@article{BadalyanDierichStibaetal.2014, author = {Badalyan, Artavazd and Dierich, Marlen and Stiba, Konstanze and Schwuchow, Viola and Leimk{\"u}hler, Silke and Wollenberger, Ulla}, title = {Electrical wiring of the aldehyde oxidoreductase PaoABC with a polymer containing osmium redox centers}, series = {Biosensors}, volume = {4}, journal = {Biosensors}, number = {4}, publisher = {MDPI}, address = {Basel}, doi = {10.3390/bios4040403}, pages = {403 -- 421}, year = {2014}, abstract = {Biosensors for the detection of benzaldehyde and g-aminobutyric acid (GABA) are reported using aldehyde oxidoreductase PaoABC from Escherichia coli immobilized in a polymer containing bound low potential osmium redox complexes. The electrically connected enzyme already electrooxidizes benzaldehyde at potentials below -0.15 V (vs. Ag|AgCl, 1 M KCl). The pH-dependence of benzaldehyde oxidation can be strongly influenced by the ionic strength. The effect is similar with the soluble osmium redox complex and therefore indicates a clear electrostatic effect on the bioelectrocatalytic efficiency of PaoABC in the osmium containing redox polymer. At lower ionic strength, the pH-optimum is high and can be switched to low pH-values at high ionic strength. This offers biosensing at high and low pH-values. A "reagentless" biosensor has been formed with enzyme wired onto a screen-printed electrode in a flow cell device. The response time to addition of benzaldehyde is 30 s, and the measuring range is between 10-150 µM and the detection limit of 5 µM (signal to noise ratio 3:1) of benzaldehyde. The relative standard deviation in a series (n = 13) for 200 µM benzaldehyde is 1.9\%. For the biosensor, a response to succinic semialdehyde was also identified. Based on this response and the ability to work at high pH a biosensor for GABA is proposed by coimmobilizing GABA-aminotransferase (GABA-T) and PaoABC in the osmium containing redox polymer.}, language = {en} } @article{ReineckeKlemmHeinken2014, author = {Reinecke, Jennifer and Klemm, Gunther and Heinken, Thilo}, title = {Vegetation change and homogenization of species composition in temperate nutrient deficient scots pine forests after 45 yr}, series = {Journal of vegetation science}, volume = {25}, journal = {Journal of vegetation science}, number = {1}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1100-9233}, doi = {10.1111/jvs.12069}, pages = {113 -- 121}, year = {2014}, abstract = {QuestionDoes eutrophication drive vegetation change in pine forests on nutrient deficient sites and thus lead to the homogenization of understorey species composition? LocationForest area (1600ha) in the Lower Spreewald, Brandenburg, Germany. MethodsResurvey of 77 semi-permanent plots after 45yr, including vascular plants, bryophytes and ground lichens. We applied multidimensional ordination of species composition, dissimilarity indices, mean Ellenberg indicator values and the concept of winner/loser species to identify vegetation change between years. Differential responses along a gradient of nutrient availability were analysed on the basis of initial vegetation type, reflecting topsoil N availability of plots. ResultsSpecies composition changed strongly and overall shifted towards higher N and slightly lower light availability. Differences in vegetation change were related to initial vegetation type, with strongest compositional changes in the oligotrophic forest type, but strongest increase of nitrophilous species in the mesotrophic forest type. Despite an overall increase in species number, species composition was homogenized between study years due to the loss of species (mainly ground lichens) on the most oligotrophic sites. ConclusionsThe response to N enrichment is confounded by canopy closure on the N-richest sites and probably by water limitation on N-poorest sites. The relative importance of atmospheric N deposition in the eutrophication effect is difficult to disentangle from natural humus accumulation after historical litter raking. However, the profound differences in species composition between study years across all forest types suggest that atmospheric N deposition contributes to the eutrophication, which drives understorey vegetation change and biotic homogenization in Central European Scots pine forests on nutrient deficient sites.}, language = {en} } @article{NicolasLecourieuxKappeletal.2014, author = {Nicolas, Philippe and Lecourieux, David and Kappel, Christian and Cluzet, Stephanie and Cramer, Grant and Delrot, Serge and Lecourieux, Fatma}, title = {The basic leucine zipper transcription factor abscisic acid responseelement-binding factor 2 is an important transcriptional regulator ofabscisic acid-dependent grape berry ripening processes}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {164}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {1}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.113.231977}, pages = {365 -- 383}, year = {2014}, abstract = {In grape (Vitis vinifera), abscisic acid (ABA) accumulates during fruit ripening and is thought to play a pivotal role in this process, but the molecular basis of this control is poorly understood. This work characterizes ABSCISIC ACID RESPONSE ELEMENT-BINDING FACTOR2 (VvABF2), a grape basic leucine zipper transcription factor belonging to a phylogenetic subgroup previously shown to be involved in ABA and abiotic stress signaling in other plant species. VvABF2 transcripts mainly accumulated in the berry, from the onset of ripening to the harvesting stage, and were up-regulated by ABA. Microarray analysis of transgenic grape cells overexpressing VvABF2 showed that this transcription factor up-regulates and/or modifies existing networks related to ABA responses. In addition, grape cells overexpressing VvABF2 exhibited enhanced responses to ABA treatment compared with control cells. Among the VvABF2-mediated responses highlighted in this study, the synthesis of phenolic compounds and cell wall softening were the most strongly affected. VvABF2 overexpression strongly increased the accumulation of stilbenes that play a role in plant defense and human health (resveratrol and piceid). In addition, the firmness of fruits from tomato (Solanum lycopersicum) plants overexpressing VvABF2 was strongly reduced. These data indicate that VvABF2 is an important transcriptional regulator of ABA-dependent grape berry ripening.}, language = {en} } @article{HeuvelingFrochauxZiomkowskaetal.2014, author = {Heuveling, Johanna and Frochaux, Violette and Ziomkowska, Joanna and Wawrzinek, Robert and Wessig, Pablo and Herrmann, Andreas and Schneider, Erwin}, title = {Conformational changes of the bacterial type I ATP-binding cassette importer HisQMP(2) at distinct steps of the catalytic cycle}, series = {Biochimica et biophysica acta : Biomembranes}, volume = {1838}, journal = {Biochimica et biophysica acta : Biomembranes}, number = {1}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0005-2736}, doi = {10.1016/j.bbamem.2013.08.024}, pages = {106 -- 116}, year = {2014}, abstract = {Prokaryotic solute binding protein-dependent ATP-binding cassette import systems are divided into type land type II and mechanistic differences in the transport process going along with this classification are under intensive investigation. Little is known about the conformational dynamics during the catalytic cycle especially concerning the transmembrane domains. The type I transporter for positively charged amino acids from Salmonella enterica serovar Typhimurium (1A0-Hi5QMP2) was studied by limited proteolysis in detergent solution in the absence and presence of co-factors including ATP, ADP, LAO/arginine, and Mg2+ ions. Stable peptide fragments could be obtained and differentially susceptible cleavage sites were determined by mass spectrometry as Lys-258 in the nucleotide-binding subunit, HisP, and Arg-217/Arg-218 in the transmembrane subunit, HisQ In contrast, transmembrane subunit HisM was gradually degraded but no stable fragment could be detected. HisP and HisQ were equally resistant under pre- and post-hydrolysis conditions in the presence of arginine-loaded solute-binding protein LAO and ATP/ADP. Some protection was also observed with LAO/arginine alone, thus reflecting binding to the transporter in the apo-state and transmembrane signaling. Comparable digestion patterns were obtained with the transporter reconstituted into proteoliposomes and nanodiscs. Fluorescence lifetime spectroscopy confirmed the change of HisQ(R218) to a more apolar microenvironment upon ATP binding and hydrolysis. Limited proteolysis was subsequently used as a tool to study the consequences of mutations on the transport cycle. Together, our data suggest similar conformational changes during the transport cycle as described for the maltose ABC transporter of Escherichia coli, despite distinct structural differences between both systems.}, language = {en} } @article{SchmitzHertzbergLieseTerjungetal.2014, author = {Schmitz-Hertzberg, Sebastian-Tim and Liese, Rick and Terjung, Carsten and Bier, Frank Fabian}, title = {Towards a smart encapsulation system for small-sized electronic devices: a new approach}, series = {International journal of polymer science}, journal = {International journal of polymer science}, publisher = {Hindawi Publishing Corp.}, address = {New York}, issn = {1687-9422}, doi = {10.1155/2014/713603}, pages = {12}, year = {2014}, abstract = {Miniaturized analytical chip devices like biosensors nowadays provide assistance in highly diverse fields of application such as point-of-care diagnostics and industrial bioprocess engineering. However, upon contact with fluids, the sensor requires a protective shell for its electrical components that simultaneously offers controlled access for the target analytes to the measuring units. We therefore developed a capsule that comprises a permeable and a sealed compartment consisting of variable polymers such as biocompatible and biodegradable polylactic acid (PLA) for medical applications or more economical polyvinyl chloride (PVC) and polystyrene (PS) polymers for bioengineering applications. Production of the sealed capsule compartments was performed by heat pressing of polymer pellets placed in individually designable molds. Controlled permeability of the opposite compartments was achieved by inclusion of NaCl inside the polymer matrix during heat pressing, followed by its subsequent release in aqueous solution. Correlating diffusion rates through the so made permeable capsule compartments were quantified for preselected model analytes: glucose, peroxidase, and polystyrene beads of three different diameters (1.4 mu m, 4.2 mu m, and 20.0 mu m). In summary, the presented capsule system turned out to provide sufficient shelter for small-sized electronic devices and gives insight into its potential permeability for defined substances of analytical interest.}, language = {en} } @article{SchellerYarmanBachmannetal.2014, author = {Scheller, Frieder W. and Yarman, Aysu and Bachmann, Till and Hirsch, Thomas and Kubick, Stefan and Renneberg, Reinhard and Schumacher, Soeren and Wollenberger, Ursula and Teller, Carsten and Bier, Frank Fabian}, title = {Future of biosensors: a personal view}, series = {Advances in biochemical engineering, biotechnology}, volume = {140}, journal = {Advances in biochemical engineering, biotechnology}, editor = {Gu, MB and Kim, HS}, publisher = {Springer}, address = {Berlin}, isbn = {978-3-642-54143-8; 978-3-642-54142-1}, issn = {0724-6145}, doi = {10.1007/10_2013_251}, pages = {1 -- 28}, year = {2014}, abstract = {Biosensors representing the technological counterpart of living senses have found routine application in amperometric enzyme electrodes for decentralized blood glucose measurement, interaction analysis by surface plasmon resonance in drug development, and to some extent DNA chips for expression analysis and enzyme polymorphisms. These technologies have already reached a highly advanced level and need minor improvement at most. The dream of the "100-dollar' personal genome may come true in the next few years provided that the technological hurdles of nanopore technology or of polymerase-based single molecule sequencing can be overcome. Tailor-made recognition elements for biosensors including membrane-bound enzymes and receptors will be prepared by cell-free protein synthesis. As alternatives for biological recognition elements, molecularly imprinted polymers (MIPs) have been created. They have the potential to substitute antibodies in biosensors and biochips for the measurement of low-molecular-weight substances, proteins, viruses, and living cells. They are more stable than proteins and can be produced in large amounts by chemical synthesis. Integration of nanomaterials, especially of graphene, could lead to new miniaturized biosensors with high sensitivity and ultrafast response. In the future individual therapy will include genetic profiling of isoenzymes and polymorphic forms of drug-metabolizing enzymes especially of the cytochrome P450 family. For defining the pharmacokinetics including the clearance of a given genotype enzyme electrodes will be a useful tool. For decentralized online patient control or the integration into everyday "consumables' such as drinking water, foods, hygienic articles, clothing, or for control of air conditioners in buildings and cars and swimming pools, a new generation of "autonomous' biosensors will emerge.}, language = {en} } @article{RadchukJohstGroeneveldetal.2014, author = {Radchuk, Viktoriia and Johst, Karin and Groeneveld, J{\"u}rgen and Turlure, Camille and Grimm, Volker and Schtickzelle, Nicolas}, title = {Appropriate resolution in time and model structure for population viability analysis: Insights from a butterfly metapopulation}, series = {: an international journal}, volume = {169}, journal = {: an international journal}, publisher = {Elsevier}, address = {Oxford}, issn = {0006-3207}, doi = {10.1016/j.biocon.2013.12.004}, pages = {345 -- 354}, year = {2014}, abstract = {The importance of a careful choice of the appropriate scale for studying ecological phenomena has been stressed repeatedly. However, issues of spatial scale in metapopulation dynamics received much more attention compared to temporal scale. Moreover, multiple calls were made to carefully choose the appropriate model structure for Population Viability Analysis (PVA). We assessed the effect of using coarser resolution in time and model structure on population dynamics. For this purpose, we compared outcomes of two PVA models differing in their time step: daily individual-based model (dIBM) and yearly stage-based model (ySBM), loaded with empirical data on a well-known metapopulation of the butterfly Boloria eunomia. Both models included the same environmental drivers of population dynamics that were previously identified as being the most important for this species. Under temperature change scenarios, both models yielded the same qualitative scenario ranking, but they quite substantially differed quantitatively with dIBM being more pessimistic in absolute viability measures. We showed that these differences stemmed from inter-individual heterogeneity in dIBM allowing for phenological shifts of individual appearance. We conclude that a finer temporal resolution and an individual-based model structure allow capturing the essential mechanisms necessary to go beyond mere PVA scenario ranking. We encourage researchers to carefully chose the temporal resolution and structure of their model aiming at (1) depicting the processes important for (meta)population dynamics of the species and (2) implementing the environmental change scenarios expected for their study system in the future, using the temporal resolution at which such changes are predicted to operate.}, language = {en} } @article{AttermeyerHornickKayleretal.2014, author = {Attermeyer, Katrin and Hornick, T. and Kayler, Zachary and Bahr, A. and Zwirnmann, E. and Grossart, Hans-Peter and Premke, K.}, title = {Enhanced bacterial decomposition with increasing addition of autochthonous to allochthonous carbon without any effect on bacterial community composition}, series = {Biogeosciences}, volume = {11}, journal = {Biogeosciences}, number = {6}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {1726-4170}, doi = {10.5194/bg-11-1479-2014}, pages = {1479 -- 1489}, year = {2014}, abstract = {Dissolved organic carbon (DOC) concentrations - mainly of terrestrial origin - are increasing worldwide in inland waters. Heterotrophic bacteria are the main consumers of DOC and thus determine DOC temporal dynamics and availability for higher trophic levels. Our aim was to study bacterial carbon (C) turnover with respect to DOC quantity and chemical quality using both allochthonous and autochthonous DOC sources. We incubated a natural bacterial community with allochthonous C (C-13-labeled beech leachate) and increased concentrations and pulses (intermittent occurrence of organic matter input) of autochthonous C (phytoplankton lysate). We then determined bacterial C consumption, activities, and community composition together with the C flow through bacteria using stable C isotopes. The chemical analysis of single sources revealed differences in aromaticity and low-and high-molecular-weight substance fractions (LMWS and HMWS, respectively) between allochthonous and autochthonous C sources. Both DOC sources (allochthonous and autochthonous DOC) were metabolized at a high bacterial growth efficiency (BGE) around 50\%. In treatments with mixed sources, rising concentrations of added autochthonous DOC resulted in a further, significant increase in bacterial DOC consumption of up to 68\% when nutrients were not limiting. This rise was accompanied by a decrease in the humic substance (HS) fraction and an increase in bacterial biomass. Changes in DOC concentration and consumption in mixed treatments did not affect bacterial community composition (BCC), but BCC differed in single vs. mixed incubations. Our study highlights that DOC quantity affects bacterial C consumption but not BCC in nutrient-rich aquatic systems. BCC shifted when a mixture of allochthonous and autochthonous C was provided simultaneously to the bacterial community. Our results indicate that chemical quality rather than source of DOC per se (allochthonous vs. autochthonous) determines bacterial DOC turnover.}, language = {en} } @article{BickelTangGrossart2014, author = {Bickel, Samantha L. and Tang, Kam W. and Grossart, Hans-Peter}, title = {Structure and function of zooplankton-associated bacterial communities in a temperate estuary change more with time than with zooplankton species}, series = {Aquatic microbial ecology : international journal}, volume = {72}, journal = {Aquatic microbial ecology : international journal}, number = {1}, publisher = {Institute of Mathematical Statistics}, address = {Oldendorf Luhe}, issn = {0948-3055}, doi = {10.3354/ame01676}, pages = {1 -- 15}, year = {2014}, abstract = {Zooplankton support distinct bacterial communities in high concentrations relative to the surrounding water, but little is known about how the compositions and functionalities of these bacterial communities change through time in relation to environmental conditions. We conducted a year-long field study of bacterial communities associated with common zooplankton groups as well as free-living bacterial communities in the York River, a tributary of Chesapeake Bay. Bacterial community genetic fingerprints and their carbon substrate usage were examined by denaturing gradient gel electrophoresis (DGGE) of amplified 16S rDNA and by Biolog EcoPlates, respectively. Zooplankton-associated communities were genetically distinct from free-living bacterial communities but utilized a similar array of carbon substrates. On average, bacteria associated with different zooplankton groups were genetically more similar to each other within each month (65.4\% similarity) than to bacterial communities of the same zooplankton group from different months (28 to 30\% similarity), which suggests the importance of ambient environmental conditions in shaping resident zooplankton-associated bacterial communities. Monthly changes in carbon substrate utilization were less variable for zooplankton-associated bacteria than for free-living bacteria, suggesting that the zooplankton microhabitat is more stable than the surrounding water and supports specific bacterial groups in the otherwise unfavorable conditions in the water column.}, language = {en} } @article{JoppSchefflerHermanussen2014, author = {Jopp, Eilin and Scheffler, Christiane and Hermanussen, Michael}, title = {Prevention and anthropology}, series = {Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft f{\"u}r Anthropologie}, volume = {71}, journal = {Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft f{\"u}r Anthropologie}, number = {1-2}, publisher = {Schweizerbart}, address = {Stuttgart}, issn = {0003-5548}, doi = {10.1127/0003-5548/2014/0384}, pages = {135 -- 141}, year = {2014}, abstract = {Screening is an important issue in medicine and is used to early identify unrecognised diseases in persons who are apparently in good health. Screening strongly relies on the concept of "normal values". Normal values are defined as values that are frequently observed in a population and usually range within certain statistical limits. Screening for obesity should start early as the prevalence of obesity consolidates already at early school age. Though widely practiced, measuring BMI is not the ultimate solution for detecting obesity. Children with high BMI may be "robust" in skeletal dimensions. Assessing skeletal robustness and in particularly assessing developmental tempo in adolescents are also important issues in health screening. Yet, in spite of the necessity of screening investigations, appropriate reference values are often missing. Meanwhile, new concepts of growth diagrams have been developed. Stage line diagrams are useful for tracking developmental processes over time. Functional data analyses have efficiently been used for analysing longitudinal growth in height and assessing the tempo of maturation. Convenient low-cost statistics have also been developed for generating synthetic national references.}, language = {en} } @article{AzumaKuekenshoenerMaetal.2014, author = {Azuma, Yusuke and Kuekenshoener, Tim and Ma, Guangyong and Yasunaga, Jun-ichiro and Imanishi, Miki and Tanaka, Gen and Nakase, Ikuhiko and Maruno, Takahiro and Kobayashi, Yuji and Arndt, Katja Maren and Matsuoka, Masao and Futaki, Shiroh}, title = {Controlling leucine-zipper partner recognition in cells through modification of a-g interactions}, series = {Chemical communications}, volume = {50}, journal = {Chemical communications}, number = {48}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1359-7345}, doi = {10.1039/c4cc00555d}, pages = {6364 -- 6367}, year = {2014}, abstract = {By focusing on the a-g interactions, successful design and selection were accomplished to obtain a leucine-zipper segment that discriminates the appropriate partner over another that provides very similar patterns of electrostatic interactions.}, language = {en} } @article{MayerUciechowskiMeyeretal.2014, author = {Mayer, Lena S. and Uciechowski, Peter and Meyer, S{\"o}ren and Schwerdtle, Tanja and Rink, Lothar and Haase, Hajo}, title = {Differential impact of zinc deficiency on phagocytosis, oxidative burst, and production of pro-inflammatory cytokines by human monocytes}, series = {Metallomics : integrated biometal science}, volume = {6}, journal = {Metallomics : integrated biometal science}, number = {7}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1756-5901}, doi = {10.1039/c4mt00051j}, pages = {1288 -- 1295}, year = {2014}, language = {en} } @article{PajoroMadrigalMuinoetal.2014, author = {Pajoro, Alice and Madrigal, Pedro and Muino, Jose M. and Tomas Matus, Jose and Jin, Jian and Mecchia, Martin A. and Debernardi, Juan M. and Palatnik, Javier F. and Balazadeh, Salma and Arif, Muhammad and Wellmer, Frank and Krajewski, Pawel and Riechmann, Jose-Luis and Angenent, Gerco C. and Kaufmann, Kerstin}, title = {Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development}, series = {Genome biology : biology for the post-genomic era}, volume = {15}, journal = {Genome biology : biology for the post-genomic era}, publisher = {BioMed Central}, address = {London}, issn = {1465-6906}, doi = {10.1186/gb-2014-15-3-r41}, pages = {18}, year = {2014}, abstract = {Background: Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood. Results: We characterized the relationship of chromatin accessibility, gene expression, and DNA binding of two MADS-domain proteins at different stages of Arabidopsis flower development. Dynamic changes in APETALA1 and SEPALLATA3 DNA binding correlated with changes in gene expression, and many of the target genes could be associated with the developmental stage in which they are transcriptionally controlled. We also observe dynamic changes in chromatin accessibility during flower development. Remarkably, DNA binding of APETALA1 and SEPALLATA3 is largely independent of the accessibility status of their binding regions and it can precede increases in DNA accessibility. These results suggest that APETALA1 and SEPALLATA3 may modulate chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes. Conclusions: Our findings indicate that different homeotic factors regulate partly overlapping, yet also distinctive sets of target genes in a partly stage-specific fashion. By combining the information from DNA-binding and gene expression data, we are able to propose models of stage-specific regulatory interactions, thereby addressing dynamics of regulatory networks throughout flower development. Furthermore, MADS-domain TFs may regulate gene expression by alternative strategies, one of which is modulation of chromatin accessibility.}, language = {en} } @article{KoehlerLutherMeyeretal.2014, author = {K{\"o}hler, Yvonne and Luther, Eva Maria and Meyer, S{\"o}ren and Schwerdtle, Tanja and Dringen, Ralf}, title = {Uptake and toxicity of arsenite and arsenate in cultured brain astrocytes}, series = {Journal of trace elements in medicine and biology}, volume = {28}, journal = {Journal of trace elements in medicine and biology}, number = {3}, publisher = {Elsevier}, address = {Jena}, issn = {0946-672X}, doi = {10.1016/j.jtemb.2014.04.007}, pages = {328 -- 337}, year = {2014}, abstract = {Inorganic arsenicals are environmental toxins that have been connected with neuropathies and impaired cognitive functions. To investigate whether such substances accumulate in brain astrocytes and affect their viability and glutathione metabolism, we have exposed cultured primary astrocytes to arsenite or arsenate. Both arsenicals compromised the cell viability of astrocytes in a time- and concentration-dependent manner. However, the early onset of cell toxicity in arsenite-treated astrocytes revealed the higher toxic potential of arsenite compared with arsenate. The concentrations of arsenite and arsenate that caused within 24 h half-maximal release of the cytosolic enzyme lactate dehydrogenase were around 0.3 mM and 10 mM, respectively. The cellular arsenic contents of astrocytes increased rapidly upon exposure to arsenite or arsenate and reached after 4 h of incubation almost constant steady state levels. These levels were about 3-times higher in astrocytes that had been exposed to a given concentration of arsenite compared with the respective arsenate condition. Analysis of the intracellular arsenic species revealed that almost exclusively arsenite was present in viable astrocytes that had been exposed to either arsenate or arsenite. The emerging toxicity of arsenite 4 h after exposure was accompanied by a loss in cellular total glutathione and by an increase in the cellular glutathione disulfide content. These data suggest that the high arsenite content of astrocytes that had been exposed to inorganic arsenicals causes an increase in the ratio of glutathione disulfide to glutathione which contributes to the toxic potential of these substances.}, language = {en} } @article{SchulzeBuchwaldHeinken2014, author = {Schulze, Kiowa Alraune and Buchwald, Rainer and Heinken, Thilo}, title = {Epizoochory via the hooves - the European bison (Bison bonasus L.) as a dispersal agent of seeds in an open-forest-mosaic}, series = {Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft}, journal = {Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft}, number = {34}, publisher = {Floristisch-Soziologische Arbeitsgemeinschaft}, address = {G{\"o}ttingen}, issn = {0722-494X}, pages = {131 -- 144}, year = {2014}, abstract = {Large herbivores are significant vectors for the long-distance dispersal of seeds in various habitats, both attached to animals (epizoochory) and via gut passage (endozoochory). The majority of studies on epizoochory have examined dispersal in the fur of domesticated ungulates. Studies on wild ungulates are important to understand dispersal processes in many habitats, but rare due to methodological constraints. We studied epizoochory of seeds by European bison in an open-forest-mosaic (nutrient-poor grassland and heathland, mixed forest) in NW Germany, where bison had been introduced for the purpose of nature conservation. At the study site it was possible to apply a method by which hoof material of free-ranging bison was non-invasively collected. We identified a total of 1082 seeds from 32 plant species in the hoof material. The three most abundant species were Polygonum aviculare, Agrostis capillaris and Betula spp. Seed species originated from various habitat types of the study area, while the majority of seeds derived from trampled areas. Compared to the non-dispersed plant species of the study area, dispersed plant species had a higher seed longevity index, suggesting that many seeds were picked up from the soil seed bank. Epizoochory ranking indices of dispersed seed species, classifying the importance of epizoochory, revealed that transport in the fur may be of minor importance for many species, i.e. epizoochory by the hooves turned out to be negatively correlated to epizoochory in the fur. We conclude that European bison disperses a considerable number of seed species through trampling. Further research should consider epizoochory via the hooves and include integrative approaches to understand the different dispersal mechanisms by ungulates and their long-term synergetic effect on plant communities.}, language = {en} } @article{ChenWangWangetal.2014, author = {Chen, Yao and Wang, Guang and Wang, Xiao-yu and Ma, Zheng-lai and Chen, You-peng and Chuai, Manli and von Websky, Karoline and Hocher, Berthold and Yang, Xuesong}, title = {Effects of high salt-exposure on the development of retina and lens in 5.5-Day Chick Embryo}, series = {Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry and pharmacology}, volume = {34}, journal = {Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry and pharmacology}, number = {3}, publisher = {Karger}, address = {Basel}, issn = {1015-8987}, doi = {10.1159/000363044}, pages = {804 -- 817}, year = {2014}, abstract = {Background/Aims: Excess maternal salt intake during pregnancy may alter fetal development. However; our knowledge on how an increased salt intake during pregnancy influences fetal eye development is limited. In this study, we investigated the effects of high salt treatment on the developing eyes in chick embryos, especially focusing on the development of the retina and the lens. Methods: 5.5 day chick embryos were exposed to 280mosm/l (n=17), or 300mosm/l (n=16) NaCl. The treated embryos were then incubated for 96 hours before they were fixed with 4\% paraformaldehyde for H\&E staining, whole mount embryo immunostaining and TUNEL staining. BrdU and PH3 incorporation experiments were performed on the chick embryos after high salt treatment. RT-PCR analyses were conducted from chick retina tissues. Results: We demonstrated that high-salt treatment altered the size of eyes in chick embryos, induced malformation of the eyes and impaired the development of the lens and the retina. We found an impaired expression of Paired box 6 (PAX6) and neuronal cells in the developing retina as revealed by neurofilament immunofluorescent staining. There was a reduction in the number of BrdU-positive cells and PH3-positive cells in the retina, indicating an impaired cell proliferation with high salt treatment. High salt treatment also resulted in an increased number of TUNEL-positive cells in the retina, indicating a higher amount of cell death. RT-PCR data displayed that the expression of the pro-apoptotic molecule nerve growth factor (NGF) in chick retina was increased and CyclinD1 was reduced with high-salt treatment. The size of the lens was reduced and Pax6 expression in the lens was significantly inhibited. High salt treatment was detrimental to the migration of neural crest cells. Conclusion: Taken together; our study demonstrated that high salt exposure of 5.5 day chick embryos led to an impairment of retina and lens development, possibly through interfering with Pax6 expression.}, language = {en} } @article{MeyerSchulzJeibmannetal.2014, author = {Meyer, S{\"o}ren and Schulz, J. and Jeibmann, A. and Taleshi, M. S. and Ebert, Franziska and Francesconi, Kevin A. and Schwerdtle, Tanja}, title = {Arsenic-containing hydrocarbons are toxic in the in vivo model Drosophila melanogaster}, series = {Metallomics : integrated biometal science}, volume = {6}, journal = {Metallomics : integrated biometal science}, number = {11}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1756-5901}, doi = {10.1039/c4mt00249k}, pages = {2010 -- 2014}, year = {2014}, abstract = {Arsenic-containing hydrocarbons (AsHC) constitute one group of arsenolipids that have been identified in seafood. In this first in vivo toxicity study for AsHCs, we show that AsHCs exert toxic effects in Drosophila melanogaster in a concentration range similar to that of arsenite. In contrast to arsenite, however, AsHCs cause developmental toxicity in the late developmental stages of Drosophila melanogaster. This work illustrates the need for a full characterisation of the toxicity of AsHCs in experimental animals to finally assess the risk to human health related to the presence of arsenolipids in seafood.}, language = {en} } @article{RoderHille2014, author = {Roder, Phillip and Hille, Carsten}, title = {ANG-2 for quantitative Na+ determination in living cells by time-resolved fluorescence microscopy}, series = {Photochemical \& photobiological sciences}, volume = {13}, journal = {Photochemical \& photobiological sciences}, number = {12}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1474-905X}, doi = {10.1039/c4pp00061g}, pages = {1699 -- 1710}, year = {2014}, abstract = {Sodium ions (Na+) play an important role in a plethora of cellular processes, which are complex and partly still unexplored. For the investigation of these processes and quantification of intracellular Na+ concentrations ([Na+](i)), two-photon coupled fluorescence lifetime imaging microscopy (2P-FLIM) was performed in the salivary glands of the cockroach Periplaneta americana. For this, the novel Na+-sensitive fluorescent dye Asante NaTRIUM Green-2 (ANG-2) was evaluated, both in vitro and in situ. In this context, absorption coefficients, fluorescence quantum yields and 2P action cross-sections were determined for the first time. ANG-2 was 2P-excitable over a broad spectral range and displayed fluorescence in the visible spectral range. Although the fluorescence decay behaviour of ANG-2 was triexponential in vitro, its analysis indicates a Na+-sensitivity appropriate for recordings in living cells. The Na+-sensitivity was reduced in situ, but the biexponential fluorescence decay behaviour could be successfully analysed in terms of quantitative [Na+](i) recordings. Thus, physiological 2P-FLIM measurements revealed a dopamine-induced [Na+](i) rise in cockroach salivary gland cells, which was dependent on a Na+-K+-2Cl-cotransporter (NKCC) activity. It was concluded that ANG-2 is a promising new sodium indicator applicable for diverse biological systems.}, language = {en} } @article{ZorHeiskanenCavigliaetal.2014, author = {Zor, K. and Heiskanen, A. and Caviglia, Claudia and Vergani, M. and Landini, E. and Shah, F. and Carminati, Marco and Martinez-Serrano, A. and Ramos Moreno, T. and Kokaia, M. and Benayahu, Dafna and Keresztes, Zs. and Papkovsky, D. and Wollenberger, Ursula and Svendsen, W. E. and Dimaki, M. and Ferrari, G. and Raiteri, R. and Sampietro, M. and Dufva, M. and Emneus, Jenny}, title = {A compact multifunctional microfluidic platform for exploring cellular dynamics in real-time using electrochemical detection}, series = {RSC Advances}, volume = {4}, journal = {RSC Advances}, number = {109}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {2046-2069}, doi = {10.1039/c4ra12632g}, pages = {63761 -- 63771}, year = {2014}, abstract = {Downscaling of microfluidic cell culture and detection devices for electrochemical monitoring has mostly focused on miniaturization of the microfluidic chips which are often designed for specific applications and therefore lack functional flexibility. We present a compact microfluidic cell culture and electrochemical analysis platform with in-built fluid handling and detection, enabling complete cell based assays comprising on-line electrode cleaning, sterilization, surface functionalization, cell seeding, cultivation and electrochemical real-time monitoring of cellular dynamics. To demonstrate the versatility and multifunctionality of the platform, we explored amperometric monitoring of intracellular redox activity in yeast (Saccharomyces cerevisiae) and detection of exocytotically released dopamine from rat pheochromocytoma cells (PC12). Electrochemical impedance spectroscopy was used in both applications for monitoring cell sedimentation and adhesion as well as proliferation in the case of PC12 cells. The influence of flow rate on the signal amplitude in the detection of redox metabolism as well as the effect of mechanical stimulation on dopamine release were demonstrated using the programmable fluid handling capability. The here presented platform is aimed at applications utilizing cell based assays, ranging from e.g. monitoring of drug effects in pharmacological studies, characterization of neural stem cell differentiation, and screening of genetically modified microorganisms to environmental monitoring.}, language = {en} } @article{Gonzalez2014, author = {Gonzalez, Javier}, title = {Phylogenetic position of the most endangered Chilean bird: the Masafuera Rayadito (Aphrastura masafuerae; Furnariidae)}, series = {Tropical conservation science}, volume = {7}, journal = {Tropical conservation science}, number = {4}, publisher = {Mongabay.com}, address = {Menlo Park}, issn = {1940-0829}, pages = {677 -- 689}, year = {2014}, abstract = {Masafuera Rayadito (Aphrastura masafuerae; Furnariidae) is a Critically Endangered species endemic to Alejandro Selkirk Island (Juan Fernandez Archipelago, Chile). Categorized as probably extinct in 1980, later estimates, ranging from 140 (in 2002) to 500 individuals (in 2006-2007), showed a fluctuating population size of the species. The grazing of goats and cattle has increased habitat loss for the species. Other threats are lack of nesting sites, introduced species such as feral cats and rats (Rattus rattus and R. norvegicus), and increased populations of natural predators like the Masafuera Hawk. In order to increase the availability of nesting sites, 81 nest boxes were installed in different habitats in 2006, with evidence of use during subsequent breeding seasons. Despite conservation concerns, however, no genetic studies are yet available for this furnariid. This study reports for the first time the levels of genetic divergence of the species, based on nucleotide sequences of the mitochondrial DNA (cytochrome oxidase subunit 1 gene; COI). Aphrastura masafuerae is closely related to a widespread species of furnariid distributed mainly in Chile on the mainland, the Thorn-tailed Rayadito (A. spinicauda). The Masafuera Rayadito diverged from its mainland sister species probably during the Pleistocene 0.57 +/- 0.19 Myr ago. Consistent with mitochondrial and nuclear molecular clocks, the estimated time of the split between A. masafuerae and A. spinicauda is in perfect agreement with the geological origin of the Juan Fernandez Archipelago, which is of volcanic origin. In order to assess genetic variability within the population of this fragile bird, further studies using a multi-locus genetic approach at the population level are necessary.}, language = {en} } @article{IvanovBeninaPetrovetal.2014, author = {Ivanov, Ivan and Benina, Maria and Petrov, Veselin and Gechev, Tsanko S. and Toneva, Valentina}, title = {Metabolic responses of gloxinia perennis to dehydration and rehydration}, series = {COMPTES RENDUS DE L ACADEMIE BULGARE DES SCIENCES}, volume = {67}, journal = {COMPTES RENDUS DE L ACADEMIE BULGARE DES SCIENCES}, number = {12}, publisher = {Publ. House of the Bulgarian Acad. of Sciences}, address = {Sofia}, issn = {1310-1331}, pages = {1657 -- 1662}, year = {2014}, abstract = {Gloxinia perennis is a species from the family Gesneriaceae with little known physiology, particularly in respect to responses to dehydration. G. perennis survived water deprivation for a month and then quickly recovered upon rehydration. The slow loss of water was in contrast with the quick dehydration of other Gesnerian species - Boea hygrometrica, Ramonda serbica, and Haber lea rhodopensis. Furthermore, a significant difference between older and younger leaves of G. perennis was observed. While the relative water content in the early stages of water deprivation was reduced to 65\% in the old leaves, it was not or slightly reduced in the young ones, implying a mechanism that protects specifically the younger leaves from dehydration. Water deprivation induced accumulation of gama-aminobutyric acid and sugars like sucrose and raffinose, but decreased the levels of amino acids such as glycine, leucine, and isoleucine. The levels of these amino acids recovered after rehydration and in some cases like glycine and isoleucine were even higher in rehydrated leaves compared with unstressed controls. We conclude that G.perennis can survive prolonged drought stress but its responses to dehydration are different from the resurrection species from Gesneriaceae. All this makes G. perennis a good model that can be used for comparative genomics and metabolomics of Gesneriads exposed to desiccation.}, language = {en} } @article{AudisioClineSolanoetal.2014, author = {Audisio, Paolo and Cline, Andrew R. and Solano, Emanuela and Mancini, Emiliano and Lamanna, Francesco and Antonini, Gloria and Trizzino, Marco}, title = {A peculiar new genus and species of pollen-beetle (Coleoptera, Nitidulidae) from eastern Africa, with a molecular phylogeny of related Meligethinae}, series = {Systematics and biodiversity}, volume = {12}, journal = {Systematics and biodiversity}, number = {1}, publisher = {Routledge, Taylor \& Francis Group}, address = {Abingdon}, issn = {1477-2000}, doi = {10.1080/14772000.2013.877539}, pages = {77 -- 91}, year = {2014}, language = {en} } @article{FeherLisecRoemischMargletal.2014, author = {Feher, Kristen and Lisec, Jan and Roemisch-Margl, Lilla and Selbig, Joachim and Gierl, Alfons and Piepho, Hans-Peter and Nikoloski, Zoran and Willmitzer, Lothar}, title = {Deducing hybrid performance from parental metabolic profiles of young primary roots of maize by using a multivariate diallel approach}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {1}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0085435}, pages = {9}, year = {2014}, language = {en} } @article{AllanBossdorfDormannetal.2014, author = {Allan, Eric and Bossdorf, Oliver and Dormann, Carsten F. and Prati, Daniel and Gossner, Martin M. and Tscharntke, Teja and Bl{\"u}thgen, Nico and Bellach, Michaela and Birkhofer, Klaus and Boch, Steffen and B{\"o}hm, Stefan and B{\"o}rschig, Carmen and Chatzinotas, Antonis and Christ, Sabina and Daniel, Rolf and Diek{\"o}tter, Tim and Fischer, Christiane and Friedl, Thomas and Glaser, Karin and Hallmann, Christine and Hodac, Ladislav and H{\"o}lzel, Norbert and Jung, Kirsten and Klein, Alexandra-Maria and Klaus, Valentin H. and Kleinebecker, Till and Krauss, Jochen and Lange, Markus and Morris, E. Kathryn and M{\"u}ller, J{\"o}rg and Nacke, Heiko and Pasalic, Esther and Rillig, Matthias C. and Rothenwoehrer, Christoph and Schally, Peter and Scherber, Christoph and Schulze, Waltraud X. and Socher, Stephanie A. and Steckel, Juliane and Steffan-Dewenter, Ingolf and T{\"u}rke, Manfred and Weiner, Christiane N. and Werner, Michael and Westphal, Catrin and Wolters, Volkmar and Wubet, Tesfaye and Gockel, Sonja and Gorke, Martin and Hemp, Andreas and Renner, Swen C. and Sch{\"o}ning, Ingo and Pfeiffer, Simone and K{\"o}nig-Ries, Birgitta and Buscot, Francois and Linsenmair, Karl Eduard and Schulze, Ernst-Detlef and Weisser, Wolfgang W. and Fischer, Markus}, title = {Interannual variation in land-use intensity enhances grassland multidiversity}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {1}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1312213111}, pages = {308 -- 313}, year = {2014}, abstract = {Although temporal heterogeneity is a well-accepted driver of biodiversity, effects of interannual variation in land-use intensity (LUI) have not been addressed yet. Additionally, responses to land use can differ greatly among different organisms; therefore, overall effects of land-use on total local biodiversity are hardly known. To test for effects of LUI (quantified as the combined intensity of fertilization, grazing, and mowing) and interannual variation in LUI (SD in LUI across time), we introduce a unique measure of whole-ecosystem biodiversity, multidiversity. This synthesizes individual diversity measures across up to 49 taxonomic groups of plants, animals, fungi, and bacteria from 150 grasslands. Multidiversity declined with increasing LUI among grasslands, particularly for rarer species and aboveground organisms, whereas common species and belowground groups were less sensitive. However, a high level of interannual variation in LUI increased overall multidiversity at low LUI and was even more beneficial for rarer species because it slowed the rate at which the multidiversity of rare species declined with increasing LUI. In more intensively managed grasslands, the diversity of rarer species was, on average, 18\% of the maximum diversity across all grasslands when LUI was static over time but increased to 31\% of the maximum when LUI changed maximally over time. In addition to decreasing overall LUI, we suggest varying LUI across years as a complementary strategy to promote biodiversity conservation.}, language = {en} } @article{HagenBaumannWagneretal.2014, author = {Hagen, Sven and Baumann, Tobias and Wagner, Hanna J. and Morath, Volker and Kaufmann, Beate and Fischer, Adrian and Bergmann, Stefan and Schindler, Patrick and Arndt, Katja Maren and Mueller, Kristian M.}, title = {Modular adeno-associated virus (rAAV) vectors used for cellular virus-directed enzyme prodrug therapy}, series = {Scientific reports}, volume = {4}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep03759}, pages = {11}, year = {2014}, abstract = {The pre-clinical and clinical development of viral vehicles for gene transfer increased in recent years, and a recombinant adeno-associated virus (rAAV) drug took center stage upon approval in the European Union. However, lack of standardization, inefficient purification methods and complicated retargeting limit general usability. We address these obstacles by fusing rAAV-2 capsids with two modular targeting molecules (DARPin or Affibody) specific for a cancer cell-surface marker (EGFR) while simultaneously including an affinity tag (His-tag) in a surface-exposed loop. Equipping these particles with genes coding for prodrug converting enzymes (thymidine kinase or cytosine deaminase) we demonstrate tumor marker specific transduction and prodrug-dependent apoptosis of cancer cells. Coding terminal and loop modifications in one gene enabled specific and scalable purification. Our genetic parts for viral production adhere to a standardized cloning strategy facilitating rapid prototyping of virus directed enzyme prodrug therapy (VDEPT).}, language = {en} } @article{OtreloCardosoSchwuchowRodriguesetal.2014, author = {Otrelo-Cardoso, Ana Rita and Schwuchow, Viola and Rodrigues, David and Cabrita, Eurico J. and Leimk{\"u}hler, Silke and Romao, Maria Joao and Santos-Silva, Teresa}, title = {Biochemical, stabilization and crystallization studies on a molecular chaperone (PaoD) involved in the maturation of molybdoenzymes}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {1}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0087295}, pages = {9}, year = {2014}, abstract = {Molybdenum and tungsten enzymes require specific chaperones for folding and cofactor insertion. PaoD is the chaperone of the periplasmic aldehyde oxidoreductase PaoABC. It is the last gene in the paoABCD operon in Escherichia coli and its presence is crucial for obtaining mature enzyme. PaoD is an unstable, 35 kDa, protein. Our biochemical studies showed that it is a dimer in solution with a tendency to form large aggregates, especially after freezing/thawing cycles. In order to improve stability, PaoD was thawed in the presence of two ionic liquids [C(4)mim]Cl and [C(2)OHmim]PF6 and no protein precipitation was observed. This allowed protein concentration and crystallization using polyethylene glycol or ammonium sulfate as precipitating agents. Saturation transfer difference - nuclear magnetic resonance (STD-NMR) experiments have also been performed in order to investigate the effect of the ionic liquids in the stabilization process, showing a clear interaction between the acidic ring protons of the cation and, most likely, negatively charged residues at the protein surface. DLS assays also show a reduction of the overall size of the protein aggregates in presence of ionic liquids. Furthermore, cofactor binding studies on PaoD showed that the protein is able to discriminate between molybdenum and tungsten bound to the molybdenum cofactor, since only a Mo-MPT form of the cofactor remained bound to PaoD.}, language = {en} } @article{ArnoldNikoloski2014, author = {Arnold, Anne and Nikoloski, Zoran}, title = {In search for an accurate model of the photosynthetic carbon metabolism}, series = {Mathematics and computers in simulation : transactions of IMACS}, volume = {96}, journal = {Mathematics and computers in simulation : transactions of IMACS}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0378-4754}, doi = {10.1016/j.matcom.2012.03.011}, pages = {171 -- 194}, year = {2014}, abstract = {The photosynthetic carbon metabolism, including the Calvin-Benson cycle, is the primary pathway in C-3-plants, producing starch and sucrose from CO2. Understanding the interplay between regulation and efficiency of this pathway requires the development of mathematical models which would explain the observed dynamics of metabolic transformations. Here, we address this question by casting the existing models of Calvin-Benson cycle and the end-product processes into an analysis framework which not only facilitates the comparison of the different models, but also allows for their ranking with respect to chosen criteria, including stability, sensitivity, robustness and/or compliance with experimental data. The importance of the photosynthetic carbon metabolism for the increase of plant biomass has resulted in many models with various levels of detail. We provide the largest compendium of 15 existing, well-investigated models together with a comprehensive classification as well as a ranking framework to determine the best-performing models for metabolic engineering and planning of in silica experiments. The classification can be additionally used, based on the model structure, as a tool to identify the models which match best the experimental design. The provided ranking is just one alternative to score models and, by changing the weighting factor, this framework also could be applied for selection of other criteria of interest.}, language = {en} } @article{LinHuthBergeretal.2014, author = {Lin, Yue and Huth, Franka and Berger, Uta and Grimm, Volker}, title = {The role of belowground competition and plastic biomass allocation in altering plant mass-density relationships}, series = {Oikos}, volume = {123}, journal = {Oikos}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0030-1299}, doi = {10.1111/j.1600-0706.2013.00921.x}, pages = {248 -- 256}, year = {2014}, language = {en} } @article{GarciaMcMahonGrossartetal.2014, author = {Garcia, Sarahi L. and McMahon, Katherine D. and Grossart, Hans-Peter and Warnecke, Falk}, title = {Successful enrichment of the ubiquitous freshwater acI Actinobacteria}, series = {Environmental microbiology reports}, volume = {6}, journal = {Environmental microbiology reports}, number = {1}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1758-2229}, doi = {10.1111/1758-2229.12104}, pages = {21 -- 27}, year = {2014}, abstract = {Actinobacteria of the acI lineage are often the numerically dominant bacterial phylum in surface freshwaters, where they can account for >50\% of total bacteria. Despite their abundance, there are no described isolates. In an effort to obtain enrichment of these ubiquitous freshwater Actinobacteria, diluted freshwater samples from Lake Grosse Fuchskuhle, Germany, were incubated in 96-well culture plates. With this method, a successful enrichment containing high abundances of a member of the lineage acI was established. Phylogenetic classification showed that the acIActinobacteria of the enrichment belonged to the acI-B2 tribe, which seems to prefer acidic lakes. This enrichment grows to low cell densities and thus the oligotrophic nature of acI-B2 was confirmed.}, language = {en} } @article{MalinovaMahlowAlseekhetal.2014, author = {Malinova, Irina and Mahlow, Sebastian and Alseekh, Saleh and Orawetz, Tom and Fernie, Alisdair R. and Baumann, Otto and Steup, Martin and Fettke, J{\"o}rg}, title = {Double knockout mutants of arabidopsis grown under normal conditions reveal that the plastidial phosphorylase isozyme participates in transitory starch metabolism}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {164}, 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.113.227843}, pages = {907 -- 921}, year = {2014}, abstract = {In leaves of two starch-related single-knockout lines lacking either the cytosolic transglucosidase (also designated as disproportionating enzyme 2, DPE2) or the maltose transporter (MEX1), the activity of the plastidial phosphorylase isozyme (PHS1) is increased. In both mutants, metabolism of starch-derived maltose is impaired but inhibition is effective at different subcellular sites. Two constitutive double knockout mutants were generated (designated as dpe2-1 x phs1a and mex1 x phs1b) both lacking functional PHS1. They reveal that in normally grown plants, the plastidial phosphorylase isozyme participates in transitory starch degradation and that the central carbon metabolism is closely integrated into the entire cell biology. All plants were grown either under continuous illumination or in a light-dark regime. Both double mutants were compromised in growth and, compared with the single knockout plants, possess less average leaf starch when grown in a light-dark regime. Starch and chlorophyll contents decline with leaf age. As revealed by transmission electron microscopy, mesophyll cells degrade chloroplasts, but degradation is not observed in plants grown under continuous illumination. The two double mutants possess similar but not identical phenotypes. When grown in a light-dark regime, mesophyll chloroplasts of dpe2-1 x phs1a contain a single starch granule but under continuous illumination more granules per chloroplast are formed. The other double mutant synthesizes more granules under either growth condition. In continuous light, growth of both double mutants is similar to that of the parental single knockout lines. Metabolite profiles and oligoglucan patterns differ largely in the two double mutants.}, language = {en} } @article{SchmidtSchippersMieuletetal.2014, author = {Schmidt, Romy and Schippers, Jos H. M. and Mieulet, Delphine and Watanabe, Mutsumi and Hoefgen, Rainer and Guiderdoni, Emmanuel and M{\"u}ller-R{\"o}ber, Bernd}, title = {Salt-Rresponsive ERF1 is a negative regulator of grain filling and gibberellin-mediated seedling establishment in rice}, series = {Molecular plant}, volume = {7}, journal = {Molecular plant}, number = {2}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1674-2052}, doi = {10.1093/mp/sst131}, pages = {404 -- 421}, year = {2014}, abstract = {Grain quality is an important agricultural trait that is mainly determined by grain size and composition. Here, we characterize the role of the rice transcription factor (TF) SALT-RESPONSIVE ERF1 (SERF1) during grain development. Through genome-wide expression profiling and chromatin immunoprecipitation, we found that SERF1 directly regulates RICE PROLAMIN-BOX BINDING FACTOR (RPBF), a TF that functions as a positive regulator of grain filling. Loss of SERF1 enhances RPBF expression resulting in larger grains with increased starch content, while SERF1 overexpression represses RPBF resulting in smaller grains. Consistently, during grain filling, starch biosynthesis genes such as GRANULE-BOUND STARCH SYNTHASEI (GBSSI), STARCH SYNTHASEI (SSI), SSIIIa, and ADP-GLUCOSE PYROPHOSPHORYLASE LARGE SUBUNIT2 (AGPL2) are up-regulated in SERF1 knockout grains. Moreover, SERF1 is a direct upstream regulator of GBSSI. In addition, SERF1 negatively regulates germination by controlling RPBF expression, which mediates the gibberellic acid (GA)-induced expression of RICE AMYLASE1A (RAmy1A). Loss of SERF1 results in more rapid seedling establishment, while SERF1 overexpression has the opposite effect. Our study reveals that SERF1 represents a negative regulator of grain filling and seedling establishment by timing the expression of RPBF.}, language = {en} } @article{SalkaWurzbacherGarciaetal.2014, author = {Salka, Ivette and Wurzbacher, Christian and Garcia, Sarahi L. and Labrenz, Matthias and Juergens, Klaus and Grossart, Hans-Peter}, title = {Distribution of acI-Actinorhodopsin genes in Baltic Sea salinity gradients indicates adaptation of facultative freshwater photoheterotrophs to brackish waters}, series = {Environmental microbiology}, volume = {16}, journal = {Environmental microbiology}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1462-2912}, pages = {586 -- 597}, year = {2014}, language = {en} } @article{HeydariBullerWischerhoffetal.2014, author = {Heydari, Esmaeil and Buller, Jens and Wischerhoff, Erik and Laschewsky, Andr{\´e} and D{\"o}ring, Sebastian and Stumpe, Joachim}, title = {Label-Free biosensor based on an all-polymer DFB laser}, series = {Advanced optical materials}, volume = {2}, journal = {Advanced optical materials}, number = {2}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {2195-1071}, doi = {10.1002/adom.201300454}, pages = {137 -- 141}, year = {2014}, language = {en} } @article{BaetenWartonVanCalsteretal.2014, author = {Baeten, Lander and Warton, David I. and Van Calster, Hans and De Frenne, Pieter and Verstraeten, Gorik and Bonte, Dries and Bernhardt-R{\"o}mermann, Markus and Cornelis, Johnny and Decocq, Guillaume and Eriksson, Ove and Hedl, Radim and Heinken, Thilo and Hermy, Martin and Hommel, Patrick and Kirby, Keith J. and Naaf, Tobias and Petrik, Petr and Walther, Gian-Reto and Wulf, Monica and Verheyen, Kris}, title = {A model-based approach to studying changes in compositional heterogeneity}, series = {Methods in ecology and evolution : an official journal of the British Ecological Society}, volume = {5}, journal = {Methods in ecology and evolution : an official journal of the British Ecological Society}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {2041-210X}, pages = {156 -- 164}, year = {2014}, language = {en} } @article{FrenchSimcockRolkeetal.2014, author = {French, Alice S. and Simcock, Kerry L. and Rolke, Daniel and Gartside, Sarah E. and Blenau, Wolfgang and Wright, Geraldine A.}, title = {The role of serotonin in feeding and gut contractions in the honeybee}, series = {Journal of insect physiology}, volume = {61}, journal = {Journal of insect physiology}, publisher = {Elsevier}, address = {Oxford}, issn = {0022-1910}, doi = {10.1016/j.jinsphys.2013.12.005}, pages = {8 -- 15}, year = {2014}, language = {en} } @article{KoesslHechavarriaVossetal.2014, author = {Koessl, M. and Hechavarria, J. C. and Voss, C. and Macias, S. and Mora, E. C. and Vater, Marianne}, title = {Neural maps for target range in the auditory cortex of echolocating bats}, series = {Current opinion in neurobiology : reviews of all advances ; evaluation of key references ; comprehensive listing of papers}, volume = {24}, journal = {Current opinion in neurobiology : reviews of all advances ; evaluation of key references ; comprehensive listing of papers}, publisher = {Elsevier}, address = {London}, issn = {0959-4388}, doi = {10.1016/j.conb.2013.08.016}, pages = {68 -- 75}, year = {2014}, abstract = {Computational brain maps as opposed to maps of receptor surfaces strongly reflect functional neuronal design principles. In echolocating bats, computational maps are established that topographically represent the distance of objects. These target range maps are derived from the temporal delay between emitted call and returning echo and constitute a regular representation of time (chronotopy). Basic features of these maps are innate, and in different bat species the map size and precision varies. An inherent advantage of target range maps is the implementation of mechanisms for lateral inhibition and excitatory feedback. Both can help to focus target ranging depending on the actual echolocation situation. However, these maps are not absolutely necessary for bat echolocation since there are bat species without cortical target-distance maps, which use alternative ensemble computation mechanisms.}, language = {en} } @article{DolgenerFreudenbergerSchlucketal.2014, author = {Dolgener, N. and Freudenberger, L. and Schluck, M. and Schneeweiss, N. and Ibisch, P. L. and Tiedemann, Ralph}, title = {Environmental niche factor analysis (ENFA) relates environmental parameters to abundance and genetic diversity in an endangered amphibian, the fire-bellied-toad (Bombina bombina)}, series = {Conservation genetics}, volume = {15}, journal = {Conservation genetics}, number = {1}, publisher = {Springer}, address = {Dordrecht}, issn = {1566-0621}, doi = {10.1007/s10592-013-0517-4}, pages = {11 -- 21}, year = {2014}, abstract = {Increasing attempts are made to understand the factors responsible for both the demographic and genetic depletion in amphibian populations. Landscape genetics aims at a spatially explicit correlation of genetic population parameters to landscape features. Using data from the endangered fire-bellied toad Bombina bombina in Brandenburg (Northeastern Germany), we performed an environmental niche factor analysis (ENFA), relating demographic (abundance) and genetic (diversity at 17 microsatellite loci and partial sequences of the mitochondrial control region in 434 individuals from 16 populations) parameters to ecological and anthropogenic variables such as temperature, precipitation, soil wetness, water runoff, vegetation density, and road/traffic impact. We found significant correlations between road disturbance and observed heterozygosity and between soil wetness and mitochondrial diversity. As the influences of the environmental variables can differ between different indicators for genetic diversity, population size and abundance data, our ENFA-based landscape genetics approach allows us to put various aspects of long- versus short term effective population size and genetic connectivity into an ecological and spatially explicit context, enabling potentially even forecast assessment under future environmental scenarios.}, language = {en} } @article{GattePicchiWeizIshidaetal.2014, author = {Gatte-Picchi, Douglas and Weiz, Annika and Ishida, Keishi and Hertweck, Christian and Dittmann-Th{\"u}nemann, Elke}, title = {Functional analysis of environmental DNA-derived microviridins provides new insights into the diversity of the tricyclic peptide family}, series = {Applied and environmental microbiology}, volume = {80}, journal = {Applied and environmental microbiology}, number = {4}, publisher = {American Society for Microbiology}, address = {Washington}, issn = {0099-2240}, doi = {10.1128/AEM.03502-13}, pages = {1380 -- 1387}, year = {2014}, abstract = {Microviridins represent a unique family of ribosomally synthesized cage-like depsipeptides from cyanobacteria with potent protease-inhibitory activities. The natural diversity of these peptides is largely unexplored. Here, we describe two methodologies that were developed to functionally characterize cryptic microviridin gene clusters from metagenomic DNA. Environmental samples were collected and enriched from cyanobacterial freshwater blooms of different geographical origins containing predominantly Microcystis sp. Microviridins were produced either directly from fosmid clones or after insertion of environmental DNA-derived gene cassettes into a minimal expression platform in Escherichia coli. Three novel microviridin variants were isolated and tested against different serine-type proteases. The comparison of the bioactivity profiles of the new congeners allows deduction of further structure-function relationships for microviridins. Moreover, this study provides new insights into microviridin processing and gene cluster organization.}, language = {en} } @article{OtreloCardosodaSilvaCorreiaSchwuchowetal.2014, author = {Otrelo-Cardoso, Ana Rita and da Silva Correia, Marcia Alexandra and Schwuchow, Viola and Svergun, Dmitri I. and Romao, Maria Joao and Leimk{\"u}hler, Silke and Santos-Silva, Teresa}, title = {Structural Data on the Periplasmic Aldehyde Oxidoreductase PaoABC from Escherichia coli: SAXS and Preliminary X-ray Crystallography Analysis}, series = {International journal of molecular sciences}, volume = {15}, journal = {International journal of molecular sciences}, number = {2}, publisher = {MDPI}, address = {Basel}, issn = {1422-0067}, doi = {10.3390/ijms15022223}, pages = {2223 -- 2236}, year = {2014}, abstract = {The periplasmic aldehyde oxidoreductase PaoABC from Escherichia coli is a molybdenum enzyme involved in detoxification of aldehydes in the cell. It is an example of an heterotrimeric enzyme of the xanthine oxidase family of enzymes which does not dimerize via its molybdenum cofactor binding domain. In order to structurally characterize PaoABC, X-ray crystallography and small angle X-ray scattering (SAXS) have been carried out. The protein crystallizes in the presence of 20\% (w/v) polyethylene glycol 3350 using the hanging-drop vapour diffusion method. Although crystals were initially twinned, several experiments were done to overcome twinning and lowering the crystallization temperature (293 K to 277 K) was the solution to the problem. The non-twinned crystals used to solve the structure diffract X-rays to beyond 1.80 angstrom and belong to the C2 space group, with cell parameters a = 109.42 angstrom, b = 78.08 angstrom, c = 151.77 angstrom, = 99.77 degrees, and one molecule in the asymmetric unit. A molecular replacement solution was found for each subunit separately, using several proteins as search models. SAXS data of PaoABC were also collected showing that, in solution, the protein is also an heterotrimer.}, language = {en} } @article{BoehmerHartmannLeimkuehler2014, author = {Boehmer, Nadine and Hartmann, Tobias and Leimk{\"u}hler, Silke}, title = {The chaperone FdsC for Rhodobacter capsulatus formate dehydrogenase binds the bis-molybdopterin guanine dinucleotide cofactor}, series = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences}, volume = {588}, journal = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences}, number = {4}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0014-5793}, doi = {10.1016/j.febslet.2013.12.033}, pages = {531 -- 537}, year = {2014}, abstract = {Molybdoenzymes are complex enzymes in which the molybdenum cofactor (Moco) is deeply buried in the enzyme. Most molybdoenzymes contain a specific chaperone for the insertion of Moco. For the formate dehydrogenase FdsGBA from Rhodobacter capsulatus the two chaperones FdsC and FdsD were identified to be essential for enzyme activity, but are not a subunit of the mature enzyme. Here, we purified and characterized the FdsC protein after heterologous expression in Escherichia coli. We were able to copurify FdsC with the bound Moco derivate bis-molybdopterin guanine dinucleotide. This cofactor successfully was used as a source to reconstitute the activity of molybdoenzymes. Structured summary of protein interactions: FdsC and FdsC bind by molecular sieving (View interaction) FdsD binds to RcMobA by surface plasmon resonance (View interaction) FdsC binds to RcMobA by surface plasmon resonance (View interaction) FdsC binds to FdsA by surface plasmon resonance (View interaction)}, language = {en} } @article{KocyanSchuiteman2014, author = {Kocyan, Alexander and Schuiteman, Andre}, title = {New combinations in Aeridinae (Orchidaceae)}, series = {Phytotaxa : a rapid international journal for accelerating the publication of botanical taxonomy}, volume = {161}, journal = {Phytotaxa : a rapid international journal for accelerating the publication of botanical taxonomy}, number = {1}, publisher = {Magnolia Press}, address = {Auckland}, issn = {1179-3155}, pages = {61 -- 85}, year = {2014}, abstract = {New combinations are made in the genera Arachnis, Brachypeza, Dimorphorchis, Grosourdya, Phalaenopsis, Renanthera, Robiquetia, Taeniophyllum, Thrixspermum, Trachoma and Trichoglottis. Two new subgenera are established in Phalaenopsis (subgen. Ornithochilus and Hygrochilus). These changes are proposed to begin aligning the genera recognized in subtribe Aeridinae with results of recent DNA analyses ( published elsewhere).}, language = {en} } @article{NietzscheSchiesslBoernke2014, author = {Nietzsche, Madlen and Schiessl, Ingrid and B{\"o}rnke, Frederik}, title = {The complex becomes more complex: protein-protein interactions of SnRK1 with DUF581 family proteins provide a framework for cell and stimulus type-specific SnRK1 signaling in plants}, series = {Frontiers in plant science}, volume = {5}, journal = {Frontiers in plant science}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2014.00054}, pages = {13}, year = {2014}, abstract = {In plants, SNF1-related kinase (SnRK1) responds to the availability of carbohydrates as well as to environmental stresses by down-regulating ATP consuming biosynthetic processes, while stimulating energy-generating catabolic reactions through gene expression and post-transcriptional regulation. The functional SnRK1 complex is a heterotrimer where the catalytic alpha subunit associates with a regulatory beta subunit and an activating gamma subunit. Several different metabolites as well as the hormone abscisic acid (ABA) have been shown to modulate SnRK1 activity in a cell- and stimulus-type specific manner. It has been proposed that tissue- or stimulus-specific expression of adapter proteins mediating SnRK1 regulation can at least partly explain the differences observed in SnRK1 signaling. By using yeast two-hybrid and in planta bi-molecular fluorescence complementation assays we were able to demonstrate that proteins containing the domain of unknown function (DUF) 581 could interact with both isoforms of the SnRK1 alpha subunit (AKIN10/11) of Arabidopsis. A structure/function analysis suggests that the DUF581 is a generic SnRK1 interaction module and co-expression with DUF581 proteins in plant cells leads to reallocation of the kinase to specific regions within the nucleus. Yeast two-hybrid analyses suggest that SnRK1 and DUF581 proteins share common interaction partners inside the nucleus. The analysis of available microarray data implies that expression of the 19 members of the DUF581 encoding gene family in Arabidopsis is differentially regulated by hormones and environmental cues, indicating specialized functions of individual family members. We hypothesize that DUF581 proteins could act as mediators conferring tissue- and stimulus-type specific differences in SnRK1 regulation.}, language = {en} } @article{BoitGaedke2014, author = {Boit, Alice and Gaedke, Ursula}, title = {Benchmarking successional progress in a quantitative food web}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {2}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0090404}, pages = {25}, year = {2014}, abstract = {Central to ecology and ecosystem management, succession theory aims to mechanistically explain and predict the assembly and development of ecological communities. Yet processes at lower hierarchical levels, e. g. at the species and functional group level, are rarely mechanistically linked to the under-investigated system-level processes which drive changes in ecosystem properties and functioning and are comparable across ecosystems. As a model system for secondary succession, seasonal plankton succession during the growing season is readily observable and largely driven autogenically. We used a long-term dataset from large, deep Lake Constance comprising biomasses, auto-and heterotrophic production, food quality, functional diversity, and mass-balanced food webs of the energy and nutrient flows between functional guilds of plankton and partly fish. Extracting population-and system-level indices from this dataset, we tested current hypotheses about the directionality of successional progress which are rooted in ecosystem theory, the metabolic theory of ecology, quantitative food web theory, thermodynamics, and information theory. Our results indicate that successional progress in Lake Constance is quantifiable, passing through predictable stages. Mean body mass, functional diversity, predator-prey weight ratios, trophic positions, system residence times of carbon and nutrients, and the complexity of the energy flow patterns increased during succession. In contrast, both the mass-specific metabolic activity and the system export decreased, while the succession rate exhibited a bimodal pattern. The weighted connectance introduced here represents a suitable index for assessing the evenness and interconnectedness of energy flows during succession. Diverging from earlier predictions, ascendency and eco-exergy did not increase during succession. Linking aspects of functional diversity to metabolic theory and food web complexity, we reconcile previously disjoint bodies of ecological theory to form a complete picture of successional progress within a pelagic food web. This comprehensive synthesis may be used as a benchmark for quantifying successional progress in other ecosystems.}, language = {en} } @article{SuttonKoerzdoerferCoropceanuetal.2014, author = {Sutton, Christopher and K{\"o}rzd{\"o}rfer, Thomas and Coropceanu, Veaceslav and Bredas, Jean-Luc}, title = {Toward a robust quantum-chemical description of organic mixed-valence systems}, series = {The journal of physical chemistry : C, Nanomaterials and interfaces}, volume = {118}, journal = {The journal of physical chemistry : C, Nanomaterials and interfaces}, number = {8}, publisher = {American Chemical Society}, address = {Washington}, issn = {1932-7447}, doi = {10.1021/jp410461v}, pages = {3925 -- 3934}, year = {2014}, abstract = {The electronic coupling between redox sites in mixed-valence systems has attracted the interest of the chemistry community for a long time. Many computational studies have focused on trying to determine its magnitude as a function of the nature of the redox sites and of the bridge(s) between them. However, in most instances, the quantum-chemical methodologies that have been employed suffer from intrinsic errors that lead to either an overlocalized or an overdelocalized character of the electronic structure. These deficiencies prevent an accurate depiction of the degree of charge (de)localization in the system and, as a result, of the extent of electronic coupling. Here we use nonempirically tuned long-range corrected density functional theory and show that it provides a robust, efficient approach to characterize organic mixed-valence systems. We first demonstrate the performance of this approach via a study of representative Robin-Day class-II (localized) and class-III (delocalized) complexes. We then examine a borderline class-II/class-III complex, which had proven difficult to describe accurately with standard density functional theory and Hartree-Fock methods.}, language = {en} } @article{KlemmeBaeumerEccardetal.2014, author = {Klemme, I. and Baeumer, J. and Eccard, Jana and Ylonen, H.}, title = {Polyandrous females produce sons that are successful at post-copulatory competition}, series = {Journal of evolutionary biology}, volume = {27}, journal = {Journal of evolutionary biology}, number = {3}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1010-061X}, pages = {457 -- 465}, year = {2014}, language = {en} } @article{LumagaCozzolinoKocyanetal.2014, author = {Lumaga, Maria Rosaria Barone and Cozzolino, Salvatore and Kocyan, Alexander and Menale, Bruno and Rudall, Paula J.}, title = {Exine micromorphology and ultrastructure in Neottieae (Epidendroideae, Orchidaceae)}, series = {Plant systematics and evolution}, volume = {300}, journal = {Plant systematics and evolution}, number = {3}, publisher = {Springer}, address = {Wien}, issn = {0378-2697}, doi = {10.1007/s00606-013-0899-2}, pages = {505 -- 515}, year = {2014}, abstract = {The diverse epidendroid orchid tribe Neottieae is characterized by multiple transitions between autotrophy and mycoheterotrophy, allogamous and autogamous mating systems, pollen released as tetrads or monads, and pollen exine tectate or semitectate. We use transmission and scanning electron microscopy on pollen of ten species of Neottieae to investigate whether the differences in pollen aggregation and exine micromorphology and ultrastructure reflect phylogenetic relationships, or whether this variation is subject to ecological constraints. Our results showed that differences in exine micromorphology are mostly concordant with phylogenetic relationships in Neottieae, i.e. an ascending tendency of pollen ornamentation from tectate (Cephalanthera) to semitectate (e.g. Neottia). In contrast, pollen aggregation, when plotted on the most recent phylogeny, shows repeated transitions between monads and tetrads that could be related to ecological constraints. Tetrads are present in species that are nectar rewarding, whereas monads are common in deceptive species. Cephalanthera is characterized by recalcitrant pollen, including the frequent occurrence of collapsed pollen. In this genus, the observed shifts from allogamous to autogamous or cleistogamous mating systems could help to reduce pollen damage caused by exposure to dry habitats.}, language = {en} } @article{MuellerRoeberBalazadeh2014, author = {M{\"u}ller-R{\"o}ber, Bernd and Balazadeh, Salma}, title = {Auxin and its role in plant senescence}, series = {Journal of plant growth regulation}, volume = {33}, journal = {Journal of plant growth regulation}, number = {1}, publisher = {Springer}, address = {New York}, issn = {0721-7595}, doi = {10.1007/s00344-013-9398-5}, pages = {21 -- 33}, year = {2014}, abstract = {Leaf senescence represents a key developmental process through which resources trapped in the photosynthetic organ are degraded in an organized manner and transported away to sustain the growth of other organs including newly forming leaves, roots, seeds, and fruits. The optimal timing of the initiation and progression of senescence are thus prerequisites for controlled plant growth, biomass accumulation, and evolutionary success through seed dispersal. Recent research has uncovered a multitude of regulatory factors including transcription factors, micro-RNAs, protein kinases, and others that constitute the molecular networks that regulate senescence in plants. The timing of senescence is affected by environmental conditions and abiotic or biotic stresses typically trigger a faster senescence. Various phytohormones, including for example ethylene, abscisic acid, and salicylic acid, promote senescence, whereas cytokinins delay it. Recently, several reports have indicated an involvement of auxin in the control of senescence, however, its mode of action and point of interference with senescence control mechanisms remain vaguely defined at present and contrasting observations regarding the effect of auxin on senescence have so far hindered the establishment of a coherent model. Here, we summarize recent studies on auxin-related genes that affect senescence in plants and highlight how these findings might be integrated into current molecular-regulatory models of senescence.}, language = {en} } @article{TrostViCzesnicketal.2014, author = {Trost, Gerda and Vi, Son Lang and Czesnick, Hj{\"o}rdis and Lange, Peggy and Holton, Nick and Giavalisco, Patrick and Zipfel, Cyril and Kappel, Christian and Lenhard, Michael}, title = {Arabidopsis poly(A) polymerase PAPS1 limits founder-cell recruitment to organ primordia and suppresses the salicylic acid-independent immune response downstream of EDS1/PAD4}, series = {The plant journal}, volume = {77}, journal = {The plant journal}, number = {5}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0960-7412}, doi = {10.1111/tpj.12421}, pages = {688 -- 699}, year = {2014}, abstract = {Polyadenylation of pre-mRNAs by poly(A) polymerase (PAPS) is a critical process in eukaryotic gene expression. As found in vertebrates, plant genomes encode several isoforms of canonical nuclear PAPS enzymes. In Arabidopsis thaliana these isoforms are functionally specialized, with PAPS1 affecting both organ growth and immune response, at least in part by the preferential polyadenylation of subsets of pre-mRNAs. Here, we demonstrate that the opposite effects of PAPS1 on leaf and flower growth reflect the different identities of these organs, and identify a role for PAPS1 in the elusive connection between organ identity and growth patterns. The overgrowth of paps1 mutant petals is due to increased recruitment of founder cells into early organ primordia, and suggests that PAPS1 activity plays unique roles in influencing organ growth. By contrast, the leaf phenotype of paps1 mutants is dominated by a constitutive immune response that leads to increased resistance to the biotrophic oomycete Hyaloperonospora arabidopsidis and reflects activation of the salicylic acid-independent signalling pathway downstream of ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1)/PHYTOALEXIN DEFICIENT4 (PAD4). These findings provide an insight into the developmental and physiological basis of the functional specialization amongst plant PAPS isoforms.}, language = {en} } @article{BauerVosKlauschiesetal.2014, author = {Bauer, Barbara and Vos, Matthijs and Klauschies, Toni and Gaedke, Ursula}, title = {Diversity, functional similarity, and top-down control drive synchronization and the reliability of ecosystem function}, series = {The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences}, volume = {183}, journal = {The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences}, number = {3}, publisher = {Univ. of Chicago Press}, address = {Chicago}, issn = {0003-0147}, doi = {10.1086/674906}, pages = {394 -- 409}, year = {2014}, abstract = {The concept that diversity promotes reliability of ecosystem function depends on the pattern that community-level biomass shows lower temporal variability than species-level biomasses. However, this pattern is not universal, as it relies on compensatory or independent species dynamics. When in contrast within--trophic level synchronization occurs, variability of community biomass will approach population-level variability. Current knowledge fails to integrate how species richness, functional distance between species, and the relative importance of predation and competition combine to drive synchronization at different trophic levels. Here we clarify these mechanisms. Intense competition promotes compensatory dynamics in prey, but predators may at the same time increasingly synchronize, under increasing species richness and functional similarity. In contrast, predators and prey both show perfect synchronization under strong top-down control, which is promoted by a combination of low functional distance and high net growth potential of predators. Under such conditions, community-level biomass variability peaks, with major negative consequences for reliability of ecosystem function.}, language = {en} } @article{LehtoAlvarezGaucketal.2014, author = {Lehto, Taavi and Alvarez, Alejandra Castillo and Gauck, Sarah and Gait, Michael J. and Coursindel, Thibault and Wood, Matthew J. A. and Lebleu, Bernard and Boisguerin, Prisca}, title = {Cellular trafficking determines the exon skipping activity of Pip6a-PMO in mdx skeletal and cardiac muscle cells}, series = {Nucleic acids research}, volume = {42}, journal = {Nucleic acids research}, number = {5}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0305-1048}, doi = {10.1093/nar/gkt1220}, pages = {3207 -- 3217}, year = {2014}, abstract = {Cell-penetrating peptide-mediated delivery of phosphorodiamidate morpholino oligomers (PMOs) has shown great promise for exon-skipping therapy of Duchenne Muscular Dystrophy (DMD). Pip6a-PMO, a recently developed conjugate, is particularly efficient in a murine DMD model, although mechanisms responsible for its increased biological activity have not been studied. Here, we evaluate the cellular trafficking and the biological activity of Pip6a-PMO in skeletal muscle cells and primary cardiomyocytes. Our results indicate that Pip6a-PMO is taken up in the skeletal muscle cells by an energy-and caveolae-mediated endocytosis. Interestingly, its cellular distribution is different in undifferentiated and differentiated skeletal muscle cells (vesicular versus nuclear). Likewise, Pip6a-PMO mainly accumulates in cytoplasmic vesicles in primary cardiomyocytes, in which clathrin-mediated endocytosis seems to be the predominant uptake pathway. These differences in cellular trafficking correspond well with the exon-skipping data, with higher activity in myotubes than in myoblasts or cardiomyocytes. These differences in cellular trafficking thus provide a possible mechanistic explanation for the variations in exon-skipping activity and restoration of dystrophin protein in heart muscle compared with skeletal muscle tissues in DMD models. Overall, Pip6a-PMO appears as the most efficient conjugate to date (low nanomolar EC50), even if limitations remain from endosomal escape.}, language = {en} }