@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}
}
@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}
}
@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}
}