@article{KnoxBrownRindfleischGuentheretal.2020, author = {Knox-Brown, Patrick and Rindfleisch, Tobias and G{\"u}nther, Anne and Balow, Kim and Bremer, Anne and Walther, Dirk and Miettinen, Markus S. and Hincha, Dirk K. and Thalhammer, Anja}, title = {Similar Yet Different}, series = {International Journal of Molecular Sciences}, volume = {21}, journal = {International Journal of Molecular Sciences}, number = {8}, publisher = {Molecular Diversity Preservation International}, address = {Basel}, issn = {1422-0067}, doi = {10.3390/ijms21082794}, pages = {25}, year = {2020}, abstract = {The importance of intrinsically disordered late embryogenesis abundant (LEA) proteins in the tolerance to abiotic stresses involving cellular dehydration is undisputed. While structural transitions of LEA proteins in response to changes in water availability are commonly observed and several molecular functions have been suggested, a systematic, comprehensive and comparative study of possible underlying sequence-structure-function relationships is still lacking. We performed molecular dynamics (MD) simulations as well as spectroscopic and light scattering experiments to characterize six members of two distinct, lowly homologous clades of LEA_4 family proteins from Arabidopsis thaliana. We compared structural and functional characteristics to elucidate to what degree structure and function are encoded in LEA protein sequences and complemented these findings with physicochemical properties identified in a systematic bioinformatics study of the entire Arabidopsis thaliana LEA_4 family. Our results demonstrate that although the six experimentally characterized LEA_4 proteins have similar structural and functional characteristics, differences concerning their folding propensity and membrane stabilization capacity during a freeze/thaw cycle are obvious. These differences cannot be easily attributed to sequence conservation, simple physicochemical characteristics or the abundance of sequence motifs. Moreover, the folding propensity does not appear to be correlated with membrane stabilization capacity. Therefore, the refinement of LEA_4 structural and functional properties is likely encoded in specific patterns of their physicochemical characteristics.}, language = {en} } @article{RajuLiebigKlemkeetal.2020, author = {Raju, Rajarshi Roy and Liebig, Ferenc and Klemke, Bastian and Koetz, Joachim}, title = {Ultralight magnetic aerogels from Janus emulsions}, series = {RSC Advances}, volume = {10}, journal = {RSC Advances}, number = {13}, publisher = {RSC Publishing}, address = {London}, issn = {2046-2069}, doi = {10.1039/c9ra10247g}, pages = {7492 -- 7499}, year = {2020}, abstract = {Magnetite containing aerogels were synthesized by freeze-drying olive oil/silicone oil-based Janus emulsion gels containing gelatin and sodium carboxymethylcellulose (NaCMC). The magnetite nanoparticles dispersed in olive oil are processed into the gel and remain in the macroporous aerogel after removing the oil components. The coexistence of macropores from the Janus droplets and mesopores from freeze-drying of the hydrogels in combination with the magnetic properties offer a special hierarchical pore structure, which is of relevance for smart supercapacitors, biosensors, and spilled oil sorption and separation. The morphology of the final structure was investigated in dependence on initial compositions. More hydrophobic aerogels with magnetic responsiveness were synthesized by bisacrylamide-crosslinking of the hydrogel. The crosslinked aerogels can be successfully used in magnetically responsive clean up experiments of the cationic dye methylene blue.}, language = {en} } @misc{FichteTruszczynskiWoltran2015, author = {Fichte, Johannes Klaus and Truszczynski, Miroslaw and Woltran, Stefan}, title = {Dual-normal logic programs}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {585}, issn = {1866-8372}, doi = {10.25932/publishup-41449}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-414490}, pages = {16}, year = {2015}, abstract = {Disjunctive Answer Set Programming is a powerful declarative programming paradigm with complexity beyond NP. Identifying classes of programs for which the consistency problem is in NP is of interest from the theoretical standpoint and can potentially lead to improvements in the design of answer set programming solvers. One of such classes consists of dual-normal programs, where the number of positive body atoms in proper rules is at most one. Unlike other classes of programs, dual-normal programs have received little attention so far. In this paper we study this class. We relate dual-normal programs to propositional theories and to normal programs by presenting several inter-translations. With the translation from dual-normal to normal programs at hand, we introduce the novel class of body-cycle free programs, which are in many respects dual to head-cycle free programs. We establish the expressive power of dual-normal programs in terms of SE- and UE-models, and compare them to normal programs. We also discuss the complexity of deciding whether dual-normal programs are strongly and uniformly equivalent.}, language = {en} } @misc{SiskaJonesJeonetal.2017, author = {Siska, Veronika and Jones, Eppie Ruth and Jeon, Sungwon and Bhak, Youngjune and Kim, Hak-Min and Cho, Yun Sung and Kim, Hyunho and Lee, Kyusang and Veselovskaya, Elizaveta and Balueva, Tatiana and Gallego-Llorente, Marcos and Hofreiter, Michael and Bradley, Daniel G. and Eriksson, Anders and Pinhasi, Ron and Bhak, Jong and Manica, Andrea}, title = {Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {791}, issn = {1866-8372}, doi = {10.25932/publishup-43997}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-439977}, pages = {11}, year = {2017}, abstract = {Ancient genomes have revolutionized our understanding of Holocene prehistory and, particularly, the Neolithic transition in western Eurasia. In contrast, East Asia has so far received little attention, despite representing a core region at which the Neolithic transition took place independently similar to 3 millennia after its onset in the Near East. We report genome-wide data from two hunter-gatherers from Devil's Gate, an early Neolithic cave site (dated to similar to 7.7 thousand years ago) located in East Asia, on the border between Russia and Korea. Both of these individuals are genetically most similar to geographically close modern populations from the Amur Basin, all speaking Tungusic languages, and, in particular, to the Ulchi. The similarity to nearby modern populations and the low levels of additional genetic material in the Ulchi imply a high level of genetic continuity in this region during the Holocene, a pattern that markedly contrasts with that reported for Europe.}, language = {en} } @misc{MohandesanSpellerPetersetal.2017, author = {Mohandesan, Elmira and Speller, Camilla F. and Peters, Joris and Uerpmann, Hans-Peter and Uerpmann, Margarethe and De Cupere, Bea and Hofreiter, Michael and Burger, Pamela A.}, title = {Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {789}, issn = {1866-8372}, doi = {10.25932/publishup-43995}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-439955}, pages = {300 -- 313}, year = {2017}, abstract = {The performance of hybridization capture combined with next-generation sequencing (NGS) has seen limited investigation with samples from hot and arid regions until now. We applied hybridization capture and shotgun sequencing to recover DNA sequences from bone specimens of ancient-domestic dromedary (Camelus dromedarius) and its extinct ancestor, the wild dromedary from Jordan, Syria, Turkey and the Arabian Peninsula, respectively. Our results show that hybridization capture increased the percentage of mitochondrial DNA (mtDNA) recovery by an average 187-fold and in some cases yielded virtually complete mitochondrial (mt) genomes at multifold coverage in a single capture experiment. Furthermore, we tested the effect of hybridization temperature and time by using a touchdown approach on a limited number of samples. We observed no significant difference in the number of unique dromedary mtDNA reads retrieved with the standard capture compared to the touchdown method. In total, we obtained 14 partial mitochondrial genomes from ancient-domestic dromedaries with 17-95\% length coverage and 1.27-47.1-fold read depths for the covered regions. Using whole-genome shotgun sequencing, we successfully recovered endogenous dromedary nuclear DNA (nuDNA) from domestic and wild dromedary specimens with 1-1.06-fold read depths for covered regions. Our results highlight that despite recent methodological advances, obtaining ancient DNA (aDNA) from specimens recovered from hot, arid environments is still problematic. Hybridization protocols require specific optimization, and samples at the limit of DNA preservation need multiple replications of DNA extraction and hybridization capture as has been shown previously for Middle Pleistocene specimens.}, language = {en} } @misc{MorrisSaltRailaetal.2012, author = {Morris, Penelope J. and Salt, Carina and Raila, Jens and Brenten, Thomas and Kohn, Barbara and Schweigert, Florian J. and Zentek, J{\"u}rgen}, title = {Safety evaluation of vitamin A in growing dogs}, series = {Potsprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Potsprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {686}, doi = {10.25932/publishup-41492}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-414929}, pages = {10}, year = {2012}, abstract = {The safe upper limit for inclusion of vitamin A in complete diets for growing dogs is uncertain, with the result that current recommendations range from 5.24 to 104.80 mu mol retinol (5000 to 100 000 IU vitamin A)/4184 kJ (1000 kcal) metabolisable energy (ME). The aim of the present study was to determine the effect of feeding four concentrations of vitamin A to puppies from weaning until 1 year of age. A total of forty-nine puppies, of two breeds, Labrador Retriever and Miniature Schnauzer, were randomly assigned to one of four treatment groups. Following weaning at 8 weeks of age, puppies were fed a complete food supplemented with retinyl acetate diluted in vegetable oil and fed at 1ml oil/100 g diet to achieve an intake of 5.24, 13.10, 78.60 and 104.80 mu mol retinol (5000, 12 500, 75 000 and 100 000 IU vitamin A)/4184 kJ (1000 kcal) ME. Fasted blood and urine samples were collected at 8, 10, 12, 14, 16, 20, 26, 36 and 52 weeks of age and analysed for markers of vitamin A metabolism and markers of safety including haematological and biochemical variables, bone-specific alkaline phosphatase, cross-linked carboxyterminal telopeptides of type I collagen and dual-energy X-ray absorptiometry. Clinical examinations were conducted every 4 weeks. Data were analysed by means of a mixed model analysis with Bonferroni corrections for multiple endpoints. There was no effect of vitamin A concentration on any of the parameters, with the exception of total serum retinyl esters, and no effect of dose on the number, type and duration of adverse events. We therefore propose that 104.80 mu mol retinol (100 000 IU vitamin A)/4184 kJ (1000 kcal) is a suitable safe upper limit for use in the formulation of diets designed for puppy growth.}, language = {en} } @misc{EggertRawelPawelzik2011, author = {Eggert, Kai and Rawel, Harshadrai Manilal and Pawelzik, Elke}, title = {In vitro degradation of wheat gluten fractions by Fusarium graminearum proteases}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {877}, issn = {1866-8372}, doi = {10.25932/publishup-43510}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-435102}, pages = {697 -- 705}, year = {2011}, abstract = {Fusarium spp. infection of cereal grain is a common problem, which leads to a dramatic loss of grain quality. The aim of the present study was to investigate the effect of Fusarium infection on the wheat storage protein gluten and its fractions, the gliadins and glutenins, in an in vitro model system. Gluten proteins were digested by F. graminearum proteases for 2, 4, 8 and 24 h, separated by Osborne fractionation and characterised by chromatographic (RP-HPLC) and electrophoretic analysis (SDS-Page). Gluten digestion by F. graminearum proteases showed in comparison with gliadins a preference for the glutenins whereas the HMW subfraction was at most affected. In comparison with a untreated control, the HMW subfraction was degraded of about 97\% after 4 h incubation with Fusarium proteases. Separate digestion of gliadin and glutenin underlined the preference for HMW-GS. Analogue to the observed change in the gluten composition, the yield of the proteins extracted changed. A higher amount of glutenin fragments was found in the gliadin extraction solution after digestion and could mask a gliadin destruction at the same time. This observation can contribute to explain the frequently reported reduced glutenin amount parallel to an increase in gliadin quantity after Fusarium infection in grains.}, language = {en} } @misc{SpricigoDronovLisdatetal.2009, author = {Spricigo, Roberto and Dronov, Roman and Lisdat, Fred and Leimk{\"u}hler, Silke and Scheller, Frieder W. and Wollenberger, Ursula}, title = {Electrocatalytic sulfite biosensor with human sulfite oxidase co-immobilized with cytochrome c in a polyelectrolyte-containing multilayer}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {945}, issn = {1866-8372}, doi = {10.25932/publishup-43117}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431176}, pages = {225 -- 233}, year = {2009}, abstract = {An efficient electrocatalytic biosensor for sulfite detection was developed by co-immobilizing sulfite oxidase and cytochrome c with polyaniline sulfonic acid in a layer-by-layer assembly. QCM, UV-Vis spectroscopy and cyclic voltammetry revealed increasing loading of electrochemically active protein with the formation of multilayers. The sensor operates reagentless at low working potential. A catalytic oxidation current was detected in the presence of sulfite at the modified gold electrode, polarized at +0.1 V ( vs. Ag/AgCl 1 M KCl). The stability of the biosensor performance was characterized and optimized. A 17-bilayer electrode has a linear range between 1 and 60 mu M sulfite with a sensitivity of 2.19 mA M-1 sulfite and a response time of 2 min. The electrode retained a stable response for 3 days with a serial reproducibility of 3.8\% and lost 20\% of sensitivity after 5 days of operation. It is possible to store the sensor in a dry state for more than 2 months. The multilayer electrode was used for determination of sulfite in unspiked and spiked samples of red and white wine. The recovery and the specificity of the signals were evaluated for each sample.}, language = {en} } @misc{BeniniSchenkel2017, author = {Benini, Marco and Schenkel, Alexander}, title = {Quantum field theories on categories fibered in groupoids}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {895}, issn = {1866-8372}, doi = {10.25932/publishup-43154}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431541}, pages = {48}, year = {2017}, abstract = {We introduce an abstract concept of quantum field theory on categories fibered in groupoids over the category of spacetimes. This provides us with a general and flexible framework to study quantum field theories defined on spacetimes with extra geometric structures such as bundles, connections and spin structures. Using right Kan extensions, we can assign to any such theory an ordinary quantum field theory defined on the category of spacetimes and we shall clarify under which conditions it satisfies the axioms of locally covariant quantum field theory. The same constructions can be performed in a homotopy theoretic framework by using homotopy right Kan extensions, which allows us to obtain first toy-models of homotopical quantum field theories resembling some aspects of gauge theories.}, language = {en} } @misc{HartungBenaryWolfetal.2017, author = {Hartung, Niklas and Benary, Uwe and Wolf, Jana and Kofahl, Bente}, title = {Paracrine and autocrine regulation of gene expression by Wnt-inhibitor Dickkopf in wild-type and mutant hepatocytes}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {886}, issn = {1866-8372}, doi = {10.25932/publishup-43077}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-430778}, pages = {18}, year = {2017}, abstract = {Background Cells are able to communicate and coordinate their function within tissues via secreted factors. Aberrant secretion by cancer cells can modulate this intercellular communication, in particular in highly organised tissues such as the liver. Hepatocytes, the major cell type of the liver, secrete Dickkopf (Dkk), which inhibits Wnt/ β-catenin signalling in an autocrine and paracrine manner. Consequently, Dkk modulates the expression of Wnt/ β-catenin target genes. We present a mathematical model that describes the autocrine and paracrine regulation of hepatic gene expression by Dkk under wild-type conditions as well as in the presence of mutant cells. Results Our spatial model describes the competition of Dkk and Wnt at receptor level, intra-cellular Wnt/ β-catenin signalling, and the regulation of target gene expression for 21 individual hepatocytes. Autocrine and paracrine regulation is mediated through a feedback mechanism via Dkk and Dkk diffusion along the porto-central axis. Along this axis an APC concentration gradient is modelled as experimentally detected in liver. Simulations of mutant cells demonstrate that already a single mutant cell increases overall Dkk concentration. The influence of the mutant cell on gene expression of surrounding wild-type hepatocytes is limited in magnitude and restricted to hepatocytes in close proximity. To explore the underlying molecular mechanisms, we perform a comprehensive analysis of the model parameters such as diffusion coefficient, mutation strength and feedback strength. Conclusions Our simulations show that Dkk concentration is elevated in the presence of a mutant cell. However, the impact of these elevated Dkk levels on wild-type hepatocytes is confined in space and magnitude. The combination of inter- and intracellular processes, such as Dkk feedback, diffusion and Wnt/ β-catenin signal transduction, allow wild-type hepatocytes to largely maintain their gene expression.}, language = {en} } @misc{ArvidssonKwasniewskiRianoPachonetal.2008, author = {Arvidsson, Samuel Janne and Kwasniewski, Miroslaw and Ria{\~n}o- Pach{\´o}n, Diego Mauricio and Mueller-Roeber, Bernd}, title = {QuantPrime}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {943}, issn = {1866-8372}, doi = {10.25932/publishup-43153}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431531}, pages = {17}, year = {2008}, abstract = {Background Medium- to large-scale expression profiling using quantitative polymerase chain reaction (qPCR) assays are becoming increasingly important in genomics research. A major bottleneck in experiment preparation is the design of specific primer pairs, where researchers have to make several informed choices, often outside their area of expertise. Using currently available primer design tools, several interactive decisions have to be made, resulting in lengthy design processes with varying qualities of the assays. Results Here we present QuantPrime, an intuitive and user-friendly, fully automated tool for primer pair design in small- to large-scale qPCR analyses. QuantPrime can be used online through the internet http://www.quantprime.de/ or on a local computer after download; it offers design and specificity checking with highly customizable parameters and is ready to use with many publicly available transcriptomes of important higher eukaryotic model organisms and plant crops (currently 295 species in total), while benefiting from exon-intron border and alternative splice variant information in available genome annotations. Experimental results with the model plant Arabidopsis thaliana, the crop Hordeum vulgare and the model green alga Chlamydomonas reinhardtii show success rates of designed primer pairs exceeding 96\%. Conclusion QuantPrime constitutes a flexible, fully automated web application for reliable primer design for use in larger qPCR experiments, as proven by experimental data. The flexible framework is also open for simple use in other quantification applications, such as hydrolyzation probe design for qPCR and oligonucleotide probe design for quantitative in situ hybridization. Future suggestions made by users can be easily implemented, thus allowing QuantPrime to be developed into a broad-range platform for the design of RNA expression assays.}, language = {en} } @misc{NeigenfindGyetvaiBasekowetal.2008, author = {Neigenfind, Jost and Gyetvai, Gabor and Basekow, Rico and Diehl, Svenja and Achenbach, Ute and Gebhardt, Christiane and Selbig, Joachim and Kersten, Birgit}, title = {Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {883}, issn = {1866-8372}, doi = {10.25932/publishup-43501}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-435011}, pages = {28}, year = {2008}, abstract = {Background: Haplotype inference based on unphased SNP markers is an important task in population genetics. Although there are different approaches to the inference of haplotypes in diploid species, the existing software is not suitable for inferring haplotypes from unphased SNP data in polyploid species, such as the cultivated potato (Solanum tuberosum). Potato species are tetraploid and highly heterozygous. Results: Here we present the software SATlotyper which is able to handle polyploid and polyallelic data. SATlo-typer uses the Boolean satisfiability problem to formulate Haplotype Inference by Pure Parsimony. The software excludes existing haplotype inferences, thus allowing for calculation of alternative inferences. As it is not known which of the multiple haplotype inferences are best supported by the given unphased data set, we use a bootstrapping procedure that allows for scoring of alternative inferences. Finally, by means of the bootstrapping scores, it is possible to optimise the phased genotypes belonging to a given haplotype inference. The program is evaluated with simulated and experimental SNP data generated for heterozygous tetraploid populations of potato. We show that, instead of taking the first haplotype inference reported by the program, we can significantly improve the quality of the final result by applying additional methods that include scoring of the alternative haplotype inferences and genotype optimisation. For a sub-population of nineteen individuals, the predicted results computed by SATlotyper were directly compared with results obtained by experimental haplotype inference via sequencing of cloned amplicons. Prediction and experiment gave similar results regarding the inferred haplotypes and phased genotypes. Conclusion: Our results suggest that Haplotype Inference by Pure Parsimony can be solved efficiently by the SAT approach, even for data sets of unphased SNP from heterozygous polyploids. SATlotyper is freeware and is distributed as a Java JAR file. The software can be downloaded from the webpage of the GABI Primary Database at http://www.gabipd.org/projects/satlotyper/. The application of SATlotyper will provide haplotype information, which can be used in haplotype association mapping studies of polyploid plants.}, language = {en} } @misc{ThomasMatuschekGrima2013, author = {Thomas, Philipp and Matuschek, Hannes and Grima, Ramon}, title = {How reliable is the linear noise approximation of gene regulatory networks?}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {876}, issn = {1866-8372}, doi = {10.25932/publishup-43502}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-435028}, pages = {17}, year = {2013}, abstract = {Background: The linear noise approximation (LNA) is commonly used to predict how noise is regulated and exploited at the cellular level. These predictions are exact for reaction networks composed exclusively of first order reactions or for networks involving bimolecular reactions and large numbers of molecules. It is however well known that gene regulation involves bimolecular interactions with molecule numbers as small as a single copy of a particular gene. It is therefore questionable how reliable are the LNA predictions for these systems. Results: We implement in the software package intrinsic Noise Analyzer (iNA), a system size expansion based method which calculates the mean concentrations and the variances of the fluctuations to an order of accuracy higher than the LNA. We then use iNA to explore the parametric dependence of the Fano factors and of the coefficients of variation of the mRNA and protein fluctuations in models of genetic networks involving nonlinear protein degradation, post-transcriptional, post-translational and negative feedback regulation. We find that the LNA can significantly underestimate the amplitude and period of noise-induced oscillations in genetic oscillators. We also identify cases where the LNA predicts that noise levels can be optimized by tuning a bimolecular rate constant whereas our method shows that no such regulation is possible. All our results are confirmed by stochastic simulations. Conclusion: The software iNA allows the investigation of parameter regimes where the LNA fares well and where it does not. We have shown that the parametric dependence of the coefficients of variation and Fano factors for common gene regulatory networks is better described by including terms of higher order than LNA in the system size expansion. This analysis is considerably faster than stochastic simulations due to the extensive ensemble averaging needed to obtain statistically meaningful results. Hence iNA is well suited for performing computationally efficient and quantitative studies of intrinsic noise in gene regulatory networks.}, language = {en} } @misc{VanDonkIanoraVos2011, author = {Van Donk, Ellen and Ianora, Adrianna and Vos, Matthijs}, title = {Induced defences in marine and freshwater phytoplankton}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {881}, issn = {1866-8372}, doi = {10.25932/publishup-43513}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-435130}, pages = {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} } @misc{ClusellaPolitiRosenblum2016, author = {Clusella, Pau and Politi, Antonio and Rosenblum, Michael}, title = {A minimal model of self-consistent partial synchrony}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {890}, issn = {1866-8372}, doi = {10.25932/publishup-43626}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-436266}, pages = {19}, year = {2016}, abstract = {We show that self-consistent partial synchrony in globally coupled oscillatory ensembles is a general phenomenon. We analyze in detail appearance and stability properties of this state in possibly the simplest setup of a biharmonic Kuramoto-Daido phase model as well as demonstrate the effect in limit-cycle relaxational Rayleigh oscillators. Such a regime extends the notion of splay state from a uniform distribution of phases to an oscillating one. Suitable collective observables such as the Kuramoto order parameter allow detecting the presence of an inhomogeneous distribution. The characteristic and most peculiar property of self-consistent partial synchrony is the difference between the frequency of single units and that of the macroscopic field.}, language = {en} } @misc{KarpuzCevikKoppitzetal.2013, author = {Karpuz, Eylem Guzel and {\c{C}}evik, Ahmet Sinan and Koppitz, J{\"o}rg and Cangul, Ismail Naci}, title = {Some fixed-point results on (generalized) Bruck-Reilly ∗-extensions of monoids}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {942}, issn = {1866-8372}, doi = {10.25932/publishup-43270}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-432701}, pages = {11}, year = {2013}, abstract = {In this paper, we determine necessary and sufficient conditions for Bruck-Reilly and generalized Bruck-Reilly ∗-extensions of arbitrary monoids to be regular, coregular and strongly π-inverse. These semigroup classes have applications in various field of mathematics, such as matrix theory, discrete mathematics and p-adic analysis (especially in operator theory). In addition, while regularity and coregularity have so many applications in the meaning of boundaries (again in operator theory), inverse monoids and Bruck-Reilly extensions contain a mixture fixed-point results of algebra, topology and geometry within the purposes of this journal.}, language = {en} } @misc{KienelWulfBowenByrneetal.2009, author = {Kienel, Ulrike and Wulf Bowen, Sabine and Byrne, Roger and Park, Jungjae and B{\"o}hnel, Harald and Dulski, Peter and Luhr, James F. and Siebert, Lee and Haug, Gerald H. and Negendank, J{\"o}rg F. W.}, title = {First lacustrine varve chronologies from Mexico}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {860}, issn = {1866-8372}, doi = {10.25932/publishup-43279}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-432794}, pages = {587 -- 609}, year = {2009}, abstract = {We present varve chronologies for sediments from two maar lakes in the Valle de Santiago region (Central Mexico): Hoya La Alberca (AD 1852-1973) and Hoya Rincn de Parangueo (AD 1839-1943). These are the first varve chronologies for Mexican lakes. The varved sections were anchored with tephras from Colima (1913) and Paricutin (1943/1944) and (210)Pb ages. We compare the sequences using the thickness of seasonal laminae and element counts (Al, Si, S, Cl, K, Ti, Mn, Fe, and Sr) determined by micro X-ray fluorescence spectrometry. The formation of the varve sublaminae is attributed to the strongly seasonal climate regime. Limited rainfall and high evaporation rates in winter and spring induce precipitation of carbonates (high Ca, Sr) enriched in (13)C and (18)O, whereas rainfall in summer increases organic and clastic input (plagioclase, quartz) with high counts of lithogenic elements (K, Al, Ti, and Si). Eolian input of Ti occurs also in the dry season. Moving correlations (5-yr windows) of the Ca and Ti counts show similar development in both sequences until the 1930s. Positive correlations indicate mixing of allochthonous Ti and autochthonous Ca, while negative correlations indicate their separation in sublaminae. Negative excursions in the correlations correspond with historic and reconstructed droughts, El Nio events, and positive SST anomalies. Based on our data, droughts (3-7 year duration) were severe and centred around the following years: the early 1850s, 1865, 1880, 1895, 1905, 1915 and the late 1920s with continuation into the 1930s. The latter dry period brought both lake systems into a critical state making them susceptible to further drying. Groundwater overexploitation due to the expansion of irrigation agriculture in the region after 1940 induced the transition from calcite to aragonite precipitation in Alberca and halite infiltration in Rincn. The proxy data indicate a faster response to increased evaporation for Rincn, the lake with the larger maar dimensions, solar radiation receipt and higher conductivity, whereas the smaller, steeper Alberca maar responded rapidly to increased precipitation.}, language = {en} } @misc{HudsonDeRuigDeRuiteretal.2019, author = {Hudson, Paul and De Ruig, Lars T. and De Ruiter, Marco C. and Kuik, Onno J. and Botzen, W. J. Wouter and Le Den, X. and Persson, Magnus and Benoist, Anthony and Nielsen, C. N.}, title = {An assessment of best practices of extreme weather insurance and directions for a more resilient society}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {757}, issn = {1866-8372}, doi = {10.25932/publishup-43351}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-433510}, pages = {22}, year = {2019}, abstract = {Extreme weather resilience has been defined as being based on three pillars: resistance (the ability to lower impacts), recovery (the ability to bounce back), and adaptive capacity (the ability to learn and improve). These resilience pillars are important both before and after the occurrence of extreme weather events. Extreme weather insurance can influence these pillars of resilience depending on how particular insurance mechanisms are structured. We explore how the lessons learnt from the current best insurance practices can improve resilience to extreme weather events. We employ an extensive inventory of private property and agricultural crop insurance mechanisms to conduct a multi-criteria analysis of insurance market outcomes. We draw conclusions regarding the patterns in the best practice from six European countries to increase resilience. We suggest that requirements to buy a bundle extreme weather event insurance with general insurance packages are strengthened and supported with structures to financing losses through public-private partnerships. Moreover, support for low income households through income vouchers could be provided. Similarly, for the agricultural sector we propose moving towards comprehensive crop yield insurance linked to general agricultural subsidies. In both cases a nationally representative body can coordinate the various stakeholders into acting in concert.}, language = {en} } @misc{FuchsGrosseStraussetal.2018, author = {Fuchs, Matthias and Grosse, Guido and Strauss, Jens and G{\"u}nther, Frank and Grigoriev, Mikhail N. and Maximov, Georgy M. and Hugelius, Gustaf}, title = {Carbon and nitrogen pools in thermokarst-affected permafrost landscapes in Arctic Siberia}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, volume = {15}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {654}, issn = {1866-8372}, doi = {10.25932/publishup-41802}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-418026}, pages = {19}, year = {2018}, abstract = {Ice-rich yedoma-dominated landscapes store con- siderable amounts of organic carbon (C) and nitrogen (N) and are vulnerable to degradation under climate warming. We investigate the C and N pools in two thermokarst-affected yedoma landscapes - on Sobo-Sise Island and on Bykovsky Peninsula in the north of eastern Siberia. Soil cores up to 3 m depth were collected along geomorphic gradients and anal- ysed for organic C and N contents. A high vertical sampling density in the profiles allowed the calculation of C and N stocks for short soil column intervals and enhanced under- standing of within-core parameter variability. Profile-level C and N stocks were scaled to the landscape level based on landform classifications from 5 m resolution, multispectral RapidEye satellite imagery. Mean landscape C and N storage in the first metre of soil for Sobo-Sise Island is estimated to be 20.2 kg C m -2 and 1.8 kg N m -2 and for Bykovsky Penin- sula 25.9 kg C m -2 and 2.2 kg N m -2 . Radiocarbon dating demonstrates the Holocene age of thermokarst basin de- posits but also suggests the presence of thick Holocene- age cover layers which can reach up to 2 m on top of in- tact yedoma landforms. Reconstructed sedimentation rates of 0.10-0.57 mm yr -1 suggest sustained mineral soil accu- mulation across all investigated landforms. Both yedoma and thermokarst landforms are characterized by limited accumu- lation of organic soil layers (peat). We further estimate that an active layer deepening of about 100 cm will increase organic C availability in a sea- sonally thawed state in the two study areas by ∼ 5.8 Tg (13.2 kg C m -2 ). Our study demonstrates the importance of increasing the number of C and N storage inventories in ice- rich yedoma and thermokarst environments in order to ac- count for high variability of permafrost and thermokarst en- vironments in pan-permafrost soil C and N pool estimates.}, language = {en} } @misc{SchnitzlerPinzoneAutenriethetal.2018, author = {Schnitzler, Joseph G. and Pinzone, Marianna and Autenrieth, Marijke and van Neer, Abbo and IJsseldijk, Lonneke L. and Barber, Jonathan L. and Deaville, Rob and Jepson, Paul and Brownlow, Andrew and Schaffeld, Tobias and Thom{\´e}, Jean-Pierre and Tiedemann, Ralph and Das, Krishna and Siebert, Ursula}, title = {Inter-individual differences in contamination profiles as tracer of social group association in stranded sperm whales}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {692}, issn = {1866-8372}, doi = {10.25932/publishup-42652}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-426525}, pages = {11}, year = {2018}, abstract = {Ecological and physiological factors lead to different contamination patterns in individual marine mammals. The objective of the present study was to assess whether variations in contamination profiles are indicative of social structures of young male sperm whales as they might reflect a variation in feeding preferences and/or in utilized feeding grounds. We used a total of 61 variables associated with organic compounds and trace element concentrations measured in muscle, liver, kidney and blubber gained from 24 sperm whales that stranded in the North Sea in January and February 2016. Combining contaminant and genetic data, there is evidence for at least two cohorts with different origin among these stranded sperm whales; one from the Canary Island region and one from the northern part of the Atlantic. While genetic data unravel relatedness and kinship, contamination data integrate over areas, where animals occured during their lifetime. Especially in long-lived animals with a large migratory potential, as sperm whales, contamination data may carry highly relevant information about aggregation through time and space.}, language = {en} } @misc{DiGiacomoDiGiacomoKligeretal.2015, author = {Di Giacomo, Adrian S. and Di Giacomo, Alejandro G. and Kliger, Rafi and Reboreda, Juan C. and Tiedemann, Ralph and Mahler, Bettina}, title = {No evidence of genetic variation in microsatellite and mitochondrial DNA markers among remaining populations of the Strange-tailed Tyrant Alectrurus risora, an endangered grassland species}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {583}, doi = {10.25932/publishup-41442}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-414427}, pages = {127 -- 138}, year = {2015}, abstract = {The Strange-tailed Tyrant Alectrurus risora (Aves: Tyrannidae) is an endemic species of southern South American grasslands that suffered a 90\% reduction of its original distribution due to habitat transformation. This has led the species to be classified as globally Vulnerable. By the beginning of the last century, populations were partially migratory and moved south during the breeding season. Currently, the main breeding population inhabits the Ibera wetlands in the province of Corrientes, north-east Argentina, where it is resident all year round. There are two remaining small populations in the province of Formosa, north-east Argentina, and in southern Paraguay, which are separated from the main population by the Parana-Paraguay River and its continuous riverine forest habitat. The populations of Corrientes and Formosa are separated by 300 km and the grasslands between populations are non-continuous due to habitat transformation. We used mtDNA sequences and eight microsatellite loci to test if there were evidences of genetic isolation between Argentinean populations. We found no evidence of genetic structure between populations (Phi(ST) = 0.004, P = 0.32; Fst = 0.01, P = 0.06), which can be explained by either retained ancestral polymorphism or by dispersal between populations. We found no evidence for a recent demographic bottleneck in nuclear loci. Our results indicate that these populations could be managed as a single conservation unit on a regional scale. Conservation actions should be focused on preserving the remaining network of areas with natural grasslands to guarantee reproduction, dispersal and prevent further decline of populations.}, language = {en} } @article{CherstvyChechkinMetzler2014, author = {Cherstvy, Andrey G. and Chechkin, Aleksei V. and Metzler, Ralf}, title = {Particle invasion, survival, and non-ergodicity in 2D diffusion processes with space-dependent diffusivity}, series = {Soft matter}, volume = {2014}, journal = {Soft matter}, number = {10}, publisher = {Royal Society of Chemistry}, issn = {2046-2069}, doi = {10.1039/c3sm52846d}, pages = {1591 -- 1601}, year = {2014}, abstract = {We study the thermal Markovian diffusion of tracer particles in a 2D medium with spatially varying diffusivity D(r), mimicking recently measured, heterogeneous maps of the apparent diffusion coefficient in biological cells. For this heterogeneous diffusion process (HDP) we analyse the mean squared displacement (MSD) of the tracer particles, the time averaged MSD, the spatial probability density function, and the first passage time dynamics from the cell boundary to the nucleus. Moreover we examine the non-ergodic properties of this process which are important for the correct physical interpretation of time averages of observables obtained from single particle tracking experiments. From extensive computer simulations of the 2D stochastic Langevin equation we present an in-depth study of this HDP. In particular, we find that the MSDs along the radial and azimuthal directions in a circular domain obey anomalous and Brownian scaling, respectively. We demonstrate that the time averaged MSD stays linear as a function of the lag time and the system thus reveals a weak ergodicity breaking. Our results will enable one to rationalise the diffusive motion of larger tracer particles such as viruses or submicron beads in biological cells.}, language = {en} } @misc{MakowiczTiedemannSteeleetal.2016, author = {Makowicz, Amber M. and Tiedemann, Ralph and Steele, Rachel N. and Schlupp, Ingo}, title = {Kin recognition in a clonal fish, Poecilia formosa}, series = {PLoS ONE}, journal = {PLoS ONE}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-411329}, pages = {20}, year = {2016}, abstract = {Relatedness strongly influences social behaviors in a wide variety of species. For most species, the highest typical degree of relatedness is between full siblings with 50\% shared genes. However, this is poorly understood in species with unusually high relatedness between individuals: clonal organisms. Although there has been some investigation into clonal invertebrates and yeast, nothing is known about kin selection in clonal vertebrates. We show that a clonal fish, the Amazon molly (Poecilia formosa), can distinguish between different clonal lineages, associating with genetically identical, sister clones, and use multiple sensory modalities. Also, they scale their aggressive behaviors according to the relatedness to other females: they are more aggressive to non-related clones. Our results demonstrate that even in species with very small genetic differences between individuals, kin recognition can be adaptive. Their discriminatory abilities and regulation of costly behaviors provides a powerful example of natural selection in species with limited genetic diversity.}, language = {en} } @misc{LaemkeBaeurle2017, author = {L{\"a}mke, J{\"o}rn and B{\"a}urle, Isabel}, title = {Epigenetic and chromatin-based mechanisms in environmental stress adaptation and stress memory in plants}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {792}, issn = {1866-8372}, doi = {10.25932/publishup-43623}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-436236}, pages = {11}, year = {2017}, abstract = {Plants frequently have to weather both biotic and abiotic stressors, and have evolved sophisticated adaptation and defense mechanisms. In recent years, chromatin modifications, nucleosome positioning, and DNA methylation have been recognized as important components in these adaptations. Given their potential epigenetic nature, such modifications may provide a mechanistic basis for a stress memory, enabling plants to respond more efficiently to recurring stress or even to prepare their offspring for potential future assaults. In this review, we discuss both the involvement of chromatin in stress responses and the current evidence on somatic, intergenerational, and transgenerational stress memory.}, language = {en} } @misc{ReibisSalzwedelBonaventuraetal.2017, author = {Reibis, Rona Katharina and Salzwedel, Annett and Bonaventura, Klaus and V{\"o}ller, Heinz and Wegscheider, Karl}, title = {Improvement of left ventricular ejection fraction in revascularized postmyocardial patients}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {882}, issn = {1866-8372}, doi = {10.25932/publishup-43509}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-435093}, pages = {10}, year = {2017}, abstract = {BACKGROUND: Reduced left ventricular ejection fraction (LVEF) ≤30\% is the most powerful prognostic indicator for sudden cardiac death (SCD) in patients after myocardial infarction (MI), but there are little data about long-term changes of LVEF after revascularization and the following implantation of a cardioverter defibrillator (ICD). METHODS: We performed a retrospective analysis of 277 patients with reduced LVEF at least 1month after MI and complete revascularization. Patients (median time post-MI 23.4months; 74.3\% after PCI, 25.7\% after CABG were assigned either to group 1 (LVEF<30\%) or group 2 (LVEF 30-40\%). Biplane echocardiography was redone after a mean follow-up of 441±220days. RESULTS: LVEF increased significantly in both two groups (group 1: 26.2±4.8\% to 32.4±8.5\%; p<0.001; group 2: 38.2±2.5\% to 44.4±9.6\%; p<0.001). However, statistical analysis of first and second LVEF measurement by means of a LOWESS regression and with an appropriate correction of the regression towards the mean effect revealed only a moderate increase of the mean LVEF from 35 to 37\% (p<0.001) with a large interindividual variation. CONCLUSIONS: The impact of early revascularization on LVEF appears to be low in the majority of post-MI heart failure patients. Owing to the high variability, a single measurement may not be reliable enough to justify a decision on ICD indication.}, language = {en} } @misc{DelikostidisEngelRetsiosetal.2013, author = {Delikostidis, Ioannis and Engel, Juri and Retsios, Bas and Elzakker, Corn{\´e} P.J.M. van and Kraak, Menno-Jan and D{\"o}llner, J{\"u}rgen Roland Friedrich}, title = {Increasing the usability of pedestrian navigation interfaces by means of landmark visibility analysis}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {599}, issn = {1866-8372}, doi = {10.25932/publishup-41550}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-415500}, pages = {523 -- 537}, year = {2013}, abstract = {Communicating location-specific information to pedestrians is a challenging task which can be aided by user-friendly digital technologies. In this paper, landmark visibility analysis, as a means for developing more usable pedestrian navigation systems, is discussed. Using an algorithmic framework for image-based 3D analysis, this method integrates a 3D city model with identified landmarks and produces raster visibility layers for each one. This output enables an Android phone prototype application to indicate the visibility of landmarks from the user's actual position. Tested in the field, the method achieves sufficient accuracy for the context of use and improves navigation efficiency and effectiveness.}, language = {en} } @misc{NagelKirschbaumEngelmannetal.2018, author = {Nagel, Rebecca and Kirschbaum, Frank and Engelmann, Jacob and Hofmann, Volker and Pawelzik, Felix and Tiedemann, Ralph}, title = {Male-mediated species recognition among African weakly electric fishes}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {645}, issn = {1866-8372}, doi = {10.25932/publishup-42501}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-425016}, pages = {8}, year = {2018}, abstract = {Effective communication among sympatric species is often instrumental for behavioural isolation, where the failure to successfully discriminate between potential mates could lead to less fit hybrid offspring. Discrimination between con- and heterospecifics tends to occur more often in the sex that invests more in offspring production, i.e. females, but males may also mediate reproductive isolation. In this study, we show that among two Campylomormyrus Africanweakly electric fish species, males preferentially associate with conspecific females during choice tests using live fish as stimuli, i.e. when all sensory modalities potentially used for communication were present. We then conducted playback experiments to determine whether the species-specific electric organ discharge (EOD) used for electrocommunication serves as the cue for this conspecific association preference. Interestingly, only C. compressirostris males associated significantly more with the conspecific EOD waveform when playback stimuli were provided, while no such association preference was observed in C. tamandua males. Given our results, the EOD appears to serve, in part, as a male-mediated pre-zygotic isolation mechanism among sympatric species. However, the failure of C. tamandua males to discriminate between con- and heterospecific playback discharges suggests that multiple modalities may be necessary for species recognition in some African weakly electric fish species.}, language = {en} } @misc{KnoxBrownRindfleischGuentheretal.2020, author = {Knox-Brown, Patrick and Rindfleisch, Tobias and G{\"u}nther, Anne and Balow, Kim and Bremer, Anne and Walther, Dirk and Miettinen, Markus S. and Hincha, Dirk K. and Thalhammer, Anja}, title = {Similar Yet Different}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {901}, issn = {1866-8372}, doi = {10.25932/publishup-46941}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-469419}, pages = {27}, year = {2020}, abstract = {The importance of intrinsically disordered late embryogenesis abundant (LEA) proteins in the tolerance to abiotic stresses involving cellular dehydration is undisputed. While structural transitions of LEA proteins in response to changes in water availability are commonly observed and several molecular functions have been suggested, a systematic, comprehensive and comparative study of possible underlying sequence-structure-function relationships is still lacking. We performed molecular dynamics (MD) simulations as well as spectroscopic and light scattering experiments to characterize six members of two distinct, lowly homologous clades of LEA_4 family proteins from Arabidopsis thaliana. We compared structural and functional characteristics to elucidate to what degree structure and function are encoded in LEA protein sequences and complemented these findings with physicochemical properties identified in a systematic bioinformatics study of the entire Arabidopsis thaliana LEA_4 family. Our results demonstrate that although the six experimentally characterized LEA_4 proteins have similar structural and functional characteristics, differences concerning their folding propensity and membrane stabilization capacity during a freeze/thaw cycle are obvious. These differences cannot be easily attributed to sequence conservation, simple physicochemical characteristics or the abundance of sequence motifs. Moreover, the folding propensity does not appear to be correlated with membrane stabilization capacity. Therefore, the refinement of LEA_4 structural and functional properties is likely encoded in specific patterns of their physicochemical characteristics.}, language = {en} } @misc{SultanaSiegKellermannetal.2018, author = {Sultana, Zakia and Sieg, Tobias and Kellermann, Patric and M{\"u}ller, Meike and Kreibich, Heidi}, title = {Assessment of business interruption of flood-affected companies using random forests}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {939}, issn = {1866-8372}, doi = {10.25932/publishup-45977}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-459778}, pages = {18}, year = {2018}, abstract = {Losses due to floods have dramatically increased over the past decades, and losses of companies, comprising direct and indirect losses, have a large share of the total economic losses. Thus, there is an urgent need to gain more quantitative knowledge about flood losses, particularly losses caused by business interruption, in order to mitigate the economic loss of companies. However, business interruption caused by floods is rarely assessed because of a lack of sufficiently detailed data. A survey was undertaken to explore processes influencing business interruption, which collected information on 557 companies affected by the severe flood in June 2013 in Germany. Based on this data set, the study aims to assess the business interruption of directly affected companies by means of a Random Forests model. Variables that influence the duration and costs of business interruption were identified by the variable importance measures of Random Forests. Additionally, Random Forest-based models were developed and tested for their capacity to estimate business interruption duration and associated costs. The water level was found to be the most important variable influencing the duration of business interruption. Other important variables, relating to the estimation of business interruption duration, are the warning time, perceived danger of flood recurrence and inundation duration. In contrast, the amount of business interruption costs is strongly influenced by the size of the company, as assessed by the number of employees, emergency measures undertaken by the company and the fraction of customers within a 50 km radius. These results provide useful information and methods for companies to mitigate their losses from business interruption. However, the heterogeneity of companies is relatively high, and sector-specific analyses were not possible due to the small sample size. Therefore, further sector-specific analyses on the basis of more flood loss data of companies are recommended.}, language = {en} } @misc{LemaireInfossiChaoucheetal.2018, author = {Lemaire, Olivier N. and Infossi, Pascale and Chaouche, Amine Ali and Espinosa, Leon and Leimk{\"u}hler, Silke and Giudici-Orticoni, Marie-Th{\´e}r{\`e}se and M{\´e}jean, Vincent and Iobbi-Nivol, Chantal}, title = {Small membranous proteins of the TorE/NapE family, crutches for cognate respiratory systems in Proteobacteria}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {933}, issn = {1866-8372}, doi = {10.25932/publishup-45920}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-459208}, pages = {15}, year = {2018}, abstract = {In this report, we investigate small proteins involved in bacterial alternative respiratory systems that improve the enzymatic efficiency through better anchorage and multimerization of membrane components. Using the small protein TorE of the respiratory TMAO reductase system as a model, we discovered that TorE is part of a subfamily of small proteins that are present in proteobacteria in which they play a similar role for bacterial respiratory systems. We reveal by microscopy that, in Shewanella oneidensis MR1, alternative respiratory systems are evenly distributed in the membrane contrary to what has been described for Escherichia coli. Thus, the better efficiency of the respiratory systems observed in the presence of the small proteins is not due to a specific localization in the membrane, but rather to the formation of membranous complexes formed by TorE homologs with their c-type cytochrome partner protein. By an in vivo approach combining Clear Native electrophoresis and fluorescent translational fusions, we determined the 4: 4 stoichiometry of the complexes. In addition, mild solubilization of the cytochrome indicates that the presence of the small protein reinforces its anchoring to the membrane. Therefore, assembly of the complex induced by this small protein improves the efficiency of the respiratory system.}, language = {en} } @misc{TotzLoeberTotzetal.2018, author = {Totz, Sonja Juliana and L{\"o}ber, Jakob and Totz, Jan Frederik and Engel, Harald}, title = {Control of transversal instabilities in reaction-diffusion systems}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {962}, issn = {1866-8372}, doi = {10.25932/publishup-46976}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-469762}, pages = {19}, year = {2018}, abstract = {In two-dimensional reaction-diffusion systems, local curvature perturbations on traveling waves are typically damped out and vanish. However, if the inhibitor diffuses much faster than the activator, transversal instabilities can arise, leading from flat to folded, spatio-temporally modulated waves and to spreading spiral turbulence. Here, we propose a scheme to induce or inhibit these instabilities via a spatio-temporal feedback loop. In a piecewise-linear version of the FitzHugh-Nagumo model, transversal instabilities and spiral turbulence in the uncontrolled system are shown to be suppressed in the presence of control, thereby stabilizing plane wave propagation. Conversely, in numerical simulations with the modified Oregonator model for the photosensitive Belousov-Zhabotinsky reaction, which does not exhibit transversal instabilities on its own, we demonstrate the feasibility of inducing transversal instabilities and study the emerging wave patterns in a well-controlled manner.}, language = {en} } @misc{KrsticGalhuberSchulzetal.2018, author = {Krstic, Jelena and Galhuber, Markus and Schulz, Tim Julius and Schupp, Michael and Prokesch, Andreas}, title = {p53 as a dichotomous regulator of liver disease}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {963}, issn = {1866-8372}, doi = {10.25932/publishup-46812}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-468127}, pages = {25}, year = {2018}, abstract = {Lifestyle-related disorders, such as the metabolic syndrome, have become a primary risk factor for the development of liver pathologies that can progress from hepatic steatosis, hepatic insulin resistance, steatohepatitis, fibrosis and cirrhosis, to the most severe condition of hepatocellular carcinoma (HCC). While the prevalence of liver pathologies is steadily increasing in modern societies, there are currently no approved drugs other than chemotherapeutic intervention in late stage HCC. Hence, there is a pressing need to identify and investigate causative molecular pathways that can yield new therapeutic avenues. The transcription factor p53 is well established as a tumor suppressor and has recently been described as a central metabolic player both in physiological and pathological settings. Given that liver is a dynamic tissue with direct exposition to ingested nutrients, hepatic p53, by integrating cellular stress response, metabolism and cell cycle regulation, has emerged as an important regulator of liver homeostasis and dysfunction. The underlying evidence is reviewed herein, with a focus on clinical data and animal studies that highlight a direct influence of p53 activity on different stages of liver diseases. Based on current literature showing that activation of p53 signaling can either attenuate or fuel liver disease, we herein discuss the hypothesis that, while hyper-activation or loss of function can cause disease, moderate induction of hepatic p53 within physiological margins could be beneficial in the prevention and treatment of liver pathologies. Hence, stimuli that lead to a moderate and temporary p53 activation could present new therapeutic approaches through several entry points in the cascade from hepatic steatosis to HCC.}, language = {en} } @misc{GoodwinMuddClubb2018, author = {Goodwin, Guillaume C. H. and Mudd, Simon M. and Clubb, Fiona J.}, title = {Unsupervised detection of salt marsh platforms}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {936}, issn = {1866-8372}, doi = {10.25932/publishup-45932}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-459329}, pages = {239 -- 255}, year = {2018}, abstract = {Salt marshes filter pollutants, protect coastlines against storm surges, and sequester carbon, yet are under threat from sea level rise and anthropogenic modification. The sustained existence of the salt marsh ecosystem depends on the topographic evolution of marsh platforms. Quantifying marsh platform topography is vital for improving the management of these valuable landscapes. The determination of platform boundaries currently relies on supervised classification methods requiring near-infrared data to detect vegetation, or demands labour-intensive field surveys and digitisation. We propose a novel, unsupervised method to reproducibly isolate salt marsh scarps and platforms from a digital elevation model (DEM), referred to as Topographic Identification of Platforms (TIP). Field observations and numerical models show that salt marshes mature into subhorizontal platforms delineated by subvertical scarps. Based on this premise, we identify scarps as lines of local maxima on a slope raster, then fill landmasses from the scarps upward, thus isolating mature marsh platforms. We test the TIP method using lidar-derived DEMs from six salt marshes in England with varying tidal ranges and geometries, for which topographic platforms were manually isolated from tidal flats. Agreement between manual and unsupervised classification exceeds 94\% for DEM resolutions of 1 m, with all but one site maintaining an accuracy superior to 90\% for resolutions up to 3 m. For resolutions of 1 m, platforms detected with the TIP method are comparable in surface area to digitised platforms and have similar elevation distributions. We also find that our method allows for the accurate detection of local block failures as small as 3 times the DEM resolution. Detailed inspection reveals that although tidal creeks were digitised as part of the marsh platform, unsupervised classification categorises them as part of the tidal flat, causing an increase in false negatives and overall platform perimeter. This suggests our method may benefit from combination with existing creek detection algorithms. Fallen blocks and high tidal flat portions, associated with potential pioneer zones, can also lead to differences between our method and supervised mapping. Although pioneer zones prove difficult to classify using a topographic method, we suggest that these transition areas should be considered when analysing erosion and accretion processes, particularly in the case of incipient marsh platforms. Ultimately, we have shown that unsupervised classification of marsh platforms from high-resolution topography is possible and sufficient to monitor and analyse topographic evolution.}, language = {en} } @misc{SchuetzWinterleitnerHuenges2018, author = {Sch{\"u}tz, Felina and Winterleitner, Gerd and Huenges, Ernst}, title = {Geothermal exploration in a sedimentary basin}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {934}, issn = {1866-8372}, doi = {10.25932/publishup-45931}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-459317}, pages = {25}, year = {2018}, abstract = {The lateral and vertical temperature distribution in Oman is so far only poorly understood, particularly in the area between Muscat and the Batinah coast, which is the area of this study and which is composed of Cenozoic sediments developed as part of a foreland basin of the Makran Thrust Zone. Temperature logs (T-logs) were run and physical rock properties of the sediments were analyzed to understand the temperature distribution, thermal and hydraulic properties, and heat-transport processes within the sedimentary cover of northern Oman. An advective component is evident in the otherwise conduction-dominated geothermal play system, and is caused by both topography and density driven flow. Calculated temperature gradients (T-gradients) in two wells that represent conductive conditions are 18.7 and 19.5 degrees C km(-1), corresponding to about 70-90 degrees C at 2000-3000 m depth. This indicates a geothermal potential that can be used for energy intensive applications like cooling or water desalinization. Sedimentation in the foreland basin was initiated after the obduction of the Semail Ophiolite in the late Campanian, and reflects the complex history of alternating periods of transgressive and regressive sequences with erosion of the Oman Mountains. Thermal and hydraulic parameters were analyzed of the basin's heterogeneous clastic and carbonate sedimentary sequence. Surface heat-flow values of 46.4 and 47.9 mW m(-2) were calculated from the T-logs and calculated thermal conductivity values in two wells. The results of this study serve as a starting point for assessing different geothermal applications that may be suitable for northern Oman.}, language = {en} } @misc{LaeppleMuenchCasadoetal.2018, author = {Laepple, Thomas and M{\"u}nch, Thomas and Casado, Mathieu and Hoerhold, Maria and Landais, Amaelle and Kipfstuhl, Sepp}, title = {On the similarity and apparent cycles of isotopic variations in East Antarctic snow pits}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {932}, issn = {1866-8372}, doi = {10.25932/publishup-44605}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-446052}, pages = {169 -- 187}, year = {2018}, abstract = {Stable isotope ratios delta O-18 and delta D in polar ice provide a wealth of information about past climate evolution. Snow-pit studies allow us to relate observed weather and climate conditions to the measured isotope variations in the snow. They therefore offer the possibility to test our understanding of how isotope signals are formed and stored in firn and ice. As delta O-18 and delta D in the snowfall are strongly correlated to air temperature, isotopes in the near-surface snow are thought to record the seasonal cycle at a given site. Accordingly, the number of seasonal cycles observed over a given depth should depend on the accumulation rate of snow. However, snow-pit studies from different accumulation conditions in East Antarctica reported similar isotopic variability and comparable apparent cycles in the delta O-18 and delta D profiles with typical wavelengths of similar to 20 cm. These observations are unexpected as the accumulation rates strongly differ between the sites, ranging from 20 to 80mmw.e.yr(-1) (similar to 6-21 cm of snow per year). Various mechanisms have been proposed to explain the isotopic variations individually at each site; however, none of these are consistent with the similarity of the different profiles independent of the local accumulation conditions. Here, we systematically analyse the properties and origins of delta O-18 and delta D variations in high-resolution firn profiles from eight East Antarctic sites. First, we confirm the suggested cycle length (mean distance between peaks) of similar to 20 cm by counting the isotopic maxima. Spectral analysis further shows a strong similarity between the sites but indicates no dominant periodic features. Furthermore, the appar-ent cycle length increases with depth for most East Antarctic sites, which is inconsistent with burial and compression of a regular seasonal cycle. We show that these results can be explained by isotopic diffusion acting on a noise-dominated isotope signal. The firn diffusion length is rather stable across the Antarctic Plateau and thus leads to similar power spectral densities of the isotopic variations. This in turn implies a similar distance between isotopic maxima in the firn profiles. Our results explain a large set of observations discussed in the literature, providing a simple explanation for the interpretation of apparent cycles in shallow isotope records, without invoking complex mechanisms. Finally, the results underline previous suggestions that isotope signals in single ice cores from low-accumulation regions have a small signal-to-noise ratio and thus likely do not allow the reconstruction of interannual to decadal climate variations.}, language = {en} } @misc{MaoNakamuraViottietal.2016, author = {Mao, Hailiang and Nakamura, Moritaka and Viotti, Corrado and Grebe, Markus}, title = {A framework for lateral membrane trafficking and polar tethering of the PEN3 ATP-Binding cassette transporter}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {909}, issn = {1866-8372}, doi = {10.25932/publishup-44130}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-441302}, pages = {2245 -- 2260}, year = {2016}, abstract = {The outermost cell layer of plants, the epidermis, and its outer (lateral) membrane domain facing the environment are continuously challenged by biotic and abiotic stresses. Therefore, the epidermis and the outer membrane domain provide important selective and protective barriers. However, only a small number of specifically outer membrane-localized proteins are known. Similarly, molecular mechanisms underlying the trafficking and the polar placement of outer membrane domain proteins require further exploration. Here, we demonstrate that ACTIN7 (ACT7) mediates trafficking of the PENETRATION3 (PEN3) outer membrane protein from the trans-Golgi network (TGN) to the plasma membrane in the root epidermis of Arabidopsis (Arabidopsis thaliana) and that actin function contributes to PEN3 endocytic recycling. In contrast to such generic ACT7-dependent trafficking from the TGN, the EXOCYST84b (EXO84b) tethering factor mediates PEN3 outer-membrane polarity. Moreover, precise EXO84b placement at the outer membrane domain itself requires ACT7 function. Hence, our results uncover spatially and mechanistically distinct requirements for ACT7 function during outer lateral membrane cargo trafficking and polarity establishment. They further identify an exocyst tethering complex mediator of outer lateral membrane cargo polarity.}, language = {en} } @misc{GorochowskiIgnatovaBovenbergetal.2015, author = {Gorochowski, Thomas E. and Ignatova, Zoya and Bovenberg, Roel A. L. and Roubos, Johannes A.}, title = {Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {816}, issn = {1866-8372}, doi = {10.25932/publishup-44134}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-441340}, pages = {13}, year = {2015}, abstract = {Translation of protein from mRNA is a complex multi-step process that occurs at a non-uniform rate. Variability in ribosome speed along an mRNA enables refinement of the proteome and plays a critical role in protein biogenesis. Detailed single protein studies have found both tRNA abundance and mRNA secondary structure as key modulators of translation elongation rate, but recent genome-wide ribosome profiling experiments have not observed significant influence of either on translation efficiency. Here we provide evidence that this results from an inherent trade-off between these factors. We find codons pairing to high-abundance tRNAs are preferentially used in regions of high secondary structure content, while codons read by significantly less abundant tRNAs are located in lowly structured regions. By considering long stretches of high and low mRNA secondary structure in Saccharomyces cerevisiae and Escherichia coli and comparing them to randomized-gene models and experimental expression data, we were able to distinguish clear selective pressures and increased protein expression for specific codon choices. The trade-off between secondary structure and tRNA-concentration based codon choice allows for compensation of their independent effects on translation, helping to smooth overall translational speed and reducing the chance of potentially detrimental points of excessively slow or fast ribosome movement.}, language = {en} } @misc{BenteleSaffertRauscheretal.2013, author = {Bentele, Kajetan and Saffert, Paul and Rauscher, Robert and Ignatova, Zoya and Bluethgen, Nils}, title = {Efficient translation initiation dictates codon usage at gene start}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {912}, issn = {1866-8372}, doi = {10.25932/publishup-44133}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-441337}, pages = {12}, year = {2013}, abstract = {The genetic code is degenerate; thus, protein evolution does not uniquely determine the coding sequence. One of the puzzles in evolutionary genetics is therefore to uncover evolutionary driving forces that result in specific codon choice. In many bacteria, the first 5-10 codons of protein-coding genes are often codons that are less frequently used in the rest of the genome, an effect that has been argued to arise from selection for slowed early elongation to reduce ribosome traffic jams. However, genome analysis across many species has demonstrated that the region shows reduced mRNA folding consistent with pressure for efficient translation initiation. This raises the possibility that unusual codon usage is a side effect of selection for reduced mRNA structure. Here we discriminate between these two competing hypotheses, and show that in bacteria selection favours codons that reduce mRNA folding around the translation start, regardless of whether these codons are frequent or rare. Experiments confirm that primarily mRNA structure, and not codon usage, at the beginning of genes determines the translation rate.}, language = {en} } @misc{RingelSomogyvariJalalietal.2019, author = {Ringel, Lisa Maria and Somogyv{\´a}ri, M{\´a}rk and Jalali, Mohammadreza and Bayer, Peter}, title = {Comparison of hydraulic and tracer tomography for discrete fracture network inversion}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {922}, issn = {1866-8372}, doi = {10.25932/publishup-44261}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-442616}, pages = {19}, year = {2019}, abstract = {Fractures serve as highly conductive preferential flow paths for fluids in rocks, which are difficult to exactly reconstruct in numerical models. Especially, in low-conductive rocks, fractures are often the only pathways for advection of solutes and heat. The presented study compares the results from hydraulic and tracer tomography applied to invert a theoretical discrete fracture network (DFN) that is based on data from synthetic cross-well testing. For hydraulic tomography, pressure pulses in various injection intervals are induced and the pressure responses in the monitoring intervals of a nearby observation well are recorded. For tracer tomography, a conservative tracer is injected in different well levels and the depth-dependent breakthrough of the tracer is monitored. A recently introduced transdimensional Bayesian inversion procedure is applied for both tomographical methods, which adjusts the fracture positions, orientations, and numbers based on given geometrical fracture statistics. The used Metropolis-Hastings-Green algorithm is refined by the simultaneous estimation of the measurement error's variance, that is, the measurement noise. Based on the presented application to invert the two-dimensional cross-section between source and the receiver well, the hydraulic tomography reveals itself to be more suitable for reconstructing the original DFN. This is based on a probabilistic representation of the inverted results by means of fracture probabilities.}, language = {en} } @misc{NueskenReichRozdeba2019, author = {N{\"u}sken, Nikolas and Reich, Sebastian and Rozdeba, Paul J.}, title = {State and parameter estimation from observed signal increments}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {916}, issn = {1866-8372}, doi = {10.25932/publishup-44260}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-442609}, pages = {25}, year = {2019}, abstract = {The success of the ensemble Kalman filter has triggered a strong interest in expanding its scope beyond classical state estimation problems. In this paper, we focus on continuous-time data assimilation where the model and measurement errors are correlated and both states and parameters need to be identified. Such scenarios arise from noisy and partial observations of Lagrangian particles which move under a stochastic velocity field involving unknown parameters. We take an appropriate class of McKean-Vlasov equations as the starting point to derive ensemble Kalman-Bucy filter algorithms for combined state and parameter estimation. We demonstrate their performance through a series of increasingly complex multi-scale model systems.}, language = {en} } @misc{RajasundaramSelbig2016, author = {Rajasundaram, Dhivyaa and Selbig, Joachim}, title = {More effort — more results}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {923}, issn = {1866-8372}, doi = {10.25932/publishup-44263}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-442639}, pages = {57 -- 61}, year = {2016}, abstract = {The development of 'omics' technologies has progressed to address complex biological questions that underlie various plant functions thereby producing copious amounts of data. The need to assimilate large amounts of data into biologically meaningful interpretations has necessitated the development of statistical methods to integrate multidimensional information. Throughout this review, we provide examples of recent outcomes of 'omics' data integration together with an overview of available statistical methods and tools.}, language = {en} } @misc{MareljaLeimkuehlerMissirlis2018, author = {Marelja, Zvonimir and Leimk{\"u}hler, Silke and Missirlis, Fanis}, title = {Iron sulfur and molybdenum cofactor enzymes regulate the Drosophila life cycle by controlling cell metabolism}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {925}, issn = {1866-8372}, doi = {10.25932/publishup-44567}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-445670}, pages = {33}, year = {2018}, abstract = {Iron sulfur (Fe-S) clusters and the molybdenum cofactor (Moco) are present at enzyme sites, where the active metal facilitates electron transfer. Such enzyme systems are soluble in the mitochondrial matrix, cytosol and nucleus, or embedded in the inner mitochondrial membrane, but virtually absent from the cell secretory pathway. They are of ancient evolutionary origin supporting respiration, DNA replication, transcription, translation, the biosynthesis of steroids, heme, catabolism of purines, hydroxylation of xenobiotics, and cellular sulfur metabolism. Here, Fe-S cluster and Moco biosynthesis in Drosophila melanogaster is reviewed and the multiple biochemical and physiological functions of known Fe-S and Moco enzymes are described. We show that RNA interference of Mocs3 disrupts Moco biosynthesis and the circadian clock. Fe-S-dependent mitochondrial respiration is discussed in the context of germ line and somatic development, stem cell differentiation and aging. The subcellular compartmentalization of the Fe-S and Moco assembly machinery components and their connections to iron sensing mechanisms and intermediary metabolism are emphasized. A biochemically active Fe-S core complex of heterologously expressed fly Nfs1, Isd11, IscU, and human frataxin is presented. Based on the recent demonstration that copper displaces the Fe-S cluster of yeast and human ferredoxin, an explanation for why high dietary copper leads to cytoplasmic iron deficiency in flies is proposed. Another proposal that exosomes contribute to the transport of xanthine dehydrogenase from peripheral tissues to the eye pigment cells is put forward, where the Vps16a subunit of the HOPS complex may have a specialized role in concentrating this enzyme within pigment granules. Finally, we formulate a hypothesis that (i) mitochondrial superoxide mobilizes iron from the Fe-S clusters in aconitase and succinate dehydrogenase; (ii) increased iron transiently displaces manganese on superoxide dismutase, which may function as a mitochondrial iron sensor since it is inactivated by iron; (iii) with the Krebs cycle thus disrupted, citrate is exported to the cytosol for fatty acid synthesis, while succinyl-CoA and the iron are used for heme biosynthesis; (iv) as iron is used for heme biosynthesis its concentration in the matrix drops allowing for manganese to reactivate superoxide dismutase and Fe-S cluster biosynthesis to reestablish the Krebs cycle.}, language = {en} } @misc{RajuLiebigKlemkeetal.2020, author = {Raju, Rajarshi Roy and Liebig, Ferenc and Klemke, Bastian and Koetz, Joachim}, title = {Ultralight magnetic aerogels from Janus emulsions}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {828}, doi = {10.25932/publishup-44552}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-445522}, pages = {10}, year = {2020}, abstract = {Magnetite containing aerogels were synthesized by freeze-drying olive oil/silicone oil-based Janus emulsion gels containing gelatin and sodium carboxymethylcellulose (NaCMC). The magnetite nanoparticles dispersed in olive oil are processed into the gel and remain in the macroporous aerogel after removing the oil components. The coexistence of macropores from the Janus droplets and mesopores from freeze-drying of the hydrogels in combination with the magnetic properties offer a special hierarchical pore structure, which is of relevance for smart supercapacitors, biosensors, and spilled oil sorption and separation. The morphology of the final structure was investigated in dependence on initial compositions. More hydrophobic aerogels with magnetic responsiveness were synthesized by bisacrylamide-crosslinking of the hydrogel. The crosslinked aerogels can be successfully used in magnetically responsive clean up experiments of the cationic dye methylene blue.}, language = {en} } @misc{ZwiebackKokeljGuentheretal.2018, author = {Zwieback, Simon and Kokelj, Steven V. and G{\"u}nther, Frank and Boike, Julia and Grosse, Guido and Hajnsek, Irena}, title = {Sub-seasonal thaw slump mass wasting is not consistently energy limited at the landscape scale}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {926}, issn = {1866-8372}, doi = {10.25932/publishup-44568}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-445688}, pages = {549 -- 564}, year = {2018}, abstract = {Predicting future thaw slump activity requires a sound understanding of the atmospheric drivers and geomorphic controls on mass wasting across a range of timescales. On sub-seasonal timescales, sparse measurements indicate that mass wasting at active slumps is often limited by the energy available for melting ground ice, but other factors such as rainfall or the formation of an insulating veneer may also be relevant. To study the sub-seasonal drivers, we derive topographic changes from single-pass radar interferometric data acquired by the TanDEM-X satellites. The estimated elevation changes at 12m resolution complement the commonly observed planimetric retreat rates by providing information on volume losses. Their high vertical precision (around 30 cm), frequent observations (11 days) and large coverage (5000 km(2)) allow us to track mass wasting as drivers such as the available energy change during the summer of 2015 in two study regions. We find that thaw slumps in the Tuktoyaktuk coastlands, Canada, are not energy limited in June, as they undergo limited mass wasting (height loss of around 0 cm day 1) despite the ample available energy, suggesting the widespread presence of early season insulating snow or debris veneer. Later in summer, height losses generally increase (around 3 cm day 1), but they do so in distinct ways. For many slumps, mass wasting tracks the available energy, a temporal pattern that is also observed at coastal yedoma cliffs on the Bykovsky Peninsula, Russia. However, the other two common temporal trajectories are asynchronous with the available energy, as they track strong precipitation events or show a sudden speed-up in late August respectively. The observed temporal patterns are poorly related to slump characteristics like the headwall height. The contrasting temporal behaviour of nearby thaw slumps highlights the importance of complex local and temporally varying controls on mass wasting.}, language = {en} } @misc{GrafeBatsiosMeyeretal.2019, author = {Grafe, Marianne and Batsios, Petros and Meyer, Irene and Lisin, Daria and Baumann, Otto and Goldberg, Martin W. and Gr{\"a}f, Ralph}, title = {Supramolecular Structures of the Dictyostelium Lamin NE81}, series = {Potsprint der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Potsprint der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {682}, issn = {1866-8372}, doi = {10.25932/publishup-42597}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-425976}, pages = {17}, year = {2019}, abstract = {Nuclear lamins are nucleus-specific intermediate filaments (IF) found at the inner nuclear membrane (INM) of the nuclear envelope (NE). Together with nuclear envelope transmembrane proteins, they form the nuclear lamina and are crucial for gene regulation and mechanical robustness of the nucleus and the whole cell. Recently, we characterized Dictyostelium NE81 as an evolutionarily conserved lamin-like protein, both on the sequence and functional level. Here, we show on the structural level that the Dictyostelium NE81 is also capable of assembling into filaments, just as metazoan lamin filament assemblies. Using field-emission scanning electron microscopy, we show that NE81 expressed in Xenopous oocytes forms filamentous structures with an overall appearance highly reminiscent of Xenopus lamin B2. The in vitro assembly properties of recombinant His-tagged NE81 purified from Dictyostelium extracts are very similar to those of metazoan lamins. Super-resolution stimulated emission depletion (STED) and expansion microscopy (ExM), as well as transmission electron microscopy of negatively stained purified NE81, demonstrated its capability of forming filamentous structures under low-ionic-strength conditions. These results recommend Dictyostelium as a non-mammalian model organism with a well-characterized nuclear envelope involving all relevant protein components known in animal cells.}, language = {en} } @article{GrafeBatsiosMeyeretal.2019, author = {Grafe, Marianne and Batsios, Petros and Meyer, Irene and Lisin, Daria and Baumann, Otto and Goldberg, Martin W. and Gr{\"a}f, Ralph}, title = {Supramolecular Structures of the Dictyostelium Lamin NE81}, series = {Cells}, volume = {8}, journal = {Cells}, number = {2}, publisher = {Molecular Diversity Preservation International}, address = {Basel}, issn = {2073-4409}, doi = {10.3390/cells8020162}, pages = {17}, year = {2019}, abstract = {Nuclear lamins are nucleus-specific intermediate filaments (IF) found at the inner nuclear membrane (INM) of the nuclear envelope (NE). Together with nuclear envelope transmembrane proteins, they form the nuclear lamina and are crucial for gene regulation and mechanical robustness of the nucleus and the whole cell. Recently, we characterized Dictyostelium NE81 as an evolutionarily conserved lamin-like protein, both on the sequence and functional level. Here, we show on the structural level that the Dictyostelium NE81 is also capable of assembling into filaments, just as metazoan lamin filament assemblies. Using field-emission scanning electron microscopy, we show that NE81 expressed in Xenopous oocytes forms filamentous structures with an overall appearance highly reminiscent of Xenopus lamin B2. The in vitro assembly properties of recombinant His-tagged NE81 purified from Dictyostelium extracts are very similar to those of metazoan lamins. Super-resolution stimulated emission depletion (STED) and expansion microscopy (ExM), as well as transmission electron microscopy of negatively stained purified NE81, demonstrated its capability of forming filamentous structures under low-ionic-strength conditions. These results recommend Dictyostelium as a non-mammalian model organism with a well-characterized nuclear envelope involving all relevant protein components known in animal cells.}, language = {en} } @misc{YarmanScheller2020, author = {Yarman, Aysu and Scheller, Frieder W.}, title = {How reliable is the electrochemical readout of MIP-sensors?}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {960}, issn = {1866-8372}, doi = {10.25932/publishup-47160}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-471608}, pages = {25}, year = {2020}, abstract = {Electrochemical methods offer the simple characterization of the synthesis of molecularly imprinted polymers (MIPs) and the readouts of target binding. The binding of electroinactive analytes can be detected indirectly by their modulating effect on the diffusional permeability of a redox marker through thin MIP films. However, this process generates an overall signal, which may include nonspecific interactions with the nonimprinted surface and adsorption at the electrode surface in addition to (specific) binding to the cavities. Redox-active low-molecular-weight targets and metalloproteins enable a more specific direct quantification of their binding to MIPs by measuring the faradaic current. The in situ characterization of enzymes, MIP-based mimics of redox enzymes or enzyme-labeled targets, is based on the indication of an electroactive product. This approach allows the determination of both the activity of the bio(mimetic) catalyst and of the substrate concentration.}, language = {en} } @misc{LopezdeGuerenuBastianWessigetal.2019, author = {L{\´o}pez de Guere{\~n}u, Anna and Bastian, Philipp and Wessig, Pablo and John, Leonard and Kumke, Michael Uwe}, title = {Energy transfer between tm-doped upconverting nanoparticles and a small organic dye with large stokes shift}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {961}, issn = {1866-8372}, doi = {10.25932/publishup-47224}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-472240}, pages = {19}, year = {2019}, abstract = {Lanthanide-doped upconverting nanoparticles (UCNP) are being extensively studied for bioapplications due to their unique photoluminescence properties and low toxicity. Interest in RET applications involving UCNP is also increasing, but due to factors such as large sizes, ion emission distributions within the particles, and complicated energy transfer processes within the UCNP, there are still many questions to be answered. In this study, four types of core and core-shell NaYF4-based UCNP co-doped with Yb3+ and Tm3+ as sensitizer and activator, respectively, were investigated as donors for the Methyl 5-(8-decanoylbenzo[1,2-d:4,5-d ']bis([1,3]dioxole)-4-yl)-5-oxopentanoate (DBD-6) dye. The possibility of resonance energy transfer (RET) between UCNP and the DBD-6 attached to their surface was demonstrated based on the comparison of luminescence intensities, band ratios, and decay kinetics. The architecture of UCNP influenced both the luminescence properties and the energy transfer to the dye: UCNP with an inert shell were the brightest, but their RET efficiency was the lowest (17\%). Nanoparticles with Tm3+ only in the shell have revealed the highest RET efficiencies (up to 51\%) despite the compromised luminescence due to surface quenching.}, language = {en} } @misc{NakamuraGrebe2018, author = {Nakamura, Moritaka and Grebe, Markus}, title = {Outer, inner and planar polarity in the Arabidopsis root}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {911}, issn = {1866-8372}, doi = {10.25932/publishup-44126}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-441266}, pages = {46 -- 53}, year = {2018}, abstract = {Plant roots control uptake of water and nutrients and cope with environmental challenges. The root epidermis provides the first selective interface for nutrient absorption, while the endodermis produces the main apoplastic diffusion barrier in the form of a structure called the Casparian strip. The positioning of root hairs on epidermal cells, and of the Casparian strip around endodermal cells, requires asymmetries along cellular axes (cell polarity). Cell polarity is termed planar polarity, when coordinated within the plane of a given tissue layer. Here, we review recent molecular advances towards understanding both the polar positioning of the proteo-lipid membrane domain instructing root hair initiation, and the cytoskeletal, trafficking and polar tethering requirements of proteins at outer or inner plasma membrane domains. Finally, we highlight progress towards understanding mechanisms of Casparian strip formation and underlying endodermal cell polarity.}, language = {en} } @misc{SchmidtSachseWalz2016, author = {Schmidt, Katja and Sachse, Ren{\´e} and Walz, Ariane}, title = {Current role of social benefits in ecosystem service assessments}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {915}, issn = {1866-8372}, doi = {10.25932/publishup-44202}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-442024}, pages = {49 -- 64}, year = {2016}, abstract = {Ecosystem services have a significant impact on human wellbeing. While ecosystem services are frequently represented by monetary values, social values and underlying social benefits remain under explored. The purpose of this study is to assess whether and how social benefits have been explicitly addressed within socio-economic and socio-cultural ecosystem services research, ultimately allowing a better understanding between ecosystem services and human well-being. In this paper, we reviewed 115 international primary valuation studies and tested four hypotheses associated to the identification of social benefits of ecosystem services using logistic regressions. Tested hypotheses were that (1) social benefits are mostly derived in studies that assess cultural ecosystem services as opposed to other ecosystem service types, (2) there is a pattern of social benefits and certain cultural ecosystem services assessed simultaneously, (3) monetary valuation techniques go beyond expressing monetary values and convey social benefits, and (4) directly addressing stakeholder's views the consideration of social benefits in ecosystem service assessments. Our analysis revealed that (1) a variety of social benefits are valued in studies that assess either of the four ecosystem service types, (2) certain social benefits are likely to co-occur in combination with certain cultural ecosystem services, (3) of the studies that employed monetary valuation techniques, simulated market approaches overlapped most frequently with the assessment of social benefits and (4) studies that directly incorporate stakeholder's views were more likely to also assess social benefits. (C) 2016 Elsevier B.V. All rights reserved.}, language = {en} }