@article{BatsiosRenBaumannetal.2016, author = {Batsios, Petros and Ren, Xiang and Baumann, Otto and Larochelle, Denis A. and Gr{\"a}f, Ralph}, title = {Src1 is a Protein of the Inner Nuclear Membrane Interacting with the Dictyostelium Lamin NE81}, series = {Cells}, volume = {5}, journal = {Cells}, number = {1}, publisher = {MDPI}, address = {Basel}, issn = {2073-4409}, doi = {10.3390/cells5010013}, year = {2016}, abstract = {The nuclear envelope (NE) consists of the outer and inner nuclear membrane (INM), whereby the latter is bound to the nuclear lamina. Src1 is a Dictyostelium homologue of the helix-extension-helix family of proteins, which also includes the human lamin-binding protein MAN1. Both endogenous Src1 and GFP-Src1 are localized to the NE during the entire cell cycle. Immuno-electron microscopy and light microscopy after differential detergent treatment indicated that Src1 resides in the INM. FRAP experiments with GFP-Src1 cells suggested that at least a fraction of the protein could be stably engaged in forming the nuclear lamina together with the Dictyostelium lamin NE81. Both a BioID proximity assay and mis-localization of soluble, truncated mRFP-Src1 at cytosolic clusters consisting of an intentionally mis-localized mutant of GFP-NE81 confirmed an interaction of Src1 and NE81. Expression GFP-Src11-646, a fragment C-terminally truncated after the first transmembrane domain, disrupted interaction of nuclear membranes with the nuclear lamina, as cells formed protrusions of the NE that were dependent on cytoskeletal pulling forces. Protrusions were dependent on intact microtubules but not actin filaments. Our results indicate that Src1 is required for integrity of the NE and highlight Dictyostelium as a promising model for the evolution of nuclear architecture.}, language = {en} } @article{WutkeBeneckeSandovalCastellanosetal.2016, author = {Wutke, Saskia and Benecke, Norbert and Sandoval-Castellanos, Edson and D{\"o}hle, Hans-J{\"u}rgen and Friederich, Susanne and Gonzalez Soto, Javier Esteban and Hallsson, Jon Hallsteinn and Hofreiter, Michael and Lougas, Lembi and Magnell, Ola and Morales-Muniz, Arturo and Orlando, Ludovic and Palsdottir, Albina Hulda and Reissmann, Monika and Ruttkay, Matej and Trinks, Alexandra and Ludwig, Arne}, title = {Spotted phenotypes in horses lost attractiveness in the Middle Ages}, series = {Scientific reports}, volume = {6}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep38548}, pages = {9}, year = {2016}, abstract = {Horses have been valued for their diversity of coat colour since prehistoric times; this is especially the case since their domestication in the Caspian steppe in similar to 3,500 BC. Although we can assume that human preferences were not constant, we have only anecdotal information about how domestic horses were influenced by humans. Our results from genotype analyses show a significant increase in spotted coats in early domestic horses (Copper Age to Iron Age). In contrast, medieval horses carried significantly fewer alleles for these phenotypes, whereas solid phenotypes (i.e., chestnut) became dominant. This shift may have been supported because of (i) pleiotropic disadvantages, (ii) a reduced need to separate domestic horses from their wild counterparts, (iii) a lower religious prestige, or (iv) novel developments in weaponry. These scenarios may have acted alone or in combination. However, the dominance of chestnut is a remarkable feature of the medieval horse population.}, language = {en} } @article{ZwickelKahlKlaffkeetal.2016, author = {Zwickel, Theresa and Kahl, Sandra M. and Klaffke, Horst and Rychlik, Michael and M{\"u}ller, Marina E. H.}, title = {Spotlight on the Underdogs-An Analysis of Underrepresented Alternaria Mycotoxins Formed Depending on Varying Substrate, Time and Temperature Conditions}, series = {Toxins}, volume = {8}, journal = {Toxins}, publisher = {MDPI}, address = {Basel}, issn = {2072-6651}, doi = {10.3390/toxins8110344}, pages = {570 -- 583}, year = {2016}, abstract = {Alternaria (A.) is a genus of widespread fungi capable of producing numerous, possibly health-endangering Alternaria toxins (ATs), which are usually not the focus of attention. The formation of ATs depends on the species and complex interactions of various environmental factors and is not fully understood. In this study the influence of temperature (7 degrees C, 25 degrees C), substrate (rice, wheat kernels) and incubation time (4, 7, and 14 days) on the production of thirteen ATs and three sulfoconjugated ATs by three different Alternaria isolates from the species groups A. tenuissima and A. infectoria was determined. High-performance liquid chromatography coupled with tandem mass spectrometry was used for quantification. Under nearly all conditions, tenuazonic acid was the most extensively produced toxin. At 25 degrees C and with increasing incubation time all toxins were formed in high amounts by the two A. tenuissima strains on both substrates with comparable mycotoxin profiles. However, for some of the toxins, stagnation or a decrease in production was observed from day 7 to 14. As opposed to the A. tenuissima strains, the A. infectoria strain only produced low amounts of ATs, but high concentrations of stemphyltoxin III. The results provide an essential insight into the quantitative in vitro AT formation under different environmental conditions, potentially transferable to different field and storage conditions.}, language = {en} } @article{EdlichGereckeGiulbudagianetal.2016, author = {Edlich, Alexander and Gerecke, Christian and Giulbudagian, Michael and Neumann, Falko and Hedtrich, Sarah and Schaefer-Korting, Monika and Ma, Nan and Calderon, Marcelo and Kleuser, Burkhard}, title = {Specific uptake mechanisms of well-tolerated thermoresponsive polyglycerol-based nanogels in antigen-presenting cells of the skin}, series = {European Journal of Pharmaceutics and Biopharmaceutics}, volume = {116}, journal = {European Journal of Pharmaceutics and Biopharmaceutics}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0939-6411}, doi = {10.1016/j.ejpb.2016.12.016}, pages = {155 -- 163}, year = {2016}, abstract = {Engineered nanogels are of high value for a targeted and controlled transport of compounds due to the ability to change their chemical properties by external stimuli. As it has been indicated that nanogels possess a high ability to penetrate the stratum corneum, it cannot be excluded that nanogels interact with dermal dendritic cells, especially in diseased skin. In this study the potential crosstalk of the thermore-sponsive nanogels (tNGs) with the dendritic cells of the skin was investigated with the aim to determine the immunotoxicological properties of the nanogels. The investigated tNGs were made of dendritic polyglycerol (dPG) and poly(glycidyl methyl ether-co-ethyl glycidyl ether) (p(GME-co-EGE)), as polymer conferring thermoresponsive properties. Although the tNGs were taken up, they displayed neither cytotoxic and genotoxic effects nor any induction of reactive oxygen species in the tested cells. Interestingly, specific uptake mechanisms of the tNGs by the dendritic cells were depending on the nanogels cloud point temperature (Tcp), which determines the phase transition of the nanoparticle. The study points to caveolae-mediated endocytosis as being the major tNGs uptake mechanism at 37 degrees C, which is above the Tcp of the tNGs. Remarkably, an additional uptake mechanism, beside caveolae-mediated endocytosis, was observed at 29 degrees C, which is the Tcp of the tNGs. At this temperature, which is characterized by two different states of the tNGs, macropinocytosis was involved as well. In summary, our study highlights the impact of thermoresponsivity on the cellular uptake mechanisms which has to be taken into account if the tNGs are used as a drug delivery system.}, language = {en} } @article{LamannaKirschbaumErnstetal.2016, author = {Lamanna, Francesco and Kirschbaum, Frank and Ernst, Anja R. R. and Feulner, Philine G. D. and Mamonekene, Victor and Paul, Christiane and Tiedemann, Ralph}, title = {Species delimitation and phylogenetic relationships in a genus of African weakly-electric fishes (Osteoglossiformes, Mormyridae, Campylomormyrus)}, series = {Molecular phylogenetics and evolution}, volume = {101}, journal = {Molecular phylogenetics and evolution}, publisher = {Elsevier}, address = {San Diego}, issn = {1055-7903}, doi = {10.1016/j.ympev.2016.04.035}, pages = {8 -- 18}, year = {2016}, abstract = {African weakly-electric fishes (Mormyridae) are able to communicate through species-specific electric signals; this feature might have favoured the evolutionary radiation observed in this family (over 200 species) by acting as an effective pre-zygotic isolation mechanism. In the present study we used mitochondria((cytb) and nuclear (rps7, scn4aa) markers in order to reconstruct a species-phylogeny and identify species boundaries for the genus Campylomormyrus, by applying inference methods based on the multispecies coalescent model. Additionally, we employed 16 microsatellite markers, landmark-based morphometric measurements, and electro-physiological analyses as independent lines of evidence to the results obtained from the sequence data. The results show that groups that are morphologically different are also significantly divergent at the genetic level, whereas morphologically similar groups, displaying dissimilar electric signals, do not show enough genetic diversity to be considered separate species. Furthermore, the data confirm the presence of a yet undescribed species within the genus Campylomormyrus. (C) 2016 Elsevier Inc. All rights reserved.}, language = {en} } @article{LahTrenseBenkeetal.2016, author = {Lah, Ljerka and Trense, Daronja and Benke, Harald and Berggren, Per and Gunnlaugsson, Porvaldur and Lockyer, Christina and {\"O}zt{\"u}rk, Ayaka and {\"O}zt{\"u}rk, Bayram and Pawliczka, Iwona and Roos, Anna and Siebert, Ursula and Skora, Krzysztof and Vikingsson, Gisli and Tiedemann, Ralph}, title = {Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise}, series = {PLoS one}, volume = {11}, journal = {PLoS one}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0162792}, pages = {23}, year = {2016}, abstract = {The population structure of the highly mobile marine mammal, the harbor porpoise (Phocoena phocoena), in the Atlantic shelf waters follows a pattern of significant isolation-by-distance. The population structure of harbor porpoises from the Baltic Sea, which is connected with the North Sea through a series of basins separated by shallow underwater ridges, however, is more complex. Here, we investigated the population differentiation of harbor porpoises in European Seas with a special focus on the Baltic Sea and adjacent waters, using a population genomics approach. We used 2872 single nucleotide polymor-phisms (SNPs), derived from double digest restriction-site associated DNA sequencing (ddRAD-seq), as well as 13 microsatellite loci and mitochondrial haplotypes for the same set of individuals. Spatial principal components analysis (sPCA), and Bayesian clustering on a subset of SNPs suggest three main groupings at the level of all studied regions: the Black Sea, the North Atlantic, and the Baltic Sea. Furthermore, we observed a distinct separation of the North Sea harbor porpoises from the Baltic Sea populations, and identified splits between porpoise populations within the Baltic Sea. We observed a notable distinction between the Belt Sea and the Inner Baltic Sea sub-regions. Improved delineation of harbor porpoise population assignments for the Baltic based on genomic evidence is important for conservation management of this endangered cetacean in threatened habitats, particularly in the Baltic Sea proper. In addition, we show that SNPs outperform microsatellite markers and demonstrate the utility of RAD-tags from a relatively small, opportunistically sampled cetacean sample set for population diversity and divergence analysis.}, language = {en} } @article{LahTrenseBenkeetal.2016, author = {Lah, Ljerka and Trense, Daronja and Benke, Harald and Berggren, Per and Gunnlaugsson, Þorvaldur and Lockyer, Christina and {\"O}zt{\"u}rk, Ayaka and {\"O}zt{\"u}rk, Bayram and Pawliczka, Iwona and Roos, Anna and Siebert, Ursula and Sk{\´o}ra, Krzysztof and V{\´i}kingsson, G{\´i}sli and Tiedemann, Ralph}, title = {Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise}, series = {PLoS one}, volume = {11}, journal = {PLoS one}, number = {10}, publisher = {PLoS}, address = {Lawrence, Kan.}, issn = {1932-6203}, doi = {10.1371/journal.pone.0162792}, pages = {23 Seiten}, year = {2016}, abstract = {The population structure of the highly mobile marine mammal, the harbor porpoise (Phocoena phocoena), in the Atlantic shelf waters follows a pattern of significant isolation-by-distance. The population structure of harbor porpoises from the Baltic Sea, which is connected with the North Sea through a series of basins separated by shallow underwater ridges, however, is more complex. Here, we investigated the population differentiation of harbor porpoises in European Seas with a special focus on the Baltic Sea and adjacent waters, using a population genomics approach. We used 2872 single nucleotide polymorphisms (SNPs), derived from double digest restriction-site associated DNA sequencing (ddRAD-seq), as well as 13 microsatellite loci and mitochondrial haplotypes for the same set of individuals. Spatial principal components analysis (sPCA), and Bayesian clustering on a subset of SNPs suggest three main groupings at the level of all studied regions: the Black Sea, the North Atlantic, and the Baltic Sea. Furthermore, we observed a distinct separation of the North Sea harbor porpoises from the Baltic Sea populations, and identified splits between porpoise populations within the Baltic Sea. We observed a notable distinction between the Belt Sea and the Inner Baltic Sea sub-regions. Improved delineation of harbor porpoise population assignments for the Baltic based on genomic evidence is important for conservation management of this endangered cetacean in threatened habitats, particularly in the Baltic Sea proper. In addition, we show that SNPs outperform microsatellite markers and demonstrate the utility of RAD-tags from a relatively small, opportunistically sampled cetacean sample set for population diversity and divergence analysis.}, language = {en} } @misc{LahTrenseBenkeetal.2016, author = {Lah, Ljerka and Trense, Daronja and Benke, Harald and Berggren, Per and Gunnlaugsson, Þorvaldur and Lockyer, Christina and {\"O}zt{\"u}rk, Ayaka and {\"O}zt{\"u}rk, Bayram and Pawliczka, Iwona and Roos, Anna and Siebert, Ursula and Sk{\´o}ra, Krzysztof and V{\´i}kingsson, G{\´i}sli and Tiedemann, Ralph}, title = {Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise}, issn = {1866-8372}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-100813}, pages = {23 Seiten}, year = {2016}, abstract = {The population structure of the highly mobile marine mammal, the harbor porpoise (Phocoena phocoena), in the Atlantic shelf waters follows a pattern of significant isolation-by-distance. The population structure of harbor porpoises from the Baltic Sea, which is connected with the North Sea through a series of basins separated by shallow underwater ridges, however, is more complex. Here, we investigated the population differentiation of harbor porpoises in European Seas with a special focus on the Baltic Sea and adjacent waters, using a population genomics approach. We used 2872 single nucleotide polymorphisms (SNPs), derived from double digest restriction-site associated DNA sequencing (ddRAD-seq), as well as 13 microsatellite loci and mitochondrial haplotypes for the same set of individuals. Spatial principal components analysis (sPCA), and Bayesian clustering on a subset of SNPs suggest three main groupings at the level of all studied regions: the Black Sea, the North Atlantic, and the Baltic Sea. Furthermore, we observed a distinct separation of the North Sea harbor porpoises from the Baltic Sea populations, and identified splits between porpoise populations within the Baltic Sea. We observed a notable distinction between the Belt Sea and the Inner Baltic Sea sub-regions. Improved delineation of harbor porpoise population assignments for the Baltic based on genomic evidence is important for conservation management of this endangered cetacean in threatened habitats, particularly in the Baltic Sea proper. In addition, we show that SNPs outperform microsatellite markers and demonstrate the utility of RAD-tags from a relatively small, opportunistically sampled cetacean sample set for population diversity and divergence analysis.}, language = {en} } @phdthesis{Korkuć2016, author = {Korkuć, Paula}, title = {Spatial investigations of protein structures with regard to compound binding and post-translational modifications}, school = {Universit{\"a}t Potsdam}, pages = {141}, year = {2016}, language = {en} } @article{MetzTielboerger2016, author = {Metz, Johannes and Tielboerger, Katja}, title = {Spatial and temporal aridity gradients provide poor proxies for plant-plant interactions under climate change: a large-scale experiment}, series = {Functional ecology : an official journal of the British Ecological Society}, volume = {30}, journal = {Functional ecology : an official journal of the British Ecological Society}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0269-8463}, doi = {10.1111/1365-2435.12599}, pages = {20 -- 29}, year = {2016}, abstract = {1. Plant-plant interactions may critically modify the impact of climate change on plant communities. However, the magnitude and even direction of potential future interactions remains highly debated, especially for water-limited ecosystems. Predictions range from increasing facilitation to increasing competition with future aridification. 2. The different methodologies used for assessing plant-plant interactions under changing environmental conditions may affect the outcome but they are not equally represented in the literature. Mechanistic experimental manipulations are rare compared with correlative approaches that infer future patterns from current observations along spatial climatic gradients. 3. Here, we utilize a unique climatic gradient in combination with a large-scale, long-term experiment to test whether predictions about plant-plant interactions yield similar results when using experimental manipulations, spatial gradients or temporal variation. We assessed shrub-annual interactions in three different sites along a natural rainfall gradient (spatial) during 9 years of varying rainfall (temporal) and 8 years of dry and wet manipulations of ambient rainfall (experimental) that closely mimicked regional climate scenarios. 4. The results were fundamentally different among all three approaches. Experimental water manipulations hardly altered shrub effects on annual plant communities for the assessed fitness parameters biomass and survival. Along the spatial gradient, shrub effects shifted from clearly negative to mildly facilitative towards drier sites, whereas temporal variation showed the opposite trend: more negative shrub effects in drier years. 5. Based on our experimental approach, we conclude that shrub-annual interaction will remain similar under climate change. In contrast, the commonly applied space-for-time approach based on spatial gradients would have suggested increasing facilitative effects with climate change. We discuss potential mechanisms governing the differences among the three approaches. 6. Our study highlights the critical importance of long-term experimental manipulations for evaluating climate change impacts. Correlative approaches, for example along spatial or temporal gradients, may be misleading and overestimate the response of plant-plant interactions to climate change.}, language = {en} } @article{HeinzeGenschWeberetal.2016, author = {Heinze, Johannes and Gensch, Sabine and Weber, Ewald and Joshi, Jasmin Radha}, title = {Soil temperature modifies effects of soil biota on plant growth}, series = {Journal of plant ecology}, volume = {10}, journal = {Journal of plant ecology}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1752-9921}, doi = {10.1093/jpe/rtw097}, pages = {808 -- 821}, year = {2016}, abstract = {Aims Plants directly and indirectly interact with many abiotic and biotic soil components. Research so far mostly focused on direct, individual abiotic or biotic effects on plant growth, but only few studies tested the indirect effects of abiotic soil factors on plant growth. Therefore, we investigated how abiotic soil conditions affect plant performance, via changes induced by soil biota. Methods In a full-factorial experiment, we grew the widespread grass Dactylis glomerata either with or without soil biota and investigated the impact of soil temperature, fertility and moisture on the soil biota effects on plant growth. We measured biomass production, root traits and colonization by arbuscular mycorrhizal fungi as well as microbial respiration. Important Findings We found significant interaction effects between abiotic soil conditions and soil biota on plant growth for fertility, but especially for soil temperature, as an increase of 10 degrees C significantly changed the soil biota effects on plant growth from positive to neutral. However, if tested individually, an increase in soil temperature and fertility per se positively affected plant biomass production, whereas soil biota per se did not affect overall plant growth, but both influenced root architecture. By affecting soil microbial activity and root architecture, soil temperature might influence both mutualistic and pathogenic interactions between plants and soil biota. Such soil temperature effects should be considered in soil feedback studies to ensure greater transferability of results from artificial and experimental conditions to natural environmental conditions.}, language = {en} } @phdthesis{HankeGogokhia2016, author = {Hanke-Gogokhia, Christin}, title = {Small GTPase ARL3-GTP is key molecule in transition zone formation and trafficking of ciliary cargo in mouse photoreceptors}, school = {Universit{\"a}t Potsdam}, pages = {166}, year = {2016}, language = {en} } @article{RadchukOppelGroeneveldetal.2016, author = {Radchuk, Viktoriia and Oppel, Steffen and Groeneveld, Juergen and Grimm, Volker and Schtickzelle, Nicolas}, title = {Simple or complex: Relative impact of data availability and model purpose on the choice of model types for population viability analyses}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {323}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2015.11.022}, pages = {87 -- 95}, year = {2016}, abstract = {Population viability analysis (PVA) models are used to estimate population extinction risk under different scenarios. Both simple and complex PVA models are developed and have their specific pros and cons; the question therefore arises whether we always use the most appropriate model type. Generally, the specific purpose of a model and the availability of data are listed as determining the choice of model type, but this has not been formally tested yet. We quantified the relative importance of model purpose and nine metrics of data availability and resolution for the choice of a PVA model type, while controlling for effects of the different life histories of the modelled species. We evaluated 37 model pairs: each consisting of a generally simpler, population-based model (PBM) and a more complex, individual-based model (IBM) developed for the same species. The choice of model type was primarily affected by the availability and resolution of demographic, dispersal and spatial data. Low-resolution data resulted in the development of less complex models. Model purpose did not affect the choice of the model type. We confirm the general assumption that poor data availability is the main reason for the wide use of simpler models, which may have limited predictive power for population responses to changing environmental conditions. Conservation biology is a crisis discipline where researchers learned to work with the data at hand. However, for threatened and poorly-known species, there is no short-cut when developing either a PBM or an IBM: investments to collect appropriately detailed data are required to ensure PVA models can assess extinction risk under complex environmental conditions. (C) 2015 Elsevier B.V. All rights reserved.}, language = {en} } @phdthesis{Friess2016, author = {Frieß, Fabian}, title = {Shape-memory polymer micronetworks}, school = {Universit{\"a}t Potsdam}, pages = {xiv, 111 S.}, year = {2016}, language = {en} } @phdthesis{Loewenberg2016, author = {L{\"o}wenberg, Candy}, title = {Shape-memory effect of gelatin-based hydrogels}, school = {Universit{\"a}t Potsdam}, pages = {122}, year = {2016}, language = {en} } @phdthesis{Bolger2016, author = {Bolger, Anthony}, title = {Sequencing the Genome of the stress-tolerant wild tomato Solanum pennellii and Novel Algorithms motivated thereby}, school = {Universit{\"a}t Potsdam}, pages = {143}, year = {2016}, language = {en} } @article{ZhuSchluppTiedemann2016, author = {Zhu, Fangjun and Schlupp, Ingo and Tiedemann, Ralph}, title = {Sequence Evolution and Expression of the Androgen Receptor and Other Pathway-Related Genes in a Unisexual Fish, the Amazon Molly, Poecilia formosa, and Its Bisexual Ancestors}, series = {PLoS one}, volume = {11}, journal = {PLoS one}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0156209}, pages = {19}, year = {2016}, abstract = {The all-female Amazon molly (Poecilia formosa) originated from a single hybridization of two bisexual ancestors, Atlantic molly (Poecilia mexicana) and sailfin molly (Poecilia latipinna). As a gynogenetic species, the Amazon molly needs to copulate with a heterospecific male, but the genetic information of the sperm-donor does not contribute to the next generation, as the sperm only acts as the trigger for the diploid eggs' embryogenesis. Here, we study the sequence evolution and gene expression of the duplicated genes coding for androgen receptors (ars) and other pathway-related genes, i.e., the estrogen receptors (ers) and cytochrome P450, family19, subfamily A, aromatase genes (cyp19as), in the Amazon molly, in comparison to its bisexual ancestors. Mollies possess-as most other teleost fish—two copies of the ar, er, and cyp19a genes, i.e., ar\&\#945;/ar\&\#946;, er\&\#945;/er\&\#946;1, and cyp19a1 (also referred as cyp19a1a)/cyp19a2 (also referred to as cyp19a1b), respectively. Non-synonymous single nucleotide polymorphisms (SNPs) among the ancestral bisexual species were generally predicted not to alter protein function. Some derived substitutions in the P. mexicana and one in P. formosa are predicted to impact protein function. We also describe the gene expression pattern of the ars and pathway-related genes in various tissues (i.e., brain, gill, and ovary) and provide SNP markers for allele specific expression research. As a general tendency, the levels of gene expression were lowest in gill and highest in ovarian tissues, while expression levels in the brain were intermediate in most cases. Expression levels in P. formosa were conserved where expression did not differ between the two bisexual ancestors. In those cases where gene expression levels significantly differed between the bisexual species, P. formosa expression was always comparable to the higher expression level among the two ancestors. Interestingly, er\&\#946;1 was expressed neither in brain nor in gill in the analyzed three molly species, which implies a more important role of er\&\#945; in the estradiol synthesis pathway in these tissues. Furthermore, our data suggest that interactions of steroid-signaling pathway genes differ across tissues, in particular the interactions of ars and cyp19as.}, language = {en} } @article{ZhuSchluppTiedemann2016, author = {Zhu, Fangjun and Schlupp, Ingo and Tiedemann, Ralph}, title = {Sequence Evolution and Expression of the Androgen Receptor and Other Pathway-Related Genes in a Unisexual Fish, the Amazon Molly, Poecilia formosa, and Its Bisexual Ancestors}, series = {PLoS one}, volume = {11}, journal = {PLoS one}, number = {6}, publisher = {PLoS}, address = {Lawrence, Kan.}, issn = {1932-6203}, doi = {10.1371/JOURNAL.PONE.0156209}, pages = {19}, year = {2016}, abstract = {The all-female Amazon molly (Poecilia formosa) originated from a single hybridization of two bisexual ancestors, Atlantic molly (Poecilia mexicana) and sailfin molly (Poecilia latipinna). As a gynogenetic species, the Amazon molly needs to copulate with a heterospecific male, but the genetic information of the sperm-donor does not contribute to the next generation, as the sperm only acts as the trigger for the diploid eggs' embryogenesis. Here, we study the sequence evolution and gene expression of the duplicated genes coding for androgen receptors (ars) and other pathway-related genes, i.e., the estrogen receptors (ers) and cytochrome P450, family19, subfamily A, aromatase genes (cyp19as), in the Amazon molly, in comparison to its bisexual ancestors. Mollies possess-as most other teleost fish—two copies of the ar, er, and cyp19a genes, i.e., arα/arβ, erα/erβ1, and cyp19a1 (also referred as cyp19a1a)/cyp19a2 (also referred to as cyp19a1b), respectively. Non-synonymous single nucleotide polymorphisms (SNPs) among the ancestral bisexual species were generally predicted not to alter protein function. Some derived substitutions in the P. mexicana and one in P. formosa are predicted to impact protein function. We also describe the gene expression pattern of the ars and pathway-related genes in various tissues (i.e., brain, gill, and ovary) and provide SNP markers for allele specific expression research. As a general tendency, the levels of gene expression were lowest in gill and highest in ovarian tissues, while expression levels in the brain were intermediate in most cases. Expression levels in P. formosa were conserved where expression did not differ between the two bisexual ancestors. In those cases where gene expression levels significantly differed between the bisexual species, P. formosa expression was always comparable to the higher expression level among the two ancestors. Interestingly, erβ1 was expressed neither in brain nor in gill in the analyzed three molly species, which implies a more important role of erα in the estradiol synthesis pathway in these tissues. Furthermore, our data suggest that interactions of steroid-signaling pathway genes differ across tissues, in particular the interactions of ars and cyp19as.}, language = {en} } @misc{ZhuSchluppTiedemann2016, author = {Zhu, Fangjun and Schlupp, Ingo and Tiedemann, Ralph}, title = {Sequence Evolution and Expression of the Androgen Receptor and Other Pathway-Related Genes in a Unisexual Fish, the Amazon Molly, Poecilia formosa, and Its Bisexual Ancestors}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-97119}, pages = {19}, year = {2016}, abstract = {The all-female Amazon molly (Poecilia formosa) originated from a single hybridization of two bisexual ancestors, Atlantic molly (Poecilia mexicana) and sailfin molly (Poecilia latipinna). As a gynogenetic species, the Amazon molly needs to copulate with a heterospecific male, but the genetic information of the sperm-donor does not contribute to the next generation, as the sperm only acts as the trigger for the diploid eggs' embryogenesis. Here, we study the sequence evolution and gene expression of the duplicated genes coding for androgen receptors (ars) and other pathway-related genes, i.e., the estrogen receptors (ers) and cytochrome P450, family19, subfamily A, aromatase genes (cyp19as), in the Amazon molly, in comparison to its bisexual ancestors. Mollies possess-as most other teleost fish—two copies of the ar, er, and cyp19a genes, i.e., arα/arβ, erα/erβ1, and cyp19a1 (also referred as cyp19a1a)/cyp19a2 (also referred to as cyp19a1b), respectively. Non-synonymous single nucleotide polymorphisms (SNPs) among the ancestral bisexual species were generally predicted not to alter protein function. Some derived substitutions in the P. mexicana and one in P. formosa are predicted to impact protein function. We also describe the gene expression pattern of the ars and pathway-related genes in various tissues (i.e., brain, gill, and ovary) and provide SNP markers for allele specific expression research. As a general tendency, the levels of gene expression were lowest in gill and highest in ovarian tissues, while expression levels in the brain were intermediate in most cases. Expression levels in P. formosa were conserved where expression did not differ between the two bisexual ancestors. In those cases where gene expression levels significantly differed between the bisexual species, P. formosa expression was always comparable to the higher expression level among the two ancestors. Interestingly, erβ1 was expressed neither in brain nor in gill in the analyzed three molly species, which implies a more important role of erα in the estradiol synthesis pathway in these tissues. Furthermore, our data suggest that interactions of steroid-signaling pathway genes differ across tissues, in particular the interactions of ars and cyp19as.}, language = {en} } @misc{SchellerSakarDasdan2016, author = {Scheller, Frieder W. and Sakar Dasdan, Dolunay}, title = {Selected papers presented on the 2nd International Conference on the New Trends in Chemistry, Zagreb, Croatia, April 19-22, 2016 Preface}, series = {Bulgarian chemical communications : journal of the Chemical Institutes of the Bulgarian Academy of Sciences and of the Bulgarian Chemical Society = Izvestija po chimija}, volume = {48}, journal = {Bulgarian chemical communications : journal of the Chemical Institutes of the Bulgarian Academy of Sciences and of the Bulgarian Chemical Society = Izvestija po chimija}, publisher = {Bulgarian Academy of Sciences}, address = {Sofia}, issn = {0324-1130}, pages = {4 -- 4}, year = {2016}, language = {en} } @article{RichterRolkeBlenauetal.2016, author = {Richter, Katharina Natalia and Rolke, Daniel and Blenau, Wolfgang and Baumann, Otto}, title = {Secretory cells in honeybee hypopharyngeal gland: polarized organization and age-dependent dynamics of plasma membrane}, series = {Cell \& tissue research}, volume = {366}, journal = {Cell \& tissue research}, publisher = {Springer}, address = {New York}, issn = {0302-766X}, doi = {10.1007/s00441-016-2423-9}, pages = {163 -- 174}, year = {2016}, abstract = {The honeybee hypopharyngeal gland consists in numerous units, each comprising a secretory cell and a canal cell. The secretory cell discharges its products into a convoluted tubular membrane system, the canaliculus, which is surrounded at regular intervals by rings of actin filaments. Using probes for various membrane components, we analyze the organization of the secretory cells relative to the apicobasal configuration of epithelial cells. The canaliculus was defined by labeling with an antibody against phosphorylated ezrin/radixin/moesin (pERM), a marker protein for the apical membrane domain of epithelial cells. Anti-phosphotyrosine visualizes the canalicular system, possibly by staining the microvillar tips. The open end of the canaliculus leads to a region in which the secretory cell is attached to the canal cell by adherens and septate junctions. The remaining plasma membrane stains for Na,K-ATPase and spectrin and represents the basolateral domain. We also used fluorophore-tagged phalloidin, anti-phosphotyrosine and anti-pERM as probes for the canaliculus in order to describe fine-structural changes in the organization of the canalicular system during the adult life cycle. These probes in conjunction with fluorescence microscopy allow the fast and detailed three-dimensional analysis of the canalicular membrane system and its structural changes in a developmental mode or in response to environmental factors.}, language = {en} } @article{HeimSchroederEccardetal.2016, author = {Heim, Olga and Schr{\"o}der, Assja and Eccard, Jana and Jung, Kirsten and Voigt, Christian C.}, title = {Seasonal activity patterns of European bats above intensively used farmland}, series = {The astrophysical journal : an international review of spectroscopy and astronomical physics ; Part 2, Letters}, volume = {233}, journal = {The astrophysical journal : an international review of spectroscopy and astronomical physics ; Part 2, Letters}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0167-8809}, doi = {10.1016/j.agee.2016.09.002}, pages = {130 -- 139}, year = {2016}, abstract = {Bats are top insect predators on farmland, yet they suffer from intensive farmland management. Here, we evaluated the seasonal activity patterns of European bats above large, arable fields and compared these patterns between ecologically distinct bat species. Using repeated passive acoustic monitoring on a total of 93 arable fields in 2 years in Brandenburg, Germany, we surveyed the activity of different bat species between early spring and autumn. We then used generalized additive mixed models to describe and compare the seasonal bat activity patterns between bat categories, which were build based on the affiliation to a functional group and migratory class, while controlling for local weather conditions. In general, the affiliation to a bat category in interaction with the season in addition to cloud cover and ambient air temperature explained a major part of bat activity. The season was also an important factor for the foraging activity of open-space specialists such as Nyctalus noctula but showed only a weak effect on species such as Pipistreilus nathusii which are adapted to edge-space habitats. Across the seasons, habitat use intensity was high during the period of swarming and migration and low during the energy demanding period of lactation. Seasonal patterns in foraging activity showed that open-space specialists foraged more intensively above agricultural fields during the migration period, while edge-space specialists foraged also during the energy demanding period of lactation. We conclude that the significant seasonal fluctuations in bat activity and significant differences between bat categories in open agricultural landscapes should be taken into consideration when designing monitoring schemes and management plans for bat species in regions dominated by agriculture. Also, management plans should be directed to improve the conditions on arable land especially for bat species which would be classified as narrow-space foragers such as Myotis species. (C) 2016 Elsevier B.V. All rights reserved.}, language = {en} } @article{MartinCzesnyWahletal.2016, author = {Martin, Benjamin T. and Czesny, Sergiusz and Wahl, David H. and Grimm, Volker}, title = {Scale-dependent role of demography and dispersal on the distribution of populations in heterogeneous landscapes}, series = {Oikos}, volume = {125}, journal = {Oikos}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0030-1299}, doi = {10.1111/oik.02345}, pages = {667 -- 673}, year = {2016}, abstract = {Both dispersal and local demographic processes determine a population's distribution among habitats of varying quality, yet most theory, experiments, and field studies have focused on the former. We use a generic model to show how both processes contribute to a population's distribution, and how the relative importance of each mechanism depends on scale. In contrast to studies only considering habitat-dependent dispersal, we show that predictions of ideal free distribution (IFD) theory are relevant even at landscape scales, where the assumptions of IFD theory are violated. This is because scales that inhibit one process, promote the other's ability to drive populations to the IFD. Furthermore, because multiple processes can generate IFDs, the pattern alone does not specify a causal mechanism. This is important because populations with IFDs generated by dispersal or demography respond much differently to shifts in resource distributions.}, language = {en} } @phdthesis{Synodinos2016, author = {Synodinos, Alexios D.}, title = {Savanna dynamics under extreme conditions}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-395000}, school = {Universit{\"a}t Potsdam}, pages = {x, 168}, year = {2016}, abstract = {Savannas cover a broad geographical range across continents and are a biome best described by a mix of herbaceous and woody plants. The former create a more or less continuous layer while the latter should be sparse enough to leave an open canopy. What has long intrigued ecologists is how these two competing plant life forms of vegetation coexist. Initially attributed to resource competition, coexistence was considered the stable outcome of a root niche differentiation between trees and grasses. The importance of environmental factors became evident later, when data from moister environments demonstrated that tree cover was often lower than what the rainfall conditions would allow for. Our current understanding relies on the interaction of competition and disturbances in space and time. Hence, the influence of grazing and fire and the corresponding feedbacks they generate have been keenly investigated. Grazing removes grass cover, initiating a self-reinforcing process propagating tree cover expansion. This is known as the encroachment phenomenon. Fire, on the other hand, imposes a bottleneck on the tree population by halting the recruitment of young trees into adulthood. Since grasses fuel fires, a feedback linking grazing, grass cover, fire, and tree cover is created. In African savannas, which are the focus of this dissertation, these feedbacks play a major role in the dynamics. The importance of these feedbacks came into sharp focus when the notion of alternative states began to be applied to savannas. Alternative states in ecology arise when different states of an ecosystem can occur under the same conditions. According to this an open savanna and a tree-dominated savanna can be classified as alternative states, since they can both occur under the same climatic conditions. The aforementioned feedbacks are critical in the creation of alternative states. The grass-fire feedback can preserve an open canopy as long as fire intensity and frequency remain above a certain threshold. Conversely, crossing a grazing threshold can force an open savanna to shift to a tree-dominated state. Critically, transitions between such alternative states can produce hysteresis, where a return to pre-transition conditions will not suffice to restore the ecosystem to its original state. In the chapters that follow, I will cover aspects relating to the coexistence mechanisms and the role of feedbacks in tree-grass interactions. Coming back to the coexistence question, due to the overwhelming focus on competition and disturbance another important ecological process was neglected: facilitation. Therefore, in the first study within this dissertation I examine how facilitation can expand the tree-grass coexistence range into drier conditions. For the second study I focus on another aspect of savanna dynamics which remains underrepresented in the literature: the impacts of inter-annual rainfall variability upon savanna trees and the resilience of the savanna state. In the third and final study within this dissertation I approach the well-researched encroachment phenomenon from a new perspective: I search for an early warning indicator of the process to be used as a prevention tool for savanna conservation. In order to perform all this work I developed a mathematical ecohydrological model of Ordinary Differential Equations (ODEs) with three variables: soil moisture content, grass cover and tree cover. Facilitation: Results showed that the removal of grass cover through grazing was detrimental to trees under arid conditions, contrary to expectation based on resource competition. The reason was that grasses preserved moisture in the soil through infiltration and shading, thus ameliorating the harsh conditions for trees in accordance with the Stress Gradient Hypothesis. The exclusion of grasses from the model further demonstrated this: tree cover was lower in the absence of grasses, indicating that the benefits of grass facilitation outweighed the costs of grass competition for trees. Thus, facilitation expanded the climatic range where savannas persisted into drier conditions. Rainfall variability: By adjusting the model to current rainfall patterns in East Africa, I simulated conditions of increasing inter-annual rainfall variability for two distinct mean rainfall scenarios: semi-arid and mesic. Alternative states of tree-less grassland and tree-dominated savanna emerged in both cases. Increasing variability reduced semi-arid savanna tree cover to the point that at high variability the savanna state was eliminated, because variability intensified resource competition and strengthened the fire disturbance during high rainfall years. Mesic savannas, on the other hand, became more resilient along the variability gradient: increasing rainfall variability created more opportunities for the rapid growth of trees to overcome the fire disturbance, boosting the chances of savannas persisting and thus increasing mesic savanna resilience. Preventing encroachment: The breakdown in the grass-fire feedback caused by heavy grazing promoted the expansion of woody cover. This could be irreversible due to the presence of alternative states of encroached and open savanna, which I found along a simulated grazing gradient. When I simulated different short term heavy grazing treatments followed by a reduction to the original grazing conditions, certain cases converged to the encroached state. Utilising woody cover changes only during the heavy grazing treatment, I developed an early warning indicator which identified these cases with a high risk of such hysteresis and successfully distinguished them from those with a low risk. Furthermore, after validating the indicator on encroachment data, I demonstrated that it appeared early enough for encroachment to be prevented through realistic grazing-reduction treatments. Though this dissertation is rooted in the theory of savanna dynamics, its results can have significant applications in savanna conservation. Facilitation has only recently become a topic of interest within savanna literature. Given the threat of increasing droughts and a general anticipation of drier conditions in parts of Africa, insights stemming from this research may provide clues for preserving arid savannas. The impacts of rainfall variability on savannas have not yet been thoroughly studied, either. Conflicting results appear as a result of the lack of a robust theoretical understanding of plant interactions under variable conditions. . My work and other recent studies argue that such conditions may increase the importance of fast resource acquisition creating a 'temporal niche'. Woody encroachment has been extensively studied as phenomenon, though not from the perspective of its early identification and prevention. The development of an encroachment forecasting tool, as the one presented in this work, could protect both the savanna biome and societies dependent upon it for (economic) survival. All studies which follow are bound by the attempt to broaden the horizons of savanna-related research in order to deal with extreme conditions and phenomena; be it through the enhancement of the coexistence debate or the study of an imminent external threat or the development of a management-oriented tool for the conservation of savannas.}, language = {en} } @phdthesis{Rolke2016, author = {Rolke, Daniel}, title = {R{\"a}umliche und zeitliche Expressionsmuster sowie Funktionen der Serotonin-Rezeptor-Subtypen der Honigbiene, Apis mellifera L., 1758}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-96667}, school = {Universit{\"a}t Potsdam}, pages = {xii, 125}, year = {2016}, abstract = {Das biogene Amin Serotonin (5-Hydroxytryptamin, 5-HT) agiert als wichtiger chemischer Botenstoff bei einer Vielzahl von Organismen. Das durch 5 HT vermittelte Signal wird dabei durch spezifische Rezeptoren wahrgenommen und in eine zellul{\"a}re Reaktion umgesetzt. Diese 5 HT Rezeptoren geh{\"o}ren {\"u}berwiegend zur Familie der G Protein gekoppelten Rezeptoren (GPCRs). Die Honigbiene Apis mellifera bietet unter anderem aufgrund ihrer eusozialen Lebensweise vielf{\"a}ltige Ansatzpunkte zur Erforschung der Funktionen des serotonergen Systems in Insekten. Bei A. mellifera wurden bereits vier 5-HT-Rezeptor-Subtypen beschrieben und molekular sowie pharmakologisch charakterisiert: Am5 HT1A, Am5 HT2α, Am5 HT2β und Am5 HT7. Ziel dieser Arbeit war es, gewebespezifische sowie alters- und tageszeitabh{\"a}ngige Expressionsmuster der 5 HT Rezeptor-Subtypen zu untersuchen, um zu einem umfassenden Verst{\"a}ndnis des serotonergen Systems der Honigbiene beizutragen und eine Basis zur Hypothesenentwicklung f{\"u}r m{\"o}gliche physiologische Funktionen zu schaffen. Es wurde die Expression der 5 HT Rezeptorgene sowohl im zentralen Nervensystem, als auch in Teilen des Verdauungs-, Exkretions- und Speicheldr{\"u}sensystems gemessen. Dabei konnte gezeigt werden, dass die untersuchten 5-HT-Rezeptor-Subtypen generell weit im Organismus der Honigbiene verbreitet sind. Interessanterweise unterschieden sich die untersuchten Gewebe hinsichtlich der mRNA-Expressionsmuster der untersuchten Rezeptoren. W{\"a}hrend beispielsweise im Gehirn Am5 ht1A und Am5 ht7 st{\"a}rker als Am5 ht2α und Am5 ht2β exprimiert wurden, zeigte sich in Darmgewebe ein umgekehrtes Muster. Es war bereits bekannt, dass es bei der Expression der Am5-ht2-Gene zu alternativem Spleißen kommt. Dies f{\"u}hrt zur Entstehung der verk{\"u}rzten mRNA-Varianten Am5 ht2αΔIII und Am5 ht2βΔII. Die daraus resultierenden Proteine k{\"o}nnen nicht als funktionelle GPCRs agieren. Es konnte gezeigt werden, dass diese verk{\"u}rzten Spleißvarianten dennoch ubiquit{\"a}r in der Honigbiene exprimiert werden. Bemerkenswerterweise wurden gewebe{\"u}bergreifende {\"A}hnlichkeiten der Expressionsmuster der Spleißvarianten gegen{\"u}ber deren zugeh{\"o}rigen Volll{\"a}ngenvarianten festgestellt, welche auf Funktionen der verk{\"u}rzten Varianten in vivo hindeuten. Im Hinblick auf die bei A. mellifera haupts{\"a}chlich altersbedingte Arbeitsteilung wurde die Expression der 5 HT Rezeptor-Subtypen in Gehirnen von unterschiedlich alten Arbeiterinnen mit unterschiedlichen sozialen Rollen verglichen. W{\"a}hrend auf mRNA-Ebene keines der vier 5 HT Rezeptor-Subtypen eine altersabh{\"a}ngig unterschiedliche Expression zeigte, konnte f{\"u}r das Am5-HT1A-Protein eine h{\"o}here Konzentration in den Gehirnen {\"a}lterer Tiere gefunden werden. Dies deutet auf eine posttranskriptionale Regulation der 5 HT1A Rezeptorexpression hin, welche im Zusammenhang mit der Arbeitsteilung stehen k{\"o}nnte. Es erfolgte die Untersuchung tageszeitlicher {\"A}nderungen sowohl der Expression der 5 HT Rezeptor-Subtypen, als auch des biogenen Amins 5 HT selbst. W{\"a}hrend es in den Gehirnen von Arbeiterinnen, welche unter nat{\"u}rlichen Bedingungen gehalten wurden, zu keiner tageszeitabh{\"a}ngigen Ver{\"a}nderung des 5 HT-Titers kam, zeigte die mRNA-Expression von Am5-ht2α und Am5-ht2β eine periodische Oszillation mit Zunahme w{\"a}hrend des Tages und Abnahme w{\"a}hrend der Nacht. Diese Regulation wird durch externe Faktoren hervorgerufen und ist nicht auf einen endogenen circadianen Rhythmus zur{\"u}ckzuf{\"u}hren. Dies ging aus der Wiederholung der Expressionsmessungen an Gehirnen von Bienen, welche unter konstanten Laborbedingungen gehalten wurden, hervor. Weiterhin wurde die Beteiligung des serotonergen Systems an der Steuerung von Aspekten des circadianen lokomotorischen Aktivit{\"a}tsrhythmus anhand von Verhaltensexperimenten untersucht. Mit 5 HT gef{\"u}tterte Arbeiterinnen zeigten dabei unter konstanten Bedingungen eine l{\"a}ngere Periode des Aktivit{\"a}tsrhythmus als Kontrolltiere. Dies deutet auf einen Einfluss von 5 HT auf die Modulation der Synchronisation der inneren Uhr hin. Die vorliegenden Ergebnisse tragen wesentlich zum tieferen Verst{\"a}ndnis des serotonergen Systems der Honigbiene bei und bieten Ansatzpunkte f{\"u}r weitergehende Studien zur Funktion von 5 HT im Zusammenhang mit der Modulation von physiologischen Prozessen, Arbeitsteilung und circadianen Rhythmen.}, language = {de} } @phdthesis{Mengin2016, author = {Mengin, Virginie}, title = {Role of the clock in the regulation of growth and metabolism in stable and fluctuating environmental conditions}, school = {Universit{\"a}t Potsdam}, pages = {284}, year = {2016}, language = {en} } @article{ZengFrascaRumschoetteletal.2016, author = {Zeng, Ting and Frasca, Stefano and Rumsch{\"o}ttel, Jens and Koetz, Joachim and Leimk{\"u}hler, Silke and Wollenberger, Ursula}, title = {Role of Conductive Nanoparticles in the Direct Unmediated Bioelectrocatalysis of Immobilized Sulfite Oxidase}, series = {Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis}, volume = {28}, journal = {Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1040-0397}, doi = {10.1002/elan.201600246}, pages = {2303 -- 2310}, year = {2016}, language = {en} } @article{SchlaegelLewis2016, author = {Schl{\"a}gel, Ulrike E. and Lewis, Mark A.}, title = {Robustness of movement models: can models bridge the gap between temporal scales of data sets and behavioural processes?}, series = {Journal of mathematical biology}, volume = {73}, journal = {Journal of mathematical biology}, publisher = {Springer}, address = {Heidelberg}, issn = {0303-6812}, doi = {10.1007/s00285-016-1005-5}, pages = {1691 -- 1726}, year = {2016}, language = {en} } @phdthesis{OnanaEloundouEpseMbebi2016, author = {Onana Eloundou Epse Mbebi, Jeanne Marie}, title = {Robustness and plasticity in chemical reaction networks}, school = {Universit{\"a}t Potsdam}, pages = {116}, year = {2016}, language = {en} } @article{GrimmBerger2016, author = {Grimm, Volker and Berger, Uta}, title = {Robustness analysis: Deconstructing computational models for ecological theory and applications}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {326}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2015.07.018}, pages = {162 -- 167}, year = {2016}, abstract = {The design of computational models is path-dependent: the choices made in each step during model development constrain the choices that are available in the subsequent steps. The actual path of model development can be extremely different, even for the same system, because the path depends on the question addressed, the availability of data, and the consideration of specific expert knowledge, in addition to the experience, background, and modelling preferences of the modellers. Thus, insights from different models are practically impossible to integrate, which hinders the development of general theory. We therefore suggest augmenting the current culture of communicating models as working just fine with a culture of presenting analyses in which we try to break models, i.e., model mechanisms explaining certain observations break down. We refer to the systematic attempts to break a model as "robustness analysis" (RA). RA is the systematic deconstruction of a model by forcefully changing the model's parameters, structure, and representation of processes. We discuss the nature and elements of RA and provide brief examples. RA cannot be completely formalized into specific techniques and instead corresponds to detective work that is driven by general questions and specific hypotheses, with strong attention focused on unusual behaviours. Both individual modellers and ecological modelling in general will benefit from RA because RA helps with understanding models and identifying "robust theories", which are general principles that are independent of the idiosyncrasies of specific models. Integrating the results of RAs from different models to address certain systems or questions will then provide a comprehensive overview of when certain mechanisms control system behaviour and when and why this control ceases. This approach can provide insights into the mechanisms that lead to regime shifts in actual ecological systems.}, language = {en} } @phdthesis{Klauschies2016, author = {Klauschies, Toni}, title = {Revealing causes and consequences of functional diversity using trait-based models}, school = {Universit{\"a}t Potsdam}, pages = {231}, year = {2016}, language = {en} } @article{GuoLohmannRatzmannetal.2016, author = {Guo, Tong and Lohmann, Dirk and Ratzmann, Gregor and Tietjen, Britta}, title = {Response of semi-arid savanna vegetation composition towards grazing along a precipitation gradient-The effect of including plant heterogeneity into an ecohydrological savanna model}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {325}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2016.01.004}, pages = {47 -- 56}, year = {2016}, abstract = {Ecohydrological models of savanna rangeland systems typically aggregate plant species to very broad plant functional types (PFTs), which are characterized by their trait combinations. However, neglecting trait variability within modelled PFTs may hamper our ability to understand the effects of climate or land use change on vegetation composition and thus on ecosystem processes. In this study we extended and parameterized the ecohydrological savanna model EcoHyD, which originally considered only three broad PFTs (perennial grasses, annuals and shrubs). We defined several sub-types of perennial grasses (sub-PFTs) to assess the effect of environmental conditions on vegetation composition and ecosystem functioning. These perennial sub-PFTs are defined by altering distinct trait values based on a trade-off approach for (i) the longevity of plants and (ii) grazing-resistance. We find that increasing grazing intensity leads to a dominance of the fast-growing and short-lived perennial grass type as well as a dominance of the poorly palatable grass type. Increasing precipitation dampens the magnitude of grazing-induced shifts between perennial grass types. The diversification of perennial grass PFTs generally increases the total perennial grass cover and ecosystem water use efficiency, but does not protect the community from shrub encroachment. We thus demonstrate that including trait heterogeneity into ecosystem models will allow for an improved representation of ecosystem responses to environmental change in savannas. This will help to better assess how ecosystem functions might be impacted under future conditions. (C) 2016 Elsevier B.V. All rights reserved.}, language = {en} } @article{SakschewskivonBlohBoitetal.2016, author = {Sakschewski, Boris and von Bloh, Werner and Boit, Alice and Poorter, Lourens and Pe~na-Claros, Marielos and Heinke, Jens and Joshi, Jasmin Radha and Thonicke, Kirsten}, title = {Resilience of Amazon forests emerges from plant trait diversity}, series = {Nature climate change}, volume = {6}, journal = {Nature climate change}, publisher = {Nature Publ. Group}, address = {London}, issn = {1758-678X}, doi = {10.1038/NCLIMATE3109}, pages = {1032 -- +}, year = {2016}, language = {en} } @article{SasMuellerKappeletal.2016, author = {Sas, Claudia and Mueller, Frank and Kappel, Christian and Kent, Tyler V. and Wright, Stephen I. and Hilker, Monika and Lenhard, Michael}, title = {Repeated Inactivation of the First Committed Enzyme Underlies the Loss of Benzaldehyde Emission after the Selfing Transition in Capsella}, series = {Current biology}, volume = {26}, journal = {Current biology}, publisher = {Cell Press}, address = {Cambridge}, issn = {0960-9822}, doi = {10.1016/j.cub.2016.10.026}, pages = {3313 -- 3319}, year = {2016}, abstract = {The enormous species richness of flowering plants is at least partly due to floral diversification driven by interactions between plants and their animal pollinators [1, 2]. Specific pollinator attraction relies on visual and olfactory floral cues [3-5]; floral scent can not only attract pollinators but also attract or repel herbivorous insects [6-8]. However, despite its central role for plant-animal interactions, the genetic control of floral scent production and its evolutionary modification remain incompletely understood [9-13]. Benzenoids are an important class of floral scent compounds that are generated from phenylalanine via several enzymatic pathways [14-17]. Here we address the genetic basis of the loss of floral scent associated with the transition from outbreeding to selfing in the genus Capsella. While the outbreeding C. grandiflora emits benzaldehyde as a major constituent of its floral scent, this has been lost in the selfing C. rubella. We identify the Capsella CNL1 gene encoding cinnamate: CoA ligase as responsible for this variation. Population genetic analysis indicates that CNL1 has been inactivated twice independently in C. rubella via different novel mutations to its coding sequence. Together with a recent study in Petunia [18], this identifies cinnamate: CoA ligase as an evolutionary hotspot for mutations causing the loss of benzenoid scent compounds in association with a shift in the reproductive strategy of Capsella from pollination by insects to self-fertilization.}, language = {en} } @article{OrawetzMalinovaOrzechowskietal.2016, author = {Orawetz, Tom and Malinova, Irina and Orzechowski, Slawomir and Fettke, J{\"o}rg}, title = {Reduction of the plastidial phosphorylase in potato (Solanum tuberosum L.) reveals impact on storage starch structure during growth at low temperature}, series = {Plant physiology and biochemistry : an official journal of the Federation of European Societies of Plant Physiology}, volume = {100}, journal = {Plant physiology and biochemistry : an official journal of the Federation of European Societies of Plant Physiology}, publisher = {Elsevier}, address = {Paris}, issn = {0981-9428}, doi = {10.1016/j.plaphy.2016.01.013}, pages = {141 -- 149}, year = {2016}, abstract = {Tubers of potato (Solanum tuberosum L.), one of the most important crops, are a prominent example for an efficient production of storage starch. Nevertheless, the synthesis of this storage starch is not completely understood. The plastidial phosphorylase (Phol; EC 2.4.11) catalyzes the reversible transfer of glucosyl residues from glucose-1-phosphate to the non-reducing end of alpha-glucans with the release of orthophosphate. Thus, the enzyme is in principle able to act during starch synthesis. However, so far under normal growth conditions no alterations in tuber starch metabolism were observed. Based on analyses of other species and also from in vitro experiments with potato tuber slices it was supposed, that Phol has a stronger impact on starch metabolism, when plants grow under low temperature conditions. Therefore, we analyzed the starch content, granule size, as well as the internal structure of starch granules isolated from potato plants grown under low temperatures. Besides wild type, transgenic potato plants with a strong reduction in the Phol activity were analyzed. No significant alterations in starch content and granule size were detected. In contrast, when plants were cultivated at low temperatures the chain length distributions of the starch granules were altered. Thus, the granules contained more short glucan chains. That was not observed in the transgenic plants, revealing that Pho1 in wild type is involved in the formation of the short glucan chains, at least at low temperatures. (C) 2016 Elsevier Masson SAS. All rights reserved.}, language = {en} } @article{CazellesLalaouiHartmannetal.2016, author = {Cazelles, R. and Lalaoui, N. and Hartmann, Tobias and Leimk{\"u}hler, Silke and Wollenberger, Ursula and Antonietti, Markus and Cosnier, S.}, title = {Ready to use bioinformatics analysis as a tool to predict immobilisation strategies for protein direct electron transfer (DET)}, series = {Polymer : the international journal for the science and technology of polymers}, volume = {85}, journal = {Polymer : the international journal for the science and technology of polymers}, publisher = {Elsevier}, address = {Oxford}, issn = {0956-5663}, doi = {10.1016/j.bios.2016.04.078}, pages = {90 -- 95}, year = {2016}, language = {en} } @article{NukarinenNaegelePedrottietal.2016, author = {Nukarinen, Ella and N{\"a}gele, Thomas and Pedrotti, Lorenzo and Wurzinger, Bernhard and Mair, Andrea and Landgraf, Ramona and B{\"o}rnke, Frederik and Hanson, Johannes and Teige, Markus and Baena-Gonzalez, Elena and Dr{\"o}ge-Laser, Wolfgang and Weckwerth, Wolfram}, title = {Quantitative phosphoproteomics reveals the role of the AMPK plant ortholog SnRK1 as a metabolic master regulator under energy deprivation}, series = {Scientific reports}, volume = {6}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep31697}, pages = {10248 -- 10252}, year = {2016}, abstract = {Since years, research on SnRK1, the major cellular energy sensor in plants, has tried to define its role in energy signalling. However, these attempts were notoriously hampered by the lethality of a complete knockout of SnRK1. Therefore, we generated an inducible amiRNA:: SnRK1 alpha 2 in a snrk1 alpha 1 knock out background (snrk1 alpha 1/alpha 2) to abolish SnRK1 activity to understand major systemic functions of SnRK1 signalling under energy deprivation triggered by extended night treatment. We analysed the in vivo phosphoproteome, proteome and metabolome and found that activation of SnRK1 is essential for repression of high energy demanding cell processes such as protein synthesis. The most abundant effect was the constitutively high phosphorylation of ribosomal protein S6 (RPS6) in the snrk1 alpha 1/alpha 2 mutant. RPS6 is a major target of TOR signalling and its phosphorylation correlates with translation. Further evidence for an antagonistic SnRK1 and TOR crosstalk comparable to the animal system was demonstrated by the in vivo interaction of SnRK1 alpha 1 and RAPTOR1B in the cytosol and by phosphorylation of RAPTOR1B by SnRK1 alpha 1 in kinase assays. Moreover, changed levels of phosphorylation states of several chloroplastic proteins in the snrk1 alpha 1/alpha 2 mutant indicated an unexpected link to regulation of photosynthesis, the main energy source in plants.}, language = {en} } @phdthesis{Reil2016, author = {Reil, Daniela}, title = {Puumala hantavirus dynamics in bank voles: identification of environmental correlates to predict human infection risk}, school = {Universit{\"a}t Potsdam}, pages = {85}, year = {2016}, language = {en} } @article{BaylisKowalskiVoigtetal.2016, author = {Baylis, Alastair M. M. and Kowalski, Gabriele Joanna and Voigt, Christian C. and Orben, Rachael A. and Trillmich, Fritz and Staniland, Iain J. and Hoffman, Joseph I.}, title = {Pup Vibrissae Stable Isotopes Reveal Geographic Differences in Adult Female Southern Sea Lion Habitat Use during Gestation}, series = {PLoS one}, volume = {11}, journal = {PLoS one}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0157394}, pages = {1824 -- 1835}, year = {2016}, abstract = {Individuals within populations often differ substantially in habitat use, the ecological consequences of which can be far reaching. Stable isotope analysis provides a convenient and often cost effective means of indirectly assessing the habitat use of individuals that can yield valuable insights into the spatiotemporal distribution of foraging specialisations within a population. Here we use the stable isotope ratios of southern sea lion (Otaria flavescens) pup vibrissae at the Falkland Islands, in the South Atlantic, as a proxy for adult female habitat use during gestation. A previous study found that adult females from one breeding colony (Big Shag Island) foraged in two discrete habitats, inshore (coastal) or offshore (outer Patagonian Shelf). However, as this species breeds at over 70 sites around the Falkland Islands, it is unclear if this pattern is representative of the Falkland Islands as a whole. In order to characterize habitat use, we therefore assayed carbon (delta C-13) and nitrogen (delta N-15) ratios from 65 southern sea lion pup vibrissae, sampled across 19 breeding colonies at the Falkland Islands. Model-based clustering of pup isotope ratios identified three distinct clusters, representing adult females that foraged inshore, offshore, and a cluster best described as intermediate. A significant difference was found in the use of inshore and offshore habitats between West and East Falkland and between the two colonies with the largest sample sizes, both of which are located in East Falkland. However, habitat use was unrelated to the proximity of breeding colonies to the Patagonian Shelf, a region associated with enhanced biological productivity. Our study thus points towards other factors, such as local oceanography and its influence on resource distribution, playing a prominent role in inshore and offshore habitat use.}, language = {en} } @misc{Matzk2016, type = {Master Thesis}, author = {Matzk, S{\"o}ren}, title = {Predictive analysis of metabolic and preventive patient data}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-406103}, school = {Universit{\"a}t Potsdam}, pages = {XI, 63}, year = {2016}, abstract = {Every day huge amounts of medical records are stored by means of hospitals' and medical offices' software. These data are generally unconsidered in research. In this work anonymized everyday medical records ascertained in a physician's office, cov- ering holistic internal medicine in combination with orthomolecular medicine, are analyzed. Due to the lack of cooperation by the provider of the medical practice software a selection of diagnoses and anthropometric parameters was extracted manually. Information about patients' treatment are not available in this study. Nevertheless, data mining approaches in- cluding machine learning techniques are used to enable research, prevention and monitoring of patients' course of treatment. The potential of these everyday medical data is demonstrated by investigating co-morbidity and pyroluria which is a metabolic dysfunction indicated by increased levels of hydroxy- hemopyrrolin-2-one (HPL). It points out that the metabolic syndrome forms a cluster of its components and cancer, as well as mental disorders are grouped with thyroid diseases including autoimmune thyroid diseases. In contrast to prevailing assumptions in which it was estimated that approximately 10 \% of the population show increased levels of HPL, in this analysis 84.9 \% of the tested patients have an increased concentration of HPL. Prevention is illustrated by using decision tree models to predict diseases. Evaluation of the obtained model for Hashimoto's disease yield an accuracy of 87.5 \%. The model generated for hypothyroidism (accuracy of 60.9 \%) reveals shortcomings due to missing information about the treatment. Dynamics in the biomolecular status of 20 patients who have visited the medical office at least one time a year between 2010 and 2014 for laboratory tests are visualized by STATIS, a consensus analysis based on an extension to principal component analysis. Thereby, one can obtain patterns which are predestinated for specific diseases as hypertension. This study demonstrates that these often overlooked everyday data are challenging due to its sparsity and heterogeneity but its analysis is a great possibility to do research on disease profiles of real patients.}, language = {de} } @article{GietlerNykielOrzechowskietal.2016, author = {Gietler, Marta and Nykiel, Malgorzata and Orzechowski, Slawomir and Zagdanska, Barbara and Fettke, J{\"o}rg}, title = {Proteomic analysis of S-nitrosylated and S-glutathionylated proteins in wheat seedlings with different dehydration tolerances}, series = {Plant physiology and biochemistry : an official journal of the Federation of European Societies of Plant Physiology}, volume = {108}, journal = {Plant physiology and biochemistry : an official journal of the Federation of European Societies of Plant Physiology}, publisher = {Elsevier}, address = {Paris}, issn = {0981-9428}, doi = {10.1016/j.plaphy.2016.08.017}, pages = {507 -- 518}, year = {2016}, abstract = {A loss of dehydration tolerance in wheat seedlings on the fifth day following imbibition is associated with a disturbance in cellular redox homeostasis, as documented by a shift of the reduced/oxidized glutathione ratio to a more oxidized state and a significant increase in the ratio of protein thiols to the total thiol group content. Therefore, the identification and characterization of redox-sensitive proteins are important steps toward understanding the molecular mechanisms of the loss of dehydration tolerance. In the present study, proteins that were differentially expressed between fully turgid (control), dehydrated tolerant (four-day-old) and dehydrated sensitive (six-day-old) wheat seedlings were analysed. Protein spots having at least a significant (p < 0.05) two-fold change in protein abundance were selected by Delta2D as differentially expressed, identified by MALDI-TOF and LC-MS/MS, and classified according to their function. The observed changes in the proteomic patterns of the differentially S-nitrosylated and S-glutathionylated proteins were highly specific in dehydration-tolerant and-sensitive wheat seedlings. The metabolic function of these proteins indicates that dehydration tolerance is mainly related to nucleic acids, protein metabolism, and energy metabolism. It has been proven that leaf-specific thionins BTH6 and DB4, chloroplastic 50S ribosomal protein L16, phospholipase A1-II delta, and chloroplastic thioredoxin M2 are both S-nitrosylated and S-glutathionylated upon water deficiency. Our results revealed the existence of interplay between S-nitrosylation and S-glutathionylation, two redox-regulated protein posttranslational modifications that could enhance plant defence mechanisms and/or facilitate the acclimation of plants to unfavourable environmental conditions. (C) 2016 Elsevier Masson SAS. All rights reserved.}, language = {en} } @phdthesis{Kersten2016, author = {Kersten, Birgit}, title = {Proteom-weite Studien zur Phosphorylierung pflanzlicher Proteine mittels Proteinmikroarrays und Bioinformatik}, school = {Universit{\"a}t Potsdam}, year = {2016}, language = {de} } @article{HilkerSchwachtjeBaieretal.2016, author = {Hilker, Monika and Schwachtje, Jens and Baier, Margarete and Balazadeh, Salma and B{\"a}urle, Isabel and Geiselhardt, Sven and Hincha, Dirk K. and Kunze, Reinhard and Mueller-Roeber, Bernd and Rillig, Matthias G. and Rolff, Jens and Schm{\"u}lling, Thomas and Steppuhn, Anke and van Dongen, Joost and Whitcomb, Sarah J. and Wurst, Susanne and Zuther, Ellen and Kopka, Joachim}, title = {Priming and memory of stress responses in organisms lacking a nervous system}, series = {Biological reviews}, volume = {91}, journal = {Biological reviews}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1464-7931}, doi = {10.1111/brv.12215}, pages = {1118 -- 1133}, year = {2016}, language = {en} } @article{IzhitskiyZavialovSapozhnikovetal.2016, author = {Izhitskiy, A. S. and Zavialov, P. O. and Sapozhnikov, P. V. and Kirillin, G. B. and Grossart, Hans-Peter and Kalinina, O. Y. and Zalota, A. K. and Goncharenko, I. V. and Kurbaniyazov, A. K.}, title = {Present state of the Aral Sea: diverging physical and biological characteristics of the residual basins}, series = {Scientific reports}, volume = {6}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep23906}, pages = {1435 -- 1442}, year = {2016}, abstract = {Latest data on the hydrophysical and biological state of the residual basins of the Aral Sea are presented and compared. Direct, quasi-simultaneous observations were carried out in the central part of the Western Large Aral Sea, the northern extremity of the Large Aral known as Chernyshev Bay, Lake Tshchebas, and the Small Aral Sea in October 2014. The Large Aral Sea and Lake Tshchebas transformed into hyperhaline water bodies with highly special taxocene structure. The Small Aral Sea was a relatively diverse brackish ecosystem, which was rather similar to the pre-desiccation environment. The Small Aral Sea and Lake Tshchebas exhibited a fully-mixed vertical structure, whereas the Western Large Aral Sea was strongly stratified. Our data show that during desiccation, different parts of the Aral Sea experienced different environmental conditions, resulting in qualitative and quantitative differences in the physical and biological regimes among the different residual basins.}, language = {en} } @article{CuongNguyenHuuKappelKelleretal.2016, author = {Cuong Nguyen Huu, and Kappel, Christian and Keller, Barbara and Sicard, Adrien and Takebayashi, Yumiko and Breuninger, Holger and Nowak, Michael D. and B{\"a}urle, Isabel and Himmelbach, Axel and Burkart, Michael and Ebbing-Lohaus, Thomas and Sakakibara, Hitoshi and Altschmied, Lothar and Conti, Elena and Lenhard, Michael}, title = {Presence versus absence of CYP734A50 underlies the style-length dimorphism in primroses}, series = {eLife}, volume = {5}, journal = {eLife}, publisher = {eLife Sciences Publications}, address = {Cambridge}, issn = {2050-084X}, doi = {10.7554/eLife.17956}, pages = {15}, year = {2016}, abstract = {Heterostyly is a wide-spread floral adaptation to promote outbreeding, yet its genetic basis and evolutionary origin remain poorly understood. In Primula (primroses), heterostyly is controlled by the S-locus supergene that determines the reciprocal arrangement of reproductive organs and incompatibility between the two morphs. However, the identities of the component genes remain unknown. Here, we identify the Primula CYP734A50 gene, encoding a putative brassinosteroid-degrading enzyme, as the G locus that determines the style-length dimorphism. CYP734A50 is only present on the short-styled S-morph haplotype, it is specifically expressed in S-morph styles, and its loss or inactivation leads to long styles. The gene arose by a duplication specific to the Primulaceae lineage and shows an accelerated rate of molecular evolution. Thus, our results provide a mechanistic explanation for the Primula style-length dimorphism and begin to shed light on the evolution of the S-locus as a prime model for a complex plant supergene.}, language = {en} } @article{CzolkosDockTonningetal.2016, author = {Czolkos, Ilja and Dock, Eva and Tonning, Erik and Christensen, Jakob and Winther-Nielsen, Margrethe and Carlsson, Charlotte and Mojzikova, Renata and Skladal, Petr and Wollenberger, Ursula and Norgaard, Lars and Ruzgas, Tautgirdas and Emneus, Jenny}, title = {Prediction of wastewater quality using amperometric bioelectronic tongues}, series = {Marine policy}, volume = {75}, journal = {Marine policy}, publisher = {Elsevier}, address = {Oxford}, issn = {0956-5663}, doi = {10.1016/j.bios.2015.08.055}, pages = {375 -- 382}, year = {2016}, abstract = {Wastewater samples from a Swedish chemi-thermo-mechanical pulp (CTMP) mill collected at different purification stages in a wastewater treatment plant (WWTP) were analyzed with an amperometric enzyme-based biosensor array in a flow-injection system. In order to resolve the complex composition of the wastewater, the array consists of several sensing elements which yield a multidimensional response. We used principal component analysis (PCA) to decompose the array's responses, and found that wastewater with different degrees of pollution can be differentiated. With the help of partial least squares regression (PLS-R), we could link the sensor responses to the toxicity parameter, as well as to global organic pollution parameters (COD, BOD, and TOC). From investigating the influences of individual sensors in the array, it was found that the best models were in most cases obtained when all sensors in the array were included in the PLS-R model. We find that fast simultaneous determination of several global environmental parameters characterizing wastewaters is possible with this kind of biosensor array, in particular because of the link between the sensor responses and the biological effect onto the ecosystem into which the wastewater would be released. In conjunction with multivariate data analysis tools, there is strong potential to reduce the total time until a result is yielded from days to a few minutes.}, language = {en} } @phdthesis{Sin2016, author = {Sin, Celine}, title = {Post-transcriptional control of gene expression}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-102469}, school = {Universit{\"a}t Potsdam}, pages = {xxv, 238}, year = {2016}, abstract = {Gene expression describes the process of making functional gene products (e.g. proteins or special RNAs) from instructions encoded in the genetic information (e.g. DNA). This process is heavily regulated, allowing cells to produce the appropriate gene products necessary for cell survival, adapting production as necessary for different cell environments. Gene expression is subject to regulation at several levels, including transcription, mRNA degradation, translation and protein degradation. When intact, this system maintains cell homeostasis, keeping the cell alive and adaptable to different environments. Malfunction in the system can result in disease states and cell death. In this dissertation, we explore several aspects of gene expression control by analyzing data from biological experiments. Most of the work following uses a common mathematical model framework based on Markov chain models to test hypotheses, predict system dynamics or elucidate network topology. Our work lies in the intersection between mathematics and biology and showcases the power of statistical data analysis and math modeling for validation and discovery of biological phenomena.}, language = {en} } @article{HoffmanKowalskiKlimovaetal.2016, author = {Hoffman, J. I. and Kowalski, Gabriele Joanna and Klimova, A. and Eberhart-Phillips, Luke J. and Staniland, Iain J. and Baylis, Alastair M. M.}, title = {Population structure and historical demography of South American sea lions provide insights into the catastrophic decline of a marine mammal population}, series = {Royal Society Open Science}, volume = {3}, journal = {Royal Society Open Science}, publisher = {Royal Society}, address = {London}, issn = {2054-5703}, doi = {10.1098/rsos.160291}, pages = {505 -- 517}, year = {2016}, abstract = {Understanding the causes of population decline is crucial for conservation management. We therefore used genetic analysis both to provide baseline data on population structure and to evaluate hypotheses for the catastrophic decline of the South American sea lion (Otaria flavescens) at the Falkland Islands (Malvinas) in the South Atlantic. We genotyped 259 animals from 23 colonies across the Falklands at 281 bp of the mitochondrial hypervariable region and 22 microsatellites. A weak signature of population structure was detected, genetic diversity was moderately high in comparison with other pinniped species, and no evidence was found for the decline being associated with a strong demographic bottleneck. By combining our mitochondrial data with published sequences from Argentina, Brazil, Chile and Peru, we also uncovered strong maternally directed population structure across the geographical range of the species. In particular, very few shared haplotypes were found between the Falklands and South America, and this was reflected in correspondingly low migration rate estimates. These findings do not support the prominent hypothesis that the decline was caused by migration to Argentina, where large-scale commercial harvesting operations claimed over half a million animals. Thus, our study not only provides baseline data for conservation management but also reveals the potential for genetic studies to shed light upon long-standing questions pertaining to the history and fate of natural populations.}, language = {en} } @article{HeinzeSitteSchindhelmetal.2016, author = {Heinze, Johannes and Sitte, Mario and Schindhelm, Anne and Wright, J. and Joshi, Jasmin Radha}, title = {Plant-soil feedbacks: a comparative study on the relative importance of soil feedbacks in the greenhouse versus the field}, series = {Oecologia}, volume = {181}, journal = {Oecologia}, publisher = {Springer}, address = {New York}, issn = {0029-8549}, doi = {10.1007/s00442-016-3591-8}, pages = {559 -- 569}, year = {2016}, abstract = {Interactions between plants and soil microorganisms influence individual plant performance and thus plant-community composition. Most studies on such plant-soil feedbacks (PSFs) have been performed under controlled greenhouse conditions, whereas no study has directly compared PSFs under greenhouse and natural field conditions. We grew three grass species that differ in local abundance in grassland communities simultaneously in the greenhouse and field on field-collected soils either previously conditioned by these species or by the general grassland community. As soils in grasslands are typically conditioned by mixes of species through the patchy and heterogeneous plant species' distributions, we additionally compared the effects of species-specific versus non-specific species conditioning on PSFs in natural and greenhouse conditions. In almost all comparisons PSFs differed between the greenhouse and field. In the greenhouse, plant growth in species-specific and non-specific soils resulted in similar effects with neutral PSFs for the most abundant species and positive PSFs for the less abundant species. In contrast, in the field all grass species tested performed best in non-specific plots, whereas species-specific PSFs were neutral for the most abundant and varied for the less abundant species. This indicates a general beneficial effect of plant diversity on PSFs in the field. Controlled greenhouse conditions might provide valuable insights on the nominal effects of soils on plants. However, the PSFs observed in greenhouse conditions may not be the determining drivers in natural plant communities where their effects may be overwhelmed by the diversity of abiotic and biotic above- and belowground interactions in the field.}, language = {en} } @article{CuadratFerreraGrossartetal.2016, author = {Cuadrat, Rafael R. C. and Ferrera, Isabel and Großart, Hans-Peter and Davila, Alberto M. R.}, title = {Picoplankton Bloom in Global South? A High Fraction of Aerobic Anoxygenic Phototrophic Bacteria in Metagenomes from a Coastal Bay (Arraial do Cabo-Brazil)}, series = {OMICS : a journal of integrative biology}, volume = {20}, journal = {OMICS : a journal of integrative biology}, publisher = {Liebert}, address = {New Rochelle}, issn = {1536-2310}, doi = {10.1089/omi.2015.0142}, pages = {76 -- 87}, year = {2016}, abstract = {Marine habitats harbor a great diversity of microorganism from the three domains of life, only a small fraction of which can be cultivated. Metagenomic approaches are increasingly popular for addressing microbial diversity without culture, serving as sensitive and relatively unbiased methods for identifying and cataloging the diversity of nucleic acid sequences derived from organisms in environmental samples. Aerobic anoxygenic phototrophic bacteria (AAP) play important roles in carbon and energy cycling in aquatic systems. In oceans, those bacteria are widely distributed; however, their abundance and importance are still poorly understood. The aim of this study was to estimate abundance and diversity of AAPs in metagenomes from an upwelling affected coastal bay in Arraial do Cabo, Brazil, using in silico screening for the anoxygenic photosynthesis core genes. Metagenomes from the Global Ocean Sample Expedition (GOS) were screened for comparative purposes. AAPs were highly abundant in the free-living bacterial fraction from Arraial do Cabo: 23.88\% of total bacterial cells, compared with 15\% in the GOS dataset. Of the ten most AAP abundant samples from GOS, eight were collected close to the Equator where solar irradiation is high year-round. We were able to assign most retrieved sequences to phylo-groups, with a particularly high abundance of Roseobacter in Arraial do Cabo samples. The high abundance of AAP in this tropical bay may be related to the upwelling phenomenon and subsequent picoplankton bloom. These results suggest a link between upwelling and light abundance and demonstrate AAP even in oligotrophic tropical and subtropical environments. Longitudinal studies in the Arraial do Cabo region are warranted to understand the dynamics of AAP at different locations and seasons, and the ecological role of these unique bacteria for biogeochemical and energy cycling in the ocean.}, language = {en} }