomass to be a useful proxy of the conservation value of agriculturally used grasslands.}, language = {en} } @article{AlbertGrasseinSchurretal.2011, author = {Albert, C{\´e}cile H. and Grassein, Fabrice and Schurr, Frank Martin and Vieilledent, Ghislain and Violle, Cyrille}, title = {When and how should intraspecific variability be considered in trait-based plant ecology?}, series = {Perspectives in plant ecology, evolution and systematics}, volume = {13}, journal = {Perspectives in plant ecology, evolution and systematics}, number = {3}, publisher = {Elsevier}, address = {Jena}, issn = {1433-8319}, doi = {10.1016/j.ppees.2011.04.003}, pages = {217 -- 225}, year = {2011}, abstract = {Trait-based studies have become extremely common in plant ecology. Trait-based approaches often rely on the tacit assumption that intraspecific trait variability (ITV) is negligible compared to interspecific variability, so that species can be characterized by mean trait values. Yet, numerous recent studies have challenged this assumption by showing that ITV significantly affects various ecological processes. Accounting for ITV may thus strengthen trait-based approaches, but measuring trait values on a large number of individuals per species and site is not feasible. Therefore, it is important and timely to synthesize existing knowledge on ITV in order to (1) decide critically when ITV should be considered, and (2) establish methods for incorporating this variability. Here we propose a practical set of rules to identify circumstances under which ITV should be accounted for. We formulate a spatial trait variance partitioning hypothesis to highlight the spatial scales at which ITV cannot be ignored in ecological studies. We then refine a set of four consecutive questions on the research question, the spatial scale, the sampling design, and the type of studied traits, to determine case-by-case if a given study should quantify ITV and test its effects. We review methods for quantifying ITV and develop a step-by-step guideline to design and interpret simulation studies that test for the importance of ITV. Even in the absence of quantitative knowledge on ITV, its effects can be assessed by varying trait values within species within realistic bounds around the known mean values. We finish with a discussion of future requirements to further incorporate ITV within trait-based approaches. This paper thus delineates a general framework to account for ITV and suggests a direction towards a more quantitative trait-based ecology.}, language = {en} } @article{KleinpeterLaemmermannKuehn2011, author = {Kleinpeter, Erich and Laemmermann, Anica and K{\"u}hn, Heiner}, title = {The anisotropic effect of functional groups in H-1 NMR spectra is the molecular response property of spatial nucleus independent chemical shifts (NICS)-Conformational equilibria of exo/endo tetrahydrodicyclopentadiene derivatives}, series = {Organic \& biomolecular chemistry : an international journal of synthetic, physical and biomolecular organic chemistry}, volume = {9}, journal = {Organic \& biomolecular chemistry : an international journal of synthetic, physical and biomolecular organic chemistry}, number = {4}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1477-0520}, doi = {10.1039/c0ob00356e}, pages = {1098 -- 1111}, year = {2011}, abstract = {The inversion of the flexible five-membered ring in tetrahydrodicyclopentadiene (TH-DCPD) derivatives remains fast on the NMR timescale even at 103 K. Since the intramolecular exchange process could not be sufficiently slowed for spectroscopic evaluation, the conformational equilibrium is thus inaccessible by dynamic NMR. Fortunately, the spatial magnetic properties of the aryl and carbonyl groups attached to the DCPD skeleton can be employed in order to evaluate the conformational state of the system. In this context, the anisotropic effects of the functional groups in the H-1 NMR spectra prove to be the molecular response property of spatial nucleus independent chemical shifts (NICS).}, language = {en} } @article{BuchmannSchurrNathanetal.2011, author = {Buchmann, Carsten M. and Schurr, Frank Martin and Nathan, Ran and Jeltsch, Florian}, title = {An allometric model of home range formation explains the structuring of animal communities exploiting heterogeneous resources}, series = {Oikos}, volume = {120}, journal = {Oikos}, number = {1}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0030-1299}, doi = {10.1111/j.1600-0706.2010.18556.x}, pages = {106 -- 118}, year = {2011}, abstract = {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.}, language = {en} } @article{RochaVasseurHaynetal.2011, author = {Rocha, Marcia R. and Vasseur, David A. and Hayn, Michael and Holschneider, Matthias and Gaedke, Ursula}, title = {Variability patterns differ between standing stock and process rates}, series = {Oikos}, volume = {120}, journal = {Oikos}, number = {1}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0030-1299}, doi = {10.1111/j.1600-0706.2010.18786.x}, pages = {17 -- 25}, year = {2011}, abstract = {Standing stocks are typically easier to measure than process rates such as production. Hence, stocks are often used as indicators of ecosystem functions although the latter are generally more strongly related to rates than to stocks. The regulation of stocks and rates and thus their variability over time may differ, as stocks constitute the net result of production and losses. Based on long-term high frequency measurements in a large, deep lake we explore the variability patterns in primary and bacterial production and relate them to those of the corresponding standing stocks, i.e. chlorophyll concentration, phytoplankton and bacterial biomass. We employ different methods (coefficient of variation, spline fitting and spectral analysis) which complement each other for assessing the variability present in the plankton data, at different temporal scales. In phytoplankton, we found that the overall variability of primary production is dominated by fluctuations at low frequencies, such as the annual, whereas in stocks and chlorophyll in particular, higher frequencies contribute substantially to the overall variance. This suggests that using standing stocks instead of rate measures leads to an under- or overestimation of food shortage for consumers during distinct periods of the year. The range of annual variation in bacterial production is 8 times greater than biomass, showing that the variability of bacterial activity (e.g. oxygen consumption, remineralisation) would be underestimated if biomass is used. The P/B ratios were variable and although clear trends are present in both bacteria and phytoplankton, no systematic relationship between stock and rate measures were found for the two groups. Hence, standing stock and process rate measures exhibit different variability patterns and care is needed when interpreting the mechanisms and implications of the variability encountered.}, language = {en} } @misc{NikoloskivanDongen2011, author = {Nikoloski, Zoran and van Dongen, Joost T.}, title = {Modeling alternatives for interpreting the change in oxygen-consumption rates during hypoxic conditions}, series = {New phytologist : international journal of plant science}, volume = {190}, journal = {New phytologist : international journal of plant science}, number = {2}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0028-646X}, doi = {10.1111/j.1469-8137.2011.03674.x}, pages = {273 -- 276}, year = {2011}, 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} } @misc{JohnsonLenhard2011, author = {Johnson, Kim L. and Lenhard, Michael}, title = {Genetic control of plant organ growth}, series = {New phytologist : international journal of plant science}, volume = {191}, journal = {New phytologist : international journal of plant science}, number = {2}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0028-646X}, doi = {10.1111/j.1469-8137.2011.03737.x}, pages = {319 -- 333}, year = {2011}, abstract = {The growth of plant organs is under genetic control. Work in model species has identified a considerable number of genes that regulate different aspects of organ growth. This has led to an increasingly detailed knowledge about how the basic cellular processes underlying organ growth are controlled, and which factors determine when proliferation gives way to expansion, with this transition emerging as a critical decision point during primordium growth. Progress has been made in elucidating the genetic basis of allometric growth and the role of tissue polarity in shaping organs. We are also beginning to understand how the mechanisms that determine organ identity influence local growth behaviour to generate organs with characteristic sizes and shapes. Lastly, growth needs to be coordinated at several levels, for example between different cell layers and different regions within one organ, and the genetic basis for such coordination is being elucidated. However, despite these impressive advances, a number of basic questions are still not fully answered, for example, whether and how a growing primordium keeps track of its size. Answering these questions will likely depend on including additional approaches that are gaining in power and popularity, such as combined live imaging and modelling.}, language = {en} } @article{LaiDentonGilesMuellerRoeberetal.2011, author = {Lai, Alvina G. and Denton-Giles, Matthew and M{\"u}ller-R{\"o}ber, Bernd and Schippers, Jos H. M. and Dijkwel, Paul P.}, title = {Positional information resolves structural variations and uncovers an evolutionarily divergent genetic locus in accessions of arabidopsis thaliana}, series = {Genome biology and evolution}, volume = {3}, journal = {Genome biology and evolution}, number = {1-2}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1759-6653}, doi = {10.1093/gbe/evr038}, pages = {627 -- 640}, year = {2011}, abstract = {Genome sequencing of closely related individuals has yielded valuable insights that link genome evolution to phenotypic variations. However, advancement in sequencing technology has also led to an escalation in the number of poor quality-drafted genomes assembled based on reference genomes that can have highly divergent or haplotypic regions. The self-fertilizing nature of Arabidopsis thaliana poses an advantage to sequencing projects because its genome is mostly homozygous. To determine the accuracy of an Arabidopsis drafted genome in less conserved regions, we performed a resequencing experiment on a similar to 371-kb genomic interval in the Landsberg erecta (Ler-0) accession. We identified novel structural variations (SVs) between Ler-0 and the reference accession Col-0 using a long-range polymerase chain reaction approach to generate an Illumina data set that has positional information, that is, a data set with reads that map to a known location. Positional information is important for accurate genome assembly and the resolution of SVs particularly in highly duplicated or repetitive regions. Sixty-one regions with misassembly signatures were identified from the Ler-0 draft, suggesting the presence of novel SVs that are not represented in the draft sequence. Sixty of those were resolved by iterative mapping using our data set. Fifteen large indels (> 100 bp) identified from this study were found to be located either within protein-coding regions or upstream regulatory regions, suggesting the formation of novel alleles or altered regulation of existing genes in Ler-0. We propose future genome-sequencing experiments to follow a clone-based approach that incorporates positional information to ultimately reveal haplotype-specific differences between accessions.}, language = {en} } @article{RyngajlloChildsLohseetal.2011, author = {Ryngajllo, Malgorzata and Childs, Liam H. and Lohse, Marc and Giorgi, Federico M. and Lude, Anja and Selbig, Joachim and Usadel, Bj{\"o}rn}, title = {SLocX predicting subcellular localization of Arabidopsis proteins leveraging gene expression data}, series = {Frontiers in plant science}, volume = {2}, journal = {Frontiers in plant science}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2011.00043}, pages = {19}, year = {2011}, abstract = {Despite the growing volume of experimentally validated knowledge about the subcellular localization of plant proteins, a well performing in silico prediction tool is still a necessity. Existing tools, which employ information derived from protein sequence alone, offer limited accuracy and/or rely on full sequence availability. We explored whether gene expression profiling data can be harnessed to enhance prediction performance. To achieve this, we trained several support vector machines to predict the subcellular localization of Arabidopsis thaliana proteins using sequence derived information, expression behavior, or a combination of these data and compared their predictive performance through a cross-validation test. We show that gene expression carries information about the subcellular localization not available in sequence information, yielding dramatic benefits for plastid localization prediction, and some notable improvements for other compartments such as the mito-chondrion, the Golgi, and the plasma membrane. Based on these results, we constructed a novel subcellular localization prediction engine, SLocX, combining gene expression profiling data with protein sequence-based information. We then validated the results of this engine using an independent test set of annotated proteins and a transient expression of GFP fusion proteins. Here, we present the prediction framework and a website of predicted localizations for Arabidopsis. The relatively good accuracy of our prediction engine, even in cases where only partial protein sequence is available (e.g., in sequences lacking the N-terminal region), offers a promising opportunity for similar application to non-sequenced or poorly annotated plant species. Although the prediction scope of our method is currently limited by the availability of expression information on the ATH1 array, we believe that the advances in measuring gene expression technology will make our method applicable for all Arabidopsis proteins.}, language = {en} } @article{RuprechtMutwilSaxeetal.2011, author = {Ruprecht, Colin and Mutwil, Marek and Saxe, Friederike and Eder, Michaela and Nikoloski, Zoran and Persson, Staffan}, title = {Large-scale co-expression approach to dissect secondary cell wall formation across plant species}, series = {Frontiers in plant science}, volume = {2}, journal = {Frontiers in plant science}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2011.00023}, pages = {13}, year = {2011}, abstract = {Plant cell walls are complex composites largely consisting of carbohydrate-based polymers, and are generally divided into primary and secondary walls based on content and characteristics. Cellulose microfibrils constitute a major component of both primary and secondary cell walls and are synthesized at the plasma membrane by cellulose synthase (CESA) complexes. Several studies in Arabidopsis have demonstrated the power of co-expression analyses to identify new genes associated with secondary wall cellulose biosynthesis. However, across-species comparative co-expression analyses remain largely unexplored. Here, we compared co-expressed gene vicinity networks of primary and secondary wall CESAsin Arabidopsis, barley, rice, poplar, soybean, Medicago, and wheat, and identified gene families that are consistently co-regulated with cellulose biosynthesis. In addition to the expected polysaccharide acting enzymes, we also found many gene families associated with cytoskeleton, signaling, transcriptional regulation, oxidation, and protein degradation. Based on these analyses, we selected and biochemically analyzed T-DNA insertion lines corresponding to approximately twenty genes from gene families that re-occur in the co-expressed gene vicinity networks of secondary wall CESAs across the seven species. We developed a statistical pipeline using principal component analysis and optimal clustering based on silhouette width to analyze sugar profiles. One of the mutants, corresponding to a pinoresinol reductase gene, displayed disturbed xylem morphology and held lower levels of lignin molecules. We propose that this type of large-scale co-expression approach, coupled with statistical analysis of the cell wall contents, will be useful to facilitate rapid knowledge transfer across plant species.}, language = {en} } @article{AstMuellerFlehretal.2011, author = {Ast, Sandra and M{\"u}ller, Holger and Flehr, Roman and Klamroth, Tillmann and Walz, Bernd and Holdt, Hans-J{\"u}rgen}, title = {High Na+ and K+-induced fluorescence enhancement of a pi-conjugated phenylaza-18-crown-6-triazol-substituted coumarin fluoroionophore}, series = {Chemical communications}, volume = {47}, journal = {Chemical communications}, number = {16}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1359-7345}, doi = {10.1039/c0cc04370b}, pages = {4685 -- 4687}, year = {2011}, abstract = {The new pi-conjugated 1,2,3-triazol-1,4-diyl fluoroionophore 1 generated via Cu(I) catalyzed [3 + 2] cycloaddition shows high fluorescence enhancement factors (FEF) in the presence of Na+ (FEF = 58) and K+ (FEF = 27) in MeCN and high selectivity towards K+ under simulated physiological conditions (160 mM K+ or Na+, respectively) with a FEF of 2.5 for K+.}, language = {en} } @article{deEspinosaMeier2011, author = {de Espinosa, Lucas Montero and Meier, Michael A. R.}, title = {Synthesis of star- and block-copolymers using ADMET head-to-tail selectivity during step-growth polymerization}, series = {Chemical communications}, volume = {47}, journal = {Chemical communications}, number = {6}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1359-7345}, doi = {10.1039/c0cc04161k}, pages = {1908 -- 1910}, year = {2011}, abstract = {Control over molecular architectures obtained via ADMET polymerization is limited by the step-growth nature of this technique. A new approach to this polycondensation method is described allowing for the synthesis of diblock and star-shaped polymers with molecular weight control by using the selectivity of olefin cross-metathesis between acrylates and terminal olefins.}, language = {en} } @article{SamereierBaumannMeyeretal.2011, author = {Samereier, Matthias and Baumann, Otto and Meyer, Irene and Gr{\"a}f, Ralph}, title = {Analysis of dictyostelium TACC reveals differential interactions with CP224 and unusual dynamics of dictyostelium microtubules}, series = {Cellular and molecular life sciences}, volume = {68}, journal = {Cellular and molecular life sciences}, number = {2}, publisher = {Springer}, address = {Basel}, issn = {1420-682X}, doi = {10.1007/s00018-010-0453-0}, pages = {275 -- 287}, year = {2011}, abstract = {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.}, language = {en} } @article{ZaupaNeffePierceetal.2011, author = {Zaupa, Alessandro and Neffe, Axel T. and Pierce, Benjamin F. and N{\"o}chel, Ulrich and Lendlein, Andreas}, title = {Influence of tyrosine-derived moieties and drying conditions on the formation of helices in gelatin}, series = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences}, volume = {12}, journal = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences}, number = {1}, publisher = {American Chemical Society}, address = {Washington}, issn = {1525-7797}, doi = {10.1021/bm101029k}, pages = {75 -- 81}, year = {2011}, abstract = {The single and triple helical organization of protein chains strongly influences the mechanical properties of gelatin-based materials. A chemical method for obtaining different degrees of helical organization in gelatin is covalent functionalization, while a physical method for achieving the same goal is the variation of the drying conditions of gelatin solutions. Here we explored how the introduction of desaminotyrosine (DAT) and desaminotyrosyl tyrosine (DATT) linked to lysine residues of gelatin influenced the kinetics and thermodynamic equilibrium of the helicalization process of single and triple helices following different drying conditions. Drying at a temperature above. the helix-to-coil transition temperature of gelatin (T > T-c, called nu(short)) generally resulted in gelatins with relatively lower triple helical content (X-c,X-t = 1-2\%) than lower temperature drying (T < T-c, called nu(long)) (X-c,X-t = 8-10\%), where the DAT(T) functional groups generally disrupted helix formation. While different helical contents affected the thermal transition temperatures only slightly, the mechanical properties were strongly affected for swollen hydrogels (E = 4-13 kPa for samples treated by nu(long) and E = 120-700 kPa for samples treated by nu(short)). This study shows that side group functionalization and different drying conditions are viable options to control the helicalization and macroscopic properties of gelatin-based materials.}, language = {en} } @article{EnsslinSandnerMatthies2011, author = {Ensslin, Andreas and Sandner, Tobias M. and Matthies, Diethart}, title = {Consequences of ex situ cultivation of plants genetic diversity, fitness and adaptation of the monocarpic Cynoglossum officinale L. in botanic gardens}, series = {: an international journal}, volume = {144}, journal = {: an international journal}, number = {1}, publisher = {Elsevier}, address = {Oxford}, issn = {0006-3207}, doi = {10.1016/j.biocon.2010.09.001}, pages = {272 -- 278}, year = {2011}, abstract = {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.}, language = {en} } @article{KaylerKaiserGessleretal.2011, author = {Kayler, Z. E. and Kaiser, Michael and Gessler, A. and Ellerbrock, Ruth H. and Sommer, Michael}, title = {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}, series = {Biogeosciences}, volume = {8}, journal = {Biogeosciences}, number = {10}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {1726-4170}, doi = {10.5194/bg-8-2895-2011}, pages = {2895 -- 2906}, year = {2011}, abstract = {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.}, language = {en} } @article{BinzerBroseCurtsdotteretal.2011, author = {Binzer, Amrei and Brose, Ulrich and Curtsdotter, Alva and Ekloef, Anna and Rall, Bjoern C. and Riede, Jens O. and de Castro, Francisco}, title = {The susceptibility of species to extinctions in model communities}, series = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, volume = {12}, journal = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, number = {7}, publisher = {Elsevier}, address = {Jena}, issn = {1439-1791}, doi = {10.1016/j.baae.2011.09.002}, pages = {590 -- 599}, year = {2011}, abstract = {Despite the fact that the loss of a species from a community has the potential to cause a dramatic decline in biodiversity, for example through cascades of secondary extinctions, little is known about the factors contributing to the extinction risk of any particular species. Here we expand earlier modeling approaches using a dynamic food-web model that accounts for bottom-up as well as top-down effects. We investigate what factors influence a species' extinction risk and time to extinction of the non-persistent species. We identified three basic properties that affect a species' risk of extinction. The highest extinction risk is born by species with (1) low energy input (e.g. high trophic level), (2) susceptibility to the loss of energy pathways (e.g. specialists with few prey species) and (3) dynamic instability (e.g. low Hill exponent and reliance on homogeneous energy channels when feeding on similarly sized prey). Interestingly, and different from field studies, we found that the trophic level and not the body mass of a species influences its extinction risk. On the other hand, body mass is the single most important factor determining the time to extinction of a species, resulting in small species dying first. This suggests that in the field the trophic level might have more influence on the extinction risk than presently recognized.}, language = {en} } @article{RiedeBinzerBroseetal.2011, author = {Riede, Jens O. and Binzer, Amrei and Brose, Ulrich and de Castro, Francisco and Curtsdotter, Alva and Rall, Bjoern C. and Ekloef, Anna}, title = {Size-based food web characteristics govern the response to species extinctions}, series = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, volume = {12}, journal = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, number = {7}, publisher = {Elsevier}, address = {Jena}, issn = {1439-1791}, doi = {10.1016/j.baae.2011.09.006}, pages = {581 -- 589}, year = {2011}, abstract = {How ecological communities react to species extinctions is a long-standing yet current question in ecology. The species constituting the basic units of ecosystems interact with each other forming complex networks of trophic relationships and the characteristics of these networks are highly important for the consequences of species extinction. Here we take a more general approach and analyze a broad range of network characteristics and their role in determining food web susceptibility to secondary extinctions. We extend previous studies, that have focused on the consequences of topological and dynamical food web parameters for food web robustness, by also defining network-wide characteristics depending on the relationships between the distribution of species body masses and other species characteristics. We use a bioenergetic dynamical model to simulate realistically structured model food webs that differ in their structural and dynamical properties as well as their size structure. In order to measure food web robustness we calculated the proportion of species going secondarily extinct. A multiple regression analysis was then used to fit a general model relating the proportion of species going secondarily extinct to the measured food web properties. Our results show that there are multiple factors from all three groups of food web characteristics that affect food web robustness. However, we find the most striking effect was related to the body mass abundance relationship which points to the importance of body mass relationships for food web stability.}, language = {en} } @article{CurtsdotterBinzerBroseetal.2011, author = {Curtsdotter, Alva and Binzer, Amrei and Brose, Ulrich and de Castro, Francisco and Ebenman, Bo and Ekloef, Anna and Riede, Jens O. and Thierry, Aaron and Rall, Bjoern C.}, title = {Robustness to secondary extinctions comparing trait-based sequential deletions in static and dynamic food webs}, series = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, volume = {12}, journal = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, number = {7}, publisher = {Elsevier}, address = {Jena}, issn = {1439-1791}, doi = {10.1016/j.baae.2011.09.008}, pages = {571 -- 580}, year = {2011}, abstract = {The loss of species from ecological communities can unleash a cascade of secondary extinctions, the risk and extent of which are likely to depend on the traits of the species that are lost from the community. To identify species traits that have the greatest impact on food web robustness to species loss we here subject allometrically scaled, dynamical food web models to several deletion sequences based on species' connectivity, generality, vulnerability or body mass. Further, to evaluate the relative importance of dynamical to topological effects we compare robustness between dynamical and purely topological models. This comparison reveals that the topological approach overestimates robustness in general and for certain sequences in particular. Top-down directed sequences have no or very low impact on robustness in topological analyses, while the dynamical analysis reveals that they may be as important as high-impact bottom-up directed sequences. Moreover, there are no deletion sequences that result, on average, in no or very few secondary extinctions in the dynamical approach. Instead, the least detrimental sequence in the dynamical approach yields an average robustness similar to the most detrimental (non-basal) deletion sequence in the topological approach. Hence, a topological analysis may lead to erroneous conclusions concerning both the relative and the absolute importance of different species traits for robustness. The dynamical sequential deletion analysis shows that food webs are least robust to the loss of species that have many trophic links or that occupy low trophic levels. In contrast to previous studies we can infer, albeit indirectly, that secondary extinctions were triggered by both bottom-up and top-down cascades.}, language = {en} } @article{KlossFischerDurka2011, author = {Kloss, Lena and Fischer, Markus and Durka, Walter}, title = {Land-use effects on genetic structure of a common grassland herb a matter of scale}, series = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, volume = {12}, journal = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, number = {5}, publisher = {Elsevier}, address = {Jena}, issn = {1439-1791}, doi = {10.1016/j.baae.2011.06.001}, pages = {440 -- 448}, year = {2011}, abstract = {The most common management practices in European grasslands are grazing by livestock and mowing for silage and hay. Grazing and mowing differ in their potential effects on plant gene flow and resulting population genetic structure. After assessing its breeding system, we investigated the effect of land use on the population genetic structure in the common grassland plant Veronica chamaedrys using 63 study populations on meadows, mown pastures and pastures in three regions in Germany, the so-called Biodiversity Exploratories. We determined plant density and analysed the genetic diversity, differentiation and small-scale genetic structure using amplified fragment length polymorphism (AFLP) markers. The breeding system of V chamaedrys turned out as self-incompatible and outcrossing. Its genetic diversity did not differ among land-use types. This may be attributed to large population sizes and the strong dispersal ability of the species, which maintains genetically diverse populations not prone to genetic drift. Genetic differentiation among populations was low (overall F(ST) = 0.075) but significant among the three regions. Land use had only weak effects on population differentiation in only one region. However, land use affected small-scale genetic structure suggesting that gene flow within plots was more restricted on meadows than on mown and unmown pastures. Our study shows that land use influences genetic structure mainly at the small scale within populations, despite high gene flow.}, language = {en} } @article{RaabovaMuenzbergovaFischer2011, author = {Raabova, Jana and Muenzbergova, Zuzana and Fischer, Markus}, title = {The role of spatial scale and soil for local adaptation in Inula hirta}, series = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, volume = {12}, journal = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, number = {2}, publisher = {Elsevier}, address = {Jena}, issn = {1439-1791}, doi = {10.1016/j.baae.2011.01.001}, pages = {152 -- 160}, year = {2011}, abstract = {Many plant populations are adapted to their local environment. Reciprocal transplant experiments in the field and in the experimental garden allow for studying different aspects of local adaptation. However, usually only one of these approaches is used. We applied both experimental approaches to study the role of spatial scale and soil conditions for local adaptation in the perennial herb Inula hirta. We reciprocally sowed seeds and transplanted juvenile plants among six field sites from two regions and, in the garden, among pots with soil from each field site. We recorded germination percentage, survival percentage, number of stems and plant height in all experiments. We also recorded above- and below-ground biomass, flowering percentage and the number of flower heads in the garden. No population-specific local adaptation was detected in germination, survival, flowering percentages or in the number of flower heads. At the regional scale in the field, however, the performance of local transplants was higher than the performance of foreign transplants by 10\% and 7\% in the two regions, respectively. Similarly, when grown in the garden in soil from the more basic and nutrient-poorer region, plant height and aboveground biomass of local transplants were higher than the corresponding values for foreign transplants by 31\% and 112\%, respectively. Congruent evidence for local adaptation from the juvenile-transplant experiments in field and garden suggests that soil conditions represent an important factor of local adaptation in I. hirta. Overall, our results show that both spatial scale and soil conditions play an important role for local adaptation in I. hirta. Moreover, we underline the importance of combining field and garden experiments to reveal factors affecting local adaptation in plants.}, language = {en} } @inproceedings{SchweigertRailaMothesetal.2011, author = {Schweigert, Florian J. and Raila, Jens and Mothes, Ralf and Frey, S.}, title = {Point of care measurements of Vitamin A in blood and breast milk for low resource settings}, series = {Annals of nutrition \& metabolism : journal of nutrition, metabolic diseases and dietetics ; an official journal of International Union of Nutritional Sciences (IUNS)}, volume = {58}, booktitle = {Annals of nutrition \& metabolism : journal of nutrition, metabolic diseases and dietetics ; an official journal of International Union of Nutritional Sciences (IUNS)}, number = {2}, publisher = {Karger}, address = {Basel}, issn = {0250-6807}, pages = {382 -- 382}, year = {2011}, language = {en} } @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{NahavandiPlathTiedemannetal.2011, author = {Nahavandi, Nahid and Plath, Martin and Tiedemann, Ralph and Mirzajani, Ali R.}, title = {Sexual and natural selection on morphological traits in a marine amphipod, Pontogammarus maeoticus (Sowinsky, 1894)}, series = {Marine biology research}, volume = {7}, journal = {Marine biology research}, number = {2}, publisher = {Taylor \& Francis Group}, address = {Oslo}, issn = {1745-1000}, doi = {10.1080/17451001003713589}, pages = {135 -- 146}, year = {2011}, abstract = {Sexual selection often leads to sexual dimorphism, where secondary sexual traits are more expressed in the male sex. This may be due, for example, to increased fighting or mate-guarding abilities of males expressing those traits. We investigated sexually dimorphic traits in four populations of a marine amphipod, Pontogammarus maeoticus (Gammaridea: Pontogammaridae), the most abundant amphipod species in the sublittoral zone along the southern shoreline of the Caspian Sea. Male amphipods are typically larger in body size than females, and have relatively larger posterior gnathopods and antennae. However, it remains to be studied for most other body appendages whether or not, and to what extent, they are sexually dimorphic. Using Analysis of Covariance (ANCOVA), we compared the relationships between body size and trait expression for 35 metric characters between males and females, and among the four populations examined by performing three different Discriminant Function Analyses (DFA). We detected several thus far undescribed sexual dimorphic traits such as the seventh peraeopods or the epimeral plates. We also found that the size of the propodus of the first and second gnathopods increases with increasing body size, and this allometric increase was stronger in males than in females. Finally, we found that the degree of sexual dimorphism in the expression of the width of the third epimeral plate varies across sites, suggesting that differences in ecology might affect the strength of sexual selection in different populations.}, language = {en} } @article{PauliukMuellerHeinken2011, author = {Pauliuk, Franziska and M{\"u}ller, J{\"o}rg and Heinken, Thilo}, title = {Bryophyte dispersal by sheep on dry grassland}, series = {Nova Hedwigia : Zeitschrift f{\"u}r Kryptogamenkunde}, volume = {92}, journal = {Nova Hedwigia : Zeitschrift f{\"u}r Kryptogamenkunde}, number = {3-4}, publisher = {Cramer}, address = {Stuttgart}, issn = {0029-5035}, doi = {10.1127/0029-5035/2011/0092-0327}, pages = {327 -- 341}, year = {2011}, abstract = {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.}, language = {en} } @article{SharmaStuckasBhaskaretal.2011, author = {Sharma, Reeta and Stuckas, Heiko and Bhaskar, Ranjana and Khan, Imran and Goyal, Surendra Prakash and Tiedemann, Ralph}, title = {Genetically distinct population of Bengal tiger (Panthera tigris tigris) in Terai Arc Landscape (TAL) of India}, series = {Mammalian biology = Zeitschrift f{\"u}r S{\"a}ugetierkunde}, volume = {76}, journal = {Mammalian biology = Zeitschrift f{\"u}r S{\"a}ugetierkunde}, number = {4}, publisher = {Elsevier}, address = {Jena}, issn = {1616-5047}, doi = {10.1016/j.mambio.2010.10.005}, pages = {484 -- 490}, year = {2011}, abstract = {We analyzed mtDNA polymorphisms (a total of 741 bp from a part of conserved control region, ND5, ND2, Cyt b and 12S) in 91 scats and 12 tissue samples of Bengal tiger (Panthera tigris tigris) populations across Terai Arc Landscape (TAL) located at the foothills of Himalayas in North Western India, Buxa Tiger Reserve (BTR), and North East India. In TAL and BTR, we found a specific haplotype at high frequency, which was absent elsewhere, indicating a genetically distinct population in these regions. Within the TAL region, there is some evidence for genetic isolation of the tiger populations west of river Ganges, i.e., in the western part of Rajaji National Park (RNP). Although the river itself might not constitute a significant barrier for tigers, recent human-induced changes in habitat and degradation of the Motichur-Chilla Corridor connecting the two sides of the tiger habitat of RNP might effectively prevent genetic exchange. A cohesive population is observed for the rest of the TAL. Even the more eastern BTR belongs genetically to this unit, despite the present lack of a migration corridor between BTR and TAL. In spite of a close geographic proximity, Chitwan (Nepal) constitutes a tiger population genetically different from TAL. Moreover, it is observed that the North East India tiger populations are genetically different from TAL and BTR, as well as from the other Bengal tiger populations in India.}, 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} } @inproceedings{KuhnertBaumannMeyeretal.2011, author = {Kuhnert, Oliver and Baumann, Otto and Meyer, Irene and Gr{\"a}f, Ralph}, title = {Functional characterization of CP148, a novel key component for centrosome integrity in Dictyostelium}, 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}, publisher = {American Society for Cell Biology}, address = {Bethesda}, issn = {1059-1524}, pages = {2}, year = {2011}, language = {en} } @article{GajdanowiczMichardSandmannetal.2011, author = {Gajdanowicz, Pawel and Michard, Erwan and Sandmann, Michael and Rocha, Marcio and Correa, Luiz Gustavo Guedes and Ramirez-Aguilar, Santiago J. and Gomez-Porras, Judith L. and Gonzalez, Wendy and Thibaud, Jean-Baptiste and van Dongen, Joost T. and Dreyer, Ingo}, title = {Potassium (K plus ) gradients serve as a mobile energy source in plant vascular tissues}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {2}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1009777108}, pages = {864 -- 869}, year = {2011}, abstract = {The essential mineral nutrient potassium (K(+)) is the most important inorganic cation for plants and is recognized as a limiting factor for crop yield and quality. Nonetheless, it is only partially understood how K(+) contributes to plant productivity. K(+) is used as a major active solute to maintain turgor and to drive irreversible and reversible changes in cell volume. K(+) also plays an important role in numerous metabolic processes, for example, by serving as an essential cofactor of enzymes. Here, we provide evidence for an additional, previously unrecognized role of K(+) in plant growth. By combining diverse experimental approaches with computational cell simulation, we show that K(+) circulating in the phloem serves as a decentralized energy storage that can be used to overcome local energy limitations. Posttranslational modification of the phloem-expressed Arabidopsis K(+) channel AKT2 taps this "potassium battery," which then efficiently assists the plasma membrane H(+)-ATPase in energizing the transmembrane phloem (re) loading processes.}, language = {en} } @article{NeumannSedukIobbiNivoletal.2011, author = {Neumann, Meina and Seduk, Farida and Iobbi-Nivol, Chantal and Leimk{\"u}hler, Silke}, title = {Molybdopterin Dinucleotide Biosynthesis in Escherichia coli identification of amino acid residues of molybdopterin dinucleotide transferases that determine specificity for binding of guanine or cytosine nucleotides}, series = {The journal of biological chemistry}, volume = {286}, journal = {The journal of biological chemistry}, number = {2}, publisher = {American Society for Biochemistry and Molecular Biology}, address = {Bethesda}, issn = {0021-9258}, doi = {10.1074/jbc.M110.155671}, pages = {1400 -- 1408}, year = {2011}, abstract = {The molybdenum cofactor is modified by the addition of GMP or CMP to the C4' phosphate of molybdopterin forming the molybdopterin guanine dinucleotide or molybdopterin cytosine dinucleotide cofactor, respectively. The two reactions are catalyzed by specific enzymes as follows: the GTP: molybdopterin guanylyltransferase MobA and the CTP: molybdopterin cytidylyltransferase MocA. Both enzymes show 22\% amino acid sequence identity and are specific for their respective nucleotides. Crystal structure analysis of MobA revealed two conserved motifs in the N-terminal domain of the protein involved in binding of the guanine base. Based on these motifs, we performed site-directed mutagenesis studies to exchange the amino acids to the sequence found in the paralogue MocA. Using a fully defined in vitro system, we showed that the exchange of five amino acids was enough to obtain activity with both GTP and CTP in either MocA or MobA. Exchange of the complete N-terminal domain of each protein resulted in the total inversion of nucleotide specificity activity, showing that the N-terminal domain determines nucleotide recognition and binding. Analysis of protein-protein interactions showed that the C-terminal domain of either MocA or MobA determines the specific binding to the respective acceptor protein.}, language = {en} } @article{SammlerBleidornTiedemann2011, author = {Sammler, Svenja and Bleidorn, Christoph and Tiedemann, Ralph}, title = {Full mitochondrial genome sequences of two endemic Philippine hornbill species (Aves: Bucerotidae) provide evidence for pervasive mitochondrial DNA recombination}, series = {BMC genomics}, volume = {12}, journal = {BMC genomics}, number = {2}, publisher = {BioMed Central}, address = {London}, issn = {1471-2164}, doi = {10.1186/1471-2164-12-35}, pages = {10}, year = {2011}, abstract = {Background: Although nowaday it is broadly accepted that mitochondrial DNA (mtDNA) may undergo recombination, the frequency of such recombination remains controversial. Its estimation is not straightforward, as recombination under homoplasmy (i.e., among identical mt genomes) is likely to be overlooked. In species with tandem duplications of large mtDNA fragments the detection of recombination can be facilitated, as it can lead to gene conversion among duplicates. Although the mechanisms for concerted evolution in mtDNA are not fully understood yet, recombination rates have been estimated from "one per speciation event" down to 850 years or even "during every replication cycle". Results: Here we present the first complete mt genome of the avian family Bucerotidae, i.e., that of two Philippine hornbills, Aceros waldeni and Penelopides panini. The mt genomes are characterized by a tandemly duplicated region encompassing part of cytochrome b, 3 tRNAs, NADH6, and the control region. The duplicated fragments are identical to each other except for a short section in domain I and for the length of repeat motifs in domain III of the control region. Due to the heteroplasmy with regard to the number of these repeat motifs, there is some size variation in both genomes; with around 21,657 bp (A. waldeni) and 22,737 bp (P. panini), they significantly exceed the hitherto longest known avian mt genomes, that of the albatrosses. We discovered concerted evolution between the duplicated fragments within individuals. The existence of differences between individuals in coding genes as well as in the control region, which are maintained between duplicates, indicates that recombination apparently occurs frequently, i. e., in every generation. Conclusions: The homogenised duplicates are interspersed by a short fragment which shows no sign of recombination. We hypothesize that this region corresponds to the so-called Replication Fork Barrier (RFB), which has been described from the chicken mitochondrial genome. As this RFB is supposed to halt replication, it offers a potential mechanistic explanation for frequent recombination in mitochondrial genomes.}, language = {en} } @article{HeinzeBochFischeretal.2011, author = {Heinze, Eric and Boch, Steffen and Fischer, Markus and Hessenm{\"o}ller, Dominik and Klenk, Bernd and M{\"u}ller, J{\"o}rg and Prati, Daniel and Schulze, Ernst-Detlef and Seele, Carolin and Socher, Stephanie and Halle, Stefan}, title = {Habitat use of large ungulates in northeastern Germany in relation to forest management}, series = {Forest ecology and management}, volume = {261}, journal = {Forest ecology and management}, number = {2}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0378-1127}, doi = {10.1016/j.foreco.2010.10.022}, pages = {288 -- 296}, year = {2011}, abstract = {Estimating large herbivore density has been a major area of research in recent decades. Previous studies monitoring ungulate density, however, focused mostly on determining animal abundance, and did not interpret animal distribution in relation to habitat parameters. We surveyed large ungulates in the Biodiversity Exploratory Schorfheide-Chorin using faecal pellet group counts. This allowed us to explore the link between relative ungulate abundance, habitat use, and browsing damage on trees in a region with several types of forest, including unharvested and age-class beech forests, as well as age-class pine forests. Our results demonstrate that roe deer and fallow deer relative abundance is negatively correlated with large tree cover, and positively correlated with the cover of small shrubs (Rubus spec., Vaccinium spec.), and winter food supply. Habitat use of roe deer and fallow deer, as estimated by counting faecal pellet groups, revealed a preference for mature pine forests, and avoidance of deciduous forests. This differential habitat use is explained by different distributions of high quality food resources during winter. The response of deer to understory cover differed between roe deer and fallow deer at high cover percentages. The amount of browsing damage we observed on coniferous trees was not consistent with the relative deer abundance. Browsing damage was consistently higher on most deciduous trees, except for beech saplings which sustained less damage when roe deer density was low. Because roe deer is a highly selective feeder, it was reported to affect tree diversity by feeding only on trees with high nutritional value. Consequently, we propose that managing the number of all deer species by hunting is necessary to allow successful forest regeneration. Such an adjustment to deer numbers would need to account for both current tree diversity and alternative food resources. Our findings may be applicable to other forest landscapes in northeastern Germany including mature pine stands and differently harvested deciduous forests.}, language = {en} } @article{HuegeGoetzeSchwarzetal.2011, author = {Huege, Jan and Goetze, Jan and Schwarz, Doreen and Bauwe, Hermann and Hagemann, Martin and Kopka, Joachim}, title = {Modulation of the major Paths of Carbon in photorespiratory mutants of synechocystis}, series = {PLoS one}, volume = {6}, journal = {PLoS one}, number = {1}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0016278}, pages = {12}, year = {2011}, abstract = {Background: Recent studies using transcript and metabolite profiles of wild-type and gene deletion mutants revealed that photorespiratory pathways are essential for the growth of Synechocystis sp. PCC 6803 under atmospheric conditions. Pool size changes of primary metabolites, such as glycine and glycolate, indicated a link to photorespiration. Methodology/Principal Findings: The (13)C labelling kinetics of primary metabolites were analysed in photoautotrophically grown cultures of Synechocystis sp. PCC 6803 by gas chromatography-mass spectrometry (GC-MS) to demonstrate the link with photorespiration. Cells pre-acclimated to high CO(2) (5\%, HC) or limited CO(2) (0.035\%, LC) conditions were pulse-labelled under very high (2\% w/w) (13)C-NaHCO(3) (VHC) conditions followed by treatment with ambient (12)C at HC and LC conditions, respectively. The (13)C enrichment, relative changes in pool size, and (13)C flux of selected metabolites were evaluated. We demonstrate two major paths of CO(2) assimilation via Rubisco in Synechocystis, i.e., from 3PGA via PEP to aspartate, malate and citrate or, to a lesser extent, from 3PGA via glucose-6-phosphate to sucrose. The results reveal evidence of carbon channelling from 3PGA to the PEP pool. Furthermore, (13)C labelling of glycolate was observed under conditions thought to suppress photorespiration. Using the glycolate-accumulating Delta glcD1 mutant, we demonstrate enhanced (13)C partitioning into the glycolate pool under conditions favouring photorespiration and enhanced (13)C partitioning into the glycine pool of the glycine-accumulating Delta gcvT mutant. Under LC conditions, the photorespiratory mutants Delta glcD1 and Delta gcvT showed enhanced activity of the additional carbon-fixing PEP carboxylase pathway. Conclusions/Significance: With our approach of non-steady-state (13)C labelling and analysis of metabolite pool sizes with respective (13)C enrichments, we identify the use and modulation of major pathways of carbon assimilation in Synechocystis in the presence of high and low inorganic carbon supplies.}, language = {en} } @article{KahmenSachseArndtetal.2011, author = {Kahmen, Ansgar and Sachse, Dirk and Arndt, Stefan K. and Tu, Kevin P. and Farrington, Heraldo and Vitousek, Peter M. and Dawson, Todd E.}, title = {Cellulose delta O-18 is an index of leaf-to-air vapor pressure difference (VPD) in tropical plants}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {5}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1018906108}, pages = {1981 -- 1986}, year = {2011}, abstract = {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.}, language = {en} } @article{DeFrenneGraaeKolbetal.2011, author = {De Frenne, Pieter and Graae, Bente J. and Kolb, Annette and Shevtsova, Anna and Baeten, Lander and Brunet, J{\"o}rg and Chabrerie, Olivier and Cousins, Sara A. O. and Decocq, Guillaume and Dhondt, Rob and Diekmann, Martin and Gruwez, Robert and Heinken, Thilo and Hermy, Martin and Oster, Mathias and Saguez, Robert and Stanton, Sharon and Tack, Wesley and Vanhellemont, Margot and Verheyen, Kris}, title = {An intraspecific application of the leaf-height-seed ecology strategy scheme to forest herbs along a latitudinal gradient}, series = {Ecography : pattern and diversity in ecology ; research papers forum}, volume = {34}, journal = {Ecography : pattern and diversity in ecology ; research papers forum}, number = {1}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0906-7590}, doi = {10.1111/j.1600-0587.2010.06399.x}, pages = {132 -- 140}, year = {2011}, abstract = {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.}, language = {en} } @misc{ZhangIgnatova2011, author = {Zhang, Gong and Ignatova, Zoya}, title = {Folding at the birth of the nascent chain: coordinating translation with co-translational folding}, series = {Current opinion in structural biology : review of all advances ; evaluation of key references ; comprehensive listing of papers}, volume = {21}, journal = {Current opinion in structural biology : review of all advances ; evaluation of key references ; comprehensive listing of papers}, number = {1}, publisher = {Elsevier}, address = {London}, issn = {0959-440X}, doi = {10.1016/j.sbi.2010.10.008}, pages = {25 -- 31}, year = {2011}, abstract = {In the living cells, the folding of many proteins is largely believed to begin co-translationally, during their biosynthesis at the ribosomes. In the ribosomal tunnel, the nascent peptide may establish local interactions and stabilize alpha-helical structures. Long-range contacts are more likely outside the ribosomes after release of larger segments of the nascent chain. Examples suggest that domains can attain native-like structure on the ribosome with and without population of folding intermediates. The co-translational folding is limited by the speed of the gradual extrusion of the nascent peptide which imposes conformational restraints on its folding landscape. Recent experimental and in silico modeling studies indicate that translation kinetics fine-tunes co-translational folding by providing a time delay for sequential folding of distinct portions of the nascent chain.}, language = {en} } @article{GrimbsArnoldKoseskaetal.2011, author = {Grimbs, Sergio and Arnold, Anne and Koseska, Aneta and Kurths, J{\"u}rgen and Selbig, Joachim and Nikoloski, Zoran}, title = {Spatiotemporal dynamics of the Calvin cycle multistationarity and symmetry breaking instabilities}, 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.2010.10.015}, pages = {212 -- 223}, year = {2011}, abstract = {The possibility of controlling the Calvin cycle has paramount implications for increasing the production of biomass. Multistationarity, as a dynamical feature of systems, is the first obvious candidate whose control could find biotechnological applications. Here we set out to resolve the debate on the multistationarity of the Calvin cycle. Unlike the existing simulation-based studies, our approach is based on a sound mathematical framework, chemical reaction network theory and algebraic geometry, which results in provable results for the investigated model of the Calvin cycle in which we embed a hierarchy of realistic kinetic laws. Our theoretical findings demonstrate that there is a possibility for multistationarity resulting from two sources, homogeneous and inhomogeneous instabilities, which partially settle the debate on multistability of the Calvin cycle. In addition, our tractable analytical treatment of the bifurcation parameters can be employed in the design of validation experiments.}, 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} } @misc{MeyerKuhnertGraef2011, author = {Meyer, Irene and Kuhnert, Oliver and Gr{\"a}f, Ralph}, title = {Functional analyses of lissencephaly-related proteins in Dictyostelium}, series = {Seminars in cell \& developmental biology}, volume = {22}, journal = {Seminars in cell \& developmental biology}, number = {1}, publisher = {Elsevier}, address = {London}, issn = {1084-9521}, doi = {10.1016/j.semcdb.2010.10.007}, pages = {89 -- 96}, year = {2011}, abstract = {Lissencephaly is a severe brain developmental disease in human infants, which is usually caused by mutations in either of two genes, LIS1 and DCX. These genes encode proteins interacting with both the microtubule and the actin systems. Here, we review the implications of data on Dictyostelium LIS1 for the elucidation of LIS1 function in higher cells and emphasize the role of LIS1 and nuclear envelope proteins in nuclear positioning, which is also important for coordinated cell migration during neocortical development. Furthermore, for the first time we characterize Dictyostelium DCX, the only bona fide orthologue of human DCX outside the animal kingdom. We show that DCX functionally interacts with LIS1 and that both proteins have a cytoskeleton-independent function in chemotactic signaling during development. Dictyostelium LIS1 is also required for proper attachment of the centrosome to the nucleus and, thus, nuclear positioning, where the association of these two organelles has turned out to be crucial. It involves not only dynein and dynein-associated proteins such as LIS1 but also SUN proteins of the nuclear envelope. Analyses of Dictyostelium SUN1 mutants have underscored the importance of these proteins for the linkage of centrosomes and nuclei and for the maintenance of chromatin integrity. Taken together, we show that Dictyostelium amoebae, which provide a well-established model to study the basic aspects of chemotaxis, cell migration and development, are well suited for the investigation of the molecular and cell biological basis of developmental diseases such as lissencephaly.}, 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} } @misc{PokornySharmaGoyaletal.2011, author = {Pokorny, Ina and Sharma, Reeta and Goyal, Surendra Prakash and Mishra, Sudanshu and Tiedemann, Ralph}, title = {MHC class I and MHC class II DRB gene variability in wild and captive Bengal tigers (Panthera tigris tigris) (vol 10, pg 667, 2010)}, series = {Immunogenetics}, volume = {63}, journal = {Immunogenetics}, number = {2}, publisher = {Springer}, address = {New York}, issn = {0093-7711}, doi = {10.1007/s00251-010-0496-2}, pages = {121 -- 121}, year = {2011}, language = {en} } @article{SarmentoBondMidgleyetal.2011, author = {Sarmento, Juliano Sarmento and Bond, William J. and Midgley, Guy F. and Rebelo, Anthony G. and Thuiller, Wilfried and Schurr, Frank Martin}, title = {Effects of harvesting flowers from shrubs on the persistence and abundance of wild shrub populations at multiple spatial extents}, series = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {25}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, number = {1}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0888-8892}, doi = {10.1111/j.1523-1739.2010.01628.x}, pages = {73 -- 84}, year = {2011}, abstract = {Wildflower harvesting is an economically important activity of which the ecological effects are poorly understood. We assessed how harvesting of flowers affects shrub persistence and abundance at multiple spatial extents. To this end, we built a process-based model to examine the mean persistence and abundance of wild shrubs whose flowers are subject to harvest (serotinous Proteaceae in the South African Cape Floristic Region). First, we conducted a general sensitivity analysis of how harvesting affects persistence and abundance at nested spatial extents. For most spatial extents and combinations of demographic parameters, persistence and abundance of flowering shrubs decreased abruptly once harvesting rate exceeded a certain threshold. At larger extents, metapopulations supported higher harvesting rates before their persistence and abundance decreased, but persistence and abundance also decreased more abruptly due to harvesting than at smaller extents. This threshold rate of harvest varied with species' dispersal ability, maximum reproductive rate, adult mortality, probability of extirpation or local extinction, strength of Allee effects, and carrying capacity. Moreover, spatial extent interacted with Allee effects and probability of extirpation because both these demographic properties affected the response of local populations to harvesting more strongly than they affected the response of metapopulations. Subsequently, we simulated the effects of harvesting on three Cape Floristic Region Proteaceae species and found that these species reacted differently to harvesting, but their persistence and abundance decreased at low rates of harvest. Our estimates of harvesting rates at maximum sustainable yield differed from those of previous investigations, perhaps because researchers used different estimates of demographic parameters, models of population dynamics, and spatial extent than we did. Good demographic knowledge and careful identification of the spatial extent of interest increases confidence in assessments and monitoring of the effects of harvesting. Our general sensitivity analysis improved understanding of harvesting effects on metapopulation dynamics and allowed qualitative assessment of the probability of extirpation of poorly studied species.}, language = {en} } @article{BurleighBansalEulensteinetal.2011, author = {Burleigh, J. Gordon and Bansal, Mukul S. and Eulenstein, Oliver and Hartmann, Stefanie and Wehe, Andre and Vision, Todd J.}, title = {Genome-Scale Phylogenetics inferring the plant tree of life from 18,896 gene trees}, series = {Systematic biology}, volume = {60}, journal = {Systematic biology}, number = {2}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1063-5157}, doi = {10.1093/sysbio/syq072}, pages = {117 -- 125}, year = {2011}, abstract = {Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony (GTP) is a phylogenetic optimization criterion in which a species tree that minimizes the number of gene duplications induced among a set of gene trees is selected. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic advances to examine the performance of GTP on a plant data set consisting of 18,896 gene trees containing 510,922 protein sequences from 136 plant taxa (giving a combined alignment length of >2.9 million characters). The relationships inferred from the GTP analysis were largely consistent with previous large-scale studies of backbone plant phylogeny and resolved some controversial nodes. The placement of taxa that were present in few gene trees generally varied the most among GTP bootstrap replicates. Excluding these taxa either before or after the GTP analysis revealed high levels of phylogenetic support across plants. The analyses supported magnoliids sister to a eudicot + monocot clade and did not support the eurosid I and II clades. This study presents a nuclear genomic perspective on the broad-scale phylogenic relationships among plants, and it demonstrates that nuclear genes with a history of duplication and loss can be phylogenetically informative for resolving the plant tree of life.}, language = {en} } @article{BalazadehKwasniewskiCaldanaetal.2011, author = {Balazadeh, Salma and Kwasniewski, Miroslaw and Caldana, Camila and Mehrnia, Mohammad and Zanor, Maria Ines and Xue, Gang-Ping and M{\"u}ller-R{\"o}ber, Bernd}, title = {ORS1, an H2O2-Responsive NAC Transcription Factor, Controls Senescence in Arabidopsis thaliana}, series = {Molecular plant}, volume = {4}, journal = {Molecular plant}, number = {2}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1674-2052}, doi = {10.1093/mp/ssq080}, pages = {346 -- 360}, year = {2011}, abstract = {We report here that ORS1, a previously uncharacterized member of the NAC transcription factor family, controls leaf senescence in Arabidopsis thaliana. Overexpression of ORS1 accelerates senescence in transgenic plants, whereas its inhibition delays it. Genes acting downstream of ORS1 were identified by global expression analysis using transgenic plants producing dexamethasone-inducible ORS1-GR fusion protein. Of the 42 up-regulated genes, 30 (similar to 70\%) were previously shown to be up-regulated during age-dependent senescence. We also observed that 32 (similar to 76\%) of the ORS1-dependent genes were induced by long-term (4 d), but not short-term (6 h) salinity stress (150 mM NaCl). Furthermore, expression of 16 and 24 genes, respectively, was induced after 1 and 5 h of treatment with hydrogen peroxide (H2O2), a reactive oxygen species known to accumulate during salinity stress. ORS1 itself was found to be rapidly and strongly induced by H2O2 treatment in both leaves and roots. Using in vitro binding site selection, we determined the preferred binding motif of ORS1 and found it to be present in half of the ORS1-dependent genes. ORS1 is a paralog of ORE1/ANAC092/AtNAC2, a previously reported regulator of leaf senescence. Phylogenetic footprinting revealed evolutionary conservation of the ORS1 and ORE1 promoter sequences in different Brassicaceae species, indicating strong positive selection acting on both genes. We conclude that ORS1, similarly to ORE1, triggers expression of senescence-associated genes through a regulatory network that may involve cross-talk with salt- and H2O2-dependent signaling pathways.}, language = {en} } @article{ZudePflanzSpinellietal.2011, author = {Zude, Manuela and Pflanz, Michael and Spinelli, Lorenzo and Dosche, Carsten and Torricelli, Alessandro}, title = {Non-destructive analysis of anthocyanins in cherries by means of Lambert-Beer and multivariate regression based on spectroscopy and scatter correction using time-resolved analysis}, series = {Journal of food engineering}, volume = {103}, journal = {Journal of food engineering}, number = {1}, publisher = {Elsevier}, address = {Oxford}, issn = {0260-8774}, doi = {10.1016/j.jfoodeng.2010.09.021}, pages = {68 -- 75}, year = {2011}, abstract = {In high-value sweet cherry (Prunus avium), the red coloration - determined by the anthocyanins content - is correlated with the fruit ripeness stage and market value. Non-destructive spectroscopy has been introduced in practice and may be utilized as a tool to assess the fruit pigments in the supply chain processes. From the fruit spectrum in the visible (Vis) wavelength range, the pigment contents are analyzed separately at their specific absorbance wavelengths. A drawback of the method is the need for re-calibration due to varying optical properties of the fruit tissue. In order to correct for the scattering differences, most often the spectral intensity in the visible spectrum is normalized by wavelengths in the near infrared (NIR) range, or pre-processing methods are applied in multivariate calibrations. In the present study, the influence of the fruit scattering properties on the Vis/NIR fruit spectrum were corrected by the effective pathlength in the fruit tissue obtained from time-resolved readings of the distribution of time-of-flight (DTOF). Pigment analysis was carried out according to Lambert-Beer law, considering fruit spectral intensities, effective pathlength, and refractive index. Results were compared to commonly applied linear color and multivariate partial least squares (PLS) regression analysis. The approaches were validated on fruits at different ripeness stages, providing variation in the scattering coefficient and refractive index exceeding the calibration sample set. In the validation, the measuring uncertainty of non-destructively analyzing fruits with Vis/NIR spectra by means of PLS or Lambert-Beer in comparison with combined application of Vis/NIR spectroscopy and DTOF measurements showed a dramatic bias reduction as well as enhanced coefficients of determination when using both, the spectral intensities and apparent information on the scattering influence by means of DTOF readings. Corrections for the refractive index did not render improved results.}, language = {en} } @article{DeFrenneBaetenGraaeetal.2011, author = {De Frenne, Pieter and Baeten, Lander and Graae, Bente J. and Brunet, Jorg and Wulf, Monika and Orczewska, Anna and Kolb, Annette and Jansen, Ivy and Jamoneau, Aurelien and Jacquemyn, Hans and Hermy, Martin and Diekmann, Martin and De Schrijver, An and De Sanctis, Michele and Decocq, Guillaume and Cousins, Sara A. O. and Verheyen, Kris}, title = {Interregional variation in the floristic recovery of post-agricultural forests}, series = {The journal of ecology}, volume = {99}, journal = {The journal of ecology}, number = {2}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0022-0477}, doi = {10.1111/j.1365-2745.2010.01768.x}, pages = {600 -- 609}, year = {2011}, abstract = {1. Worldwide, the floristic composition of temperate forests bears the imprint of past land use for decades to centuries as forests regrow on agricultural land. Many species, however, display significant interregional variation in their ability to (re)colonize post-agricultural forests. This variation in colonization across regions and the underlying factors remain largely unexplored. 2. We compiled data on 90 species and 812 species x study combinations from 18 studies across Europe that determined species' distribution patterns in ancient (i.e. continuously forested since the first available land use maps) and post-agricultural forests. The recovery rate (RR) of species in each landscape was quantified as the log-response ratio of the percentage occurrence in post-agricultural over ancient forest and related to the species-specific life-history traits and local (soil characteristics and light availability) and regional factors (landscape properties as habitat availability, time available for colonization, and climate). 3. For the herb species, we demonstrate a strong (interactive) effect of species' life-history traits and forest habitat availability on the RR of post-agricultural forest. In graminoids, however, none of the investigated variables were significantly related to the RR. 4. The better colonizing species that mainly belonged to the short-lived herbs group showed the largest interregional variability. Their recovery significantly increased with the amount of forest habitat within the landscape, whereas, surprisingly, the time available for colonization, climate, soil characteristics and light availability had no effect. 5. Synthesis. By analysing 18 independent studies across Europe, we clearly showed for the first time on a continental scale that the recovery of short-lived forest herbs increased with the forest habitat availability in the landscape. Small perennial forest herbs, however, were generally unsuccessful in colonizing post-agricultural forest even in relatively densely forested landscapes. Hence, our results stress the need to avoid ancient forest clearance to preserve the typical woodland flora.}, language = {en} } @unpublished{WalzAdrianGilbertetal.2011, author = {Walz, Norbert and Adrian, Rita and Gilbert, John J. and Monaghan, Michael T. and Weithoff, Guntram and Zimmermann-Timm, Heike}, title = {Preface}, series = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica}, volume = {662}, journal = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica}, number = {1}, publisher = {Springer}, address = {Dordrecht}, issn = {0018-8158}, doi = {10.1007/s10750-010-0514-2}, pages = {1 -- 4}, year = {2011}, language = {en} } @misc{NathanHorvitzHeetal.2011, author = {Nathan, Ran and Horvitz, Nir and He, Yanping and Kuparinen, Anna and Schurr, Frank Martin and Katul, Gabriel G.}, title = {Spread of North American wind-dispersed trees in future environments}, series = {Ecology letters}, volume = {14}, journal = {Ecology letters}, number = {3}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {1461-023X}, doi = {10.1111/j.1461-0248.2010.01573.x}, pages = {211 -- 219}, year = {2011}, abstract = {P>Despite ample research, understanding plant spread and predicting their ability to track projected climate changes remain a formidable challenge to be confronted. We modelled the spread of North American wind-dispersed trees in current and future (c. 2060) conditions, accounting for variation in 10 key dispersal, demographic and environmental factors affecting population spread. Predicted spread rates vary substantially among 12 study species, primarily due to inter-specific variation in maturation age, fecundity and seed terminal velocity. Future spread is predicted to be faster if atmospheric CO2 enrichment would increase fecundity and advance maturation, irrespective of the projected changes in mean surface windspeed. Yet, for only a few species, predicted wind-driven spread will match future climate changes, conditioned on seed abscission occurring only in strong winds and environmental conditions favouring high survival of the farthest-dispersed seeds. Because such conditions are unlikely, North American wind-dispersed trees are expected to lag behind the projected climate range shift.}, language = {en} } @article{SchleuningTemplinHuamanetal.2011, author = {Schleuning, Matthias and Templin, Mathias and Huaman, Vicky and Vadillo, Giovana P. and Becker, Thomas and Durka, Walter and Fischer, Markus and Matthies, Diethart}, title = {Effects of inbreeding, outbreeding, and supplemental pollen on the reproduction of a hummingbird-pollinated clonal amazonian herb}, series = {Biotropica : a publication of the Association for Tropical Biology}, volume = {43}, journal = {Biotropica : a publication of the Association for Tropical Biology}, number = {2}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0006-3606}, doi = {10.1111/j.1744-7429.2010.00663.x}, pages = {183 -- 191}, year = {2011}, abstract = {Understory herbs are an essential part of tropical rain forests, but little is known about factors limiting their reproduction. Many of these herbs are clonal, patchily distributed, and produce large floral displays of nectar-rich 1-d flowers to attract hummingbird pollinators that may transport pollen over long distances. The aim of this study was to investigate the effects of clonality, cross-proximity, and patchy distribution on the reproduction of the hummingbird-pollinated Amazonian herb Heliconia metallica. We experimentally pollinated flowers within populations with self-pollen and with pollen of different diversity, crossed flowers between populations, and added supplemental pollen to ramets growing solitarily or in conspecific patches. Only flowers pollinated early in the morning produced seeds. Selfed flowers produced seeds, but seed number and mass were strongly reduced, suggesting partial sterility and inbreeding depression after selfing. Because of pollen competition, flowers produced more seeds after crosses with several than with single donor plants. Crosses between populations mostly resulted in lower seed production than those within populations, suggesting outbreeding depression. Ramets in patches produced fewer seeds than solitary ramets and were more pollen-limited, possibly due to geitonogamy and biparental inbreeding in patches. We conclude that high rates of geitonogamy due to clonality and pollen limitation due to the short receptivity of flowers and patchy distribution constrain the reproduction of this clonal herb. Even in unfragmented rain forests with highly mobile pollinators, outbreeding depression may be a widespread phenomenon in plant reproduction.}, language = {en} } @article{Scheffler2011, author = {Scheffler, Christiane}, title = {The change of skeletal robustness of 6-12 years old children in Brandenburg (Germany) - Comparison of body composition 1999-2009}, series = {Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft f{\"u}r Anthropologie}, volume = {68}, journal = {Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft f{\"u}r Anthropologie}, number = {2}, publisher = {Schweizerbart}, address = {Stuttgart}, issn = {0003-5548}, doi = {10.1127/0003-5548/2011/0095}, pages = {153 -- 165}, year = {2011}, abstract = {Overweight as a global problem is a challenge to the health systems today and in the future. Detailed information about the development of body composition in children can help to design preventive measures to stop this trend. In the present study 1397 German children aged 6-12 complete years were investigated with anthropometric methods (i.e. height, weight, BMI, skeleton robustness, and percentage of body fat) in 2008/09. The results were compared with a 10 years old identical study. Today, the investigated children are a little bit smaller and the range of BMI and percentage of body fat is increasing. The large decrease of the skeletal robustness especially in the 10(th) and 3(rd) percentile is important. Decrease of physical activity as the most important reason for shrinking skeletal robustness is discussed.}, language = {en} } @article{KuechlyMuellerReinfelderetal.2011, author = {Kuechly, Helga Ursula and Mueller, Julia Sophie and Reinfelder, Vanessa Luisa and Wiedemann, Stephan and Blaum, Niels}, title = {Rodent-mediated dispersal of Acacia seeds in Kalahari savannah rangelands - implications for bush encroachment}, series = {African journal of ecology}, volume = {49}, journal = {African journal of ecology}, number = {1}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0141-6707}, doi = {10.1111/j.1365-2028.2010.01230.x}, pages = {119 -- 121}, year = {2011}, language = {en} } @article{VoigtScheffler2011, author = {Voigt, Andrea and Scheffler, Christiane}, title = {Manual abilities of the elderly - handgrip strength, finger and thumb push strength and opening strength in age comparison}, series = {Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft f{\"u}r Anthropologie}, volume = {68}, journal = {Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft f{\"u}r Anthropologie}, number = {2}, publisher = {Schweizerbart}, address = {Stuttgart}, issn = {0003-5548}, doi = {10.1127/0003-5548/2011/0090}, pages = {167 -- 173}, year = {2011}, abstract = {The purpose of this paper is to display the static strength capacities of healthy adults in different age categories. A total of 279 healthy German adults at the ages of 20 to 29 years, 50 to 59 years and 60 to 69 years generated their maximum static handgrip, index finger and thumb push strength, as well as their maximum opening strength on a smooth jar lid of 85 mm diameter and on a knurled bottle lid of 31 mm with their right hand. The results show larger male strength than female strength. Significant age-induced differences appear primarily in opening strengths between the age groups 20 to 29 and 50 to 59 years in male subjects and in female opening strengths between the age groups 20 to 29 and 60 to 69 years as well as between the age groups 50 to 59 and 60 to 69 years. Of greatest interest is that elderly men show the largest opening strengths.}, language = {en} } @article{PavesiDeMatthaeisTiedemannetal.2011, author = {Pavesi, Laura and De Matthaeis, Elvira and Tiedemann, Ralph and Ketmaier, Valerio}, title = {Temporal population genetics and COI phylogeography of the sandhopper macarorchestia remyi (Amphipoda: Talitridae)}, series = {Zoological studies}, volume = {50}, journal = {Zoological studies}, number = {2}, publisher = {Institute of Zoology, Academia Sinica}, address = {Taipei}, issn = {1021-5506}, pages = {220 -- 229}, year = {2011}, abstract = {Laura Pavesi, Elvira De Matthaeis, Ralph Tiedemann, and Valerio Ketmaier (2011) Temporal population genetics and COI phylogeography of the sandhopper Macarorchestia remyi (Amphipoda: Talitridae). Zoological Studies 50(2): 220-229. In this study we assessed levels of genetic divergence and variability in 208 individuals of the supralittoral sandhopper Macarorchestia remyi, a species strictly associated with rotted wood stranded on sand beaches, by analyzing sequence polymorphisms in a fragment of the mitochondrial DNA (mtDNA) gene coding cytochrome oxidase subunit I (COI). The geographical distribution and ecology of the species are poorly known. The study includes 1 Tyrrhenian and 2 Adriatic populations sampled along the Italian peninsula plus a single individual found on Corfu Is. (Greece). The Tyrrhenian population was sampled monthly for 1 yr. Genetic data revealed a deep phylogeographic break between the Tyrrhenian and Adriatic populations with no shared haplotypes. The single individual collected on Corfu Is. carried the most common haplotype found in the Tyrrhenian population. A mismatch analysis could not reject the hypothesis of a sudden demographic expansion in almost all but 2 monthly samples. When compared to previous genetic data centered on a variety of Mediterranean talitrids, our results place M. remyi among those species with profound intraspecific divergence (sandhoppers) and dissimilar from beachfleas, which generally display little population genetic structuring.}, language = {en} } @article{VaterKoessl2011, author = {Vater, Marianne and Koessl, Manfred}, title = {Comparative aspects of cochlear functional organization in mammals}, series = {Hearing research}, volume = {273}, journal = {Hearing research}, number = {1-2}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0378-5955}, doi = {10.1016/j.heares.2010.05.018}, pages = {89 -- 99}, year = {2011}, abstract = {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.}, language = {en} } @article{StoofLeichsenringJungingerOlakaetal.2011, author = {Stoof-Leichsenring, Kathleen Rosemarie and Junginger, Annett and Olaka, Lydia A. and Tiedemann, Ralph and Trauth, Martin H.}, title = {Environmental variability in Lake Naivasha, Kenya, over the last two centuries}, series = {Journal of paleolimnolog}, volume = {45}, journal = {Journal of paleolimnolog}, number = {3}, publisher = {Springer}, address = {Dordrecht}, issn = {0921-2728}, doi = {10.1007/s10933-011-9502-4}, pages = {353 -- 367}, year = {2011}, abstract = {Lake Naivasha, Kenya, is one of a number of freshwater lakes in the East African Rift System. Since the beginning of the twentieth century, it has experienced greater anthropogenic influence as a result of increasingly intensive farming of coffee, tea, flowers, and other horticultural crops within its catchment. The water-level history of Lake Naivasha over the past 200 years was derived from a combination of instrumental records and sediment data. In this study, we analysed diatoms in a lake sediment core to infer past lacustrine conductivity and total phosphorus concentrations. We also measured total nitrogen and carbon concentrations in the sediments. Core chronology was established by (210)Pb dating and covered a similar to 186-year history of natural (climatic) and human-induced environmental changes. Three stratigraphic zones in the core were identified using diatom assemblages. There was a change from littoral/epiphytic diatoms such as Gomphonema gracile and Cymbella muelleri, which occurred during a prolonged dry period from ca. 1820 to 1896 AD, through a transition period, to the present planktonic Aulacoseira sp. that favors nutrient-rich waters. This marked change in the diatom assemblage was caused by climate change, and later a strong anthropogenic overprint on the lake system. Increases in sediment accumulation rates since 1928, from 0.01 to 0.08 g cm(-2) year(-1) correlate with an increase in diatom-inferred total phosphorus concentrations since the beginning of the twentieth century. The increase in phosphorus accumulation suggests increasing eutrophication of freshwater Lake Naivasha. This study identified two major periods in the lake's history: (1) the period from 1820 to 1950 AD, during which the lake was affected mainly by natural climate variations, and (2) the period since 1950, during which the effects of anthropogenic activity overprinted those of natural climate variation.}, language = {en} } @article{SchiffersTielboergerTietjenetal.2011, author = {Schiffers, Katja and Tielboerger, Katja and Tietjen, Britta and Jeltsch, Florian}, title = {Root plasticity buffers competition among plants theory meets experimental data}, series = {Ecology : a publication of the Ecological Society of America}, volume = {92}, journal = {Ecology : a publication of the Ecological Society of America}, number = {3}, publisher = {Wiley}, address = {Washington}, issn = {0012-9658}, pages = {610 -- 620}, year = {2011}, abstract = {Morphological plasticity is a striking characteristic of plants in natural communities. In the context of foraging behavior particularly, root plasticity has been documented for numerous species. Root plasticity is known to mitigate competitive interactions by reducing the overlap of the individuals' rhizospheres. But despite its obvious effect on resource acquisition, plasticity has been generally neglected in previous empirical and theoretical studies estimating interaction intensity among plants. In this study, we developed a semi-mechanistic model that addresses this shortcoming by introducing the idea of compensatory growth into the classical-zone-of influence (ZOI) and field-of-neighborhood (FON) approaches. The model parameters describing the belowground plastic sphere of influence (PSI) were parameterized using data from an accompanying field experiment. Measurements of the uptake of a stable nutrient analogue at distinct distances to the neighboring plants showed that the study species responded plastically to belowground competition by avoiding overlap of individuals' rhizospheres. An unexpected finding was that the sphere of influence of the study species Bromus hordeaceus could be best described by a unimodal function of distance to the plant's center and not with a continuously decreasing function as commonly assumed. We employed the parameterized model to investigate the interplay between plasticity and two other important factors determining the intensity of competitive interactions: overall plant density and the distribution of individuals in space. The simulation results confirm that the reduction of competition intensity due to morphological plasticity strongly depends on the spatial structure of the competitive environment. We advocate the use of semi-mechanistic simulations that explicitly consider morphological plasticity to improve our mechanistic understanding of plant interactions.}, language = {en} } @article{StruckPaulHilletal.2011, author = {Struck, Torsten H. and Paul, Christiane and Hill, Natascha and Hartmann, Stefanie and Hoesel, Christoph and Kube, Michael and Lieb, Bernhard and Meyer, Achim and Tiedemann, Ralph and Purschke, Guenter and Bleidorn, Christoph}, title = {Phylogenomic analyses unravel annelid evolution}, series = {Nature : the international weekly journal of science}, volume = {471}, journal = {Nature : the international weekly journal of science}, number = {7336}, publisher = {Nature Publ. Group}, address = {London}, issn = {0028-0836}, doi = {10.1038/nature09864}, pages = {95 -- U113}, year = {2011}, abstract = {Annelida, the ringed worms, is a highly diverse animal phylum that includes more than 15,000 described species and constitutes the dominant benthic macrofauna from the intertidal zone down to the deep sea. A robust annelid phylogeny would shape our understanding of animal body-plan evolution and shed light on the bilaterian ground pattern. Traditionally, Annelida has been split into two major groups: Clitellata (earthworms and leeches) and polychaetes (bristle worms), but recent evidence suggests that other taxa that were once considered to be separate phyla (Sipuncula, Echiura and Siboglinidae (also known as Pogonophora)) should be included in Annelida(1-4). However, the deep-level evolutionary relationships of Annelida are still poorly understood, and a robust reconstruction of annelid evolutionary history is needed. Here we show that phylogenomic analyses of 34 annelid taxa, using 47,953 amino acid positions, recovered a well-supported phylogeny with strong support for major splits. Our results recover chaetopterids, myzostomids and sipunculids in the basal part of the tree, although the position of Myzostomida remains uncertain owing to its long branch. The remaining taxa are split into two clades: Errantia (which includes the model annelid Platynereis), and Sedentaria (which includes Clitellata). Ancestral character trait reconstructions indicate that these clades show adaptation to either an errant or a sedentary lifestyle, with alteration of accompanying morphological traits such as peristaltic movement, parapodia and sensory perception. Finally, life history characters in Annelida seem to be phylogenetically informative.}, language = {en} } @article{ZilligesKehrMeissneretal.2011, author = {Zilliges, Yvonne and Kehr, Jan-Christoph and Meissner, Sven and Ishida, Keishi and Mikkat, Stefan and Hagemann, Martin and Kaplan, Aaron and B{\"o}rner, Thomas and Dittmann-Th{\"u}nemann, Elke}, title = {The cyanobacterial hepatotoxin microcystin binds to proteins and increases the fitness of microcystis under oxidative stress conditions}, series = {PLoS one}, volume = {6}, journal = {PLoS one}, number = {3}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0017615}, pages = {11}, year = {2011}, abstract = {Microcystins are cyanobacterial toxins that represent a serious threat to drinking water and recreational lakes worldwide. Here, we show that microcystin fulfils an important function within cells of its natural producer Microcystis. The microcystin deficient mutant Delta mcyB showed significant changes in the accumulation of proteins, including several enzymes of the Calvin cycle, phycobiliproteins and two NADPH-dependent reductases. We have discovered that microcystin binds to a number of these proteins in vivo and that the binding is strongly enhanced under high light and oxidative stress conditions. The nature of this binding was studied using extracts of a microcystin-deficient mutant in vitro. The data obtained provided clear evidence for a covalent interaction of the toxin with cysteine residues of proteins. A detailed investigation of one of the binding partners, the large subunit of RubisCO showed a lower susceptibility to proteases in the presence of microcystin in the wild type. Finally, the mutant defective in microcystin production exhibited a clearly increased sensitivity under high light conditions and after hydrogen peroxide treatment. Taken together, our data suggest a protein-modulating role for microcystin within the producing cell, which represents a new addition to the catalogue of functions that have been discussed for microbial secondary metabolites.}, language = {en} } @article{KalimuthuLeimkuehlerBernhardt2011, author = {Kalimuthu, Palraj and Leimk{\"u}hler, Silke and Bernhardt, Paul V.}, title = {Xanthine dehydrogenase electrocatalysis autocatalysis and novel activity}, series = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, volume = {115}, journal = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, number = {11}, publisher = {American Chemical Society}, address = {Washington}, issn = {1520-6106}, doi = {10.1021/jp111809f}, pages = {2655 -- 2662}, year = {2011}, abstract = {The enzyme xanthine dehydrogenase (XDH) from the purple photosynthetic bacterium Rhodobacter capsulatus catalyzes the oxidation of hypoxanthine to xanthine and xanthine to uric acid as part of purine metabolism. The native electron acceptor is NAD(+) but herein we show that uric acid in its 2-electron oxidized form is able to act as an artificial electron acceptor from XDH in an electrochemically driven catalytic system. Hypoxanthine oxidation is also observed with the novel production of uric acid in a series of two consecutive 2-electron oxidation reactions via xanthine. XDH exhibits native activity in terms of its pH optimum and inhibition by allopurinol.}, language = {en} } @article{BorwankarRoethleinZhangetal.2011, author = {Borwankar, Tejas and Roethlein, Christoph and Zhang, Gong and Techen, Anne and Dosche, Carsten and Ignatova, Zoya}, title = {Natural osmolytes remodel the aggregation pathway of mutant huntingtin exon 1}, series = {Biochemistry}, volume = {50}, journal = {Biochemistry}, number = {12}, publisher = {American Chemical Society}, address = {Washington}, issn = {0006-2960}, doi = {10.1021/bi1018368}, pages = {2048 -- 2060}, year = {2011}, abstract = {In response to stress small organic compounds termed osmolytes are ubiquitously accumulated in all cell types to regulate the intracellular solvent quality and to counteract the deleterious effect on the stability and function of cellular proteins. Given the evidence that destabilization of the native state of a protein either by mutation or by environmental changes triggers the aggregation in the neurodegenerative pathologies, the modulation of the intracellular solute composition with osmolytes is an attractive strategy to stabilize an aggregating protein. Here we report the effect of three natural osmolytes on the in vivo and in vitro aggregation landscape of huntingtin exon 1 implicated in the Huntington's disease. Trimethylamine N-oxide (TMAO) and proline redirect amyloid fibrillogenesis of the pathological huntingtin exon 1 to nonamyloidogenic amorphous assemblies via two dissimilar molecular mechanisms. TMAO causes a rapid formation of bulky amorphous aggregates with minimally exposed surface area, whereas proline solubilizes the monomer and suppresses the accumulation of early transient aggregates. Conversely, glycine betaine enhances fibrillization in a fashion reminiscent of the genesis of functional amyloids. Strikingly, none of the natural osmolytes can completely abrogate the aggregate formation; however, they redirect the amyloidogenesis into alternative, nontoxic aggregate species. Our study reveals new insights into the complex interactions of osmoprotectants with polyQaggregates.}, language = {en} } @article{WagnerAntunesRistowetal.2011, author = {Wagner, Viktoria and Antunes, Pedro M. and Ristow, Michael and Lechner, Ute and Hensen, Isabell}, title = {Prevailing negative soil biota effect and no evidence for local adaptation in a widespread eurasian grass}, series = {PLoS one}, volume = {6}, journal = {PLoS one}, number = {3}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0017580}, pages = {8}, year = {2011}, abstract = {Background: Soil biota effects are increasingly accepted as an important driver of the abundance and distribution of plants. While biogeographical studies on alien invasive plant species have indicated coevolution with soil biota in their native distribution range, it is unknown whether adaptation to soil biota varies among populations within the native distribution range. The question of local adaptation between plants and their soil biota has important implications for conservation of biodiversity and may justify the use of seed material from local provenances in restoration campaigns. Methodology/Principal Findings: We studied soil biota effects in ten populations of the steppe grass Stipa capillata from two distinct regions, Europe and Asia. We tested for local adaptation at two different scales, both within (ca. 10-80 km) and between (ca. 3300 km) regions, using a reciprocal inoculation experiment in the greenhouse for nine months. Generally, negative soil biota effects were consistent. However, we did not find evidence for local adaptation: both within and between regions, growth of plants in their 'home soil' was not significantly larger relative to that in soil from other, more distant, populations. Conclusions/Significance: Our study suggests that negative soil biota effects can prevail in different parts of a plant species' range. Absence of local adaptation points to the possibility of similar rhizosphere biota composition across populations and regions, sufficient gene flow to prevent coevolution, selection in favor of plasticity, or functional redundancy among different soil biota. From the point of view of plant - soil biota interactions, our findings indicate that the current practice of using seeds exclusively from local provenances in ecosystem restoration campaigns may not be justified.}, language = {en} } @article{TschoepeWallschlaegerBurkartetal.2011, author = {Tsch{\"o}pe, Okka and Wallschl{\"a}ger, Hans-Dieter and Burkart, Michael and Tielb{\"o}rger, Katja}, title = {Managing open habitats by wild ungulate browsing and grazing a case-study in North-Eastern Germany}, series = {Applied vegetation science : official organ of the International Association for Vegetation Science}, volume = {14}, journal = {Applied vegetation science : official organ of the International Association for Vegetation Science}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1402-2001}, doi = {10.1111/j.1654-109X.2010.01119.x}, pages = {200 -- 209}, year = {2011}, abstract = {Question: Can wild ungulates efficiently maintain and restore open habitats? Location: Brandenburg, NE Germany. Methods: The effect of wild ungulate grazing and browsing was studied in three successional stages: (1) Corynephorus canescens-dominated grassland; (2) ruderal tall forb vegetation dominated by Tanacetum vulgare; and (3) Pinus sylvestris-pioneer forest. The study was conducted over 3 yr. In each successional stage, six paired 4 m(2)-monitoring plots of permanently grazed versus ungrazed plots were arranged in three random blocks. Removal of grazing was introduced de novo for the study. In each plot, percentage cover of each plant and lichen species and total cover of woody plants was recorded. Results: Wild ungulates considerably affected successional pathways and species composition in open habitats but this influence became evident in alteration of abundances of only a few species. Grazing effects differed considerably between successional stages: species richness was higher in grazed versus ungrazed ruderal and pioneer forest plots, but not in the Corynephorus sites. Herbivory affected woody plant cover only in the Pioneer forest sites. Although the study period was too short to observe drastic changes in species richness and woody plant cover, notable changes in species composition were still detected in all successional stages. Conclusion: Wild ungulate browsing is a useful tool to inhibit encroachment of woody vegetation and to conserve a species-rich, open landscape.}, language = {en} } @inproceedings{SmithMattosBarbiz2011, author = {Smith, Mychal Daijon and Mattos, Carla and Barbiz, Stefanie}, title = {The multiple solvent crystal structures of P22TSP}, series = {The FASEB journal : the official journal of the Federation of American Societies for Experimental Biology}, volume = {25}, booktitle = {The FASEB journal : the official journal of the Federation of American Societies for Experimental Biology}, number = {2}, publisher = {Federation of American Societies for Experimental Biology}, address = {Bethesda}, issn = {0892-6638}, pages = {1}, year = {2011}, language = {en} } @article{SchmidtStaude2011, author = {Schmidt, Bernd and Staude, Lucia}, title = {Desymmetrization of (R,R)-Hexa-1,5-diene-3,4-diol via Monofunctionallization and Rhodium-Catalyzed Allylic Substitution}, series = {The journal of organic chemistry}, volume = {76}, journal = {The journal of organic chemistry}, number = {7}, publisher = {American Chemical Society}, address = {Washington}, issn = {0022-3263}, doi = {10.1021/jo2001337}, pages = {2220 -- 2226}, year = {2011}, abstract = {A sequence of selective monoprotection and Rh-catalyzed enantioconservative allylic subEtitution is established as a desymmetrization strategy for C-2-symmetric hexa-1,5-diene-3,4-diol. A benzyl protecting group and ethyl carbonate as a leaving group emerged as the most useful combination with respect to reproducibility, stereoselectivity, and yield: A remarkable deviation from the normally observed regiospecificity of Rh-catalyzed allylic alkylations was observed for unprotected carbonates. In this case, a linear, rather than a branched alkylation product was obtained exclusively.}, language = {en} } @article{NikoloskiGrimbsKlieetal.2011, author = {Nikoloski, Zoran and Grimbs, Sergio and Klie, Sebastian and Selbig, Joachim}, title = {Complexity of automated gene annotation}, series = {Biosystems : journal of biological and information processing sciences}, volume = {104}, journal = {Biosystems : journal of biological and information processing sciences}, number = {1}, publisher = {Elsevier}, address = {Oxford}, issn = {0303-2647}, doi = {10.1016/j.biosystems.2010.12.003}, pages = {1 -- 8}, year = {2011}, abstract = {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.}, language = {en} } @article{NeffeLoebusZaupaetal.2011, author = {Neffe, Axel T. and Loebus, Axel and Zaupa, Alessandro and St{\"o}tzel, Christian and M{\"u}ller, Frank A. and Lendlein, Andreas}, title = {Gelatin functionalization with tyrosine derived moieties to increase the interaction with hydroxyapatite fillers}, series = {Acta biomaterialia}, volume = {7}, journal = {Acta biomaterialia}, number = {4}, publisher = {Elsevier}, address = {Oxford}, issn = {1742-7061}, doi = {10.1016/j.actbio.2010.11.025}, pages = {1693 -- 1701}, year = {2011}, abstract = {Combining gelatins functionalized with the tyrosine-derived groups desaminotyrosine or desaminotyrosyl tyrosine with hydroxyapatite (HAp) led to the formation of composite materials with much lower swelling ratios than those of the pure matrices. Shifts of the infra-red (IR) bands related to the free carboxyl groups could be observed in the presence of HAp, which suggested a direct interaction of matrix and filler that formed additional physical cross-links in the material. In tensile tests and rheological measurements the composites equilibrated in water had increased Young's moduli (from 200 kPa up to 2 MPa) and tensile strengths (from 57 kPa up to 1.1 MPa) compared with the matrix polymers without affecting the elongation at break. Furthermore, an increased thermal stability of the networks from 40 to 85 degrees C could be demonstrated. The differences in the behaviour of the functionalized gelatins compared with pure gelatin as a matrix suggested an additional stabilizing bond between the incorporated aromatic groups and the HAp as supported by the IR results. The composites can potentially be applied as bone fillers.}, language = {en} } @article{FettkeMalinovaAlbrechtetal.2011, author = {Fettke, J{\"o}rg and Malinova, Irina and Albrecht, Tanja and Hejazi, Mahdi and Steup, Martin}, title = {Glucose-1-Phosphate transport into protoplasts and chloroplasts from leaves of arabidopsis}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {155}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {4}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.110.168716}, pages = {1723 -- 1734}, year = {2011}, abstract = {Almost all glucosyl transfer reactions rely on glucose-1-phosphate (Glc-1-P) that either immediately acts as glucosyl donor or as substrate for the synthesis of the more widely used Glc dinucleotides, ADPglucose or UDPglucose. In this communication, we have analyzed two Glc-1-P-related processes: the carbon flux from externally supplied Glc-1-P to starch by either mesophyll protoplasts or intact chloroplasts from Arabidopsis (Arabidopsis thaliana). When intact protoplasts or chloroplasts are incubated with [U-C-14]Glc-1-P, starch is rapidly labeled. Incorporation into starch is unaffected by the addition of unlabeled Glc-6-P or Glc, indicating a selective flux from Glc-1-P to starch. However, illuminated protoplasts incorporate less C-14 into starch when unlabeled bicarbonate is supplied in addition to the C-14-labeled Glc-1-P. Mesophyll protoplasts incubated with [U-C-14] Glc-1-P incorporate C-14 into the plastidial pool of adenosine diphosphoglucose. Protoplasts prepared from leaves of mutants of Arabidopsis that lack either the plastidial phosphorylase or the phosphoglucomutase isozyme incorporate C-14 derived from external Glc-1-P into starch, but incorporation into starch is insignificant when protoplasts from a mutant possessing a highly reduced ADPglucose pyrophosphorylase activity are studied. Thus, the path of assimilatory starch biosynthesis initiated by extraplastidial Glc-1-P leads to the plastidial pool of adenosine diphosphoglucose, and at this intermediate it is fused with the Calvin cycle-driven route. Mutants lacking the plastidial phosphoglucomutase contain a small yet significant amount of transitory starch.}, language = {en} } @article{WinckKwasniewskiWienkoopetal.2011, author = {Winck, Flavia Vischi and Kwasniewski, Miroslaw and Wienkoop, Stefanie and M{\"u}ller-R{\"o}ber, Bernd}, title = {An optimized method for the isolation of nuclei from chlamydomas Reinhardtii (Chlorophyceae)}, series = {Journal of phycology}, volume = {47}, journal = {Journal of phycology}, number = {2}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0022-3646}, doi = {10.1111/j.1529-8817.2011.00967.x}, pages = {333 -- 340}, year = {2011}, abstract = {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.}, language = {en} } @article{ZhangLukoszekMuellerRoeberetal.2011, author = {Zhang, Gong and Lukoszek, Radoslaw and M{\"u}ller-R{\"o}ber, Bernd and Ignatova, Zoya}, title = {Different sequence signatures in the upstream regions of plant and animal tRNA genes shape distinct modes of regulation}, series = {Nucleic acids research}, volume = {39}, journal = {Nucleic acids research}, number = {8}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0305-1048}, doi = {10.1093/nar/gkq1257}, pages = {3331 -- 3339}, year = {2011}, abstract = {In eukaryotes, the transcription of tRNA genes is initiated by the concerted action of transcription factors IIIC (TFIIIC) and IIIB (TFIIIB) which direct the recruitment of polymerase III. While TFIIIC recognizes highly conserved, intragenic promoter elements, TFIIIB binds to the non-coding 5'-upstream regions of the tRNA genes. Using a systematic bioinformatic analysis of 11 multicellular eukaryotic genomes we identified a highly conserved TATA motif followed by a CAA-motif in the tRNA upstream regions of all plant genomes. Strikingly, the 5'-flanking tRNA regions of the animal genomes are highly heterogeneous and lack a common conserved sequence signature. Interestingly, in the animal genomes the tRNA species that read the same codon share conserved motifs in their upstream regions. Deep-sequencing analysis of 16 human tissues revealed multiple splicing variants of two of the TFIIIB subunits, Bdp1 and Brf1, with tissue-specific expression patterns. These multiple forms most likely modulate the TFIIIB-DNA interactions and explain the lack of a uniform signature motif in the tRNA upstream regions of animal genomes. The anticodon-dependent 5'-flanking motifs provide a possible mechanism for independent regulation of the tRNA transcription in various human tissues.}, 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} } @article{DortayAkulaWestphaletal.2011, author = {Dortay, Hakan and Akula, Usha Madhuri and Westphal, Christin and Sittig, Marie and M{\"u}ller-R{\"o}ber, Bernd}, title = {High-throughput protein expression using a combination of ligation-independent cloning (LIC) and infrared fluorescent protein (IFP) detection}, series = {PLoS one}, volume = {6}, journal = {PLoS one}, number = {4}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0018900}, pages = {19}, year = {2011}, abstract = {Protein expression in heterologous hosts for functional studies is a cumbersome effort. Here, we report a superior platform for parallel protein expression in vivo and in vitro. The platform combines highly efficient ligation-independent cloning (LIC) with instantaneous detection of expressed proteins through N- or C-terminal fusions to infrared fluorescent protein (IFP). For each open reading frame, only two PCR fragments are generated (with three PCR primers) and inserted by LIC into ten expression vectors suitable for protein expression in microbial hosts, including Escherichia coli, Kluyveromyces lactis, Pichia pastoris, the protozoon Leishmania tarentolae, and an in vitro transcription/translation system. Accumulation of IFP-fusion proteins is detected by infrared imaging of living cells or crude protein extracts directly after SDS-PAGE without additional processing. We successfully employed the LIC-IFP platform for in vivo and in vitro expression of ten plant and fungal proteins, including transcription factors and enzymes. Using the IFP reporter, we additionally established facile methods for the visualisation of protein-protein interactions and the detection of DNA-transcription factor interactions in microtiter and gel-free format. We conclude that IFP represents an excellent reporter for high-throughput protein expression and analysis, which can be easily extended to numerous other expression hosts using the setup reported here.}, 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{ZuppingerDingleySchmidChenetal.2011, author = {Zuppinger-Dingley, D. and Schmid, Bernhard and Chen, Y. and Brandl, H. and van der Heijden, M. G. A. and Joshi, Jasmin Radha}, title = {In their native range, invasive plants are held in check by negative soil-feedbacks}, series = {Ecosphere : the magazine of the International Ecology University}, volume = {2}, journal = {Ecosphere : the magazine of the International Ecology University}, number = {5}, publisher = {Wiley}, address = {Washington}, issn = {2150-8925}, doi = {10.1890/ES11-00061.1}, pages = {12}, year = {2011}, abstract = {The ability of some plant species to dominate communities in new biogeographical ranges has been attributed to an innate higher competitive ability and release from co-evolved specialist enemies. Specifically, invasive success in the new range might be explained by release from biotic negative soil-feedbacks, which control potentially dominant species in their native range. To test this hypothesis, we grew individuals from sixteen phylogenetically paired European grassland species that became either invasive or naturalized in new ranges, in either sterilized soil or in sterilized soil with unsterilized soil inoculum from their native home range. We found that although the native members of invasive species generally performed better than those of naturalized species, these native members of invasive species also responded more negatively to native soil inoculum than did the native members of naturalized species. This supports our hypothesis that potentially invasive species in their native range are held in check by negative soil-feedbacks. However, contrary to expectation, negative soil-feedbacks in potentially invasive species were not much increased by interspecific competition. There was no significant variation among families between invasive and naturalized species regarding their feedback response (negative vs. neutral). Therefore, we conclude that the observed negative soil feedbacks in potentially invasive species may be quite widespread in European families of typical grassland species.}, language = {en} } @article{HagemannVaterKoessl2011, author = {Hagemann, Cornelia and Vater, Marianne and Koessl, Manfred}, title = {Comparison of properties of cortical echo delay-tuning in the short-tailed fruit bat and the mustached bat}, series = {Journal of comparative physiology : A, Neuroethology, sensory, neural, and behavioral physiology}, volume = {197}, journal = {Journal of comparative physiology : A, Neuroethology, sensory, neural, and behavioral physiology}, number = {5}, publisher = {Springer}, address = {New York}, issn = {0340-7594}, doi = {10.1007/s00359-010-0530-8}, pages = {605 -- 613}, year = {2011}, abstract = {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.}, language = {en} } @misc{LeimkuehlerWuebbensRajagopalan2011, author = {Leimk{\"u}hler, Silke and Wuebbens, Margot M. and Rajagopalan, K. V.}, title = {The history of the discovery of the molybdenum cofactor and novel aspects of its biosynthesis in bacteria}, series = {Coordination chemistry reviews}, volume = {255}, journal = {Coordination chemistry reviews}, number = {9-10}, publisher = {Elsevier}, address = {Lausanne}, issn = {0010-8545}, doi = {10.1016/j.ccr.2010.12.003}, pages = {1129 -- 1144}, year = {2011}, abstract = {The biosynthesis of the molybdenum cofactor in bacteria is described with a detailed analysis of each individual reaction leading to the formation of stable intermediates during the synthesis of molybdopterin from GTP. As a starting point, the discovery of molybdopterin and the elucidation of its structure through the study of stable degradation products are described. Subsequent to molybdopterin synthesis, the molybdenum atom is added to the molybdopterin dithiolene group to form the molybdenum cofactor. This cofactor is either inserted directly into specific molybdoenzymes or is further modified by the addition of nucleotides to molybdopterin phosphate group or the replacement of ligands at the molybdenum center.}, language = {en} } @article{SchmidtHoelterKellingetal.2011, author = {Schmidt, Bernd and H{\"o}lter, Frank and Kelling, Alexandra and Schilde, Uwe}, title = {Pd-Catalyzed arylation reactions with phenol diazonium salts application in the synthesis of diarylheptanoids}, series = {The journal of organic chemistry}, volume = {76}, journal = {The journal of organic chemistry}, number = {9}, publisher = {American Chemical Society}, address = {Washington}, issn = {0022-3263}, doi = {10.1021/jo2002787}, pages = {3357 -- 3365}, year = {2011}, abstract = {The first total synthesis of the natural product (3S,7R)-5,6-dehydro-de-O-methyl centrolobine and various analogues is reported, using a highly regio- and diastereoselective Mizoroki-Heck reaction of phenol diazonium salts and enantiopure dihydropyrans. The assigned relative configuration was confirmed by single-crystal X-ray structure analysis, but a revision of the absolute configuration is proposed based on polarimetric measurement.}, language = {en} } @article{BaslerEbenhoehSelbigetal.2011, author = {Basler, Georg and Ebenhoeh, Oliver and Selbig, Joachim and Nikoloski, Zoran}, title = {Mass-balanced randomization of metabolic networks}, series = {Bioinformatics}, volume = {27}, journal = {Bioinformatics}, number = {10}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btr145}, pages = {1397 -- 1403}, year = {2011}, abstract = {Motivation: Network-centered studies in systems biology attempt to integrate the topological properties of biological networks with experimental data in order to make predictions and posit hypotheses. For any topology-based prediction, it is necessary to first assess the significance of the analyzed property in a biologically meaningful context. Therefore, devising network null models, carefully tailored to the topological and biochemical constraints imposed on the network, remains an important computational problem. Results: We first review the shortcomings of the existing generic sampling scheme-switch randomization-and explain its unsuitability for application to metabolic networks. We then devise a novel polynomial-time algorithm for randomizing metabolic networks under the (bio)chemical constraint of mass balance. The tractability of our method follows from the concept of mass equivalence classes, defined on the representation of compounds in the vector space over chemical elements. We finally demonstrate the uniformity of the proposed method on seven genome-scale metabolic networks, and empirically validate the theoretical findings. The proposed method allows a biologically meaningful estimation of significance for metabolic network properties.}, language = {en} } @article{BanksNishiyamaHasebeetal.2011, author = {Banks, Jo Ann and Nishiyama, Tomoaki and Hasebe, Mitsuyasu and Bowman, John L. and Gribskov, Michael and dePamphilis, Claude and Albert, Victor A. and Aono, Naoki and Aoyama, Tsuyoshi and Ambrose, Barbara A. and Ashton, Neil W. and Axtell, Michael J. and Barker, Elizabeth and Barker, Michael S. and Bennetzen, Jeffrey L. and Bonawitz, Nicholas D. and Chapple, Clint and Cheng, Chaoyang and Correa, Luiz Gustavo Guedes and Dacre, Michael and DeBarry, Jeremy and Dreyer, Ingo and Elias, Marek and Engstrom, Eric M. and Estelle, Mark and Feng, Liang and Finet, Cedric and Floyd, Sandra K. and Frommer, Wolf B. and Fujita, Tomomichi and Gramzow, Lydia and Gutensohn, Michael and Harholt, Jesper and Hattori, Mitsuru and Heyl, Alexander and Hirai, Tadayoshi and Hiwatashi, Yuji and Ishikawa, Masaki and Iwata, Mineko and Karol, Kenneth G. and Koehler, Barbara and Kolukisaoglu, Uener and Kubo, Minoru and Kurata, Tetsuya and Lalonde, Sylvie and Li, Kejie and Li, Ying and Litt, Amy and Lyons, Eric and Manning, Gerard and Maruyama, Takeshi and Michael, Todd P. and Mikami, Koji and Miyazaki, Saori and Morinaga, Shin-ichi and Murata, Takashi and M{\"u}ller-R{\"o}ber, Bernd and Nelson, David R. and Obara, Mari and Oguri, Yasuko and Olmstead, Richard G. and Onodera, Naoko and Petersen, Bent Larsen and Pils, Birgit and Prigge, Michael and Rensing, Stefan A. and Mauricio Riano-Pachon, Diego and Roberts, Alison W. and Sato, Yoshikatsu and Scheller, Henrik Vibe and Schulz, Burkhard and Schulz, Christian and Shakirov, Eugene V. and Shibagaki, Nakako and Shinohara, Naoki and Shippen, Dorothy E. and Sorensen, Iben and Sotooka, Ryo and Sugimoto, Nagisa and Sugita, Mamoru and Sumikawa, Naomi and Tanurdzic, Milos and Theissen, Guenter and Ulvskov, Peter and Wakazuki, Sachiko and Weng, Jing-Ke and Willats, William W. G. T. and Wipf, Daniel and Wolf, Paul G. and Yang, Lixing and Zimmer, Andreas D. and Zhu, Qihui and Mitros, Therese and Hellsten, Uffe and Loque, Dominique and Otillar, Robert and Salamov, Asaf and Schmutz, Jeremy and Shapiro, Harris and Lindquist, Erika and Lucas, Susan and Rokhsar, Daniel and Grigoriev, Igor V.}, title = {The selaginella genome identifies genetic changes associated with the evolution of vascular plants}, series = {Science}, volume = {332}, journal = {Science}, number = {6032}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington}, issn = {0036-8075}, doi = {10.1126/science.1203810}, pages = {960 -- 963}, year = {2011}, abstract = {Vascular plants appeared similar to 410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.}, language = {en} } @article{NaafWulf2011, author = {Naaf, Tobias and Wulf, Monika}, title = {Traits of winner and loser species indicate drivers of herb layer changes over two decades in forests of NW Germany}, series = {Journal of vegetation science}, volume = {22}, journal = {Journal of vegetation science}, number = {3}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {1100-9233}, doi = {10.1111/j.1654-1103.2011.01267.x}, pages = {516 -- 527}, year = {2011}, abstract = {Questions What are the most likely environmental drivers for compositional herb layer changes as indicated by trait differences between winner and loser species? Location Weser-Elbe region (NW Germany). Methods We resurveyed the herb layer communities of ancient forest patches on base-rich sites of 175 semi-permanent plots. Species traits were tested for their ability to discriminate between winner and loser species using logistic regression analyses and deviance partitioning. Results Of 115 species tested, 31 were identified as winner species and 30 as loser species. Winner species had higher seed longevity, flowered later in the season and more often had an oceanic distribution compared to loser species. Loser species tended to have a higher specific leaf area, were more susceptible to deer browsing and had a performance optimum at higher soil pH compared to winner species. The loser species also represented several ancient forest and threatened species. Deviance partitioning indicated that local drivers (i.e. disturbance due to forest management) were primarily responsible for the species shifts, while regional drivers (i.e. browsing pressure and acidification from atmospheric deposition) and global drivers (i.e. climate warming) had moderate effects. There was no evidence that canopy closure, drainage or eutrophication contributed to herb layer changes. Conclusions The relative importance of the different drivers as indicated by the winner and loser species differs from that found in previous long-term studies. Relating species traits to species performance is a valuable tool that provides insight into the environmental drivers that are most likely responsible for herb layer changes.}, language = {en} } @article{GriessnerHartigChristmannetal.2011, author = {Griessner, Matthias and Hartig, Dave and Christmann, Alexander and Pohl, Carsten and Schellhase, Michaela and Ehrentreich-F{\"o}rster, Eva}, title = {Development and characterization of a disposable plastic microarray printhead}, series = {Biomedical microdevices : bioMEMS and biomedical nanotechnology}, volume = {13}, journal = {Biomedical microdevices : bioMEMS and biomedical nanotechnology}, number = {3}, publisher = {Springer}, address = {Dordrecht}, issn = {1387-2176}, doi = {10.1007/s10544-011-9522-x}, pages = {533 -- 538}, year = {2011}, abstract = {During the last decade microarrays have become a powerful analytical tool. Commonly microarrays are produced in a non-contact manner using silicone printheads. However, silicone printheads are expensive and not able to be used as a disposable. Here, we show the development and functional characterization of 8-channel plastic microarray printheads that overcome both disadvantages of their conventional silicone counterparts. A combination of injection-molding and laser processing allows us to produce a high quantity of cheap, customizable and disposable microarray printheads. The use of plastics (e.g., polystyrene) minimizes the need for surface modifications required previously for proper printing results. Time-consuming regeneration processes, cleaning procedures and contaminations caused by residual samples are avoided. The utilization of plastic printheads for viscous liquids, such as cell suspensions or whole blood, is possible. Furthermore, functional parts within the plastic printhead (e.g., particle filters) can be included. Our printhead is compatible with commercially available TopSpot devices but provides additional economic and technical benefits as compared to conventional TopSpot printheads, while fulfilling all requirements demanded on the latter. All in all, this work describes how the field of traditional microarray spotting can be extended significantly by low cost plastic printheads.}, language = {en} } @misc{VanDonkIanoraVos2011, author = {Van Donk, Ellen and Ianora, Adrianna and Vos, Matthijs}, title = {Induced defences in marine and freshwater phytoplankton a review}, series = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica}, volume = {668}, journal = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica}, number = {1}, publisher = {Springer}, address = {Dordrecht}, issn = {0018-8158}, doi = {10.1007/s10750-010-0395-4}, pages = {3 -- 19}, year = {2011}, abstract = {Many organisms have developed defences to avoid predation by species at higher trophic levels. The capability of primary producers to defend themselves against herbivores affects their own survival, can modulate the strength of trophic cascades and changes rates of competitive exclusion in aquatic communities. Algal species are highly flexible in their morphology, growth form, biochemical composition and production of toxic and deterrent compounds. Several of these variable traits in phytoplankton have been interpreted as defence mechanisms against grazing. Zooplankton feed with differing success on various phytoplankton species, depending primarily on size, shape, cell wall structure and the production of toxins and deterrents. Chemical cues associated with (i) mechanical damage, (ii) herbivore presence and (iii) grazing are the main factors triggering induced defences in both marine and freshwater phytoplankton, but most studies have failed to disentangle the exact mechanism(s) governing defence induction in any particular species. Induced defences in phytoplankton include changes in morphology (e.g. the formation of spines, colonies and thicker cell walls), biochemistry (such as production of toxins, repellents) and in life history characteristics (formation of cysts, reduced recruitment rate). Our categorization of inducible defences in terms of the responsible induction mechanism provides guidance for future work, as hardly any of the available studies on marine or freshwater plankton have performed all the treatments that are required to pinpoint the actual cue(s) for induction. We discuss the ecology of inducible defences in marine and freshwater phytoplankton with a special focus on the mechanisms of induction, the types of defences, their costs and benefits, and their consequences at the community level.}, language = {en} } @article{SpeckArndtMueller2011, author = {Speck, Janina and Arndt, Katja Maren and M{\"u}ller, Kristian M.}, title = {Efficient phage display of intracellularly folded proteins mediated by the TAT pathway}, series = {Protein engineering design \& selection}, volume = {24}, journal = {Protein engineering design \& selection}, number = {6}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1741-0126}, doi = {10.1093/protein/gzr001}, pages = {473 -- 484}, year = {2011}, abstract = {Phage display with filamentous phages is widely applied and well developed, yet proteins requiring a cytoplasmic environment for correct folding still defy attempts at functional display. To extend applicability of phage display, we employed the twin-arginine translocation (TAT) pathway to incorporate proteins fused to the C-terminal domain of the geneIII protein into phage particles. We investigated functionality and display level of fluorescent proteins depending on the translocation pathway, which was the TAT, general secretory (SEC) or signal recognition particle (SRP) pathway mediated by the TorA, PelB or DsbA signal sequences, respectively. Importantly, for green fluorescent protein, yellow fluorescent protein and cyan fluorescent protein, only TAT, but not SEC or SRP, translocation led to fluorescence of purified phage particles, although all three proteins could be displayed regardless of the translocation pathway. In contrast, the monomeric red fluorescent protein mCherry was functionally displayed regardless of the translocation pathway. Hence, correct folding and fluorophor formation of mCherry is not limited to the cytosol. Furthermore, we successfully displayed firefly luciferase as well as an 83 kDa argonaute protein, both containing free cysteines. This demonstrates broad applicability of the TAT-mediated phagemid system for the display of proteins requiring cytoplasmic factors for correct folding and should prove useful for the display of proteins requiring incorporation of co-factors or oligomerization to gain function.}, language = {en} } @article{FerirVermeireHuskensetal.2011, author = {Ferir, Geoffrey and Vermeire, Kurt and Huskens, Dana and Balzarini, Jan and Van Damme, Els J. M. and Kehr, Jan-Christoph and Dittmann-Th{\"u}nemann, Elke and Swanson, Michael D. and Markovitz, David M. and Schols, Dominique}, title = {Synergistic in vitro anti-HIV type 1 activity of tenofovir with carbohydrate-binding agents (CBAs)}, series = {Antiviral research}, volume = {90}, journal = {Antiviral research}, number = {3}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0166-3542}, doi = {10.1016/j.antiviral.2011.03.188}, pages = {200 -- 204}, year = {2011}, abstract = {Tenofovir, a well-known and highly prescribed anti-HIV-1 drug for the treatment of HIV/AIDS infections, has recently also shown its effectiveness as a potential microbicide drug in the prevention of HIV transmission. Here, we evaluated the combination of tenofovir with various members of the class of carbohydrate-binding agents (CBAs) targeting the glycans on the viral envelope gp120 for their anti-HIV efficacy. The tenofovir/CBA combinations predominantly showed synergistic antiviral activity using the median effect principle. These findings illustrate that combination of tenofovir with CBAs may increase the antiviral potency of the individual drugs and reducing the risk on potential side-effects.}, 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} } @misc{SicardLenhard2011, author = {Sicard, Adrien and Lenhard, Michael}, title = {The selfing syndrome a model for studying the genetic and evolutionary basis of morphological adaptation in plants}, series = {Annals of botany}, volume = {107}, journal = {Annals of botany}, number = {9}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0305-7364}, doi = {10.1093/aob/mcr023}, pages = {1433 -- 1443}, year = {2011}, abstract = {Background In angiosperm evolution, autogamously selfing lineages have been derived from outbreeding ancestors multiple times, and this transition is regarded as one of the most common evolutionary tendencies in flowering plants. In most cases, it is accompanied by a characteristic set of morphological and functional changes to the flowers, together termed the selfing syndrome. Two major areas that have changed during evolution of the selfing syndrome are sex allocation to male vs. female function and flower morphology, in particular flower (mainly petal) size and the distance between anthers and stigma. Scope A rich body of theoretical, taxonomic, ecological and genetic studies have addressed the evolutionary modification of these two trait complexes during or after the transition to selfing. Here, we review our current knowledge about the genetics and evolution of the selfing syndrome. Conclusions We argue that because of its frequent parallel evolution, the selfing syndrome represents an ideal model for addressing basic questions about morphological evolution and adaptation in flowering plants, but that realizing this potential will require the molecular identification of more of the causal genes underlying relevant trait variation.}, language = {en} } @inproceedings{KuekenshoenerJeanChristophSpecketal.2011, author = {K{\"u}kensh{\"o}ner, Tim and Jean-Christoph, N. and Speck, J. and M{\"u}ller, Kristian M. and Arndt, Katja Maren}, title = {Targeting the microphthalmia associated transcription factor coiled coil domain with interfering peptides}, series = {The FEBS journal}, volume = {278}, booktitle = {The FEBS journal}, number = {6}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {1742-464X}, pages = {159 -- 159}, year = {2011}, language = {en} } @article{DavidMarashiLarhlimietal.2011, author = {David, Laszlo and Marashi, Sayed-Amir and Larhlimi, Abdelhalim and Mieth, Bettina and Bockmayr, Alexander}, title = {FFCA a feasibility-based method for flux coupling analysis of metabolic networks}, series = {BMC bioinformatics}, volume = {12}, journal = {BMC bioinformatics}, number = {12}, publisher = {BioMed Central}, address = {London}, issn = {1471-2105}, doi = {10.1186/1471-2105-12-236}, pages = {7}, year = {2011}, abstract = {Background: Flux coupling analysis (FCA) is a useful method for finding dependencies between fluxes of a metabolic network at steady-state. FCA classifies reactions into subsets (called coupled reaction sets) in which activity of one reaction implies activity of another reaction. Several approaches for FCA have been proposed in the literature. Results: We introduce a new FCA algorithm, FFCA (Feasibility-based Flux Coupling Analysis), which is based on checking the feasibility of a system of linear inequalities. We show on a set of benchmarks that for genome-scale networks FFCA is faster than other existing FCA methods. Conclusions: We present FFCA as a new method for flux coupling analysis and prove it to be faster than existing approaches. A corresponding software tool is freely available for non-commercial use at http://www.bioinformatics.org/ffca/.}, language = {en} } @article{FranckvonBlohMuelleretal.2011, author = {Franck, Siegfried and von Bloh, Werner and M{\"u}ller, Christoph and Bondeau, Alberte and Sakschewski, B.}, title = {Harvesting the sun new estimations of the maximum population of planet Earth}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {222}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, number = {12}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2011.03.030}, pages = {2019 -- 2026}, year = {2011}, abstract = {The maximum population, also called Earth's carrying capacity, is the maximum number of people that can live on the food and other resources available on planet Earth. Previous investigations estimated the maximum carrying capacity as large as about 1 trillion people under the assumption that photosynthesis is the limiting process. Here we use a present state-of-the-art dynamic global vegetation model with managed planetary land surface, Lund-Potsdam-Jena managed Land (LPJmL), to calculate the yields of the most productive crops on a global 0.5 degrees x 0.5 degrees grid. Using the 2005 crop distribution the model predicts total harvested calories that are sufficient for the nutrition of 11.4 billion people. We define scenarios where humankind uses the whole land area for agriculture, saves the rain forests and the boreal evergreen forests or cultivates only pasture to feed animals. Every scenario is run in an extreme version with no allowance for urban and recreational needs and in two soft versions with a certain area per person for non-agricultural use. We find that there are natural limits of the maximum carrying capacity which are independent of any increase in agricultural productivity, if non-agricultural land use is accounted for. Using all land planet Earth can sustain 282 billion people. The save-forests-scenario yields 150 billion people. The scenario that cultivates only pasture to feed animals yields 96 billion people. Nevertheless, we should always have in mind that all our calculated numbers for the carrying capacity refer to extreme scenarios where humankind may only vegetate on this planet. Our numbers are considerably higher than the general median estimate of upper bounds of human population found in the literature in the order of 10 billion.}, language = {en} } @article{DortaySchmoeckelFettkeetal.2011, author = {Dortay, Hakan and Schm{\"o}ckel, Sandra M. and Fettke, J{\"o}rg and M{\"u}ller-R{\"o}ber, Bernd}, title = {Expression of human c-reactive protein in different systems and its purification from Leishmania tarentolae}, series = {Protein expression and purification}, volume = {78}, journal = {Protein expression and purification}, number = {1}, publisher = {Elsevier}, address = {San Diego}, issn = {1046-5928}, doi = {10.1016/j.pep.2011.03.010}, pages = {55 -- 60}, year = {2011}, abstract = {With its homo-pentameric structure and calcium-dependent specificity for phosphocholine (PCh), human c-reactive protein (CRP) is produced by the liver and secreted in elevated quantities in response to inflammation. CRP is widely accepted as a cardiac marker, e.g. in point-of-care diagnostics, however, its heterologous expression has proven difficult. Here, we demonstrate the expression of CRP in different Escherichia coli strains as well as by in vitro transcription/translation. Although expression in these systems was straightforward, most of the protein that accumulated was insoluble. We therefore expanded our study to include the expression of CRP in two eukaryotic hosts, namely the yeast Kluyveromyces lactis and the protozoon Leishmania tarentolae. Both expression systems are optimized for secretion of recombinant proteins and here allowed successful expression of soluble CRP. We also demonstrate the purification of recombinant CRP from Leishmania growth medium; the purification of protein expressed from K. lactis was not successful. Functional and intact CRP pentamer is known to interact with PCh in Ca(2+)-dependent manner. In this report we verify the binding specificity of recombinant CRP from L tarentolae (2 mu g/mL culture medium) for PCh.}, language = {en} } @article{PopovaHundertmarkSeckleretal.2011, author = {Popova, Antoaneta V. and Hundertmark, Michaela and Seckler, Robert and Hincha, Dirk K.}, title = {Structural transitions in the intrinsically disordered plant dehydration stress protein LEA7 upon drying are modulated by the presence of membranes}, series = {Biochimica et biophysica acta : Biomembranes}, volume = {1808}, journal = {Biochimica et biophysica acta : Biomembranes}, number = {7}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0005-2736}, doi = {10.1016/j.bbamem.2011.03.009}, pages = {1879 -- 1887}, year = {2011}, abstract = {Dehydration stress-related late embryogenesis abundant (LEA) proteins have been found in plants, invertebrates and bacteria. Most LEA proteins are unstructured in solution, but some fold into amphipathic a-helices during drying. The Pfam LEA_4 (Group 3) protein LEA7 from the higher plant Arabidopsis thaliana was predicted to be 87\% alpha-helical, while CD spectroscopy showed it to be largely unstructured in solution and only 35\% alpha-helical in the dry state. However, the dry protein contained 15\% beta-sheets. FTIR spectroscopy revealed the (beta-sheets to be largely due to aggregation. beta-Sheet content was reduced and alpha-helix content increased when LEA7 was dried in the presence of liposomes with secondary structure apparently influenced by lipid composition. Secondary structure was also affected by the presence of membranes in the fully hydrated state. A temperature-induced increase in the flexibility of the dry protein was also only observed in the presence of membranes. Functional interactions of LEA7 with membranes in the dry state were indicated by its influence on the thermotropic phase transitions of the lipids and interactions with the lipid headgroup phosphates.}, language = {en} } @article{KocyanSnijmanForestetal.2011, author = {Kocyan, Alexander and Snijman, Deirdre A. and Forest, Felix and Devey, Dion S. and Freudenstein, John V. and Wiland-Szymanska, Justyna and Chase, Mark W. and Rudall, Paula J.}, title = {Molecular phylogenetics of Hypoxidaceae - Evidence from plastid DNA data and inferences on morphology and biogeography}, series = {Molecular phylogenetics and evolution}, volume = {60}, journal = {Molecular phylogenetics and evolution}, number = {1}, publisher = {Elsevier}, address = {San Diego}, issn = {1055-7903}, doi = {10.1016/j.ympev.2011.02.021}, pages = {122 -- 136}, year = {2011}, abstract = {Phylogenetic relationships of the monocot family Hypoxidaceae (Asparagales), which occurs mainly in the Southern Hemisphere, were reconstructed using four plastid DNA regions (rbcL, trnL intron, trnL-F intergenic spacer, and trnS-G intergenic spacer) for 56 ingroup taxa including all currently accepted genera and seven species of the closely related families Asteliaceae, Blandfordiaceae, and Lanariaceae. Data were analyzed by applying parsimony, maximum likelihood and Bayesian methods. The intergenic spacer trnS-G - only rarely used in monocot research - contributed a substantial number of potentially parsimony informative characters. Hypoxidaceae consist of three well-supported major clades, but their interrelationships remain unresolved. Our data indicate that in the Pauridia clade one long-distance dispersal event occurred from southern Africa to Australia. Long-distance dispersal scenarios may also be likely for the current distribution of Hypoxis, which occurs on four continents. In the Curculigo clade, the present distribution of Curculigo s.s. on four continents could support a Gondwanan origin, but the level of divergence is too low for this hypothesis to be likely. The main clades correspond well with some floral characters, habit and palynological data, whereas chromosomal data exhibit plasticity and probably result from polyploidization and subsequent dysploidy and/or aneuploidy. Evolutionary flexibility is also suggested by the number of reported pollination syndromes: melittophily, myophily, sapromyophily, and cantharophily. Based on our phylogenetic results, we suggest cautious nomenclatural reorganization to generate monophyly at the generic level.}, language = {en} } @article{SchroederLissoMuessig2011, author = {Schr{\"o}der, Florian and Lisso, Janina and Muessig, Carsten}, title = {Exordium-Like1 promotes growth during low carbon availability in arabidopsis}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {156}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {3}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.111.177204}, pages = {1620 -- 1630}, year = {2011}, abstract = {Little is known about genes that control growth and development under low carbon (C) availability. The Arabidopsis (Arabidopsis thaliana) EXORDIUM-LIKE1 (EXL1) gene (At1g35140) was identified as a brassinosteroid-regulated gene in a previous study. We show here that the EXL1 protein is required for adaptation to C-and energy-limiting growth conditions. In-depth analysis of EXL1 transcript levels under various environmental conditions indicated that EXL1 expression is controlled by the C and energy status. Sugar starvation, extended night, and anoxia stress induced EXL1 gene expression. The C status also determined EXL1 protein levels. These results suggested that EXL1 is involved in the C-starvation response. Phenotypic changes of an exl1 loss-of-function mutant became evident only under corresponding experimental conditions. The mutant showed diminished biomass production in a short-day/low-light growth regime, impaired survival during extended night, and impaired survival of anoxia stress. Basic metabolic processes and signaling pathways are presumed to be barely impaired in exl1, because the mutant showed wild-type levels of major sugars, and transcript levels of only a few genes such as QUA-QUINE STARCH were altered. Our data suggest that EXL1 is part of a regulatory pathway that controls growth and development when C and energy supply is poor.}, language = {en} } @article{HeldPascaudEckertetal.2011, author = {Held, Katrin and Pascaud, Francois and Eckert, Christian and Gajdanowicz, Pawel and Hashimoto, Kenji and Corratge-Faillie, Claire and Offenborn, Jan Niklas and Lacombe, Benoit and Dreyer, Ingo and Thibaud, Jean-Baptiste and Kudla, J{\"o}rg}, title = {Calcium-dependent modulation and plasma membrane targeting of the AKT2 potassium channel by the CBL4/CIPK6 calcium sensor/protein kinase complex}, series = {Cell research}, volume = {21}, journal = {Cell research}, number = {7}, publisher = {Nature Publ. Group}, address = {Shanghai}, issn = {1001-0602}, doi = {10.1038/cr.2011.50}, pages = {1116 -- 1130}, year = {2011}, abstract = {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.}, language = {en} }