@phdthesis{Adamla2015, author = {Adamla, Frauke}, title = {Polyglutamine- and aging-dependent aberrancies in transcription and translation}, school = {Universit{\"a}t Potsdam}, pages = {109}, year = {2015}, language = {en} } @article{AdamlaIgnatova2015, author = {Adamla, Frauke and Ignatova, Zoya}, title = {Somatic expression of unc-54 and vha-6 mRNAs declines but not pan-neuronal rgef-1 and unc-119 expression in aging Caenorhabditis elegans}, series = {Scientific reports}, volume = {5}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep10692}, pages = {10}, year = {2015}, abstract = {Aging is a highly controlled biological process characterized by a progressive deterioration of various cellular activities. One of several hallmarks of aging describes a link to transcriptional alteration, suggesting that it may impact the steady-state mRNA levels. We analyzed the mRNA steady-state levels of polyCAG-encoding transgenes and endogenous genes under the control of well-characterized promoters for intestinal (vha-6), muscular (unc-54, unc-15) and pan-neuronal (rgef-1, unc-119) expression in the nematode Caenorhabditis elegans. We find that there is not a uniform change in transcriptional profile in aging, but rather a tissue-specific difference in the mRNA levels of these genes. While levels of mRNA in the intestine (vha-6) and muscular (unc-54, unc-15) cells decline with age, pan-neuronal tissue shows more stable mRNA expression (rgef-1, unc-119) which even slightly increases with the age of the animals. Our data on the variations in the mRNA abundance from exemplary cases of endogenous and transgenic gene expression contribute to the emerging evidence for tissue-specific variations in the aging process.}, language = {en} } @article{AlbertAuffretCosynsetal.2015, author = {Albert, Aurelie and Auffret, Alistair G. and Cosyns, Eric and Cousins, Sara A. O. and Eichberg, Carsten and Eycott, Amy E. and Heinken, Thilo and Hoffmann, Maurice and Jaroszewicz, Bogdan and Malo, Juan E. and Marell, Anders and Mouissie, Maarten and Pakeman, Robin J. and Picard, Melanie and Plue, Jan and Poschlod, Peter and Provoost, Sam and Schulze, Kiowa Alraune and Baltzinger, Christophe}, title = {Seed dispersal by ungulates as an ecological filter: a trait-based meta-analysis}, series = {Oikos}, volume = {124}, journal = {Oikos}, number = {9}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0030-1299}, doi = {10.1111/oik.02512}, pages = {1109 -- 1120}, year = {2015}, abstract = {Plant communities are often dispersal-limited and zoochory can be an efficient mechanism for plants to colonize new patches of potentially suitable habitat. We predicted that seed dispersal by ungulates acts as an ecological filter - which differentially affects individuals according to their characteristics and shapes species assemblages - and that the filter varies according to the dispersal mechanism (endozoochory, fur-epizoochory and hoof-epizoochory). We conducted two-step individual participant data meta-analyses of 52 studies on plant dispersal by ungulates in fragmented landscapes, comparing eight plant traits and two habitat indicators between dispersed and non-dispersed plants. We found that ungulates dispersed at least 44\% of the available plant species. Moreover, some plant traits and habitat indicators increased the likelihood for plant of being dispersed. Persistent or nitrophilous plant species from open habitats or bearing dry or elongated diaspores were more likely to be dispersed by ungulates, whatever the dispersal mechanism. In addition, endozoochory was more likely for diaspores bearing elongated appendages whereas epizoochory was more likely for diaspores released relatively high in vegetation. Hoof-epizoochory was more likely for light diaspores without hooked appendages. Fur-epizoochory was more likely for diaspores with appendages, particularly elongated or hooked ones. We thus observed a gradient of filtering effect among the three dispersal mechanisms. Endozoochory had an effect of rather weak intensity (impacting six plant characteristics with variations between ungulate-dispersed and non-dispersed plant species mostly below 25\%), whereas hoof-epizoochory had a stronger effect (eight characteristics included five ones with above 75\% variation), and fur-epizoochory an even stronger one (nine characteristics included six ones with above 75\% variation). Our results demonstrate that seed dispersal by ungulates is an ecological filter whose intensity varies according to the dispersal mechanism considered. Ungulates can thus play a key role in plant community dynamics and have implications for plant spatial distribution patterns at multiple scales.}, language = {en} } @article{AllanManningAltetal.2015, author = {Allan, Eric and Manning, Pete and Alt, Fabian and Binkenstein, Julia and Blaser, Stefan and Bl{\"u}thgen, Nico and B{\"o}hm, Stefan and Grassein, Fabrice and H{\"o}lzel, Norbert and Klaus, Valentin H. and Kleinebecker, Till and Morris, E. Kathryn and Oelmann, Yvonne and Prati, Daniel and Renner, Swen C. and Rillig, Matthias C. and Schaefer, Martin and Schloter, Michael and Schmitt, Barbara and Sch{\"o}ning, Ingo and Schrumpf, Marion and Solly, Emily and Sorkau, Elisabeth and Steckel, Juliane and Steffen-Dewenter, Ingolf and Stempfhuber, Barbara and Tschapka, Marco and Weiner, Christiane N. and Weisser, Wolfgang W. and Werner, Michael and Westphal, Catrin and Wilcke, Wolfgang and Fischer, Markus}, title = {Land use intensification alters ecosystem multifunctionality via loss of biodiversity and changes to functional composition}, series = {Ecology letters}, volume = {18}, journal = {Ecology letters}, number = {8}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1461-023X}, doi = {10.1111/ele.12469}, pages = {834 -- 843}, year = {2015}, abstract = {Global change, especially land-use intensification, affects human well-being by impacting the delivery of multiple ecosystem services (multifunctionality). However, whether biodiversity loss is a major component of global change effects on multifunctionality in real-world ecosystems, as in experimental ones, remains unclear. Therefore, we assessed biodiversity, functional composition and 14 ecosystem services on 150 agricultural grasslands differing in land-use intensity. We also introduce five multifunctionality measures in which ecosystem services were weighted according to realistic land-use objectives. We found that indirect land-use effects, i.e. those mediated by biodiversity loss and by changes to functional composition, were as strong as direct effects on average. Their strength varied with land-use objectives and regional context. Biodiversity loss explained indirect effects in a region of intermediate productivity and was most damaging when land-use objectives favoured supporting and cultural services. In contrast, functional composition shifts, towards fast-growing plant species, strongly increased provisioning services in more inherently unproductive grasslands.}, language = {en} } @article{AllhoffRitterskampRalletal.2015, author = {Allhoff, Korinna Theresa and Ritterskamp, Daniel and Rall, Bj{\"o}rn C. and Drossel, Barbara and Guill, Christian}, title = {Evolutionary food web model based on body masses gives realistic networks with permanent species turnover}, series = {Scientific reports}, volume = {5}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep10955}, pages = {12}, year = {2015}, abstract = {The networks of predator-prey interactions in ecological systems are remarkably complex, but nevertheless surprisingly stable in terms of long term persistence of the system as a whole. In order to understand the mechanism driving the complexity and stability of such food webs, we developed an eco-evolutionary model in which new species emerge as modifications of existing ones and dynamic ecological interactions determine which species are viable. The food-web structure thereby emerges from the dynamical interplay between speciation and trophic interactions. The proposed model is less abstract than earlier evolutionary food web models in the sense that all three evolving traits have a clear biological meaning, namely the average body mass of the individuals, the preferred prey body mass, and the width of their potential prey body mass spectrum. We observed networks with a wide range of sizes and structures and high similarity to natural food webs. The model networks exhibit a continuous species turnover, but massive extinction waves that affect more than 50\% of the network are not observed.}, language = {en} } @phdthesis{Alseekh2015, author = {Alseekh, Saleh}, title = {Identification and mode of inheritance of quantitative trait loci (QTL) for metabolite abundance in tomato}, school = {Universit{\"a}t Potsdam}, pages = {134}, year = {2015}, language = {en} } @article{AlseekhTohgeWendenbergetal.2015, author = {Alseekh, Saleh and Tohge, Takayuki and Wendenberg, Regina and Scossa, Federico and Omranian, Nooshin and Li, Jie and Kleessen, Sabrina and Giavalisco, Patrick and Pleban, Tzili and M{\"u}ller-R{\"o}ber, Bernd and Zamir, Dani and Nikoloski, Zoran and Fernie, Alisdair R.}, title = {Identification and Mode of Inheritance of Quantitative Trait Loci for Secondary Metabolite Abundance in Tomato}, series = {The plant cell}, volume = {27}, journal = {The plant cell}, number = {3}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {1040-4651}, doi = {10.1105/tpc.114.132266}, pages = {485 -- 512}, year = {2015}, abstract = {A large-scale metabolic quantitative trait loci (mQTL) analysis was performed on the well-characterized Solanum pennellii introgression lines to investigate the genomic regions associated with secondary metabolism in tomato fruit pericarp. In total, 679 mQTLs were detected across the 76 introgression lines. Heritability analyses revealed that mQTLs of secondary metabolism were less affected by environment than mQTLs of primary metabolism. Network analysis allowed us to assess the interconnectivity of primary and secondary metabolism as well as to compare and contrast their respective associations with morphological traits. Additionally, we applied a recently established real-time quantitative PCR platform to gain insight into transcriptional control mechanisms of a subset of the mQTLs, including those for hydroxycinnamates, acyl-sugar, naringenin chalcone, and a range of glycoalkaloids. Intriguingly, many of these compounds displayed a dominant-negative mode of inheritance, which is contrary to the conventional wisdom that secondary metabolite contents decreased on domestication. We additionally performed an exemplary evaluation of two candidate genes for glycolalkaloid mQTLs via the use of virus-induced gene silencing. The combined data of this study were compared with previous results on primary metabolism obtained from the same material and to other studies of natural variance of secondary metabolism.}, language = {en} } @article{AlterMeyerPostetal.2015, author = {Alter, S. Elizabeth and Meyer, Matthias and Post, Klaas and Czechowski, Paul and Gravlund, Peter and Gaines, Cork and Rosenbaum, Howard C. and Kaschner, Kristin and Turvey, Samuel T. and van der Plicht, Johannes and Shapiro, Beth and Hofreiter, Michael}, title = {Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100}, series = {Molecular ecology}, volume = {24}, journal = {Molecular ecology}, number = {7}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0962-1083}, doi = {10.1111/mec.13121}, pages = {1510 -- 1522}, year = {2015}, abstract = {Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is known about the history of Atlantic gray whales or their relationship to the extant Pacific population, the extirpation of the Atlantic population during historical times has been attributed to whaling. We used a combination of ancient and modern DNA, radiocarbon dating and predictive habitat modelling to better understand the distribution of gray whales during the Pleistocene and Holocene. Our results reveal that dispersal between the Pacific and Atlantic was climate dependent and occurred both during the Pleistocene prior to the last glacial period and the early Holocene immediately following the opening of the Bering Strait. Genetic diversity in the Atlantic declined over an extended interval that predates the period of intensive commercial whaling, indicating this decline may have been precipitated by Holocene climate or other ecological causes. These first genetic data for Atlantic gray whales, particularly when combined with predictive habitat models for the year 2100, suggest that two recent sightings of gray whales in the Atlantic may represent the beginning of the expansion of this species' habitat beyond its currently realized range.}, language = {en} } @phdthesis{Apelt2015, author = {Apelt, Federico}, title = {Implementation of an imaging-based approach using a 3D light-field camera to analyse plant growth behaviour}, school = {Universit{\"a}t Potsdam}, pages = {227}, year = {2015}, language = {en} } @article{ApeltBreuerNikoloskietal.2015, author = {Apelt, Federico and Breuer, David and Nikoloski, Zoran and Stitt, Mark and Kragler, Friedrich}, title = {Phytotyping(4D): a light-field imaging system for non-invasive and accurate monitoring of spatio-temporal plant growth}, series = {The plant journal}, volume = {82}, journal = {The plant journal}, number = {4}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0960-7412}, doi = {10.1111/tpj.12833}, pages = {693 -- 706}, year = {2015}, abstract = {Integrative studies of plant growth require spatially and temporally resolved information from high-throughput imaging systems. However, analysis and interpretation of conventional two-dimensional images is complicated by the three-dimensional nature of shoot architecture and by changes in leaf position over time, termed hyponasty. To solve this problem, Phytotyping(4D) uses a light-field camera that simultaneously provides a focus image and a depth image, which contains distance information about the object surface. Our automated pipeline segments the focus images, integrates depth information to reconstruct the three-dimensional architecture, and analyses time series to provide information about the relative expansion rate, the timing of leaf appearance, hyponastic movement, and shape for individual leaves and the whole rosette. Phytotyping(4D) was calibrated and validated using discs of known sizes, and plants tilted at various orientations. Information from this analysis was integrated into the pipeline to allow error assessment during routine operation. To illustrate the utility of Phytotyping(4D), we compare diurnal changes in Arabidopsis thaliana wild-type Col-0 and the starchless pgm mutant. Compared to Col-0, pgm showed very low relative expansion rate in the second half of the night, a transiently increased relative expansion rate at the onset of light period, and smaller hyponastic movement including delayed movement after dusk, both at the level of the rosette and individual leaves. Our study introduces light-field camera systems as a tool to accurately measure morphological and growth-related features in plants. Significance Statement Phytotyping(4D) is a non-invasive and accurate imaging system that combines a 3D light-field camera with an automated pipeline, which provides validated measurements of growth, movement, and other morphological features at the rosette and single-leaf level. In a case study in which we investigated the link between starch and growth, we demonstrated that Phytotyping(4D) is a key step towards bridging the gap between phenotypic observations and the rich genetic and metabolic knowledge.}, language = {en} } @phdthesis{Arabi2015, author = {Arabi, Fayezeh}, title = {Functional characterization of Sulfur Deficiency Induced genes, SDI1 and SDI2, in Arabidopsis thaliana}, school = {Universit{\"a}t Potsdam}, pages = {97}, year = {2015}, language = {en} } @article{AttermeyerTittelAllgaieretal.2015, author = {Attermeyer, Katrin and Tittel, Joerg and Allgaier, Martin and Frindte, Katharina and Wurzbacher, Christian and Hilt, Sabine and Kamjunke, Norbert and Grossart, Hans-Peter}, title = {Effects of Light and Autochthonous Carbon Additions on Microbial Turnover of Allochthonous Organic Carbon and Community Composition}, series = {Microbial ecology}, volume = {69}, journal = {Microbial ecology}, number = {2}, publisher = {Springer}, address = {New York}, issn = {0095-3628}, doi = {10.1007/s00248-014-0549-4}, pages = {361 -- 371}, year = {2015}, abstract = {The fate of allochthonous dissolved organic carbon (DOC) in aquatic systems is primarily controlled by the turnover of heterotrophic bacteria. However, the roles that abiotic and biotic factors such as light and DOC release by aquatic primary producers play in the microbial decomposition of allochthonous DOC is not well understood. We therefore tested if light and autochthonous DOC additions would increase allochthonous DOC decomposition rates and change bacterial growth efficiencies and community composition (BCC). We established continuous growth cultures with different inocula of natural bacterial communities and alder leaf leachates (DOCleaf) with and without light exposure before amendment. Furthermore, we incubated DOCleaf together with autochthonous DOC from lysed phytoplankton cultures (DOCphyto). Our results revealed that pretreatments of DOCleaf with light resulted in a doubling of bacterial growth efficiency (BGE), whereas additions of DOCphyto or combined additions of DOCphyto and light had no effect on BGE. The change in BGE was not accompanied by shifts in the phylogenetic structure of the BCC, but BCC was influenced by the DOC source. Our results highlight that a doubling of BGE is not necessarily accompanied by a shift in BCC and that BCC is more strongly affected by resource properties.}, language = {en} } @phdthesis{Balazadeh2015, author = {Balazadeh, Salma}, title = {New insights into the molecular mechanisms of leaf senescence}, school = {Universit{\"a}t Potsdam}, year = {2015}, language = {en} } @phdthesis{Balk2015, author = {Balk, Maria}, title = {3D structured shape-memory hydrogels with enzymatically-induced shape shifting}, school = {Universit{\"a}t Potsdam}, pages = {128}, year = {2015}, language = {en} } @misc{BeninaRibeiroGechevetal.2015, author = {Benina, Maria and Ribeiro, Dimas Mendes and Gechev, Tsanko S. and M{\"u}ller-R{\"o}ber, Bernd and Schippers, Jos H. M.}, title = {A cell type-specific view on the translation of mRNAs from ROS-responsive genes upon paraquat treatment of Arabidopsis thaliana leaves}, series = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology}, volume = {38}, journal = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0140-7791}, doi = {10.1111/pce.12355}, pages = {349 -- 363}, year = {2015}, abstract = {Oxidative stress causes dramatic changes in the expression levels of many genes. The formation of a functional protein through successful mRNA translation is central to a coordinated cellular response. To what extent the response towards reactive oxygen species (ROS) is regulated at the translational level is poorly understood. Here we analysed leaf- and tissue-specific translatomes using a set of transgenic Arabidopsis thaliana lines expressing a FLAG-tagged ribosomal protein to immunopurify polysome-bound mRNAs before and after oxidative stress. We determined transcript levels of 171 ROS-responsive genes upon paraquat treatment, which causes formation of superoxide radicals, at the whole-organ level. Furthermore, the translation of mRNAs was determined for five cell types: mesophyll, bundle sheath, phloem companion, epidermal and guard cells. Mesophyll and bundle sheath cells showed the strongest response to paraquat treatment. Interestingly, several ROS-responsive transcription factors displayed cell type-specific translation patterns, while others were translated in all cell types. In part, cell type-specific translation could be explained by the length of the 5-untranslated region (5-UTR) and the presence of upstream open reading frames (uORFs). Our analysis reveals insights into the translational regulation of ROS-responsive genes, which is important to understanding cell-specific responses and functions during oxidative stress. The study illustrates the response of different Arabidopsis thaliana leaf cells and tissues to oxidative stress at the translational level, an aspect of reactive oxygen species (ROS) biology that has been little studied in the past. Our data reveal insights into how translational regulation of ROS-responsive genes is fine-tuned at the cellular level, a phenomenon contributing to the integrated physiological response of leaves to stresses involving changes in ROS levels.}, language = {en} } @article{BergholzJeltschWeissetal.2015, author = {Bergholz, Kolja and Jeltsch, Florian and Weiß, Lina and Pottek, Janine and Geißler, Katja and Ristow, Michael}, title = {Fertilization affects the establishment ability of species differing in seed mass via direct nutrient addition and indirect competition effects}, series = {Oikos}, volume = {124}, journal = {Oikos}, number = {11}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0030-1299}, doi = {10.1111/oik.02193}, pages = {1547 -- 1554}, year = {2015}, abstract = {Fertilization causes species loss and species dominance changes in plant communities worldwide. However, it still remains unclear how fertilization acts upon species functional traits, e.g. seed mass. Seed mass is a key trait of the regeneration strategy of plants, which influences a range of processes during the seedling establishment phase. Fertilization may select upon seed mass, either directly by increased nutrient availability or indirectly by increased competition. Since previous research has mainly analyzed the indirect effects of fertilization, we disentangled the direct and indirect effects to examine how nutrient availability and competition influence the seed mass relationships on four key components during seedling establishment: seedling emergence, time of seedling emergence, seedling survival and seedling growth. We conducted a common garden experiment with 22 dry grassland species with a two-way full factorial design that simulated additional nutrient supply and increased competition. While we found no evidence that fertilization either directly by additional nutrient supply or indirectly by increased competition alters the relationship between seed mass and (time of) seedling emergence, we revealed that large seed mass is beneficial under nutrient-poor conditions (seedlings have greater chances of survival, particularly in nutrient-poor soils) as well as under competition (large-seeded species produced larger seedlings, which suffered less from competition than small-seeded species). Based on these findings, we argue that both factors, i.e. nutrient availability and competition intensity, ought to be considered to understand how fertilization influences seedling establishment and species composition with respect to seed mass in natural communities. We propose a simple conceptual model, in which seed mass in natural communities is determined by competition intensity and nutrient availability. Here, we hypothesize that seed mass shows a U-shaped pattern along gradients of soil fertility, which may explain the contrasting soil fertility-seed mass relationships found in the recent literature.}, language = {en} } @article{BernhardtRoemermannBaetenCravenetal.2015, author = {Bernhardt-R{\"o}mermann, Markus and Baeten, Lander and Craven, Dylan and De Frenne, Pieter and Hedl, Radim and Lenoir, Jonathan and Bert, Didier and Brunet, Jorg and Chudomelova, Marketa and Decocq, Guillaume and Dierschke, Hartmut and Dirnboeck, Thomas and D{\"o}rfler, Inken and Heinken, Thilo and Hermy, Martin and Hommel, Patrick and Jaroszewicz, Bogdan and Keczynski, Andrzej and Kelly, Daniel L. and Kirby, Keith J. and Kopecky, Martin and Macek, Martin and Malis, Frantisek and Mirtl, Michael and Mitchell, Fraser J. G. and Naaf, Tobias and Newman, Miles and Peterken, George and Petrik, Petr and Schmidt, Wolfgang and Standovar, Tibor and Toth, Zoltan and Van Calster, Hans and Verstraeten, Gorik and Vladovic, Jozef and Vild, Ondrej and Wulf, Monika and Verheyen, Kris}, title = {Drivers of temporal changes in temperate forest plant diversity vary across spatial scales}, series = {Global change biology}, volume = {21}, journal = {Global change biology}, number = {10}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1354-1013}, doi = {10.1111/gcb.12993}, pages = {3726 -- 3737}, year = {2015}, abstract = {Global biodiversity is affected by numerous environmental drivers. Yet, the extent to which global environmental changes contribute to changes in local diversity is poorly understood. We investigated biodiversity changes in a meta-analysis of 39 resurvey studies in European temperate forests (3988 vegetation records in total, 17-75years between the two surveys) by assessing the importance of (i) coarse-resolution (i.e., among sites) vs. fine-resolution (i.e., within sites) environmental differences and (ii) changing environmental conditions between surveys. Our results clarify the mechanisms underlying the direction and magnitude of local-scale biodiversity changes. While not detecting any net local diversity loss, we observed considerable among-site variation, partly explained by temporal changes in light availability (a local driver) and density of large herbivores (a regional driver). Furthermore, strong evidence was found that presurvey levels of nitrogen deposition determined subsequent diversity changes. We conclude that models forecasting future biodiversity changes should consider coarse-resolution environmental changes, account for differences in baseline environmental conditions and for local changes in fine-resolution environmental conditions.}, language = {en} } @article{BhaskarMaLendleinetal.2015, author = {Bhaskar, Thanga Bhuvanesh Vijaya and Ma, Nan and Lendlein, Andreas and Roch, Toralf}, title = {The interaction of human macrophage subsets with silicone as a biomaterial}, series = {Clinical hemorheology and microcirculation : blood flow and vessels}, volume = {61}, journal = {Clinical hemorheology and microcirculation : blood flow and vessels}, number = {2}, publisher = {IOS Press}, address = {Amsterdam}, issn = {1386-0291}, doi = {10.3233/CH-151991}, pages = {119 -- 133}, year = {2015}, abstract = {Silicones are widely used as biomaterials for medical devices such as extracorporeal equipments. However, there is often conflicting evidence about their supposed cell-and histocompatibility. Macrophages could mediate silicone-induced adverse responses such as foreign body reaction and fibrous encapsulation. The polarization behaviour of macrophages could determine the clinical outcome after implantation of biomaterials. Induction of classically activated macrophages (CAM) may induce and support uncontrolled inflammatory responses and undesired material degradation. In contrast, polarization into alternatively activated macrophages (AAM) is assumed to support healing processes and implant integration. This study compared the interaction of non-polarized macrophages (M0), CAM, and AAM with commercially available tissue culture polystyrene (TCP) and a medical grade silicone-based biomaterial, regarding the secretion of inflammatory mediators such as cytokines and chemokines. Firstly, by using the Limulus amoebocyte lysate (LAL) test the silicone films were shown to be free of soluble endotoxins, which is the prerequisite to investigate their interaction with primary immune cells. Primary human monocyte-derived macrophages (M0) were polarized into CAM and AAM by addition of suitable differentiation factors. These macrophage subsets were incubated on the materials for 24 hours and their viability and cytokine secretion was assessed. In comparison to TCP, cell adhesion was lower on silicone after 24 hours for all three macrophage subsets. However, compared to TCP, silicone induced higher levels of certain inflammatory and chemotactic cytokines in M0, CAM, and AAM macrophage subsets. Conclusively, it was shown that silicone has the ability to induce a pro-inflammatory state to different magnitudes dependent on the macrophage subsets. This priming of the macrophage phenotype by silicone could explain the incidence of severe foreign body complications observed in vivo.}, language = {en} } @article{BizicIonescuZederIonescuetal.2015, author = {Bizic-Ionescu, Mina and Zeder, Michael and Ionescu, Danny and Orlic, Sandi and Fuchs, Bernhard M. and Grossart, Hans-Peter and Amann, Rudolf}, title = {Comparison of bacterial communities on limnic versus coastal marine particles reveals profound differences in colonization}, series = {Environmental microbiology}, volume = {17}, journal = {Environmental microbiology}, number = {10}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1462-2912}, doi = {10.1111/1462-2920.12466}, pages = {3500 -- 3514}, year = {2015}, abstract = {Marine and limnic particles are hotspots of organic matter mineralization significantly affecting biogeochemical element cycling. Fluorescence in-situ hybridization and pyrosequencing of 16S rRNA genes were combined to investigate bacterial diversity and community composition on limnic and coastal marine particles >5 and >10m respectively. Limnic particles were more abundant (average: 1x10(7)l(-1)), smaller in size (average areas: 471 versus 2050m(2)) and more densely colonized (average densities: 7.3 versus 3.6 cells 100m(-2)) than marine ones. Limnic particle-associated (PA) bacteria harboured Alphaproteobacteria and Betaproteobacteria, and unlike previously suggested sizeable populations of Gammaproteobacteria, Actinobacteria and Bacteroidetes. Marine particles were colonized by Planctomycetes and Betaproteobacteria additionally to Alphaproteobacteria, Bacteroidetes and Gammaproteobacteria. Large differences in individual particle colonization could be detected. High-throughput sequencing revealed a significant overlap of PA and free-living (FL) bacteria highlighting an underestimated connectivity between both fractions. PA bacteria were in 14/21 cases more diverse than FL bacteria, reflecting a high heterogeneity in the particle microenvironment. We propose that a ratio of Chao 1 indices of PA/FL<1 indicates the presence of rather homogeneously colonized particles. The identification of different bacterial families enriched on either limnic or marine particles demonstrates that, despite the seemingly similar ecological niches, PA communities of both environments differ substantially.}, language = {en} } @article{BlankenburgBalfanzHayashietal.2015, author = {Blankenburg, Stefanie and Balfanz, Sabine and Hayashi, Y. and Shigenobu, S. and Miura, T. and Baumann, Otto and Baumann, Arnd and Blenau, Wolfgang}, title = {Cockroach GABA(B) receptor subtypes: Molecular characterization, pharmacological properties and tissue distribution}, series = {Neuropharmacology}, volume = {88}, journal = {Neuropharmacology}, publisher = {Elsevier}, address = {Oxford}, issn = {0028-3908}, doi = {10.1016/j.neuropharm.2014.08.022}, pages = {134 -- 144}, year = {2015}, abstract = {gamma-aminobutyric acid (GABA) is the predominant inhibitory neurotransmitter in the central nervous system (CNS). Its effects are mediated by either ionotropic GABA(A) receptors or metabotropic GABA(B) receptors. GABA(B) receptors regulate, via Gi/o, G-proteins, ion channels, and adenylyl cyclases. In humans, GABA(B) receptor subtypes are involved in the etiology of neurologic and psychiatric disorders. In arthropods, however, these members of the G-protein-coupled receptor family are only inadequately characterized. Interestingly, physiological data have revealed important functions of GABA(B) receptors in the American cockroach, Periplaneta americana. We have cloned cDNAs coding for putative GABA(B) receptor subtypes 1 and 2 of P. americana (PeaGB1 and PeaGB2). When both receptor proteins are co-expressed in mammalian cells, activation of the receptor heteromer with GABA leads to a dose-dependent decrease in cAMP production. The pharmacological profile differs from that of mammalian and Drosophila GABA(B) receptors. Western blot analyses with polyclonal antibodies have revealed the expression of PeaGB1 and PeaGB2 in the CNS of the American cockroach. In addition to the widespread distribution in the brain, PeaGB1 is expressed in salivary glands and male accessory glands. Notably, PeaGB1-like immunoreactivity has been detected in the GABAergic salivary neuron 2, suggesting that GABA(B) receptors act as autoreceptors in this neuron.}, language = {en} } @article{BogenBenderLoeweetal.2015, author = {Bogen, Oliver and Bender, Olaf and Loewe, Jana and Blenau, Wolfgang and Thevis, Beatrice and Schroeder, Wolfgang and Margolis, Richard U. and Levine, Jon D. and Hucho, Ferdinand}, title = {Neuronally produced versican V2 renders C-fiber nociceptors IB4-positive}, series = {Journal of neurochemistry}, volume = {134}, journal = {Journal of neurochemistry}, number = {1}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0022-3042}, doi = {10.1111/jnc.13113}, pages = {147 -- 155}, year = {2015}, abstract = {A subpopulation of nociceptors, the glial cell line-derived neurotrophic factor (GDNF)-dependent, non-peptidergic C-fibers, expresses a cell-surface glycoconjugate that can be selectively labeled with isolectin B4 (IB4), a homotetrameric plant lectin from Griffonia simplicifolia. We show that versican is an IB4-binding molecule in rat dorsal root ganglion neurons. Using reverse transcriptase polymerase chain reaction (RT-PCR), insitu hybridization and immunofluorescence experiments on rat lumbar dorsal root ganglion, we provide the first demonstration that versican is produced by neurons. In addition, by probing Western blots with splice variant-specific antibodies we show that the IB4-binding versican contains only the glycosaminoglycan alpha domain. Our data support V2 as the versican isoform that renders this subpopulation of nociceptors IB4-positive (+). A subset of nociceptors, the GDNF-dependent non-peptidergic C-fibers can be characterized by its reactivity for isolectin B4 (IB4), a plant lectin from Griffonia simplicifolia. We have previously demonstrated that versican V2 binds IB4 in a Ca2+-dependent manner. However, given that versican is thought to be the product of glial cells, it was questionable whether versican V2 can be accountable for the IB4-reactivity of this subset of nociceptors. The results presented here prove - for the first time - a neuronal origin of versican and suggest that versican V2 is the molecule that renders GDNF-dependent non-peptidergic C-fibers IB4-positive.}, language = {en} } @article{BordagKlieJuerchottetal.2015, author = {Bordag, Natalie and Klie, Sebastian and J{\"u}rchott, Kathrin and Vierheller, Janine and Schiewe, Hajo and Albrecht, Valerie and Tonn, J{\"o}rg-Christian and Schwartz, Christoph and Schichor, Christian and Selbig, Joachim}, title = {Glucocorticoid (dexamethasone)-induced metabolome changes in healthy males suggest prediction of response and side effects}, series = {Scientific reports}, volume = {5}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep15954}, pages = {12}, year = {2015}, abstract = {Glucocorticoids are indispensable anti-inflammatory and decongestant drugs with high prevalence of use at (similar to)0.9\% of the adult population. Better holistic insights into glucocorticoid-induced changes are crucial for effective use as concurrent medication and management of adverse effects. The profiles of 214 metabolites from plasma of 20 male healthy volunteers were recorded prior to and after ingestion of a single dose of 4 mg dexamethasone (+20 mg pantoprazole). Samples were drawn at three predefined time points per day: seven untreated (day 1 midday - day 3 midday) and four treated (day 3 evening - day 4 evening) per volunteer. Statistical analysis revealed tremendous impact of dexamethasone on the metabolome with 150 of 214 metabolites being significantly deregulated on at least one time point after treatment (ANOVA, Benjamini-Hochberg corrected, q < 0.05). Inter-person variability was high and remained uninfluenced by treatment. The clearly visible circadian rhythm prior to treatment was almost completely suppressed and deregulated by dexamethasone. The results draw a holistic picture of the severe metabolic deregulation induced by single-dose, short-term glucocorticoid application. The observed metabolic changes suggest a potential for early detection of severe side effects, raising hope for personalized early countermeasures increasing quality of life and reducing health care costs.}, language = {en} } @phdthesis{Borschewski2015, author = {Borschewski, Aljona}, title = {Bedeutung der Interaktion von Calcineurin und SORLA f{\"u}r die Regulation des Na⁺,K⁺,2Cl⁻-Kotransporters (NKCC2) in der Niere}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-89205}, school = {Universit{\"a}t Potsdam}, pages = {II, 86}, year = {2015}, abstract = {Der Na⁺-K⁺-2Cl⁻-Kotransporter (NKCC2) wird im distalen Nephron der Niere exprimiert. Seine Verteilung umfasst die Epithelien der medull{\"a}ren und kortikalen Teile der dicken aufsteigenden Henle-Schleife (Thick ascending limb, TAL) und die Macula densa. Resorptiver NaCl-Transport {\"u}ber den NKCC2 dient dem renalen Konzentrierungsmechanismus und reguliert systemisch auch Volumenstatus und Blutdruck. Die Aktivit{\"a}t des NKCC2 ist mit der Phosphorylierung seiner N-terminalen Aminos{\"a}urereste Serin 126 und Threonin 96/101 verbunden. Vermittelt wird diese durch die homologen Kinasen SPAK (SPS-related proline/alanine-rich kinase) und OSR1 (Oxidative stress responsive kinase 1), die hierzu ihrerseits phosphoryliert werden m{\"u}ssen. Der regulatorische Kontext dieser Kinasen ist mittlerweile gut charakterisiert. {\"U}ber Mechanismen und Produkte, die den NKCC2 deaktivieren, war hingegen weniger bekannt. Ziel der Arbeit war daher zu untersuchen, welche Wege zur Deaktivierung des Transporters f{\"u}hren. Der intrazellul{\"a}re Sortierungsrezeptor SORLA (Sorting-protein-related receptor with A-type repeats) war zuvor in seiner Bedeutung f{\"u}r das Nephron charakterisiert worden. Ein SORLA-defizientes Mausmodell weist unter anderem eine stark verringerte NKCC2-Phosphorylierung auf. Unter osmotischem Stress k{\"o}nnen SORLA-defiziente M{\"a}use ihren Urin weniger effizient konzentrieren. Meine Resultate zeigen mit hochaufl{\"o}sender Technik, dass SORLA apikal im TAL lokalisiert ist und dass mit NKCC2 eine anteilige Kolokalisation besteht. Unter SORLA Defizienz war die f{\"u}r die NKCC2 Aktivit{\"a}t maßgebliche SPAK/OSR1-Phosphorylierung gegen{\"u}ber dem Wildtyp nicht ver{\"a}ndert. Jedoch war die ebenfalls im TAL exprimierte Phosphatase Calcineurin Aβ (CnAβ) per Western blot um das zweifache gesteigert. Parallel hierzu wurde immunhistochemisch die Kolokalisation von verst{\"a}rktem CnAβ-Signal und NKCC2 best{\"a}tigt. Beide Befunde geben zusammen den Hinweis auf einen Bezug zwischen der reduzierten NKCC2-Phosphorylierung und der gesteigerten Pr{\"a}senz von CnAβ bei SORLA Defizienz. Die parallel induzierte {\"U}berexpression von SORLA in HEK-Zellen zeigte entsprechend eine Halbierung der CnAβ Proteinmenge. SORLA steuert demzufolge sowohl die Abundanz als auch die zellul{\"a}re Verteilung der Phosphatase. Weiterhin ließ sich die Interaktion zwischen CnAβ und SORLA (intrazellul{\"a}re Dom{\"a}ne) mittels Co-Immunpr{\"a}zipitation bzw. GST-pulldown assay nachweisen. Auch die Interaktion zwischen CnAβ und NKCC2 wurde auf diesem Weg belegt. Da allerdings weder SORLA noch NKCC2 ein spezifisches Bindungsmuster f{\"u}r CnAβ aufweisen, sind vermutlich intermedi{\"a}re Adapterproteine bei ihrer Bindung involviert. Die pharmakologische Inhibition von CnAβ mittels Cyclosporin A (CsA; 1 h) f{\"u}hrte bei SORLA Defizienz zur Normalisierung der NKCC2-Phosphorylierung. Entsprechend f{\"u}hrte in vitro die Gabe von CsA bei TAL Zellen zu einer 7-fach gesteigerten NKCC2-Phosphorylierung. Zusammenfassend zeigen die Ergebnisse, dass die Phosphatase CnAβ {\"u}ber ihre Assoziation mit NKCC2 diesen im adluminalen Zellkompartiment deaktivieren kann. Gesteuert wird dieser Vorgang durch die Eigenschaft von SORLA, CnAβ apikal zu reduzieren und damit die adluminale Phosphorylierung und Aktivit{\"a}t von NKCC2 zu unterst{\"u}tzen. Da Calcineurin-Inhibitoren derzeit die Grundlage der immunsupprimierenden Therapie darstellen, haben die Ergebnisse eine klinische Relevanz. Angesichts der Co-Expression von SORLA und CnAβ in verschiedenen anderen Organen k{\"o}nnen die Ergebnisse auch {\"u}ber die Niere hinaus Bedeutung erlangen.}, language = {de} } @article{BreitkopfOnsteinCafassoetal.2015, author = {Breitkopf, Hendrik and Onstein, Renske E. and Cafasso, Donata and Schl{\"u}ter, Philipp M. and Cozzolino, Salvatore}, title = {Multiple shifts to different pollinators fuelled rapid diversification in sexually deceptive Ophrys orchids}, series = {New phytologist : international journal of plant science}, volume = {207}, journal = {New phytologist : international journal of plant science}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0028-646X}, doi = {10.1111/nph.13219}, pages = {377 -- 389}, year = {2015}, abstract = {Episodes of rapid speciation provide unique insights into evolutionary processes underlying species radiations and patterns of biodiversity. Here we investigated the radiation of sexually deceptive bee orchids (Ophrys). Based on a time-calibrated phylogeny and by means of ancestral character reconstruction and divergence time estimation, we estimated the tempo and mode of this radiation within a state-dependent evolutionary framework. It appears that, in the Pleistocene, the evolution of Ophrys was marked by episodes of rapid diversification coinciding with shifts to different pollinator types: from wasps to Eucera bees to Andrena and other bees. An abrupt increase in net diversification rate was detected in three clades. Among these, two phylogenetically distant lineages switched from Eucera to Andrena and other bees in a parallel fashion and at about the same time in their evolutionary history. Lack of early radiation associated with the evolution of the key innovation of sexual deception suggests that Ophrys diversification was mainly driven by subsequent ecological opportunities provided by the exploitation of novel pollinator groups, encompassing many bee species slightly differing in their sex pheromone communication systems, and by spatiotemporal fluctuations in the pollinator mosaic.}, language = {en} } @article{BudzikZuwalaKupferetal.2015, author = {Budzik, Karolina A. and Zuwala, Krystyna and Kupfer, Alexander and Gower, David J. and Wilkinson, Mark}, title = {Diverse anatomy of the tongue and taste organs in five species of caecilian (Amphibia: Gymnophiona)}, series = {Zoologischer Anzeiger = Journal of comparative zoology : morphology, systematics, biogeography}, volume = {257}, journal = {Zoologischer Anzeiger = Journal of comparative zoology : morphology, systematics, biogeography}, publisher = {Elsevier}, address = {Jena}, issn = {0044-5231}, doi = {10.1016/j.jcz.2015.04.007}, pages = {103 -- 109}, year = {2015}, abstract = {Limited previous studies on caecilian taste organs have demonstrated the presence of very few taste buds in the oral epithelium, while providing somewhat contradictory reports of their distribution within the oropharynx and across taxa. Here we report on the gross morphology of the tongue and explore the distribution, number and morphology of taste organs of five caecilian species representing five families, focusing upon variation within the group and investigating whether larvae and adults have the same type of taste organs. We find that taste buds are widespread in the oropharynx of caecilians and that they occur both in adults and larvae of a species with a biphasic life history. Thus Gymnophiona differ substantially from Batriachia, which have distinct larval and adult taste organs.}, language = {en} } @article{CamargodosReisRiccardiTeixeiraRibeiroetal.2015, author = {Camargo, Rodolfo Gonzalez and dos Reis Riccardi, Daniela Mendes and Teixeira Ribeiro, Henrique Quintas and Carnevali Junior, Luiz Carlos and de Matos-Neto, Emidio Marques and Enjiu, Lucas and Neves, Rodrigo Xavier and Carola Correia Lima, Joanna Darck and Figueredo, Raquel Galvao and Martins de Alcantara, Paulo Sergio and Maximiano, Linda and Otoch, Jose and Batista Jr., Miguel Luiz and P{\"u}schel, Gerhard Paul and Seelaender, Marilia}, title = {NF-kappa Bp65 and Expression of Its Pro-Inflammatory Target Genes Are Upregulated in the Subcutaneous Adipose Tissue of Cachectic Cancer Patients}, series = {Nutrients}, volume = {7}, journal = {Nutrients}, number = {6}, publisher = {MDPI}, address = {Basel}, issn = {2072-6643}, doi = {10.3390/nu7064465}, pages = {4465 -- 4479}, year = {2015}, abstract = {Cancer cachexia, of which the most notable symptom is severe and rapid weight loss, is present in the majority of patients with advanced cancer. Inflammatory mediators play an important role in the development of cachexia, envisaged as a chronic inflammatory syndrome. The white adipose tissue (WAT) is one of the first compartments affected in cancer cachexia and suffers a high rate of lipolysis. It secretes several cytokines capable of directly regulating intermediate metabolism. A common pathway in the regulation of the expression of pro-inflammatory cytokines in WAT is the activation of the nuclear transcription factor kappa-B (NF-B). We have examined the gene expression of the subunits NF-Bp65 and NF-Bp50, as well as NF-Bp65 and NF-Bp50 binding, the gene expression of pro-inflammatory mediators under NF-B control (IL-1, IL-6, INF-, TNF-, MCP-1), and its inhibitory protein, nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha (IB-). The observational study involved 35 patients (control group, n = 12 and cancer group, n = 23, further divided into cachectic and non-cachectic). NF-Bp65 and its target genes expression (TNF-, IL-1, MCP-1 and IB-) were significantly higher in cachectic cancer patients. Moreover, NF-Bp65 gene expression correlated positively with the expression of its target genes. The results strongly suggest that the NF-B pathway plays a role in the promotion of WAT inflammation during cachexia.}, language = {en} } @misc{CampbellHofreiter2015, author = {Campbell, Kevin L. and Hofreiter, Michael}, title = {Resurrecting phenotypes from ancient DNA sequences: promises and perspectives}, series = {Canadian journal of zoology = Revue canadienne de zoologie}, volume = {93}, journal = {Canadian journal of zoology = Revue canadienne de zoologie}, number = {9}, publisher = {NRC Research Press}, address = {Ottawa}, issn = {0008-4301}, doi = {10.1139/cjz-2014-0337}, pages = {701 -- 710}, year = {2015}, abstract = {Anatomical changes in extinct mammalian lineages over evolutionary time, such as the loss of fingers and teeth and the rapid increase in body size that accompanied the late Miocene dispersal of the progenitors of Steller's sea cows (Hydrodamalis gigas (Zimmermann, 1780)) into North Pacific waters and the convergent development of a thick pelage and accompanying reductions in ear and tail surface area of woolly mammoths (Mammuthus primigenius (Blumenbach, 1799)) and woolly rhinoceros (Coelodonta antiquitatis (Blumenbach, 1799)), are prime examples of adaptive evolution underlying the exploitation of new habitats. It is likely, however, that biochemical specializations adopted during these evolutionary transitions were of similar or even greater biological importance. As these "living" processes do not fossilize, direct information regarding the physiological attributes of extinct species has largely remained beyond the range of scientific inquiry. However, the ability to retrieve genomic sequences from ancient DNA samples, combined with ectopic expression systems, now permit the evolutionary origins and structural and functional properties of authentic prehistoric proteins to be examined in great detail. Exponential technical advances in ancient DNA retrieval, enrichment, and sequencing will soon permit targeted generation of complete genomes from hundreds of extinct species across the last one million years that, in combination with emerging in vitro expression, genome engineering, and cell differentiation techniques, promises to herald an exciting new trajectory of evolutionary research at the interface of biochemistry, genomics, palaeontology, and cell biology.}, language = {en} } @article{CaronDeFrenneChabrerieetal.2015, author = {Caron, Maria Mercedes and De Frenne, P. and Chabrerie, Olivier and Cousins, S. A. O. and De Backer, L. and Decocq, G. and Diekmann, M. and Heinken, Thilo and Kolb, A. and Naaf, T. and Plue, J. and Selvi, F. and Strimbeck, G. R. and Wulf, M. and Verheyen, Kris}, title = {Impacts of warming and changes in precipitation frequency on the regeneration of two Acer species}, series = {Flora : morphology, distribution, functional ecology of plants}, volume = {214}, journal = {Flora : morphology, distribution, functional ecology of plants}, publisher = {Elsevier}, address = {Jena}, issn = {0367-2530}, doi = {10.1016/j.flora.2015.05.005}, pages = {24 -- 33}, year = {2015}, language = {en} } @article{CaronDeFrenneBrunetetal.2015, author = {Caron, Maria Mercedes and De Frenne, Pieter and Brunet, J. and Chabrerie, Olivier and Cousins, S. A. O. and De Backer, L. and Decocq, G. and Diekmann, M. and Heinken, Thilo and Kolb, A. and Naaf, T. and Plue, J. and Selvi, Federico and Strimbeck, G. R. and Wulf, Monika and Verheyen, Kris}, title = {Interacting effects of warming and drought on regeneration and early growth of Acer pseudoplatanus and A. platanoides}, series = {Plant biology}, volume = {17}, journal = {Plant biology}, number = {1}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1435-8603}, doi = {10.1111/plb.12177}, pages = {52 -- 62}, year = {2015}, abstract = {Climate change is acting on several aspects of plant life cycles, including the sexual reproductive stage, which is considered amongst the most sensitive life-cycle phases. In temperate forests, it is expected that climate change will lead to a compositional change in community structure due to changes in the dominance of currently more abundant forest tree species. Increasing our understanding of the effects of climate change on currently secondary tree species recruitment is therefore important to better understand and forecast population and community dynamics in forests. Here, we analyse the interactive effects of rising temperatures and soil moisture reduction on germination, seedling survival and early growth of two important secondary European tree species, Acer pseudoplatanus and A.platanoides. Additionally, we analyse the effect of the temperature experienced by the mother tree during seed production by collecting seeds of both species along a 2200-km long latitudinal gradient. For most of the responses, A.platanoides showed higher sensitivity to the treatments applied, and especially to its joint manipulation, which for some variables resulted in additive effects while for others only partial compensation. In both species, germination and survival decreased with rising temperatures and/or soil moisture reduction while early growth decreased with declining soil moisture content. We conclude that although A.platanoides germination and survival were more affected after the applied treatments, its initial higher germination and larger seedlings might allow this species to be relatively more successful than A.pseudoplatanus in the face of climate change.}, language = {en} } @article{CaronDeFrenneBrunetetal.2015, author = {Caron, Maria Mercedes and De Frenne, Pieter and Brunet, J{\"o}rg and Chabrerie, Olivier and Cousins, Sara A. O. and Decocq, Guillaume and Diekmann, Martin and Graae, Bente Jessen and Heinken, Thilo and Kolb, Annette and Lenoir, Jonathan and Naaf, Tobias and Plue, Jan and Selvi, Federico and Wulf, Monika and Verheyen, Kris}, title = {Divergent regeneration responses of two closely related tree species to direct abiotic and indirect biotic effects of climate change}, series = {Forest ecology and management}, volume = {342}, journal = {Forest ecology and management}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0378-1127}, doi = {10.1016/j.foreco.2015.01.003}, pages = {21 -- 29}, year = {2015}, abstract = {Changing temperature and precipitation can strongly influence plant reproduction. However, also biotic interactions might indirectly affect the reproduction and recruitment success of plants in the context of climate change. Information about the interactive effects of changes in abiotic and biotic factors is essential, but still largely lacking, to better understand the potential effects of a changing climate on plant populations. Here we analyze the regeneration from seeds of Acer platanoides and Acer pseudoplatanus, two currently secondary forest tree species from seven regions along a 2200 km-wide latitudinal gradient in Europe. We assessed the germination, seedling survival and growth during two years in a common garden experiment where temperature, precipitation and competition with the understory vegetation were manipulated. A. platanoides was more sensitive to changes in biotic conditions while A. pseudoplatanus was affected by both abiotic and biotic changes. In general, competition reduced (in A. platanoides) and warming enhanced (in A. pseudoplatanus) germination and survival, respectively. Reduced competition strongly increased the growth of A. platanoides seedlings. Seedling responses were independent of the conditions experienced by the mother tree during seed production and maturation. Our results indicate that, due to the negative effects of competition on the regeneration of A. platanoides, it is likely that under stronger competition (projected under future climatic conditions) this species will be negatively affected in terms of germination, survival and seedling biomass. Climate-change experiments including both abiotic and biotic factors constitute a key step forward to better understand the response of tree species' regeneration to climate change. (C) 2015 Elsevier B.V. All rights reserved.}, language = {en} } @article{CastelliniPaltrinieriManca2015, author = {Castellini, Alberto and Paltrinieri, Daniele and Manca, Vincenzo}, title = {MP-GeneticSynth: inferring biological network regulations from time series}, series = {Bioinformatics}, volume = {31}, journal = {Bioinformatics}, number = {5}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btu694}, pages = {785 -- 787}, year = {2015}, abstract = {MP-GeneticSynth is a Java tool for discovering the logic and regulation mechanisms responsible for observed biological dynamics in terms of finite difference recurrent equations. The software makes use of: (i) metabolic P systems as a modeling framework, (ii) an evolutionary approach to discover flux regulation functions as linear combinations of given primitive functions, (iii) a suitable reformulation of the least squares method to estimate function parameters considering simultaneously all the reactions involved in complex dynamics. The tool is available as a plugin for the virtual laboratory MetaPlab. It has graphical and interactive interfaces for data preparation, a priori knowledge integration, and flux regulator analysis.}, language = {en} } @unpublished{ChattopadhyayChakrabortyGrossartetal.2015, author = {Chattopadhyay, Madhab K. and Chakraborty, Ranadhir and Grossart, Hans-Peter and Reddy, Gundlapally S. and Jagannadham, Medicharla V.}, title = {Antibiotic resistance of bacteria}, series = {BioMed research international}, journal = {BioMed research international}, publisher = {Hindawi Publishing Corp.}, address = {New York}, issn = {2314-6133}, doi = {10.1155/2015/501658}, pages = {2}, year = {2015}, language = {en} } @article{ChoiKlostermanKummeretal.2015, author = {Choi, Young-Joon and Klosterman, Steven J. and Kummer, Volker and Voglmayr, Hermann and Shin, Hyeon-Dong and Thines, Marco}, title = {Multi-locus tree and species tree approaches toward resolving a complex clade of downy mildews (Straminipila, Oomycota), including pathogens of beet and spinach}, series = {Molecular phylogenetics and evolution}, volume = {86}, journal = {Molecular phylogenetics and evolution}, publisher = {Elsevier}, address = {San Diego}, issn = {1055-7903}, doi = {10.1016/j.ympev.2015.03.003}, pages = {24 -- 34}, year = {2015}, abstract = {Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The family Peronosporaceae (Straminipila; Oomycota) consists of obligate biotrophic pathogens that cause downy mildew disease on angiosperms, including a large number of cultivated plants. In the largest downy mildew genus Peronospora, a phylogenetically complex clade includes the economically important downy mildew pathogens of spinach and beet, as well as the type species of the genus Peronospora. To resolve this complex clade at the species level and to infer evolutionary relationships among them, we used multi-locus phylogenetic analysis and species tree estimation. Both approaches discriminated all nine currently accepted species and revealed four previously unrecognized lineages, which are specific to a host genus or species. This is in line with a narrow species concept, i.e. that a downy mildew species is associated with only a particular host plant genus or species. Instead of applying the dubious name Peronospora farinosa, which has been proposed for formal rejection, our results provide strong evidence that Peronospora schachtii is an independent species from lineages on Atriplex and apparently occurs exclusively on Beta vulgaris. The members of the clade investigated, the Peronospora rumicis clade, associate with three different host plant families, Amaranthaceae, Caryophyllaceae, and Polygonaceae, suggesting that they may have speciated following at least two recent inter-family host shifts, rather than contemporary cospeciation with the host plants. (C) 2015 Elsevier Inc. All rights reserved.}, language = {en} } @article{CisekTokarzSteupetal.2015, author = {Cisek, Richard and Tokarz, Danielle and Steup, Martin and Tetlow, Ian J. and Emes, Michael J. and Hebelstrup, Kim H. and Blennow, Andreas and Barzda, Virginijus}, title = {Second harmonic generation microscopy investigation of the crystalline ultrastructure of three barley starch lines affected by hydration}, series = {Biomedical optics express}, volume = {6}, journal = {Biomedical optics express}, number = {10}, publisher = {Optical Society of America}, address = {Washington}, issn = {2156-7085}, doi = {10.1364/BOE.6.003694}, pages = {3694 -- 3700}, year = {2015}, abstract = {Second harmonic generation (SHG) microscopy is employed to study changes in crystalline organization due to altered gene expression and hydration in barley starch granules. SHG intensity and susceptibility ratio values (R'(SHG)) are obtained using reduced Stokes-Mueller polarimetric microscopy. The maximum R'(SHG) values occur at moderate moisture indicating the narrowest orientation distribution of nonlinear dipoles from the cylindrical axis of glucan helices. The maximum SHG intensity occurs at the highest moisture and amylopectin content. These results support the hypothesis that SHG is caused by ordered hydrogen and hydroxyl bond networks which increase with hydration of starch granules. (C) 2015 Optical Society of America}, language = {en} } @article{CochardEdwardsWeber2015, author = {Cochard, Roland and Edwards, Peter J. and Weber, Ewald}, title = {Post-ranching tree-grass interactions in secondary Acacia zanzibarica woodlands in coastal Tanzania - an experimental study}, series = {Applied vegetation science : official organ of the International Association for Vegetation Science}, volume = {18}, journal = {Applied vegetation science : official organ of the International Association for Vegetation Science}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1402-2001}, doi = {10.1111/avsc.12134}, pages = {297 -- 310}, year = {2015}, abstract = {Questions: We studied a humid savanna rangeland., abandoned in 2000, where intensive cattle grazing had led to widespread encroachment by Acacia zanzibarica. We asked whether the acacia trees were able to regenerate in the absence of domesJic livestock, either beneath acacia canopies or in artificial clearings. Location: Tropical coastal Tanzania (former Mkwaja Ranch, now in Saadani National Park). Methods: We set out a total of 48 plots on four sites in November 2001, and assigned them to three treatments: trees felled (FN), trees felled and the stumps poisoned (FP) with Triclopyr, and no intervention (controls, NN). We analysed soils of plots for texture and nutrients. In two wet (July 2002 and 2003) and one dry (February 2003) seasons we assessed grass and tree leaf biomass and transpiration rates, and counted acacia seedlings and resprouts. The effects of treatments (controlled for site and other co-variables) on grass growth and acacia rectaiitment were determined statistically using general linear models (GLM). Results: Acacia leaves had a much higher stomatal conductance than grasses, with the consequence that total evapotranspiration in woodland was higher than in clearings. In the wet seasons, grass biomass and seedling densities were significantly higher in clearings than in control plots, which we attributed to more.favourable moisture conditions, In the dry season, by contrast, we found no differences, and all seedlings had died. On FN plots, 71\% of stumps, and on FP plots, 11\% resprouted (coppicing), but only a quarter of these shoots survived until July 2003. Root suckering occurred spontaneously at low densities. No root suckers or resprouts grew beyond the grass layer. Conclusions: Acacia woodlands do not regenerate in the absence of cattle grazing, and tree cutting in combination with appropriate fire management could potentially accelerate re-establishment of open grassland. However, regeneration might occur in the future due to the increasing wildlife populations within the new national park.}, language = {en} } @article{CoelhoFotiHartmannetal.2015, author = {Coelho, Catarina and Foti, Alessandro and Hartmann, Tobias and Santos-Silva, Teresa and Leimk{\"u}hler, Silke and Romao, Maria Joao}, title = {Structural insights into xenobiotic and inhibitor binding to human aldehyde oxidase}, series = {Nature chemical biology}, volume = {11}, journal = {Nature chemical biology}, number = {10}, publisher = {Nature Publ. Group}, address = {New York}, issn = {1552-4450}, doi = {10.1038/NCHEMBIO.1895}, pages = {779 -- +}, year = {2015}, abstract = {Aldehyde oxidase (AOX) is a xanthine oxidase (XO)-related enzyme with emerging importance due to its role in the metabolism of drugs and xenobiotics. We report the first crystal structures of human AOX1, substrate free (2.6-angstrom resolution) and in complex with the substrate phthalazine and the inhibitor thioridazine (2.7-angstrom resolution). Analysis of the protein active site combined with steady-state kinetic studies highlight the unique features, including binding and substrate orientation at the active site, that characterize human AOX1 as an important drug-metabolizing enzyme. Structural analysis of the complex with the noncompetitive inhibitor thioridazine revealed a new, unexpected and fully occupied inhibitor-binding site that is structurally conserved among mammalian AOXs and XO. The new structural insights into the catalytic and inhibition mechanisms of human AOX that we now report will be of great value for the rational analysis of clinical drug interactions involving inhibition of AOX1 and for the prediction and design of AOX-stable putative drugs.}, language = {en} } @article{ContinFrascaVivekananthanetal.2015, author = {Contin, Andrea and Frasca, Stefano and Vivekananthan, Jeevanthi and Leimk{\"u}hler, Silke and Wollenberger, Ursula and Plumere, Nicolas and Schuhmann, Wolfgang}, title = {A pH Responsive Redox Hydrogel for Electrochemical Detection of Redox Silent Biocatalytic Processes. Control of Hydrogel Solvation}, series = {Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis}, volume = {27}, journal = {Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis}, number = {4}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1040-0397}, doi = {10.1002/elan.201400621}, pages = {938 -- 944}, year = {2015}, abstract = {The control of bioelectrocatalytic processes by external stimuli for the indirect detection of non-redox active species was achieved using an esterase and a redox enzyme both integrated within a redox hydrogel. The poly( vinyl) imidazole Os(bpy)(2)Cl hydrogel displays pH-responsive properties. The esterase catalysed reaction leads to a local pH decrease causing protonation of imidazole moieties thus increasing hydrogel solvation and mobility of the tethered Os-complexes. This is the key step to enable improved electron transfer between an aldehyde oxidoreductase and the polymer-bound Os-complexes. The off-on switch is further integrated in a biofuel cell system for self-powered signal generation.}, language = {en} } @article{CornettiValenteDunningetal.2015, author = {Cornetti, Luca and Valente, Luis M. and Dunning, Luke T. and Quan, Xueping and Black, Richard A. and Hebert, Olivier and Savolainen, Vincent}, title = {The Genome of the "Great Speciator" Provides Insights into Bird Diversification}, series = {Genome biology and evolution}, volume = {7}, journal = {Genome biology and evolution}, number = {9}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1759-6653}, doi = {10.1093/gbe/evv168}, pages = {2680 -- 2691}, year = {2015}, abstract = {Among birds, white-eyes (genusZosterops) have diversified so extensively that Jared Diamond and Ernst Mayr referred to them as the 'great speciator." The Zosterops lineage exhibits some of the fastest rates of species diversification among vertebrates, and its members are the most prolific passerine island colonizers. We present a high-quality genome assembly for the silvereye (Zosterops lateralis), a white-eye species consisting of several subspecies distributed across multiple islands. We investigate the genetic basis of rapid diversification in white-eyes by conducting genomic analyses at varying taxonomic levels. First, we compare the silvereye genome with those of birds from different families and searched for genomic features that may be unique to Zosterops. Second, we compare the genomes of different species of white-eyes from Lifou island (South Pacific), using whole genome resequencing and restriction site associated DNA. Third, we contrast the genomes of two subspecies of silvereye that differ in plumage color. In accordance with theory, we show that white-eyes have high rates of substitutions, gene duplication, and positive selection relative to other birds. Below genus level, we find that genomic differentiation accumulates rapidly and reveals contrasting demographic histories between sympatric species on Lifou, indicative of past interspecific interactions. Finally, we highlight genes possibly involved in color polymorphism between the subspecies of silvereye. By providing the first whole-genome sequence resources for white-eyes and by conducting analyses at different taxonomic levels, we provide genomic evidence underpinning this extraordinary bird radiation.}, language = {en} } @article{CornoSalkaPohlmannetal.2015, author = {Corno, Gianluca and Salka, Ivette and Pohlmann, Kirsten and Hall, Alex R. and Grossart, Hans-Peter}, title = {Interspecific interactions drive chitin and cellulose degradation by aquatic microorganisms}, series = {Aquatic microbial ecology : international journal}, volume = {76}, journal = {Aquatic microbial ecology : international journal}, number = {1}, publisher = {Institute of Mathematical Statistics}, address = {Oldendorf Luhe}, issn = {0948-3055}, doi = {10.3354/ame01765}, pages = {27 -- +}, year = {2015}, abstract = {Complex biopolymers (BPs) such as chitin and cellulose provide the majority of organic carbon in aquatic ecosystems, but the mechanisms by which communities of bacteria in natural systems exploit them are unclear. Previous degradation experiments in artificial systems predominantly used microcosms containing a single bacterial species, neglecting effects of interspecific interactions. By constructing simplified aquatic microbial communities, we tested how the addition of other bacterial species, of a nanoflagellate protist capable of consuming bacteria, or of both, affect utilization of BPs. Surprisingly, total abundance of resident bacteria in mixed communities increased upon addition of the protist. Concomitantly, bacteria shifted from free-living to aggregated morphotypes that seemed to promote utilization of BPs. In our model system, these interactions significantly increased productivity in terms of overall bacterial numbers and carbon transfer efficiency. This indicates that interactions on microbial aggregates may be crucial for chitin and cellulose degradation. We therefore suggest that interspecific microbial interactions must be considered when attempting to model the turnover of the vast pool of complex biopolymers in aquatic ecosystems.}, language = {en} } @article{CuiLvChenetal.2015, author = {Cui, Xiao and Lv, Yang and Chen, Miaolin and Nikoloski, Zoran and Twell, David and Zhang, Dabing}, title = {Young Genes out of the Male: An Insight from Evolutionary Age Analysis of the Pollen Transcriptome}, series = {Molecular plant}, volume = {8}, journal = {Molecular plant}, number = {6}, publisher = {Cell Press}, address = {Cambridge}, issn = {1674-2052}, doi = {10.1016/j.molp.2014.12.008}, pages = {935 -- 945}, year = {2015}, abstract = {The birth of new genes in genomes is an important evolutionary event. Several studies reveal that new genes in animals tend to be preferentially expressed in male reproductive tissues such as testis (Betran et al., 2002; Begun et al., 2007; Dubruille et al., 2012), and thus an "out of testis' hypothesis for the emergence of new genes has been proposed (Vinckenbosch et al., 2006; Kaessmann, 2010). However, such phenomena have not been examined in plant species. Here, by employing a phylostratigraphic method, we dated the origin of protein-coding genes in rice and Arabidopsis thaliana and observed a number of young genes in both species. These young genes tend to encode short extracellular proteins, which may be involved in rapid evolving processes, such as reproductive barriers, species specification, and antimicrobial processes. Further analysis of transcriptome age indexes across different tissues revealed that male reproductive cells express a phylogenetically younger transcriptome than other plant tissues. Compared with sporophytic tissues, the young transcriptomes of the male gametophyte displayed greater complexity and diversity, which included a higher ratio of anti-sense and inter-genic transcripts, reflecting a pervasive transcription state that facilitated the emergence of new genes. Here, we propose that pollen may act as an "innovation incubator' for the birth of de novo genes. With cases of male-biased expression of young genes reported in animals, the "new genes out of the male' model revealed a common evolutionary force that drives reproductive barriers, species specification, and the upgrading of defensive mechanisms against pathogens.}, language = {en} } @article{CzesnickLenhard2015, author = {Czesnick, Hj{\"o}rdis and Lenhard, Michael}, title = {Size Control in Plants-Lessons from Leaves and Flowers}, series = {Cold Spring Harbor perspectives in biology}, volume = {7}, journal = {Cold Spring Harbor perspectives in biology}, number = {8}, publisher = {Cold Spring Harbor Laboratory Press}, address = {Cold Spring Harbor, NY}, issn = {1943-0264}, doi = {10.1101/cshperspect.a019190}, pages = {16}, year = {2015}, abstract = {To achieve optimal functionality, plant organs like leaves and petals have to grow to a certain size. Beginning with a limited number of undifferentiated cells, the final size of an organ is attained by a complex interplay of cell proliferation and subsequent cell expansion. Regulatory mechanisms that integrate intrinsic growth signals and environmental cues are required to enable optimal leaf and flower development. This review focuses on plant-specific principles of growth reaching from the cellular to the organ level. The currently known genetic pathways underlying these principles are summarized and network connections are highlighted. Putative non-cell autonomously acting mechanisms that might coordinate plant-cell growth are discussed.}, language = {en} } @article{DammhahnRakotondramananaGoodman2015, author = {Dammhahn, Melanie and Rakotondramanana, Claude Fabienne and Goodman, Steven M.}, title = {Coexistence of morphologically similar bats (Vespertilionidae) on Madagascar: stable isotopes reveal fine-grained niche differentiation among cryptic species}, series = {Journal of tropical ecology}, volume = {31}, journal = {Journal of tropical ecology}, publisher = {Cambridge Univ. Press}, address = {New York}, issn = {0266-4674}, doi = {10.1017/S0266467414000741}, pages = {153 -- 164}, year = {2015}, abstract = {Based on niche theory, closely related and morphologically similar species are not predicted to coexist due to overlap in resource and habitat use. Local assemblages of bats often contain cryptic taxa, which co-occur despite notable similarities in morphology and ecology. We measured in two different habitat types on Madagascar levels of stable carbon and nitrogen isotopes in hair (n = 103) and faeces (n = 57) of cryptic Vespertilionidae taxa to indirectly examine whether fine-grained trophic niche differentiation explains their coexistence. In the dry deciduous forest (Kirindy), six sympatric species ranged over 6.0\% in delta N-15, i.e. two trophic levels, and 4.2\% in delta C-13 with a community mean of 11.3\% in delta N-15 and - 21.0\% in delta C-13. In the mesic forest (Antsahabe), three sympatric species ranged over one trophic level (delta N-15: 2.4\%, delta C-13: 1.0\%) with a community mean of 8.0\% delta N-15 and - 21.7\% in delta C-13. Multivariate analyses and residual permutation of Euclidian distances in delta C-13- delta N-15 bi-plots revealed in both communities distinct stable isotope signatures and species separation for the hair samples among coexisting Vespertilionidae. Intraspecific variation in faecal and hair stable isotopes did not indicate that seasonal migration might relax competition and thereby facilitate the local co-occurrence of sympatric taxa.}, language = {en} } @article{DelCampoBartholomaeusFedyuninetal.2015, author = {Del Campo, Cristian and Bartholom{\"a}us, Alexander and Fedyunin, Ivan and Ignatova, Zoya}, title = {Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function}, series = {PLoS Genetics : a peer-reviewed, open-access journal}, volume = {11}, journal = {PLoS Genetics : a peer-reviewed, open-access journal}, number = {10}, publisher = {PLoS}, address = {San Fransisco}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1005613}, pages = {23}, year = {2015}, abstract = {Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity. Although individual examples show that specific structural features of mRNA regulate translation and transcript stability, their role and function throughout the bacterial transcriptome remains unknown. Combining three sequencing approaches to provide a high resolution view of global mRNA secondary structure, translation efficiency and mRNA abundance, we unraveled structural features in E. coli mRNA with implications in translation and mRNA degradation. A poorly structured site upstream of the coding sequence serves as an additional unspecific binding site of the ribosomes and the degree of its secondary structure propensity negatively correlates with gene expression. Secondary structures within coding sequences are highly dynamic and influence translation only within a very small subset of positions. A secondary structure upstream of the stop codon is enriched in genes terminated by UAA codon with likely implications in translation termination. The global analysis further substantiates a common recognition signature of RNase E to initiate endonucleolytic cleavage. This work determines for the first time the E. coli RNA structurome, highlighting the contribution of mRNA secondary structure as a direct effector of a variety of processes, including translation and mRNA degradation.}, language = {en} } @article{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 = {Bird conservation international}, volume = {25}, journal = {Bird conservation international}, number = {2}, publisher = {Cambridge Univ. Press}, address = {New York}, issn = {0959-2709}, doi = {10.1017/S0959270914000203}, 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{DiekmannMuellerHeinkenetal.2015, author = {Diekmann, Martin and M{\"u}ller, Josef and Heinken, Thilo and Dupre, Cecilia}, title = {Survey and statistical analysis of plant reintroductions in Germany}, series = {Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft}, journal = {Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft}, number = {35}, publisher = {Floristisch-Soziologische Arbeitsgemeinschaft}, address = {G{\"o}ttingen}, issn = {0722-494X}, pages = {249 -- 265}, year = {2015}, abstract = {Aim - Plant reintroductions and other forms of targeted species translocations will in the future gain growing importance for nature conservation. In fragmented habitats, species reintroductions offer one of the most efficient tools for preserving or restoring plant diversity. In our study, we have compiled available data about plant reintroduction projects in Germany to answer the following questions: (1) What are the characteristics, habitat preferences and ecological strategies of species considered in plant reintroduction trials, and are these representative of the entire class of threatened species in Germany? (2) Is the judgment of the success or failure of plant reintroductions biased by the choice of species used in the experiments? (3) Do reintroduction efforts focus on those species for which Germany has a particularly high responsibility for conservation? Methods - Information about reintroduction projects in Germany were obtained from published and internet sources as well as unpublished reports. In our search we focused on single-species trials in the framework of scientific or conservation projects. For all threatened species included in our database, we compiled information on their systematics, life form, ecological strategies and habitat preferences. A list of all species being threatened nationally or regionally, comprising both reintroduced and not reintroduced species, served as a reference for statistical analysis. Results - The list of vascular plants used in conservation-oriented reintroductions consisted of 196 taxa. Species of families with large and conspicuous, mostly insect-pollinated flowers (for example, Orchidaceae) were over-represented among the reintroduced species compared to those threatened species not included in reintroduction trials. Species considered were also more often than expected found in semi-natural open habitats such as heathlands and grasslands. Notably, many projects focused on calcareous grasslands, characterized by dry, high-pH and infertile soils. In contrast, species of more near-natural vegetation (alpine and rocky formations, forests) were under-represented. About 25\% of the species that were reintroduced are not threatened on the national scale. Out of 150 species for which Germany has a particularly high responsibility for conservation, only 14 (9.3\%) were reintroduced. For only about 1/3 of all reintroduction attempts, success or failure were documented; whereas the success rate appears to be relatively low in nutrient-poor environments, trials with nutrient-demanding and competitive species were more successful. Conclusions - We conclude that conservation-oriented reintroduction attempts should focus more on species for which the country or a region has a particular high responsibility. Reintroductions, to a larger extent than at present, also need to consider the different chances of success in different habitat types and environments.}, language = {de} } @misc{DittmannThuenemannGuggerSivonenetal.2015, author = {Dittmann-Th{\"u}nemann, Elke and Gugger, Muriel and Sivonen, Kaarina and Fewer, David P.}, title = {Natural Product Biosynthetic Diversity and Comparative Genomics of the Cyanobacteria}, series = {Trends in microbiology}, volume = {23}, journal = {Trends in microbiology}, number = {10}, publisher = {Elsevier}, address = {Oxford}, issn = {0966-842X}, doi = {10.1016/j.tim.2015.07.008}, pages = {642 -- 652}, year = {2015}, abstract = {Cyanobacteria are an ancient lineage of slow-growing photosynthetic bacteria and a prolific source of natural products with intricate chemical structures and potent biological activities. The bulk of these natural products are known from just a handful of genera. Recent efforts have elucidated the mechanisms underpinning the biosynthesis of a diverse array of natural products from cyanobacteria. Many of the biosynthetic mechanisms are unique to cyanobacteria or rarely described from other organisms. Advances in genome sequence technology have precipitated a deluge of genome sequences for cyanobacteria. This makes it possible to link known natural products to biosynthetic gene clusters but also accelerates the discovery of new natural products through genome mining. These studies demonstrate that cyanobacteria encode a huge variety of cryptic gene clusters for the production of natural products, and the known chemical diversity is likely to be just a fraction of the true biosynthetic capabilities of this fascinating and ancient group of organisms.}, language = {en} } @inproceedings{DonohueSmithBroekeretal.2015, author = {Donohue, Patrick and Smith, Mychal Daijon and Br{\"o}ker, Nina Kristin and Doering, Carolin and Mattos, Carla and Barbirz, Stefanie}, title = {Multiple Solvent Crystal Structures of phage P22 tailspike protein: An analysis of binding site hot spots and surface hydration}, series = {The FASEB journal : the official journal of the Federation of American Societies for Experimental Biology}, volume = {29}, booktitle = {The FASEB journal : the official journal of the Federation of American Societies for Experimental Biology}, publisher = {Federation of American Societies for Experimental Biology}, address = {Bethesda}, issn = {0892-6638}, pages = {1}, year = {2015}, language = {en} } @article{DubovskayaTangGladyshevetal.2015, author = {Dubovskaya, Olga P. and Tang, Kam W. and Gladyshev, Michail I. and Kirillin, Georgiy and Buseva, Zhanna and Kasprzak, Peter and Tolomeev, Aleksandr P. and Grossart, Hans-Peter}, title = {Estimating In Situ Zooplankton Non-Predation Mortality in an Oligo-Mesotrophic Lake from Sediment Trap Data: Caveats and Reality Check}, series = {PLoS one}, volume = {10}, journal = {PLoS one}, number = {7}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0131431}, pages = {17}, year = {2015}, abstract = {Background Mortality is a main driver in zooplankton population biology but it is poorly constrained in models that describe zooplankton population dynamics, food web interactions and nutrient dynamics. Mortality due to non-predation factors is often ignored even though anecdotal evidence of non-predation mass mortality of zooplankton has been reported repeatedly. One way to estimate non-predation mortality rate is to measure the removal rate of carcasses, for which sinking is the primary removal mechanism especially in quiescent shallow water bodies. Objectives and Results We used sediment traps to quantify in situ carcass sinking velocity and non-predation mortality rate on eight consecutive days in 2013 for the cladoceran Bosmina longirostris in the oligo-mesotrophic Lake Stechlin; the outcomes were compared against estimates derived from in vitro carcass sinking velocity measurements and an empirical model correcting in vitro sinking velocity for turbulence resuspension and microbial decomposition of carcasses. Our results show that the latter two approaches produced unrealistically high mortality rates of 0.58-1.04 d(-1), whereas the sediment trap approach, when used properly, yielded a mortality rate estimate of 0.015 d(-1), which is more consistent with concurrent population abundance data and comparable to physiological death rate from the literature. Ecological implications Zooplankton carcasses may be exposed to water column microbes for days before entering the benthos; therefore, non-predation mortality affects not only zooplankton population dynamics but also microbial and benthic food webs. This would be particularly important for carbon and nitrogen cycles in systems where recurring mid-summer decline of zooplankton population due to non-predation mortality is observed.}, language = {en} } @article{EggersArensFirlaetal.2015, author = {Eggers, Ute and Arens, Michael and Firla, Mario and Wallschl{\"a}ger, Hans-Dieter}, title = {To fledge or not to fledge: factors influencing the number of eggs and the eggs-to-fledglings rate in White Storks Ciconia ciconia in an agricultural environment}, series = {Journal of ornithology}, volume = {156}, journal = {Journal of ornithology}, number = {3}, publisher = {Springer}, address = {New York}, issn = {0021-8375}, doi = {10.1007/s10336-015-1182-9}, pages = {711 -- 723}, year = {2015}, abstract = {Numerous studies have explored the relationship between environmental factors and White Stork Ciconia ciconia reproduction, mainly expressing breeding success as the number of fledglings. Nonetheless, one of the most critical life-history stages in birds falls between egg-laying and fledging, and identifying the factors causing offspring mortality during this period provides valuable knowledge. We quantified the number of laid White Stork eggs and the proportion of eggs that turned into fledglings in an agriculture-dominated region in Eastern Germany. Moreover, we identified the factors among land cover, weather and arrival dates, which influenced these two reproductive measures the most, and analysed the monitored mortality causes. On average, four eggs were laid per nest, and 57.8 \% of the eggs turned into fledglings. The number of eggs laid was best explained by the negative effect of the arrival date of the second stork, while the percentage of eggs that turned into fledglings was more dependent on weather: most important parameters were mean temperature in the fifth and seventh weeks after the assumed breeding start (i.e. around the assumed hatching date), and the number of consecutive days with precipitation when nestlings are assumed to be approximately 3 weeks old. In an agricultural environment, weather effects that potentially disturb food availability might be more important than effects directly affecting the survival of White Stork offspring. The most frequent observed mortality cause, nest fights, furthermore revealed the relevance of intraspecific competition in the study population.}, language = {en} } @article{ElsnerSchiblerHofreiteretal.2015, author = {Elsner, Julia and Schibler, Joerg and Hofreiter, Michael and Schlumbaum, Angela}, title = {Burial condition is the most important factor for mtDNA PCR amplification success in Palaeolithic equid remains from the Alpine foreland}, series = {Archaeological and anthropological sciences}, volume = {7}, journal = {Archaeological and anthropological sciences}, number = {4}, publisher = {Springer}, address = {Heidelberg}, issn = {1866-9557}, doi = {10.1007/s12520-014-0213-4}, pages = {505 -- 515}, year = {2015}, abstract = {Faunal remains from Palaeolithic sites are important genetic sources to study preglacial and postglacial populations and to investigate the effect of climate change and human impact. Post mortem decay, resulting in fragmented and chemically modified DNA, is a key obstacle in ancient DNA analyses. In the absence of reliable methods to determine the presence of endogenous DNA in sub-fossil samples, temporal and spatial surveys of DNA survival on a regional scale may help to estimate the potential of faunal remains from a given time period and region. We therefore investigated PCR amplification success, PCR performance and post mortem damage in c. 47,000 to c. 12,000-year-old horse remains from 14 Palaeolithic sites along the Swiss Jura Mountains in relation to depositional context, tissue type, storage time and age, potentially influencing DNA preservation. The targeted 75 base pair mitochondrial DNA fragment could be amplified solely from equid remains from caves and not from any of the open dry and (temporary) wetland sites. Whether teeth are better than bones cannot be ultimately decided; however, both storage time after excavation and age significantly affect PCR amplification and performance, albeit not in a linear way. This is best explained by the-inevitable-heterogeneity of the data set. The extent of post mortem damage is not related to any of the potential impact factors. The results encourage comprehensive investigations of Palaeolithic cave sites, even from temperate regions.}, language = {en} } @misc{ElsnerSchiblerHofreiteretal.2015, author = {Elsner, Julia and Schibler, J{\"o}rg and Hofreiter, Michael and Schlumbaum, Angela}, title = {Burial condition is the most important factor for mtDNA PCR amplification success in Palaeolithic equid remains from the Alpine foreland}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {727}, issn = {1866-8372}, doi = {10.25932/publishup-42976}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-429763}, pages = {505 -- 515}, year = {2015}, abstract = {Faunal remains from Palaeolithic sites are important genetic sources to study preglacial and postglacial populations and to investigate the effect of climate change and human impact. Post mortem decay, resulting in fragmented and chemically modified DNA, is a key obstacle in ancient DNA analyses. In the absence of reliable methods to determine the presence of endogenous DNA in sub-fossil samples, temporal and spatial surveys of DNA survival on a regional scale may help to estimate the potential of faunal remains from a given time period and region. We therefore investigated PCR amplification success, PCR performance and post mortem damage in c. 47,000 to c. 12,000-year-old horse remains from 14 Palaeolithic sites along the Swiss Jura Mountains in relation to depositional context, tissue type, storage time and age, potentially influencing DNA preservation. The targeted 75 base pair mitochondrial DNA fragment could be amplified solely from equid remains from caves and not from any of the open dry and (temporary) wetland sites. Whether teeth are better than bones cannot be ultimately decided; however, both storage time after excavation and age significantly affect PCR amplification and performance, albeit not in a linear way. This is best explained by the—inevitable—heterogeneity of the data set. The extent of post mortem damage is not related to any of the potential impact factors. The results encourage comprehensive investigations of Palaeolithic cave sites, even from temperate regions.}, language = {en} } @article{EngqvistSchmitzGertzmannetal.2015, author = {Engqvist, Martin K. M. and Schmitz, Jessica and Gertzmann, Anke and Florian, Alexandra and Jaspert, Nils and Arif, Muhammad and Balazadeh, Salma and M{\"u}ller-R{\"o}ber, Bernd and Fernie, Alisdair R. and Maurino, Veronica G.}, title = {GLYCOLATE OXIDASE3, a Glycolate Oxidase Homolog of Yeast L-Lactate Cytochrome c Oxidoreductase, Supports L-Lactate Oxidation in Roots of Arabidopsis}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {169}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {2}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.15.01003}, pages = {1042 -- 1061}, year = {2015}, abstract = {In roots of Arabidopsis (Arabidopsis thaliana), L-lactate is generated by the reduction of pyruvate via L-lactate dehydrogenase, but this enzyme does not efficiently catalyze the reverse reaction. Here, we identify the Arabidopsis glycolate oxidase (GOX) paralogs GOX1, GOX2, and GOX3 as putative L-lactate-metabolizing enzymes based on their homology to CYB2, the L-lactate cytochrome c oxidoreductase from the yeast Saccharomyces cerevisiae. We found that GOX3 uses L-lactate with a similar efficiency to glycolate; in contrast, the photorespiratory isoforms GOX1 and GOX2, which share similar enzymatic properties, use glycolate with much higher efficiencies than L-lactate. The key factor making GOX3 more efficient with L-lactate than GOX1 and GOX2 is a 5- to 10-fold lower Km for the substrate. Consequently, only GOX3 can efficiently metabolize L-lactate at low intracellular concentrations. Isotope tracer experiments as well as substrate toxicity tests using GOX3 loss-of-function and overexpressor plants indicate that L-lactate is metabolized in vivo by GOX3. Moreover, GOX3 rescues the lethal growth phenotype of a yeast strain lacking CYB2, which cannot grow on L-lactate as a sole carbon source. GOX3 is predominantly present in roots and mature to aging leaves but is largely absent from young photosynthetic leaves, indicating that it plays a role predominantly in heterotrophic rather than autotrophic tissues, at least under standard growth conditions. In roots of plants grown under normoxic conditions, loss of function of GOX3 induces metabolic rearrangements that mirror wild-type responses under hypoxia. Thus, we identified GOX3 as the enzyme that metabolizes L-lactate to pyruvate in vivo and hypothesize that it may ensure the sustainment of low levels of L-lactate after its formation under normoxia.}, language = {en} } @unpublished{EnsslinTschoepeBurkartetal.2015, author = {Ensslin, Andreas and Tschoepe, Okka and Burkart, Michael and Joshi, Jasmin Radha}, title = {Fitness decline and adaptation to novel environments in ex situ plant collections: Current knowledge and future perspectives}, series = {: an international journal}, volume = {192}, journal = {: an international journal}, publisher = {Elsevier}, address = {Oxford}, issn = {0006-3207}, doi = {10.1016/j.biocon.2015.10.012}, pages = {394 -- 401}, year = {2015}, abstract = {The conservation of rare plant species as living collections in botanic gardens and arboreta has become an established tool in the battle against worldwide species' extinctions. However, the establishment of ex situ collections with a high conservation value requires a sound understanding of the evolutionary processes that may reduce the suitability of these collections for future reintroductions. Particularly, risks such as fitness decline of cultivated plants over time, trait shifts and loss of adaptation to the original habitat due to changes in selection regimes have rarely been addressed so far. Based on a literature review and results of our own project we show that genetic drift can lead to fitness decline in ex situ cultivated plants, but these drift effects strongly depend on the conditions and cultivation history in the ex situ facility. Furthermore, we provide evidence that shifts in traits such as germination and flowering time, and a decrease in stress tolerance to drought and competition can reduce the conservation value of ex situ collections. These threats associated with ex situ conditions require more attention by researchers, curators and conservationists. We need to increase knowledge on traits that are subject to novel selection pressures in ex situ collections, and to define population sizes that prevent genetic drift. Establishing conservation networks with replicated collections across gardens and balancing the seed contribution of mother plants to the next generation within a collection are suggested as first steps to increase the conservation value of ex situ plant collections. (C) 2015 Elsevier Ltd. All rights reserved.}, language = {en} } @misc{FettkeFernie2015, author = {Fettke, J{\"o}rg and Fernie, Alisdair R.}, title = {Intracellular and cell-to-apoplast compartmentation of carbohydrate metabolism}, series = {Trends in plant science}, volume = {20}, journal = {Trends in plant science}, number = {8}, publisher = {Elsevier}, address = {London}, issn = {1360-1385}, doi = {10.1016/j.tplants.2015.04.012}, pages = {490 -- 497}, year = {2015}, abstract = {In most plants, carbohydrates represent the major energy store as well as providing the building blocks for essential structural polymers. Although the major pathways for carbohydrate biosynthesis, degradation, and transport are well characterized, several key steps have only recently been discovered. In addition, several novel minor metabolic routes have been uncovered in the past few years. Here we review current studies of plant carbohydrate metabolism detailing the expanding compendium of functionally characterized transport proteins as well as our deeper comprehension of more minor and conditionally activated metabolic pathways. We additionally explore the pertinent questions that will allow us to enhance our understanding of the response of both major and minor carbohydrate fluxes to changing cellular circumstances.}, language = {en} } @article{FrindteAllgaierGrossartetal.2015, author = {Frindte, Katharina and Allgaier, Martin and Grossart, Hans-Peter and Eckert, Werner}, title = {Microbial response to experimentally controlled redox transitions at the sediment water interface}, series = {PLoS one}, volume = {10}, journal = {PLoS one}, number = {11}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0143428}, pages = {17}, year = {2015}, abstract = {The sediment-water interface of freshwater lakes is characterized by sharp chemical gradients, shaped by the interplay between physical, chemical and microbial processes. As dissolved oxygen is depleted in the uppermost sediment, the availability of alternative electron acceptors, e.g. nitrate and sulfate, becomes the limiting factor. We performed a time series experiment in a mesocosm to simulate the transition from aerobic to anaerobic conditions at the sediment-water interface. Our goal was to identify changes in the microbial activity due to redox transitions induced by successive depletion of available electron acceptors. Monitoring critical hydrochemical parameters in the overlying water in conjunction with a new sampling strategy for sediment bacteria enabled us to correlate redox changes in the water to shifts in the active microbial community and the expression of functional genes representing specific redox-dependent microbial processes. Our results show that during several transitions from oxic-heterotrophic condition to sulfate-reducing condition, nitrate-availability and the on-set of sulfate reduction strongly affected the corresponding functional gene expression. There was evidence of anaerobic methane oxidation with NOx. DGGE analysis revealed redox-related changes in microbial activity and expression of functional genes involved in sulfate and nitrite reduction, whereas methanogenesis and methanotrophy showed only minor changes during redox transitions. The combination of high-frequency chemical measurements and molecular methods provide new insights into the temporal dynamics of the interplay between microbial activity and specific redox transitions at the sediment-water interface.}, language = {en} } @phdthesis{FuentesTaladriz2015, author = {Fuentes Taladriz, Paulina Andrea}, title = {High-level production of the antimalarial drug precursor artemisinic acid in plastids and in vivo visualization of plastid-to-nucleus gene transfer}, school = {Universit{\"a}t Potsdam}, pages = {148}, year = {2015}, language = {en} } @phdthesis{Fuenfgeld2015, author = {F{\"u}nfgeld, Maximilian}, title = {Compartmentation of adenine nucleotide metabolism}, school = {Universit{\"a}t Potsdam}, pages = {113}, year = {2015}, language = {en} } @article{GarapatiFeilLunnetal.2015, author = {Garapati, Prashanth and Feil, Regina and Lunn, John Edward and Van Dijck, Patrick and Balazadeh, Salma and M{\"u}ller-R{\"o}ber, Bernd}, title = {Transcription Factor Arabidopsis Activating Factor1 Integrates Carbon Starvation Responses with Trehalose Metabolism}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {169}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {1}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.15.00917}, pages = {379 -- 390}, year = {2015}, abstract = {Plants respond to low carbon supply by massive reprogramming of the transcriptome and metabolome. We show here that the carbon starvation-induced NAC (for NO APICAL MERISTEM/ARABIDOPSIS TRANSCRIPTION ACTIVATION FACTOR/CUP-SHAPED COTYLEDON) transcription factor Arabidopsis (Arabidopsis thaliana) Transcription Activation Factor1 (ATAF1) plays an important role in this physiological process. We identified TREHALASE1, the only trehalase-encoding gene in Arabidopsis, as a direct downstream target of ATAF1. Overexpression of ATAF1 activates TREHALASE1 expression and leads to reduced trehalose-6-phosphate levels and a sugar starvation metabolome. In accordance with changes in expression of starch biosynthesis-and breakdown-related genes, starch levels are generally reduced in ATAF1 overexpressors but elevated in ataf1 knockout plants. At the global transcriptome level, genes affected by ATAF1 are broadly associated with energy and carbon starvation responses. Furthermore, transcriptional responses triggered by ATAF1 largely overlap with expression patterns observed in plants starved for carbon or energy supply. Collectively, our data highlight the existence of a positively acting feedforward loop between ATAF1 expression, which is induced by carbon starvation, and the depletion of cellular carbon/energy pools that is triggered by the transcriptional regulation of downstream gene regulatory networks by ATAF1.}, language = {en} } @article{GarapatiXueMunneBoschetal.2015, author = {Garapati, Prashanth and Xue, Gang-Ping and Munne-Bosch, Sergi and Balazadeh, Salma}, title = {Transcription Factor ATAF1 in Arabidopsis Promotes Senescence by Direct Regulation of Key Chloroplast Maintenance and Senescence Transcriptional Cascades}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {168}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {3}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.15.00567}, pages = {1122 -- +}, year = {2015}, abstract = {Senescence represents a fundamental process of late leaf development. Transcription factors (TFs) play an important role for expression reprogramming during senescence; however, the gene regulatory networks through which they exert their functions, and their physiological integration, are still largely unknown. Here, we identify the Arabidopsis (Arabidopsis thaliana) abscisic acid (ABA)- and hydrogen peroxide-activated TF Arabidopsis thaliana ACTIVATING FACTOR1 (ATAF1) as a novel upstream regulator of senescence. ATAF1 executes its physiological role by affecting both key chloroplast maintenance and senescence-promoting TFs, namely GOLDEN2-LIKE1 (GLK1) and ORESARA1 (ARABIDOPSIS NAC092), respectively. Notably, while ATAF1 activates ORESARA1, it represses GLK1 expression by directly binding to their promoters, thereby generating a transcriptional output that shifts the physiological balance toward the progression of senescence. We furthermore demonstrate a key role of ATAF1 for ABA- and hydrogen peroxide-induced senescence, in accordance with a direct regulatory effect on ABA homeostasis genes, including NINE-CIS-EPOXYCAROTENOID DIOXYGENASE3 involved in ABA biosynthesis and ABC TRANSPORTER G FAMILY MEMBER40, encoding an ABA transport protein. Thus, ATAF1 serves as a core transcriptional activator of senescence by coupling stress-related signaling with photosynthesis- and senescence-related transcriptional cascades.}, language = {en} } @article{GarciaBuckMcMahonetal.2015, author = {Garcia, Sarahi L. and Buck, Moritz and McMahon, Katherine D. and Grossart, Hans-Peter and Eiler, Alexander and Warnecke, Falk}, title = {Auxotrophy and intrapopulation complementary in the "interactome' of a cultivated freshwater model community}, series = {Molecular ecology}, volume = {24}, journal = {Molecular ecology}, number = {17}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0962-1083}, doi = {10.1111/mec.13319}, pages = {4449 -- 4459}, year = {2015}, abstract = {Microorganisms are usually studied either in highly complex natural communities or in isolation as monoclonal model populations that we manage to grow in the laboratory. Here, we uncover the biology of some of the most common and yet-uncultured bacteria in freshwater environments using a mixed culture from Lake Grosse Fuchskuhle. From a single shotgun metagenome of a freshwater mixed culture of low complexity, we recovered four high-quality metagenome-assembled genomes (MAGs) for metabolic reconstruction. This analysis revealed the metabolic interconnectedness and niche partitioning of these naturally dominant bacteria. In particular, vitamin- and amino acid biosynthetic pathways were distributed unequally with a member of Crenarchaeota most likely being the sole producer of vitamin B12 in the mixed culture. Using coverage-based partitioning of the genes recovered from a single MAG intrapopulation metabolic complementarity was revealed pointing to social' interactions for the common good of populations dominating freshwater plankton. As such, our MAGs highlight the power of mixed cultures to extract naturally occurring interactomes' and to overcome our inability to isolate and grow the microbes dominating in nature.}, language = {en} } @article{GeisslerPoyarkovGrismeretal.2015, author = {Geissler, Peter and Poyarkov, Nikolay A. and Grismer, Lee and Nguyen, Truong Q. and An, Hang T. and Neang, Thy and Kupfer, Alexander and Ziegler, Thomas and B{\"o}hme, Wolfgang and M{\"u}ller, Hendrik}, title = {New Ichthyophis species from Indochina (Gymnophiona, Ichthyophiidae): 1. The unstriped forms with descriptions of three new species and the redescriptions of I-acuminatus Taylor, 1960, I-youngorum Taylor, 1960 and I-laosensis Taylor, 1969}, series = {Organisms, diversity \& evolution : official journal of the Gesellschaft f{\"u}r Biologische Systematik}, volume = {15}, journal = {Organisms, diversity \& evolution : official journal of the Gesellschaft f{\"u}r Biologische Systematik}, number = {1}, publisher = {Springer}, address = {Heidelberg}, issn = {1439-6092}, doi = {10.1007/s13127-014-0190-6}, pages = {143 -- 174}, year = {2015}, abstract = {Caecilians of the genus Ichthyophis Fitzinger, 1826 are among the most poorly known amphibian taxa within Southeast Asia. Populations of Ichthyophis from the Indochina region (comprising Cambodia, Laos, and Vietnam) have been assigned to five taxa: Ichthyophis acuminatus, Ichthyophis bannanicus, Ichthyophis kohtaoensis, Ichthyophis laosensis, and Ichthyophis nguyenorum. Barcoding of recently collected specimens indicates that Indochinese congeners form a clade that includes several morphologically and genetically distinct but yet undescribed species. Although body coloration is supported by the molecular analyses as a diagnostic character at species level, unstriped forms are paraphyletic with respect to striped Ichthyophis. Based on our morphological and molecular analyses, three distinct unstriped ichthyophiid species, Ichthyophis cardamomensis sp. nov. from western Cambodia, Ichthyophis catlocensis sp. nov. from southern Vietnam, and Ichthyophis chaloensis sp. nov. from central Vietnam are described as new herein, almost doubling the number of Ichthyophis species known from the Indochinese region. All three new species differ from their unstriped congeners in a combination of morphological and molecular traits. In addition, redescriptions of three unstriped Ichthyophis species (Ichthyophis acuminatus, I. laosensis, I. youngorum) from Indochina and adjacent Thailand are provided.}, language = {en} } @article{GermonpreSablinLaznickovaGaletovaetal.2015, author = {Germonpre, Mietje and Sablin, Mikhail V. and Laznickova-Galetova, Martina and Despres, Viviane and Stevens, Rhiannon E. and Stiller, Mathias and Hofreiter, Michael}, title = {Palaeolithic dogs and Pleistocene wolves revisited: a reply to Morey (2014)}, series = {Journal of archaeological science}, volume = {54}, journal = {Journal of archaeological science}, publisher = {Elsevier}, address = {London}, issn = {0305-4403}, doi = {10.1016/j.jas.2014.11.035}, pages = {210 -- 216}, year = {2015}, abstract = {This is a reply to the comments of Morey (2014) on our identification of Palaeolithic dogs from several European Palaeolithic sites. In his comments Morey (2014) presents some misrepresentations and misunderstandings that we remedy here. In contrast to what Morey (2014) propounds, our results suggest that the domestication of the wolf was a long process that started early in the Upper Palaeolithic and that since that time two sympatric canid morphotypes can be seen in Eurasian sites: Pleistocene wolves and Palaeolithic dogs. Contrary to Morey (2014), we are convinced that the study of this domestication process should be multidisciplinary. (C) 2014 Elsevier Ltd. All rights reserved.}, language = {en} } @article{GeyerStrixnerKreftetal.2015, author = {Geyer, Juliane and Strixner, Lena and Kreft, Stefan and Jeltsch, Florian and Ibisch, Pierre L.}, title = {Adapting conservation to climate change: a case study on feasibility and implementation in Brandenburg, Germany}, series = {Regional environmental change}, volume = {15}, journal = {Regional environmental change}, number = {1}, publisher = {Springer}, address = {Heidelberg}, issn = {1436-3798}, doi = {10.1007/s10113-014-0609-9}, pages = {139 -- 153}, year = {2015}, abstract = {Conservation actions need to account for global climate change and adapt to it. The body of the literature on adaptation options is growing rapidly, but their feasibility and current state of implementation are rarely assessed. We discussed the practicability of adaptation options with conservation managers analysing three fields of action: reducing the vulnerability of conservation management, reducing the vulnerability of conservation targets (i.e. biodiversity) and climate change mitigation. For all options, feasibility, current state of implementation and existing obstacles to implementation were analysed, using the Federal State of Brandenburg, Germany, as a case study. Practitioners considered a large number of options useful, most of which have already been implemented at least in part. Those options considered broadly implemented resemble mainly conventional measures of conservation without direct relation to climate change. Managers are facing several obstacles for adapting to climate change, including political reluctance to change, financial and staff shortages in conservation administrations and conflictive EU funding schemes in agriculture. A certain reluctance to act, due to the high degree of uncertainty with regard to climate change scenarios and impacts, is widespread. A lack of knowledge of appropriate methods such as adaptive management often inhibits the implementation of adaptation options in the field of planning and management. Based on the findings for Brandenburg, we generally conclude that it is necessary to focus in particular on options that help to reduce vulnerability of conservation management itself, i.e. those that enhance management effectiveness. For instance, adaptive and proactive risk management can be applied as a no-regrets option, independently from specific climate change scenarios or impacts, strengthening action under uncertainty.}, language = {en} } @article{GludGrossartLarsenetal.2015, author = {Glud, Ronnie N. and Grossart, Hans-Peter and Larsen, Morten and Tang, Kam W. and Arendt, Kristine E. and Rysgaard, Soren and Thamdrup, Bo and Gissel Nielsen, Torkel}, title = {Copepod carcasses as microbial hot spots for pelagic denitrification}, series = {Limnology and oceanography}, volume = {60}, journal = {Limnology and oceanography}, number = {6}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0024-3590}, doi = {10.1002/lno.10149}, pages = {2026 -- 2036}, year = {2015}, abstract = {Copepods are exposed to a high non-predatory mortality and their decomposing carcasses act as microniches with intensified microbial activity. Sinking carcasses could thereby represent anoxic microenvironment sustaining anaerobic microbial pathways in otherwise oxic water columns. Using non-invasive O-2 imaging, we document that carcasses of Calanus finmarchicus had an anoxic interior even at fully air-saturated ambient O-2 level. The extent of anoxia gradually expanded with decreasing ambient O-2 levels. Concurrent microbial sampling showed the expression of nitrite reductase genes (nirS) in all investigated carcass samples and thereby documented the potential for microbial denitrification in carcasses. The nirS gene was occasionally expressed in live copepods, but not as consistently as in carcasses. Incubations of sinking carcasses in (15)NO3-amended seawater demonstrated denitrification, of which on average 34\%+/- 17\% (n=28) was sustained by nitrification. However, the activity was highly variable and was strongly dependent on the ambient O-2 levels. While denitrification was present even at air-saturation (302 mol L-1), the average carcass specific activity increased several orders of magnitude to approximate to 1 nmol d(-1) at 20\% air-saturation (55 mol O-2 L-1) at an ambient temperature of 7 degrees C. Sinking carcasses of C. finmarchicus therefore represent hotspots of pelagic denitrification, but the quantitative importance as a sink for bioavailable nitrogen is strongly dependent on the ambient O-2 level. The importance of carcass associated denitrification could be highly significant in O-2 depleted environments such as Oxygen Minimum Zones (OMZ).}, language = {en} } @article{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 = {Nucleic acids research}, volume = {43}, journal = {Nucleic acids research}, number = {6}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0305-1048}, doi = {10.1093/nar/gkv199}, pages = {3022 -- 3032}, 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} } @article{GroeneveldJohstKawaguchietal.2015, author = {Groeneveld, J{\"u}rgen and Johst, Karin and Kawaguchi, So and Meyer, Bettina and Teschke, Mathias and Grimm, Volker}, title = {How biological clocks and changing environmental conditions determine local population growth and species distribution in Antarctic krill (Euphausia superba): a conceptual model}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {303}, 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.2015.02.009}, pages = {78 -- 86}, year = {2015}, abstract = {The Southern Ocean ecosystem is characterized by extreme seasonal changes in environmental factors such as day length, sea ice extent and food availability. The key species Antarctic krill (Euphausia superba) has evolved metabolic and behavioural seasonal rhythms to cope with these seasonal changes. We investigate the switch between a physiological less active and active period for adult krill, a rhythm which seems to be controlled by internal biological clocks. These biological clocks can be synchronized by environmental triggers such as day length and food availability. They have evolved for particular environmental regimes to synchronize predictable seasonal environmental changes with important life cycle functions of the species. In a changing environment the time when krill is metabolically active and the time of peak food availability may not overlap if krill's seasonal activity is solely determined by photoperiod (day length). This is especially true for the Atlantic sector of the Southern Ocean where the spatio-temporal ice cover dynamics are changing substantially with rising average temperatures. We developed an individual-based model for krill to explore the impact of photoperiod and food availability on the growth and demographics of krill. We simulated dynamics of local krill populations (with no movement of krill assumed) along a south-north gradient for different triggers of metabolic activity and different levels of food availability below the ice. We also observed the fate of larval krill which cannot switch to low metabolism and therefore are likely to overwinter under ice. Krill could only occupy the southern end of the gradient, where algae bloom only lasts for a short time, when alternative food supply under the ice was high and metabolic activity was triggered by photoperiod. The northern distribution was limited by lack of overwintering habitat for krill larvae due to short duration of sea ice cover even for high food content under the ice. The variability of the krill's length-frequency distributions varied for different triggers of metabolic activity, but did not depend on the sea ice extent. Our findings suggest a southward shift of krill populations due to reduction in the spatial sea ice extent, which is consistent with field observations. Overall, our results highlight the importance of the explicit consideration of spatio-temporal sea ice dynamics especially for larval krill together with temporal synchronization through internal clocks, triggered by environmental factors (photoperiod and food) in adult krill for the population modelling of krill. (C) 2015 Elsevier B.V. All rights reserved.}, language = {en} } @phdthesis{Grune2015, author = {Grune, Jana}, title = {Effects of a novel non-steroidal mineralocorticoid receptor antagonist on cardiac hypertrophy}, school = {Universit{\"a}t Potsdam}, pages = {98}, year = {2015}, language = {en} } @article{GraefBatsiosMeyer2015, author = {Gr{\"a}f, Ralph and Batsios, Petros and Meyer, Irene}, title = {Evolution of centrosomes and the nuclear lamina: Amoebozoan assets}, series = {European journal of cell biology}, volume = {94}, journal = {European journal of cell biology}, number = {6}, publisher = {Elsevier}, address = {Jena}, issn = {0171-9335}, doi = {10.1016/j.ejcb.2015.04.004}, pages = {249 -- 256}, year = {2015}, abstract = {The current eukaryotic tree of life groups most eukaryotes into one of five supergroups, the Opisthokonta, Amoebozoa, Archaeplastida, Excavata and SAR (Stramenopile, Alveolata, Rhizaria). Molecular and comparative morphological analyses revealed that the last eukaryotic common ancestor (LECA) already contained a rather sophisticated equipment of organelles including a mitochondrion, an endomembrane system, a nucleus with a lamina, a microtubule-organizing center (MTOC), and a flagellar apparatus. Recent studies of MTOCs, basal bodies/centrioles, and nuclear envelope organization of organisms in different supergroups have clarified our picture of how the nucleus and MTOCs co-evolved from LECA to extant eukaryotes. In this review we summarize these findings with special emphasis on valuable contributions of research on a lamin-like protein, nuclear envelope proteins, and the MTOC in the amoebozoan model organism Dictyostelium discoideum. (C) 2015 Elsevier GmbH. All rights reserved.}, language = {en} } @article{GuhaWarsinkeTientcheuetal.2015, author = {Guha, S. and Warsinke, Axel and Tientcheu, Charles Merlin and Schmalz, K. and Meliani, C. and Wenger, Ch.}, title = {Label free sensing of creatinine using a 6 GHz CMOS near-field dielectric immunosensor}, series = {The analyst : the analytical journal of the Royal Society of Chemistry}, volume = {140}, journal = {The analyst : the analytical journal of the Royal Society of Chemistry}, number = {9}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {0003-2654}, doi = {10.1039/c4an02194k}, pages = {3019 -- 3027}, year = {2015}, abstract = {In this work we present a CMOS high frequency direct immunosensor operating at 6 GHz (C-band) for label free determination of creatinine. The sensor is fabricated in standard 0.13 mu m SiGe:C BiCMOS process. The report also demonstrates the ability to immobilize creatinine molecules on a Si3N4 passivation layer of the standard BiCMOS/CMOS process, therefore, evading any further need of cumbersome post processing of the fabricated sensor chip. The sensor is based on capacitive detection of the amount of non-creatinine bound antibodies binding to an immobilized creatinine layer on the passivated sensor. The chip bound antibody amount in turn corresponds indirectly to the creatinine concentration used in the incubation phase. The determination of creatinine in the concentration range of 0.88-880 mu M is successfully demonstrated in this work. A sensitivity of 35 MHz/10 fold increase in creatinine concentration (during incubation) at the centre frequency of 6 GHz is gained by the immunosensor. The results are compared with a standard optical measurement technique and the dynamic range and sensitivity is of the order of the established optical indication technique. The C-band immunosensor chip comprising an area of 0.3 mm(2) reduces the sensing area considerably, therefore, requiring a sample volume as low as 2 mu l. The small analyte sample volume and label free approach also reduce the experimental costs in addition to the low fabrication costs offered by the batch fabrication technique of CMOS/BiCMOS process.}, language = {en} } @unpublished{HagelbergHofreiterKeyser2015, author = {Hagelberg, Erika and Hofreiter, Michael and Keyser, Christine}, title = {Ancient DNA: the first three decades}, series = {Philosophical transactions of the Royal Society of London : B, Biological sciences}, volume = {370}, journal = {Philosophical transactions of the Royal Society of London : B, Biological sciences}, number = {1660}, publisher = {Royal Society}, address = {London}, issn = {0962-8436}, doi = {10.1098/rstb.2013.0371}, pages = {6}, year = {2015}, language = {en} } @article{HahnEngelhardReschkeetal.2015, author = {Hahn, Aaron and Engelhard, Christopher and Reschke, Stefan and Teutloff, Christian and Bittl, Robert and Leimk{\"u}hler, Silke and Risse, Thomas}, title = {Structural Insights into the Incorporation of the Mo Cofactor into Sulfite Oxidase from Site-Directed Spin Labeling}, series = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition}, volume = {54}, journal = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition}, number = {40}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1433-7851}, doi = {10.1002/anie.201504772}, pages = {11865 -- 11869}, year = {2015}, abstract = {Mononuclear molybdoenzymes catalyze a broad range of redox reactions and are highly conserved in all kingdoms of life. This study addresses the question of how the Mo cofactor (Moco) is incorporated into the apo form of human sulfite oxidase (hSO) by using site-directed spin labeling to determine intramolecular distances in the nanometer range. Comparative measurements of the holo and apo forms of hSO enabled the localization of the corresponding structural changes, which are localized to a short loop (residues 263-273) of the Moco-containing domain. A flap-like movement of the loop provides access to the Moco binding-pocket in the apo form of the protein and explains the earlier studies on the in vitro reconstitution of apo-hSO with Moco. Remarkably, the loop motif can be found in a variety of structurally similar molybdoenzymes among various organisms, thus suggesting a common mechanism of Moco incorporation.}, language = {en} } @article{HahnSolomunWellhausenetal.2015, author = {Hahn, Marc Benjamin and Solomun, Tihomir and Wellhausen, Robert and Hermann, Sabrina and Seitz, Harald and Meyer, Susann and Kunte, Hans-J{\"o}rg and Zeman, Johannes and Uhlig, Frank and Smiatek, Jens and Sturm, Heinz}, title = {Influence of the Compatible Solute Ectoine on the Local Water Structure: Implications for the Binding of the Protein G5P to DNA}, series = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, volume = {119}, journal = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, number = {49}, publisher = {American Chemical Society}, address = {Washington}, issn = {1520-6106}, doi = {10.1021/acs.jpcb.5b09506}, pages = {15212 -- 15220}, year = {2015}, abstract = {Microorganisms accumulate molar concentrations of compatible solutes like ectoine to prevent proteins from denaturation. Direct structural or spectroscopic information on the mechanism and about the hydration shell around ectoine are scarce. We combined surface plasmon resonance (SPR), confocal Raman spectroscopy, molecular dynamics simulations, and density functional theory (DFT) calculations to study the local hydration shell around ectoine and its influence on the binding of a gene-S-protein (G5P) to a single-stranded DNA (dT(25)). Due to the very high hygroscopicity of ectoine, it was possible to analyze the highly stable hydration shell by confocal Raman spectroscopy. Corresponding molecular dynamics simulation results revealed a significant change of the water dielectric constant in the presence of a high molar ectoine concentration as compared to pure water. The SPR data showed that the amount of protein bound to DNA decreases in the presence of ectoine, and hence, the protein-DNA dissociation constant increases in a concentration-dependent manner. Concomitantly, the Raman spectra in terms of the amide I region revealed large changes in the protein secondary structure. Our results indicate that ectoine strongly affects the molecular recognition between the protein and the oligonudeotide, which has important consequences for osmotic regulation mechanisms.}, language = {en} } @article{HamalainenDammhahnAujardetal.2015, author = {Hamalainen, Anni and Dammhahn, Melanie and Aujard, Fabienne and Kraus, Cornelia}, title = {Losing grip: Senescent decline in physical strength in a small-bodied primate in captivity and in the wild}, series = {Experimental gerontology}, volume = {61}, journal = {Experimental gerontology}, publisher = {Elsevier}, address = {Oxford}, issn = {0531-5565}, doi = {10.1016/j.exger.2014.11.017}, pages = {54 -- 61}, year = {2015}, abstract = {Muscle strength reflects physical functioning, declines at old age and predicts health and survival in humans and laboratory animals. Age-associated muscle deterioration causes loss of strength and may impair fitness of wild animals. However, the effects of age and life-history characteristics on muscle strength in wild animals are unknown. We investigated environment-and sex-specific patterns of physical functioning by measuring grip strength in wild and captive gray mouse lemurs. We expected more pronounced strength senescence in captivity due to condition-dependent, extrinsic mortality found in nature. Males were predicted to be stronger but potentially experience more severe senescence than females as predicted by life history theory. We found similar senescent declines in captive males and females as well as wild females, whereas wild males showed little decline, presumably due to their early mortality. Captive animals were generally weaker and showed earlier declines than wild animals. Unexpectedly, females tended to be stronger than males, especially in the reproductive season. Universal intrinsic mechanisms (e. g. sarcopenia) likely cause the similar patterns of strength loss across settings. The female advantage in muscle strength merits further study; it may follow higher reproductive investment by males, or be an adaptation associated with female social dominance.}, language = {en} } @inproceedings{HankeGogokhiaFrederickZhangetal.2015, author = {Hanke-Gogokhia, Christin and Frederick, Jeanne M. and Zhang, Houbin and Baehr, Wolfgang}, title = {ARL3 regulates transport of prenylated and acylated proteins to photoreceptor outer segment in mouse retina}, series = {Investigative ophthalmology \& visual science}, volume = {56}, booktitle = {Investigative ophthalmology \& visual science}, number = {7}, publisher = {Association for Research in Vision and Opthalmology}, address = {Rockville}, issn = {0146-0404}, pages = {2}, year = {2015}, language = {en} } @misc{HartmannHasenkampMayeretal.2015, author = {Hartmann, Stefanie and Hasenkamp, Natascha and Mayer, Jens and Michaux, Johan and Morand, Serge and Mazzoni, Camila J. and Roca, Alfred L. and Greenwood, Alex D.}, title = {Endogenous murine leukemia retroviral variation across wild European and inbred strains of house mouse}, series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1329}, issn = {1866-8372}, doi = {10.25932/publishup-43120}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431200}, pages = {13}, year = {2015}, abstract = {Background: Endogenous murine leukemia retroviruses (MLVs) are high copy number proviral elements difficult to comprehensively characterize using standard low throughput sequencing approaches. However, high throughput approaches generate data that is challenging to process, interpret and present. Results: Next generation sequencing (NGS) data was generated for MLVs from two wild caught Mus musculus domesticus (from mainland France and Corsica) and for inbred laboratory mouse strains C3H, LP/J and SJL. Sequence reads were grouped using a novel sequence clustering approach as applied to retroviral sequences. A Markov cluster algorithm was employed, and the sequence reads were queried for matches to specific xenotropic (Xmv), polytropic (Pmv) and modified polytropic (Mpmv) viral reference sequences. Conclusions: Various MLV subtypes were more widespread than expected among the mice, which may be due to the higher coverage of NGS, or to the presence of similar sequence across many different proviral loci. The results did not correlate with variation in the major MLV receptor Xpr1, which can restrict exogenous MLVs, suggesting that endogenous MLV distribution may reflect gene flow more than past resistance to infection.}, language = {en} } @article{HartmannHasenkampMayeretal.2015, author = {Hartmann, Stefanie and Hasenkamp, Natascha and Mayer, Jens and Michaux, Johan and Morand, Serge and Mazzoni, Camila J. and Roca, Alfred L. and Greenwood, Alex D.}, title = {Endogenous murine leukemia retroviral variation across wild European and inbred strains of house mouse}, series = {BMC genomics}, volume = {16}, journal = {BMC genomics}, publisher = {BioMed Central}, address = {London}, issn = {1471-2164}, doi = {10.1186/s12864-015-1766-z}, pages = {13}, year = {2015}, abstract = {Background: Endogenous murine leukemia retroviruses (MLVs) are high copy number proviral elements difficult to comprehensively characterize using standard low throughput sequencing approaches. However, high throughput approaches generate data that is challenging to process, interpret and present. Results: Next generation sequencing (NGS) data was generated for MLVs from two wild caught Mus musculus domesticus (from mainland France and Corsica) and for inbred laboratory mouse strains C3H, LP/J and SJL. Sequence reads were grouped using a novel sequence clustering approach as applied to retroviral sequences. A Markov cluster algorithm was employed, and the sequence reads were queried for matches to specific xenotropic (Xmv), polytropic (Pmv) and modified polytropic (Mpmv) viral reference sequences. Conclusions: Various MLV subtypes were more widespread than expected among the mice, which may be due to the higher coverage of NGS, or to the presence of similar sequence across many different proviral loci. The results did not correlate with variation in the major MLV receptor Xpr1, which can restrict exogenous MLVs, suggesting that endogenous MLV distribution may reflect gene flow more than past resistance to infection.}, language = {en} } @misc{HartmannSchwanholdLeimkuehler2015, author = {Hartmann, Tobias and Schwanhold, Nadine and Leimk{\"u}hler, Silke}, title = {Assembly and catalysis of molybdenum or tungsten-containing formate dehydrogenases from bacteria}, series = {Biochimica et biophysica acta : Proteins and proteomics}, volume = {1854}, journal = {Biochimica et biophysica acta : Proteins and proteomics}, number = {9}, publisher = {Elsevier}, address = {Amsterdam}, issn = {1570-9639}, doi = {10.1016/j.bbapap.2014.12.006}, pages = {1090 -- 1100}, year = {2015}, abstract = {The global carbon cycle depends on the biological transformations of C-1 compounds, which include the reductive incorporation of CO2 into organic molecules (e.g. in photosynthesis and other autotrophic pathways), in addition to the production of CO2 from formate, a reaction that is catalyzed by formate dehydrogenases (FDHs). FDHs catalyze, in general, the oxidation of formate to CO2 and H+. However, selected enzymes were identified to act as CO2 reductases, which are able to reduce CO2 to formate under physiological conditions. This reaction is of interest for the generation of formate as a convenient storage form of H-2 for future applications. Cofactor-containing FDHs are found in anaerobic bacteria and archaea, in addition to facultative anaerobic or aerobic bacteria. These enzymes are highly diverse and employ different cofactors such as the molybdenum cofactor (Moco), FeS clusters and flavins, or cytochromes. Some enzymes include tungsten (W) in place of molybdenum (Mo) at the active site. For catalytic activity, a selenocysteine (SeCys) or cysteine (Cys) ligand at the Mo atom in the active site is essential for the reaction. This review will focus on the characterization of Mo- and W-containing FDHs from bacteria, their active site structure, subunit compositions and its proposed catalytic mechanism. We will give an overview on the different mechanisms of substrate conversion available so far, in addition to providing an outlook on bio-applications of FDHs. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications. (C) 2014 Elsevier B.V. All rights reserved.}, language = {en} } @article{HeinzeBergmannRilligetal.2015, author = {Heinze, Johannes and Bergmann, Joana and Rillig, Matthias C. and Joshi, Jasmin Radha}, title = {Negative biotic soil-effects enhance biodiversity by restricting potentially dominant plant species in grasslands}, series = {Perspectives in plant ecology, evolution and systematics}, volume = {17}, journal = {Perspectives in plant ecology, evolution and systematics}, number = {3}, publisher = {Elsevier}, address = {Jena}, issn = {1433-8319}, doi = {10.1016/j.ppees.2015.03.002}, pages = {227 -- 235}, year = {2015}, abstract = {Interactions between soil microorganisms and plants can play a vital role for plant fitness and therefore also for plant community composition and biodiversity. However, little is known about how biotic plant soil interactions influence the local dominance and abundance of plant species and whether specific taxonomic or functional groups of plants are differentially affected by such biotic soil-effects. In two greenhouse experiments, we tested the biotic soil-effects of 33 grassland species differing in individual size and local abundance. We hypothesized that large plants that are not locally dominant (despite their size-related competitive advantage enabling them to potentially outshade competitors) are most strongly limited by negative biotic soil-effects. We sampled soils at the opposite ends of a gradient in land-use intensity in temperate grasslands to account for putative modulating effects of land-use intensity on biotic soil-effects. As hypothesized, large, but non-dominant species (especially grasses) experienced more negative biotic soil-effects compared with small and abundant plant species. Land-use intensity had contrasting effects on grasses and herbs resulting in more negative biotic soil-effects for grasses in less intensively managed grasslands. We conclude that biotic soil-effects contribute to the control of potentially dominant plants and hence enable species coexistence and biodiversity especially in species-rich less intensively managed grasslands.}, language = {en} } @article{HeinzeWernerWeberetal.2015, author = {Heinze, Johannes and Werner, Tony and Weber, Ewald and Rillig, Matthias C. and Joshi, Jasmin Radha}, title = {Soil biota effects on local abundances of three grass species along a land-use gradient}, series = {Oecologia}, volume = {179}, journal = {Oecologia}, number = {1}, publisher = {Springer}, address = {New York}, issn = {0029-8549}, doi = {10.1007/s00442-015-3336-0}, pages = {249 -- 259}, year = {2015}, abstract = {Biotic plant-soil interactions and land-use intensity are known to affect plant individual fitness as well as competitiveness and therefore plant-species abundances in communities. Therefore, a link between soil biota and land-use intensity on local abundance of plant species in grasslands can be expected. In two greenhouse experiments, we investigated the effects of soil biota from grassland sites differing in land-use intensity on three grass species that vary in local abundances along this land-use gradient. We were interested in those soil-biota effects that are associated with land-use intensity, and whether these effects act directly or indirectly. Therefore, we grew the three plant species in two separate experiments as single individuals and in mixtures and compared their performance. As single plants, all three grasses showed a similar performance with and without soil biota. In contrast, in mixtures growth of the species in response to the presence or absence of soil biota differed. This resulted in different soil-biota effects that tend to correspond with patterns of species-specific abundances in the field for two of the three species tested. Our results highlight the importance of indirect interactions between plants and soil microorganisms and suggest that combined effects of soil biota and plant-plant interactions are involved in structuring plant communities. In conclusion, our experiments suggest that soil biota may have the potential to alter effects of plant-plant interactions and therefore influence plant-species abundances and diversity in grasslands.}, language = {en} } @article{HenryNeillBeckeretal.2015, author = {Henry, Brian D. and Neill, Daniel R. and Becker, Katrin Anne and Gore, Suzanna and Bricio-Moreno, Laura and Ziobro, Regan and Edwards, Michael J. and Muehlemann, Kathrin and Steinmann, Joerg and Kleuser, Burkhard and Japtok, Lukasz and Luginbuehl, Miriam and Wolfmeier, Heidi and Scherag, Andre and Gulbins, Erich and Kadioglu, Aras and Draeger, Annette and Babiychuk, Eduard B.}, title = {Engineered liposomes sequester bacterial exotoxins and protect from severe invasive infections in mice}, series = {Nature biotechnology : the science and business of biotechnology}, volume = {33}, journal = {Nature biotechnology : the science and business of biotechnology}, number = {1}, publisher = {Nature Publ. Group}, address = {New York}, issn = {1087-0156}, doi = {10.1038/nbt.3037}, pages = {81 -- U295}, year = {2015}, abstract = {Gram-positive bacterial pathogens that secrete cytotoxic pore-forming toxins, such as Staphylococcus aureus and Streptococcus pneumoniae, cause a substantial burden of disease. Inspired by the principles that govern natural toxin-host interactions, we have engineered artificial liposomes that are tailored to effectively compete with host cells for toxin binding. Liposome-bound toxins are unable to lyse mammalian cells in vitro. We use these artificial liposomes as decoy targets to sequester bacterial toxins that are produced during active infection in vivo. Administration of artificial liposomes within 10 h after infection rescues mice from septicemia caused by S. aureus and S. pneumoniae, whereas untreated mice die within 24-33 h. Furthermore, liposomes protect mice against invasive pneumococcal pneumonia. Composed exclusively of naturally occurring lipids, tailored liposomes are not bactericidal and could be used therapeutically either alone or in conjunction with antibiotics to combat bacterial infections and to minimize toxin-induced tissue damage that occurs during bacterial clearance.}, language = {en} } @phdthesis{Herde2015, author = {Herde, Antje}, title = {Individual differences and seasonal variation in behaviour}, school = {Universit{\"a}t Potsdam}, pages = {111}, year = {2015}, language = {en} } @misc{HermanussenSchefflerGrothetal.2015, author = {Hermanussen, Michael and Scheffler, Christiane and Groth, Detlef and Aßmann, Christian}, title = {Height and skeletal morphology in relation to modern life style}, series = {Journal of physiological anthropology}, volume = {34}, journal = {Journal of physiological anthropology}, publisher = {BioMed Central}, address = {London}, issn = {1880-6805}, doi = {10.1186/s40101-015-0080-4}, pages = {5}, year = {2015}, abstract = {Height and skeletal morphology strongly relate to life style. Parallel to the decrease in physical activity and locomotion, modern people are slimmer in skeletal proportions. In German children and adolescents, elbow breadth and particularly relative pelvic breadth (50th centile of bicristal distance divided by body height) have significantly decreased in recent years. Even more evident than the changes in pelvic morphology are the rapid changes in body height in most modern countries since the end-19th and particularly since the mid-20th century. Modern Japanese mature earlier; the age at take-off (ATO, the age at which the adolescent growth spurt starts) decreases, and they are taller at all ages. Preece-Baines modelling of six national samples of Japanese children and adolescents, surveyed between 1955 and 2000, shows that this gain in height is largely an adolescent trend, whereas height at take-off (HTO) increased by less than 3 cm since 1955; adolescent growth (height gain between ATO and adult age) increased by 6 cm. The effect of globalization on the modern post-war Japanese society ("community effect in height") on adolescent growth is discussed.}, language = {en} } @article{HerterMcKennaFrazeretal.2015, author = {Herter, Susanne and McKenna, Shane M. and Frazer, Andrew R. and Leimk{\"u}hler, Silke and Carnell, Andrew J. and Turner, Nicholas J.}, title = {Galactose Oxidase Variants for the Oxidation of Amino Alcohols in Enzyme Cascade Synthesis}, series = {ChemCatChem : heterogeneous \& homogeneous \& bio- \& nano-catalysis ; a journal of ChemPubSoc Europe}, volume = {7}, journal = {ChemCatChem : heterogeneous \& homogeneous \& bio- \& nano-catalysis ; a journal of ChemPubSoc Europe}, number = {15}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1867-3880}, doi = {10.1002/cctc.201500218}, pages = {2313 -- 2317}, year = {2015}, abstract = {The use of selected engineered galactose oxidase (GOase) variants for the oxidation of amino alcohols to aldehydes under mild conditions in aqueous systems is reported. GOase variant F-2 catalyses the regioselective oxidation of N-carbobenzyloxy (Cbz)-protected 3-amino-1,2-propanediol to the corresponding -hydroxyaldehyde which was then used in an aldolase reaction. Another variant, M3-5, was found to exhibit activity towards free and N-Cbz-protected aliphatic and aromatic amino alcohols allowing the synthesis of lactams such as 3,4-dihydronaphthalen-1(2H)-one, 2-pyrrolidone and valerolactam in one-pot tandem reactions with xanthine dehydrogenase (XDH) or aldehyde oxidase (PaoABC).}, language = {en} } @article{HessSaffertLiebetonetal.2015, author = {Hess, Anne-Katrin and Saffert, Paul and Liebeton, Klaus and Ignatova, Zoya}, title = {Optimization of Translation Profiles Enhances Protein Expression and Solubility}, series = {PLoS one}, volume = {10}, journal = {PLoS one}, number = {5}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0127039}, pages = {14}, year = {2015}, abstract = {mRNA is translated with a non-uniform speed that actively coordinates co-translational folding of protein domains. Using structure-based homology we identified the structural domains in epoxide hydrolases (EHs) and introduced slow-translating codons to delineate the translation of single domains. These changes in translation speed dramatically improved the solubility of two EHs of metagenomic origin in Escherichia coli. Conversely, the importance of transient attenuation for the folding, and consequently solubility, of EH was evidenced with a member of the EH family from Agrobacterium radiobacter, which partitions in the soluble fraction when expressed in E. coli. Synonymous substitutions of codons shaping the slow-transiting regions to fast-translating codons render this protein insoluble. Furthermore, we show that low protein yield can be enhanced by decreasing the free folding energy of the initial 5'-coding region, which can disrupt mRNA secondary structure and enhance ribosomal loading. This study provides direct experimental evidence that mRNA is not a mere messenger for translation of codons into amino acids but bears an additional layer of information for folding, solubility and expression level of the encoded protein. Furthermore, it provides a general frame on how to modulate and fine-tune gene expression of a target protein.}, language = {en} } @phdthesis{Heyneke2015, author = {Heyneke, Elmien}, title = {The role of the calcineurin B-like interacting protein kinase, CIPK14 in regulating plant nutrient metabolism}, school = {Universit{\"a}t Potsdam}, pages = {135}, year = {2015}, language = {en} } @misc{HixsonSharmaKainzetal.2015, author = {Hixson, Stefanie M. and Sharma, Bhanu and Kainz, Martin J. and Wacker, Alexander and Arts, Michael T.}, title = {Production, distribution, and abundance of long-chain omega-3 polyunsaturated fatty acids: a fundamental dichotomy between freshwater and terrestrial ecosystems}, series = {Environmental reviews = Dossiers environnement}, volume = {23}, journal = {Environmental reviews = Dossiers environnement}, number = {4}, publisher = {NRC Research Press}, address = {Ottawa}, issn = {1208-6053}, doi = {10.1139/er-2015-0029}, pages = {414 -- 424}, year = {2015}, abstract = {Long-chain polyunsaturated fatty acids (LC-PUFA) are critical for the health of aquatic and terrestrial organisms; therefore, understanding the production, distribution, and abundance of these compounds is imperative. Although the dynamics of LC-PUFA production and distribution in aquatic environments has been well documented, a systematic and comprehensive comparison to LC-PUFA in terrestrial environments has not been rigorously investigated. Here we use a data synthesis approach to compare and contrast fatty acid profiles of 369 aquatic and terrestrial organisms. Habitat and trophic level were interacting factors that determined the proportion of individual omega-3 (n-3) or omega-6 (n-6) PUFA in aquatic and terrestrial organisms. Higher total n-3 content compared with n-6 PUFA and a strong prevalence of the n-3 PUFA eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) characterized aquatic versus terrestrial organisms. Conversely, terrestrial organisms had higher linoleic acid (LNA) and alpha-linolenic acid (ALA) contents than aquatic organisms; however, the ratio of ALA: LNA was higher in aquatic organisms. The EPA + DHA content was higher in aquatic animals than terrestrial organisms, and increased from algae to invertebrates to vertebrates in the aquatic environment. An analysis of covariance (ANCOVA) revealed that fatty acid composition was highly dependent on the interaction between habitat and trophic level. We conclude that freshwater ecosystems provide an essential service through the production of n-3 LC-PUFA that are required to maintain the health of terrestrial organisms including humans.}, language = {en} } @inproceedings{HofreiterBarlowPaijmansetal.2015, author = {Hofreiter, Michael and Barlow, Axel and Paijmans, Johanna L. A. and Westbury, Michael V.}, title = {Genomic analyses from highly degraded DNA}, series = {Genome}, volume = {58}, booktitle = {Genome}, number = {5}, publisher = {NRC Research Press}, address = {Ottawa}, issn = {0831-2796}, pages = {228 -- 228}, year = {2015}, language = {en} } @article{HofreiterPaijmansGoodchildetal.2015, author = {Hofreiter, Michael and Paijmans, Johanna L. A. and Goodchild, Helen and Speller, Camilla F. and Barlow, Axel and Gonz{\´a}lez-Fortes, Gloria M. and Thomas, Jessica A. and Ludwig, Arne and Collins, Matthew J.}, title = {The future of ancient DNA: Technical advances and conceptual shifts}, series = {Bioessays : ideas that push the boundaries}, volume = {37}, journal = {Bioessays : ideas that push the boundaries}, number = {3}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0265-9247}, doi = {10.1002/bies.201400160}, pages = {284 -- 293}, year = {2015}, abstract = {Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7x coverage (mammoth) in 2008 to more than 50x coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics.}, language = {en} } @article{HornHempelRistowetal.2015, author = {Horn, Sebastian and Hempel, Stefan and Ristow, Michael and Rillig, Matthias C. and Kowarik, Ingo and Caruso, Tancredi}, title = {Plant community assembly at small scales: Spatial vs. environmental factors in a European grassland}, series = {Acta oecologica : international journal of ecology}, volume = {63}, journal = {Acta oecologica : international journal of ecology}, publisher = {Elsevier}, address = {Paris}, issn = {1146-609X}, doi = {10.1016/j.actao.2015.01.004}, pages = {56 -- 62}, year = {2015}, abstract = {Dispersal limitation and environmental conditions are crucial drivers of plant species distribution and establishment. As these factors operate at different spatial scales, we asked: Do the environmental factors known to determine community assembly at broad scales operate at fine scales (few meters)? How much do these factors account for community variation at fine scales? In which way do biotic and abiotic interactions drive changes in species composition? We surveyed the plant community within a dry grassland along a very steep gradient of soil characteristics like pH and nutrients. We used a spatially explicit sampling design, based on three replicated macroplots of 15 x 15, 12 x 12 and 12 x 12 m in extent. Soil samples were taken to quantify several soil properties (carbon, nitrogen, plant available phosphorus, pH, water content and dehydrogenase activity as a proxy for overall microbial activity). We performed variance partitioning to assess the effect of these variables on plant composition and statistically controlled for spatial autocorrelation via eigenvector mapping. We also applied null model analysis to test for non-random patterns in species co-occurrence using randomization schemes that account for patterns expected under species interactions. At a fine spatial scale, environmental factors explained 18\% of variation when controlling for spatial autocorrelation in the distribution of plant species, whereas purely spatial processes accounted for 14\% variation. Null model analysis showed that species spatially segregated in a non-random way and these spatial patterns could be due to a combination of environmental filtering and biotic interactions. Our grassland study suggests that environmental factors found to be directly relevant in broad scale studies are present also at small scales, but are supplemented by spatial processes and more direct interactions like competition. (C) 2015 Elsevier Masson SAS. All rights reserved.}, language = {en} } @article{HuVoellerSussmuthetal.2015, author = {Hu, Chenlin and V{\"o}ller, Ginka and Sussmuth, Roderich and Dittmann-Th{\"u}nemann, Elke and Kehr, Jan-Christoph}, title = {Functional assessment of mycosporine-like amino acids in Microcystis aeruginosa strain PCC 7806}, series = {Environmental microbiology}, volume = {17}, journal = {Environmental microbiology}, number = {5}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1462-2912}, doi = {10.1111/1462-2920.12577}, pages = {1548 -- 1559}, year = {2015}, abstract = {The biological role of the widespread mycosporine-like amino acids (MAAs) in cyanobacteria is under debate. Here, we have constructed and characterized two mutants impaired in MAA biosynthesis in the bloom-forming cyanobacterium Microcystis aeruginosaPCC 7806. We could identify shinorine as the sole MAA type of the strain, which is exclusively located in the extracellular matrix. Bioinformatic studies as wells as polymerase chain reaction screening revealed that the ability to produce MAAs is sporadically distributed within the genus. Growth experiments and reactive oxygen species quantification with wild-type and mutant strains did not support a role of shinorine in protection against UV or other stress conditions in M.aeruginosaPCC 7806. The shinorine content per dry weight of cells as well as transcription of the mys gene cluster was not significantly elevated in response to UV-A, UV-B or any other stress condition tested. Remarkably, both mutants exhibited pronounced morphological changes compared with the wild type. We observed an increased accumulation and an enhanced hydrophobicity of the extracellular matrix. Our study suggests that MAAs in Microcystis play a negligible role in protection against UV radiation but might be a strain-specific trait involved in extracellular matrix formation and cell-cell interaction.}, language = {en} } @article{HoenickeBlissMoritz2015, author = {H{\"o}nicke, Christiane and Bliss, Peter and Moritz, Robin F. A.}, title = {Effect of density on traffic and velocity on trunk trails of Formica pratensis}, series = {The science of nature}, volume = {102}, journal = {The science of nature}, number = {3-4}, publisher = {Springer}, address = {Heidelberg}, issn = {0028-1042}, doi = {10.1007/s00114-015-1267-6}, pages = {9}, year = {2015}, abstract = {The allocation of large numbers of workers facilitates the swift intake of locally available resources which is essential for ant colony survival. To organise the traffic between nest and food source, the black-meadow ant Formica pratensis establishes permanent trunk trails, which are maintained by the ants. To unravel the ant organisation and potential traffic rules on these trails, we analysed velocity and lane segregation under various densities by experimentally changing feeding regimes. Even under the highest ant densities achieved, we never observed any traffic jams. On the contrary, velocity increased after supplementary feeding despite an enhanced density. Furthermore, inbound ants returning to the nest had a higher velocity than those leaving the colony. Whilst at low and medium density the ants used the centre of the trail, they used the full width of the trail at high density. Outbound ants also showed some degree of lane segregation which contributes to traffic organisation.}, language = {en} } @article{HuettlHettrichRiedeletal.2015, author = {H{\"u}ttl, Christine and Hettrich, Cornelia and Riedel, Melanie and Henklein, Petra and Rawel, Harshadrai Manilal and Bier, Frank Fabian}, title = {Development of Peptidyl Lysine Dendrons: 1,3-Dipolar Cycloaddition for Peptide Coupling and Antibody Recognition}, series = {Chemical biology \& drug design}, volume = {85}, journal = {Chemical biology \& drug design}, number = {5}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1747-0277}, doi = {10.1111/cbdd.12444}, pages = {565 -- 573}, year = {2015}, abstract = {A straightforward synthesis strategy to multimerize a peptide mimotopes for antibody B13-DE1 recognition is described based on lysine dendrons as multivalent scaffolds. Lysine dendrons that possess N-terminal alkyne residues at the periphery were quantitative functionalized with azido peptides using click chemistry. The solid-phase peptide synthesis (SPPS) allows preparing the peptide dendron in high purity and establishing the possibility of automation. The presented peptide dendron is a promising candidate as multivalent ligand and was used for antibody B13-DE1 recognition. The binding affinity increases with higher dendron generation without loss of specificity. The analysis of biospecific interaction between the synthesized peptide dendron and the antibody was done via surface plasmon resonance (SPR) technique. The presented results show a promising tool for investigations of antigen-antibody reactions.}, language = {en} } @article{ImholtReilEccardetal.2015, author = {Imholt, Christian and Reil, Daniela and Eccard, Jana and Jacob, Daniela and Hempelmann, Nils and Jacob, Jens}, title = {Quantifying the past and future impact of climate on outbreak patterns of bank voles (Myodes glareolus)}, series = {Pest management science}, volume = {71}, journal = {Pest management science}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1526-498X}, doi = {10.1002/ps.3838}, pages = {166 -- 172}, year = {2015}, abstract = {BACKGROUND Central European outbreak populations of the bank vole (Myodes glareolus Schreber) are known to cause damage in forestry and to transmit the most common type of Hantavirus (Puumala virus, PUUV) to humans. A sound estimation of potential effects of future climate scenarios on population dynamics is a prerequisite for long-term management strategies. Historic abundance time series were used to identify the key weather conditions associated with bank vole abundance, and were extrapolated to future climate scenarios to derive potential long-term changes in bank vole abundance dynamics. RESULTS Classification and regression tree analysis revealed the most relevant weather parameters associated with high and low bank vole abundances. Summer temperatures 2 years prior to trapping had the highest impact on abundance fluctuation. Extrapolation of the identified parameters to future climate conditions revealed an increase in years with high vole abundance. CONCLUSION Key weather patterns associated with vole abundance reflect the importance of superabundant food supply through masting to the occurrence of bank vole outbreaks. Owing to changing climate, these outbreaks are predicted potentially to increase in frequency 3-4-fold by the end of this century. This may negatively affect damage patterns in forestry and the risk of human PUUV infection in the long term. (c) 2014 Society of Chemical Industry}, language = {en} } @article{IonescuBizicIonescuKhalilietal.2015, author = {Ionescu, Danny and Bizic-Ionescu, Mina and Khalili, Arzhang and Malekmohammadi, Reza and Morad, Reza Mohammad and de Beer, Dirk and Grossart, Hans-Peter}, title = {A new tool for long-term studies of POM-bacteria interactions: overcoming the century-old Bottle Effect}, series = {Scientific reports}, volume = {5}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep14706}, pages = {12}, year = {2015}, abstract = {Downward fluxes of particulate organic matter (POM) are the major process for sequestering atmospheric CO2 into aquatic sediments for thousands of years. Budget calculations of the biological carbon pump are heavily based on the ratio between carbon export (sedimentation) and remineralization (release to the atmosphere). Current methodologies determine microbial dynamics on POM using closed vessels, which are strongly biased towards heterotrophy due to rapidly changing water chemistry (Bottle Effect). We developed a flow-through rolling tank for long term studies that continuously maintains POM at near in-situ conditions. There, bacterial communities resembled in-situ communities and greatly differed from those in the closed systems. The active particle-associated community in the flow-through system was stable for days, contrary to hours previously reported for closed incubations. In contrast to enhanced respiration rates, the decrease in photosynthetic rates on particles throughout the incubation was much slower in our system than in traditional ones. These results call for reevaluating experimentally-derived carbon fluxes estimated using traditional methods.}, language = {en} } @article{IshidaNozakiGrossartetal.2015, author = {Ishida, Seiji and Nozaki, Daiki and Grossart, Hans-Peter and Kagami, Maiko}, title = {Novel basal, fungal lineages from freshwater phytoplankton and lake samples}, series = {Environmental microbiology reports}, volume = {7}, journal = {Environmental microbiology reports}, number = {3}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1758-2229}, doi = {10.1111/1758-2229.12268}, pages = {435 -- 441}, year = {2015}, abstract = {Zoosporic fungal parasites are known to control the extent and development of blooms of numerous phytoplankton species. Despite the obvious importance of ecological interactions between parasitic fungi and their phytoplanktonic hosts, their diversity remains largely unknown due to methodological limitations. Here, a method to genetically analyse fungi directly from single, infected colonies of the phytoplanktonic host was applied to field samples of large diatom species from mesotrophic Lake Biwa and eutrophic Lake Inba, Japan. Although previous research on interaction between lacustrine fungi and large phytoplankton has mainly focused on the role of parasitic Chytridiomycota, our results revealed that fungi attached to large diatoms included not only members of Chytridiomycota, but also members of Aphelida, Cryptomycota and yeast. The fungi belonging to Chytridiomycota and Aphelida form novel, basal lineages. Environmental clone libraries also support the occurrence of these lineages in Japanese lakes. The presented method enables us to better characterize individual fungal specimens on phytoplankton, and thus facilitate and improve the investigation of ecological relationships between fungi and phytoplankton in aquatic ecosystems.}, language = {en} } @article{JetzschmannJagerszkiDechtriratetal.2015, author = {Jetzschmann, Katharina J. and Jagerszki, Gyula and Dechtrirat, Decha and Yarman, Aysu and Gajovic-Eichelmann, Nenad and Gilsing, Hans-Detlev and Schulz, Burkhard and Gyurcsanyi, Robert E. and Scheller, Frieder W.}, title = {Vectorially Imprinted Hybrid Nanofilm for Acetylcholinesterase Recognition}, series = {Advanced functional materials}, volume = {25}, journal = {Advanced functional materials}, number = {32}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1616-301X}, doi = {10.1002/adfm.201501900}, pages = {5178 -- 5183}, year = {2015}, abstract = {Effective recognition of enzymatically active tetrameric acetylcholinesterase (AChE) is accomplished by a hybrid nanofilm composed of a propidium-terminated self-assembled monolayer (Prop-SAM) which binds AChE via its peripheral anionic site (PAS) and an ultrathin electrosynthesized molecularly imprinted polymer (MIP) cover layer of a novel carboxylate-modified derivative of 3,4-propylenedioxythiophene. The rebinding of the AChE to the MIP/Prop-SAM nanofilm covered electrode is detected by measuring in situ the enzymatic activity. The oxidative current of the released thiocholine is dependent on the AChE concentration from approximate to 0.04 x 10(-6) to 0.4 x 10(-6)m. An imprinting factor of 9.9 is obtained for the hybrid MIP, which is among the best values reported for protein imprinting. The dissociation constant characterizing the strength of the MIP-AChE binding is 4.2 x 10(-7)m indicating the dominant role of the PAS-Prop-SAM interaction, while the benefit of the MIP nanofilm covering the Prop-SAM layer is the effective suppression of the cross-reactivity toward competing proteins as compared with the Prop-SAM. The threefold selectivity gain provided by i) the shape-specific MIP filter, ii) the propidium-SAM, iii) signal generation only by the AChE bound to the nanofilm shows promise for assessing AChE activity levels in cerebrospinal fluid.}, language = {en} } @phdthesis{Jin2015, author = {Jin, Chenyu}, title = {Theoretical and experimental study of capillary effect on melting}, pages = {97}, year = {2015}, language = {en} } @article{JohnsonRammKappeletal.2015, author = {Johnson, Kim L. and Ramm, Sascha and Kappel, Christian and Ward, Sally and Leyser, Ottoline and Sakamoto, Tomoaki and Kurata, Tetsuya and Bevan, Michael W. and Lenhard, Michael}, title = {The Tinkerbell (Tink) Mutation Identifies the Dual-Specificity MAPK Phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) as a Novel Regulator of Organ Size in Arabidopsis}, series = {PLoS one}, volume = {10}, journal = {PLoS one}, number = {7}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0131103}, pages = {17}, year = {2015}, abstract = {Mitogen-activated dual-specificity MAPK phosphatases are important negative regulators in the MAPK signalling pathways responsible for many essential processes in plants. In a screen for mutants with reduced organ size we have identified a mutation in the active site of the dual-specificity MAPK phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) that we named tinkerbell (tink) due to its small size. Analysis of the tink mutant indicates that IBR5 acts as a novel regulator of organ size that changes the rate of growth in petals and leaves. Organ size and shape regulation by IBR5 acts independently of the KLU growth-regulatory pathway. Microarray analysis of tink/ibr5-6 mutants identified a likely role for this phosphatase in male gametophyte development. We show that IBR5 may influence the size and shape of petals through auxin and TCP growth regulatory pathways.}, language = {en} } @article{JonesGonzalezFortesConnelletal.2015, author = {Jones, Eppie R. and Gonz{\´a}lez-Fortes, Gloria M. and Connell, Sarah and Siska, Veronika and Eriksson, Anders and Martiniano, Rui and McLaughlin, Russell L. and Llorente, Marcos Gallego and Cassidy, Lara M. and Gamba, Cristina and Meshveliani, Tengiz and Bar-Yosef, Ofer and Mueller, Werner and Belfer-Cohen, Anna and Matskevich, Zinovi and Jakeli, Nino and Higham, Thomas F. G. and Currat, Mathias and Lordkipanidze, David and Hofreiter, Michael and Manica, Andrea and Pinhasi, Ron and Bradley, Daniel G.}, title = {Upper Palaeolithic genomes reveal deep roots of modern Eurasians}, series = {Nature Communications}, volume = {6}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/ncomms9912}, pages = {8}, year = {2015}, abstract = {We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic-Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers similar to 45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers similar to 25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe similar to 3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.}, language = {en} } @misc{JonesGonzalezFortesConnelletal.2015, author = {Jones, Eppie R. and Gonz{\´a}lez-Fortes, Gloria M. and Connell, Sarah and Siska, Veronika and Eriksson, Anders and Martiniano, Rui and McLaughlin, Russell L. and Llorente, Marcos Gallego and Cassidy, Lara M. and Gamba, Cristina and Meshveliani, Tengiz and Bar-Yosef, Ofer and M{\"u}ller, Werner and Belfer-Cohen, Anna and Matskevich, Zinovi and Jakeli, Nino and Higham, Thomas F. G. and Currat, Mathias and Lordkipanidze, David and Hofreiter, Michael and Manica, Andrea and Pinhasi, Ron and Bradley, Daniel G.}, title = {Upper Palaeolithic genomes reveal deep roots of modern Eurasians}, series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1334}, issn = {1866-8372}, doi = {10.25932/publishup-43931}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-439317}, pages = {8}, year = {2015}, abstract = {We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic-Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ∼45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ∼25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ∼3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.}, language = {en} }