TY - GEN A1 - Breitenstein, Michael A1 - Nielsen, Peter E. A1 - Hölzel, Ralph A1 - Bier, Frank Fabian T1 - DNA-nanostructure-assembly by sequential spotting T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1027 KW - atomic force microscope KW - peptide nucleic acid KW - persistence length KW - adapter oligonucleotide KW - high fluorescence signal Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431108 SN - 1866-8372 IS - 1027 ER - TY - GEN A1 - Bierbach, David A1 - Schulte, Matthias A1 - Herrmann, Nina A1 - Tobler, Michael A1 - Stadler, Stefan A1 - Jung, Christian T. A1 - Kunkel, Benjamin A1 - Riesch, Rüdiger A1 - Klaus, Sebastian A1 - Ziege, Madlen A1 - Indy, Jeane Rimber A1 - Arias-Rodriguez, Lenin A1 - Plath, Martin T1 - Predator-induced changes of female mating preferences BT - innate and experiential effects T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - 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-naïve (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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 984 KW - sexual selection KW - female choice KW - non-independent mate choice KW - predator recognition KW - Poecilia mexicana Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431099 SN - 1866-8372 IS - 984 ER - TY - GEN A1 - Eccard, Jana A1 - Fey, Karen A1 - Caspers, Barbara A. A1 - Ylönen, Hannu T1 - Breeding state and season affect interspecific interaction types BT - indirect resource competition and direct interference T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Indirect resource competition and interference are widely occurring mechanisms of interspecific interactions. We have studied the seasonal expression of these two interaction types within a two-species, boreal small mammal system. Seasons differ by resource availability, individual breeding state and intraspecific social system. Live-trapping methods were used to monitor space use and reproduction in 14 experimental populations of bank voles Myodes glareolus in large outdoor enclosures with and without a dominant competitor, the field vole Microtus agrestis. We further compared vole behaviour using staged dyadic encounters in neutral arenas in both seasons. Survival of the non-breeding overwintering bank voles was not affected by competition. In the spring, the numbers of male bank voles, but not of females, were reduced significantly in the competition populations. Bank vole home ranges expanded with vole density in the presence of competitors, indicating food limitation. A comparison of behaviour between seasons based on an analysis of similarity revealed an avoidance of costly aggression against opponents, independent of species. Interactions were more aggressive during the summer than during the winter, and heterospecific encounters were more aggressive than conspecific encounters. Based on these results, we suggest that interaction types and their respective mechanisms are not either–or categories and may change over the seasons. During the winter, energy constraints and thermoregulatory needs decrease direct aggression, but food constraints increase indirect resource competition. Direct interference appears in the summer, probably triggered by each individual’s reproductive and hormonal state and the defence of offspring against conspecific and heterospecific intruders. Both interaction forms overlap in the spring, possibly contributing to spring declines in the numbers of subordinate species. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 729 KW - rodents KW - aggression KW - seasonality KW - space use KW - winter biology Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-429398 SN - 1866-8372 IS - 729 SP - 623 EP - 633 ER - TY - JOUR A1 - Feher, Kristen A1 - Whelan, James A1 - Müller, Samuel T1 - Assessing modularity using a random matrix theory approach JF - Statistical applications in genetics and molecular biology N2 - Random matrix theory (RMT) is well suited to describing the emergent properties of systems with complex interactions amongst their constituents through their eigenvalue spectrums. Some RMT results are applied to the problem of clustering high dimensional biological data with complex dependence structure amongst the variables. It will be shown that a gene relevance or correlation network can be constructed by choosing a correlation threshold in a principled way, such that it corresponds to a block diagonal structure in the correlation matrix, if such a structure exists. The structure is then found using community detection algorithms, but with parameter choice guided by RMT predictions. The resulting clustering is compared to a variety of hierarchical clustering outputs and is found to the most generalised result, in that it captures all the features found by the other considered methods. KW - random matrix theory KW - clustering KW - modularity Y1 - 2011 U6 - https://doi.org/10.2202/1544-6115.1667 SN - 2194-6302 SN - 1544-6115 VL - 10 IS - 1 PB - De Gruyter CY - Berlin ER - TY - JOUR A1 - Sangoro, J. R. A1 - Iacob, C. A1 - Naumov, S. A1 - Valiullin, R. A1 - Rexhausen, Hans A1 - Hunger, J. A1 - Buchner, R. A1 - Strehmel, Veronika A1 - Kaerger, J. A1 - Kremer, F. T1 - Diffusion in ionic liquids the interplay between molecular structure and dynamics JF - Soft matter N2 - 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. Y1 - 2011 U6 - https://doi.org/10.1039/c0sm01404d SN - 1744-683X VL - 7 IS - 5 SP - 1678 EP - 1681 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Lilie, Hauke A1 - Baer, Dorit A1 - Kettner, Karina A1 - Weininger, Ulrich A1 - Balbach, Jochen A1 - Naumann, Manfred A1 - Mueller, Eva-Christina A1 - Otto, Albrecht A1 - Gast, Klaus A1 - Golbik, Ralph A1 - Kriegel, Thomas T1 - Yeast hexokinase isoenzyme ScHxk2 stability of a two-domain protein with discontinuous domains JF - Protein engineering design & selection N2 - 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). KW - dynamic light scattering KW - NMR KW - ScHxk2 KW - stability KW - transition intermediate Y1 - 2011 U6 - https://doi.org/10.1093/protein/gzq098 SN - 1741-0126 VL - 24 IS - 1-2 SP - 79 EP - 87 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Klaus, Valentin H. A1 - Kleinebecker, Till A1 - Hoelzel, Norbert A1 - Bluethgen, Nico A1 - Boch, Steffen A1 - Müller, Jörg A1 - Socher, Stephanie A. A1 - Prati, Daniel A1 - Fischer, Markus T1 - Nutrient concentrations and fibre contents of plant community biomass reflect species richness patterns along a broad range of land-use intensities among agricultural grasslands JF - Perspectives in plant ecology, evolution and systematics N2 - 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. KW - Biodiversity exploratories KW - Fertilization KW - Grazing KW - Land use KW - Mowing KW - Nitrogen KW - Nutrient limitation KW - Phosphorus KW - Productivity Y1 - 2011 U6 - https://doi.org/10.1016/j.ppees.2011.07.001 SN - 1433-8319 VL - 13 IS - 4 SP - 287 EP - 295 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Albert, Cécile H. A1 - Grassein, Fabrice A1 - Schurr, Frank Martin A1 - Vieilledent, Ghislain A1 - Violle, Cyrille T1 - When and how should intraspecific variability be considered in trait-based plant ecology? JF - Perspectives in plant ecology, evolution and systematics N2 - 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. KW - Comparative ecology KW - Functional ecology KW - Genetic variability KW - Intraspecific functional variability KW - Phenotypic plasticity KW - Plant functional hairs KW - Within-species variability Y1 - 2011 U6 - https://doi.org/10.1016/j.ppees.2011.04.003 SN - 1433-8319 VL - 13 IS - 3 SP - 217 EP - 225 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Kleinpeter, Erich A1 - Laemmermann, Anica A1 - Kühn, Heiner T1 - 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 JF - Organic & biomolecular chemistry : an international journal of synthetic, physical and biomolecular organic chemistry N2 - 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). Y1 - 2011 U6 - https://doi.org/10.1039/c0ob00356e SN - 1477-0520 VL - 9 IS - 4 SP - 1098 EP - 1111 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Buchmann, Carsten M. A1 - Schurr, Frank Martin A1 - Nathan, Ran A1 - Jeltsch, Florian T1 - An allometric model of home range formation explains the structuring of animal communities exploiting heterogeneous resources JF - Oikos N2 - Understanding and predicting the composition and spatial structure of communities is a central challenge in ecology. An important structural property of animal communities is the distribution of individual home ranges. Home range formation is controlled by resource heterogeneity, the physiology and behaviour of individual animals, and their intra- and interspecific interactions. However, a quantitative mechanistic understanding of how home range formation influences community composition is still lacking. To explore the link between home range formation and community composition in heterogeneous landscapes we combine allometric relationships for physiological properties with an algorithm that selects optimal home ranges given locomotion costs, resource depletion and competition in a spatially-explicit individual-based modelling framework. From a spatial distribution of resources and an input distribution of animal body mass, our model predicts the size and location of individual home ranges as well as the individual size distribution (ISD) in an animal community. For a broad range of body mass input distributions, including empirical body mass distributions of North American and Australian mammals, our model predictions agree with independent data on the body mass scaling of home range size and individual abundance in terrestrial mammals. Model predictions are also robust against variation in habitat productivity and landscape heterogeneity. The combination of allometric relationships for locomotion costs and resource needs with resource competition in an optimal foraging framework enables us to scale from individual properties to the structure of animal communities in heterogeneous landscapes. The proposed spatially-explicit modelling concept not only allows for detailed investigation of landscape effects on animal communities, but also provides novel insights into the mechanisms by which resource competition in space shapes animal communities. Y1 - 2011 U6 - https://doi.org/10.1111/j.1600-0706.2010.18556.x SN - 0030-1299 VL - 120 IS - 1 SP - 106 EP - 118 PB - Wiley-Blackwell CY - Malden ER -