TY - THES A1 - Otto, Sebastian T1 - Zulassungskonforme und schnelle massenspektronomische Analytik und präklinische Pharmakokinetik neuer Wirkstoffkandidaten Y1 - 2013 CY - Potsdam ER - TY - JOUR A1 - Mirhaj, M. A1 - Boit, Alice A1 - Razzak, M. A. A1 - Wahab, M. A. T1 - Yield performance comparison between cultures of rice cum prawn (Macrobrachium rosenbergii) and rice cum fish (Cyprinus carpio, Oreochromis niloticus) in North-Eastern Bangladesh JF - Aquaculture : an international journal devoted to research on the exploration and improvement of all aquatic food resources, both floristic and faunistic, from freshwater, brackish and marine environment, related directly or indirectly to human consumption N2 - Integrated and concurrent cultures in rice fields are a promising approach to sustainable farming as the demand for aquacultural and agricultural products continues to grow while land and water resources become increasingly scarce. Prawn farming mainly takes place in coastal regions in improved extensive to semi-intensive aquacultures but a trend to shift the industry to inland regions has been noticed. This inland study in Northern Bangladesh used different input regimes such as fertilizer and additional feed to compare the performance of prawn and fish in flooded paddy fields in regard to water quality measurements. Maximal net yields and body weight gain with minimized negative impact on water quality were found when initial body weights of prawn were optimized. Regarding yield factors in reference to the reduction of costs due to the avoidance of expensive fertilizer/feed and effort, prawn performed better than integrated fish cultures considering a higher market value of prawn with net yields of up to 97 +/- 55 kg ha(-1) for unfed and 151 +/- 61 kg ha(-1) for fed treatments. Rice yields of up to 4.7 +/- 0.1 t ha(-1) for unfed and 4.4 +/- 0.1 t ha(-1) were achieved for fed treatments. The findings suggest that for small scale farmers, prawn cum rice cultures are an economically profitable and comparatively easily manageable alternative to rice cum fish cultures. KW - Rice cum prawn culture KW - Macrobrachium rosenbergii KW - Sustainable aquaculture KW - Polyculture Y1 - 2013 U6 - https://doi.org/10.1016/j.aquaculture.2013.01.038 SN - 0044-8486 VL - 392 IS - 5 SP - 26 EP - 33 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Klingstrom, Tomas A1 - Soldatova, Larissa A1 - Stevens, Robert A1 - Roos, T. Erik A1 - Swertz, Morris A. A1 - Müller, Kristian M. A1 - Kalas, Matus A1 - Lambrix, Patrick A1 - Taussig, Michael J. A1 - Litton, Jan-Eric A1 - Landegren, Ulf A1 - Bongcam-Rudloff, Erik T1 - Workshop on laboratory protocol standards for the molecular methods database JF - New biotechnology N2 - Management of data to produce scientific knowledge is a key challenge for biological research in the 21st century. Emerging high-throughput technologies allow life science researchers to produce big data at speeds and in amounts that were unthinkable just a few years ago. This places high demands on all aspects of the workflow: from data capture (including the experimental constraints of the experiment), analysis and preservation, to peer-reviewed publication of results. Failure to recognise the issues at each level can lead to serious conflicts and mistakes; research may then be compromised as a result of the publication of non-coherent protocols, or the misinterpretation of published data. In this report, we present the results from a workshop that was organised to create an ontological data-modelling framework for Laboratory Protocol Standards for the Molecular Methods Database (MolMeth). The workshop provided a set of short- and long-term goals for the MolMeth database, the most important being the decision to use the established EXACT description of biomedical ontologies as a starting point. Y1 - 2013 U6 - https://doi.org/10.1016/j.nbt.2012.05.019 SN - 1871-6784 VL - 30 IS - 2 SP - 109 EP - 113 PB - Elsevier CY - Amsterdam ER - TY - THES A1 - Frömmel, Ulrike T1 - Vergleichende geno- und phänotypische Charakterisierung von Escherichia coli aus Menschen, Hausschweinen und Wildtieren T1 - Comparative genotypic and phenotypic characterization of Escherichia coli from humans, domestic pigs and wild animals N2 - Escherichia (E.) coli ist als kommensales Bakterium ein wichtiger Bestandteil des Mikrobioms von Säugern, jedoch zudem der häufigste Infektionserreger des Menschen. Entsprechend des Infektionsortes werden intestinal (InPEC) und extraintestinal pathogene E. coli (ExPEC) unterschieden. Die Pathogenese von E. coli-Infektionen ist durch Virulenzfaktoren determiniert, welche von jeweils spezifischen virulenzassoziierten Genen (inVAGs und exVAGs) kodiert werden. Häufig werden exVAGs auch in E. coli-Isolaten aus dem Darm gesunder Wirte nachgewiesen. Dies führte zu der Vermutung, dass exVAGs die intestinale Kolonisierung des Wirtes durch E. coli unterstützen. Das Hauptziel dieser Arbeit bestand darin, das Wissen über den Einfluss von exVAGs auf die Besiedlung und damit die Adhäsion von E. coli an Epithelzellen des Darmtraktes zu erweitern. Die Durchführung einer solch umfassenden E. coli-Populationsstudie erforderte die Etablierung neuer Screeningmethoden. Für die genotypische Charakterisierung wurden mikropartikelbasierte Multiplex-PCR-Assays zum Nachweis von 44 VAGs und der Phylogenie etabliert. Für die phänotypische Charakterisierung wurden Adhäsions- und Zytotoxizitätsassays etabliert. Die Screeningmethoden basieren auf der VideoScan-Technologie, einem automatisierten bildbasierten Multifluoreszenzdetektionssystem. Es wurden 398 E. coli-Isolate aus 13 Wildsäugerarten und 5 Wildvogelarten sowie aus gesunden und harnwegserkrankten Menschen und Hausschweinen charakterisiert. Die Adhäsionsassays hatten zum Ziel, sowohl die Adhäsionsraten als auch die Adhäsionsmuster der 317 nicht hämolytischen Isolate auf 5 Epithelzelllinien zu bestimmen. Die Zytotoxizität der 81 hämolytischen Isolate wurde in Abhängigkeit der Inkubationszeit auf 4 Epithelzelllinien geprüft. In den E. coli-Isolaten wurde eine Reihe von VAGs nachgewiesen. Potentielle InPEC, insbesondere shigatoxinproduzierende und enteropathogene E. coli wurden aus Menschen, Hausschweinen und Wildtieren, vor allem aus Rehen und Feldhasen isoliert. exVAGs wurden mit stark variierender Prävalenz in Isolaten aus allen Arten detektiert. Die größte Anzahl und das breiteste Spektrum an exVAGs wurde in Isolaten aus Urin harnwegserkrankter Menschen, gefolgt von Isolaten aus Dachsen und Rehen nachgewiesen. In Isolaten der phylogenetischen Gruppe B2 wurden mehr exVAGs detektiert als in den Isolaten der phylogenetischen Gruppen A, B1 und D. Die Ergebnisse der Adhäsionsassays zeigten, dass die meisten Isolate zelllinien-, gewebe- oder wirtsspezifisch adhärierten. Ein Drittel der Isolate adhärierte an keiner Zelllinie und nur zwei Isolate adhärierten stark an allen Zelllinien. Grundsätzlich adhärierten mehr Isolate an humanen sowie an intestinalen Zelllinien. Besonders Isolate aus Eichhörnchen und Amseln sowie aus Urin harnwegserkrankter Menschen und Hausschweine waren in der Lage, stark zu adhärieren. Hierbei bildeten die Isolate als Adhäsionsmuster diffuse Adhäsion, Mikrokolonien, Ketten und Agglomerationen. Mittels statistischer Analysen wurden Assoziationen zwischen exVAGs und einer hohen Adhäsionsrate ersichtlich. So war beispielsweise das Vorkommen von afa/dra mit einer höheren Adhäsionsrate auf Caco-2- und 5637-Zellen und von sfa/foc auf IPEC-J2-Zellen assoziiert. Die Ergebnisse der Zytotoxizitätsassays zeigten eine sehr starke und zeitabhängige Zerstörung der Monolayer aller Epithelzelllinien durch die α-Hämolysin-positiven Isolate. Auffallend war die hohe Toxizität hämolytischer Isolate aus Wildtieren gegenüber den humanen Zelllinien. Mit den innerhalb dieser Arbeit entwickelten Screeningmethoden war es möglich, große Mengen an Bakterien zu charakterisieren. Es konnte ein Überblick über die Verbreitung von VAGs in E. coli aus unterschiedlichen Wirten gewonnen werden. Besonders Wildtiere wurden sowohl durch den Nachweis von VAGs in den entsprechenden Isolaten, verbunden mit deren Adhäsionsfähigkeit und ausgeprägter Zytotoxizität als Reservoire pathogener E. coli identifiziert. Ebenso wurde eine zelllinienspezifische Adhäsion von Isolaten mit bestimmten exVAGs deutlich. Damit konnte der mögliche Einfluss von exVAGs auf die intestinale Kolonisierung bestätigt werden. In weiterführenden Arbeiten sind jedoch Expressions- und Funktionsanalysen der entsprechenden Proteine unerlässlich. Es wird anhand der Mikrokoloniebildung durch kommensale E. coli vermutet, dass Adhäsionsmuster und demzufolge Kolonisierungsstrategien, die bisher pathogenen E. coli zugeschrieben wurden, eher als generelle Kolonisierungsstrategien zu betrachten sind. Das E. coli-α-Hämolysin wirkt im Allgemeinen zytotoxisch auf Epithelzellen. Ein in der Fachliteratur diskutierter adhäsionsunterstützender Mechanismus dieses Toxins ist demnach fragwürdig. Innerhalb dieser Arbeit konnte gezeigt werden, dass die entwickelten Screeningmethoden umfassende Analysen einer großen Anzahl an E. coli-Isolaten ermöglichen. N2 - Escherichia (E.) coli is as commensal bacterium an important component of the microbiome of humans and animals, but also the most common infectious agent of human. According to the site of infection intestinal pathogenic (InPEC) and extraintestinal pathogenic E. coli (ExPEC) are differentiated. The pathogenesis of E. coli infections is determined by virulence factors encoded by specific virulence-associated genes (inVAGs and exVAGs). Frequently, exVAGs also be detected in E. coli isolates from the intestine of clinically healthy hosts. This led to the assumption that exVAGs support the intestinal colonization of the host by E. coli. The main objective of this work was to extend the knowledge about the influence of exVAGs on the settlement and adhesion of E. coli to epithelial cells of the intestinal tract. The implementation of such a comprehensive E. coli population study required the establishment of new screening methods. For the genotypic characterization novel microbead-based multiplex PCR assays were established to detect 44 VAGs and phylogeny. For the phenotypic characterization novel in vitro adhesion and cytotoxicity assays were established. These screening methods based on the VideoScan technology, which is an automated image-based multi-fluorescence detection system. There have been characterized 398 E. coli isolates from 13 wild mammal species and 5 species of wild birds as well as from healthy and urinary diseased humans and domestic pigs. The adhesion assays were aimed at both the adhesion rates and the adhesion patterns of the 317 non-hemolytic isolates on intestinal human Caco-2 and porcine IPEC-J2 cells and on human urinary bladder 5637, porcine kidney PK-15 epithelial and HEp-2 cells. The cytotoxicity of 81 hemolytic isolates was compared on the human intestinal epithelium LoVo, and on 5637, IPEC-J2 and PK-15 according to the incubation period. The E. coli isolates showed a series of VAGs. Potential InPEC, especially shigatoxin-producing and enteropathogenic E. coli were isolated from humans, domestic pigs and wild animals, especially from deers (Capreolus capreolus) and hares (Lepus europaeus). exVAGs were detected with widely varying prevalence in E. coli isolates from all species studied. The largest number and the widest range of exVAGs were shown in isolates from urine of urinary diseased patients, followed by isolates from badgers (Meles meles) and deer. Within the isolates of the phylogenetic group B2 more exVAGs were detected as within the isolates of the phylogenetic groups A, B1, and D. Adhesion of the E. coli isolates was specific to cells, host, and tissue, though it was also unspecific. A third of the isolates adhered to any cell line and only two isolates adhered strongly to all cell lines. Basically, more bacteria adhered to human as well as to intestinal cell lines. Especially isolates from squirrels (Sciurus vulgaris) and blackbirds (Turdus merula) and from the urine of urinary diseased humans and domestic pigs were able to strongly adhere. Commensal and pathogenic isolates can adhere in various forms, including diffuse distribution, microcolonies, chains and clumps. Using statistical analyzes associations between the occurrence of some VAGs and a high adhesion rates were seen. Several known adhesins were associated with host cell specific adhesion. Other new potential adhesion genes were described. The results of the cytotoxicity assays showed a very strong and time-dependent degradation of the epithelial cell monolayer of all the α-hemolysin-positive E. coli isolates. The high toxicity of hemolytic isolates from wild animals against the human cell lines was striking. The screening methods enabled both, the genotypic and phenotypic characterisation of large amounts of bacterial isolates. An overview of the distribution of VAGs in E. coli from different hosts was obtained. Especially wild animals were either by the detection of VAGs in the corresponding E. coli isolates, combined with the adhesion and marked cytotoxicity identified as reservoirs of pathogenic E. coli. As well, a cell-line specific adhesion of E. coli isolates with certain exVAGs became clear. Thus, the possible influence on the intestinal colonization of exVAGs could be confirmed. In further work, however, expression and functional analysis of the corresponding proteins are essential. It is suspected on the basis of microcolony formation by commensal E. coli that adhesion patterns and consequently colonization strategies that were previously attributed to pathogenic E. coli, are to be regarded rather as a general colonization strategy. The E. coli α-hemolysin acts generally cytotoxic to epithelial cells. An in the literature discussed adhesion supporting mechanism of this toxin is therefore questionable. Within this work it was shown that the developed screening methods enable comprehensive analyzes of a large number of E. coli isolates. KW - Escherichia coli KW - Adhäsion KW - virulenzassoziierte Gene KW - Hämolyse KW - ExPEC KW - Escherichia coli KW - adhesion KW - virulence-associated genes KW - hemolysis KW - ExPEC Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-69147 ER - TY - THES A1 - Czech, Andreas T1 - Variations in the tRNA pool of mammalian cells upon differentiation and oxidative stress Y1 - 2013 CY - Potsdam ER - TY - JOUR A1 - Scheffler, Christiane T1 - Variable and Invariable Proportions in the Ontogenesis of the Human Face Y1 - 2013 ER - TY - JOUR A1 - Scheffler, Christiane T1 - Variable and invariable proportions in the ontogenesis of the human face JF - The journal of craniofacial surgery : an international journal dedicated to the practice of the art and science of craniofacial surgery ; official publication of the American Association of Pediatric Plastic Surgeons N2 - The human face shows individual features and features that are characteristic for sex and age (the loss of childlike characteristics during maturation). The analysis of facial dimensions is essential for identifying individual features also for forensic issues. The analysis of facial proportions was performed on photogrammetric data from front views of 125 children. The data were pooled from 2 different studies. The children's data were obtained from a longitudinal study and reduced by random generator to ensure the data of adults from a separate cross-sectional study. We applied principal component analysis on photogrammetric facial proportions of 169 individuals: 125 children (63 boys and 62 girls) aged 2-7 years and 44 adults (18 men and 26 women) aged 18-65 years. Facial proportions depend on age and sex. Three components described age: (1) proportions of facial height to head height, (2) proportions that involve endocanthal breadth, and (3) bigonial to bizygonial proportions. Proportions that associate with sex are connected with nasal distances and nasal to bizygonial distances. Twenty-three percent of the variance, particularly variance that are connected with proportions of lower and middle face heights to head height, do neither depend on sex nor on age and thus appear useful for screening purposes, eg, for dysmorphic genetic syndromes. KW - Human face KW - face proportions KW - ontogenesis KW - principal component analysis Y1 - 2013 U6 - https://doi.org/10.1097/SCS.0b013e31826d07a3 SN - 1049-2275 VL - 24 IS - 1 SP - 237 EP - 241 PB - Lippincott Williams & Wilkins CY - Philadelphia ER - TY - JOUR A1 - Neumann-Schaal, Meina A1 - Messerschmidt, Katrin A1 - Grenz, Nicole A1 - Heilmann, Katja T1 - Use of antibody gene library for the isolation of specific single chain antibodies. by ampicillin-antigen conjugates JF - Immunology letters : an international journal providing for the rapid publication of short reports in immunology N2 - Isolation of recombinant antibodies from antibody libraries is commonly performed by different molecular display formats including phage display and ribosome display or different cell-surface display formats. We describe a new method which allows the selection of Escherichia coil cells producing the required single chain antibody by cultivation in presence of ampicillin conjugated to the antigen of interest. The method utilizes the neutralization of the conjugate by the produced single chain antibody which is secreted to the periplasm. Therefore, a new expression system based on the pET26b vector was designed and a library was constructed. The method was successfully established first for the selection of E. coli BL21 Star (DE3) cells expressing a model single chain antibody (anti-fluorescein) by a simple selection assay on LB-agar plates. Using this selection assay, we could identify a new single chain antibody binding biotin by growing E. coil BL21 Star (DE3) containing the library in presence of a biotin-ampicillin conjugate. In contrast to methods as molecular or cell surface display our selection system applies the soluble single chain antibody molecule and thereby avoids undesired effects, e.g. by the phage particle or the yeast fusion protein. By selecting directly in an expression strain, production and characterization of the selected single chain antibody is possible without any further cloning or transformation steps. KW - Single chain antibody KW - Selection method KW - Anti-biotin antibody KW - Naive single chain library Y1 - 2013 U6 - https://doi.org/10.1016/j.imlet.2013.02.005 SN - 0165-2478 VL - 151 IS - 1-2 SP - 39 EP - 43 PB - Elsevier CY - Amsterdam ER - TY - CHAP A1 - Messerschmidt, Katrin A1 - Neumann-Schaal, Meina A1 - Heilmann, Katja T1 - Use of antibody gene library for the isolation of specific single chain antibodies by ampicillinantigen conjugates T2 - The journal of immunology Y1 - 2013 SN - 0022-1767 VL - 190 PB - American Assoc. of Immunologists CY - Bethesda ER - TY - JOUR A1 - Boch, Steffen A1 - Müller, Jörg A1 - Pratil, Daniel A1 - Blaser, Stefan A1 - Fischer, Markus T1 - Up in the tree - the overlooked richness of bryophytes and lichens in Tree Crowns JF - PLoS one N2 - Assessing diversity is among the major tasks in ecology and conservation science. In ecological and conservation studies, epiphytic cryptogams are usually sampled up to accessible heights in forests. Thus, their diversity, especially of canopy specialists, likely is underestimated. If the proportion of those species differs among forest types, plot-based diversity assessments are biased and may result in misleading conservation recommendations. We sampled bryophytes and lichens in 30 forest plots of 20 m x 20 m in three German regions, considering all substrates, and including epiphytic litter fall. First, the sampling of epiphytic species was restricted to the lower 2 m of trees and shrubs. Then, on one representative tree per plot, we additionally recorded epiphytic species in the crown, using tree climbing techniques. Per tree, on average 54% of lichen and 20% of bryophyte species were overlooked if the crown was not been included. After sampling all substrates per plot, including the bark of all shrubs and trees, still 38% of the lichen and 4% of the bryophyte species were overlooked if the tree crown of the sampled tree was not included. The number of overlooked lichen species varied strongly among regions. Furthermore, the number of overlooked bryophyte and lichen species per plot was higher in European beech than in coniferous stands and increased with increasing diameter at breast height of the sampled tree. Thus, our results indicate a bias of comparative studies which might have led to misleading conservation recommendations of plot-based diversity assessments. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0084913 SN - 1932-6203 VL - 8 IS - 12 PB - PLoS CY - San Fransisco ER - TY - THES A1 - Fünfhaus, Anne T1 - Untersuchungen zur molekularen Pathogenese der amerikanischen Faulbrut der Honigbiene Y1 - 2013 CY - Potsdam ER - TY - THES A1 - Reschke, Stefan T1 - Untersuchungen zur Bildung und Modifizierung des Molybdäncofaktors und dessen Einbau in Molybdoenzyme Y1 - 2013 CY - Potsdam ER - TY - THES A1 - Schmidt, Stefanie T1 - Untersuchung des Einflusses der stressregulierten rei1 homologen Proteine auf die Physiologie und den Metabolismus von Arabidopsis thaliana Y1 - 2013 CY - Potsdam ER - TY - JOUR A1 - Scheffler, Christiane T1 - Types of Body Shape JF - Auxology : Studying Human Growth and Development Y1 - 2013 SN - 978-3-510-65278-5 SP - 28 EP - 29 PB - Schweizerbart Science Publishers CY - Stuttgart ER - TY - CHAP A1 - Gracceva, Giulia A1 - Herde, Antje A1 - Koolhaas, J. M. A1 - Palme, R. A1 - Eccard, Jana A1 - Groothuis, T. G. G. T1 - Turning shy on winter's day effects of season on personality and stress response in Microtus arvalis T2 - Integrative and comparative biology Y1 - 2013 SN - 1540-7063 VL - 53 SP - E80 EP - E80 PB - Oxford Univ. Press CY - Cary ER - TY - JOUR A1 - Sivanesan, Arumugam A1 - Ly, Khoa H. A1 - Adamkiewicz, Witold A1 - Stiba, Konstanze A1 - Leimkühler, Silke A1 - Weidinger, Inez M. T1 - Tunable electric field enhancement and redox chemistry on TiO2 Island films via covalent attachment to Ag or Au nanostructures JF - The journal of physical chemistry : C, Nanomaterials and interfaces N2 - Ag-TiO2 and Au-TiO2 hybrid electrodes were designed by covalent attachment of TiO2 nanoparticles to Ag or Au electrodes via an organic linker. The optical and electronic properties of these systems were investigated using the cytochrome b(5) (Cyt b(5)) domain of sulfite oxidase, exclusively attached to the TiO2 surface, as a Raman marker and model redox enzyme. Very strong SERR signals of Cyt b(5) were obtained for Ag-supported systems due to plasmonic field enhancement of Ag. Time-resolved surface-enhanced resonance Raman spectroscopic measurements yielded a remarkably fast electron transfer kinetic (k = 60 s(-1)) of Cyt b(5) to Ag. A much lower Raman intensity was observed for Au-supported systems with undefined and slow redox behavior. We explain this phenomenon on the basis of the different potential of zero charge of the two metals that largely influence the electronic properties of the TiO2 island film. Y1 - 2013 U6 - https://doi.org/10.1021/jp4032578 SN - 1932-7447 VL - 117 IS - 22 SP - 11866 EP - 11872 PB - American Chemical Society CY - Washington ER - TY - THES A1 - Duensing, Nina T1 - Transport processes in the arbuscular mycorrhizal symbiosis T1 - Transportprozesse in der arbuskulären Mykorrhizasymbiose N2 - The nutrient exchange between plant and fungus is the key element of the arbuscular mycorrhizal (AM) symbiosis. The fungus improves the plant’s uptake of mineral nutrients, mainly phosphate, and water, while the plant provides the fungus with photosynthetically assimilated carbohydrates. Still, the knowledge about the mechanisms of the nutrient exchange between the symbiotic partners is very limited. Therefore, transport processes of both, the plant and the fungal partner, are investigated in this study. In order to enhance the understanding of the molecular basis underlying this tight interaction between the roots of Medicago truncatula and the AM fungus Rhizophagus irregularis, genes involved in transport processes of both symbiotic partners are analysed here. The AM-specific regulation and cell-specific expression of potential transporter genes of M. truncatula that were found to be specifically regulated in arbuscule-containing cells and in non-arbusculated cells of mycorrhizal roots was confirmed. A model for the carbon allocation in mycorrhizal roots is suggested, in which carbohydrates are mobilized in non-arbusculated cells and symplastically provided to the arbuscule-containing cells. New insights into the mechanisms of the carbohydrate allocation were gained by the analysis of hexose/H+ symporter MtHxt1 which is regulated in distinct cells of mycorrhizal roots. Metabolite profiling of leaves and roots of a knock-out mutant, hxt1, showed that it indeed does have an impact on the carbohydrate balance in the course of the symbiosis throughout the whole plant, and on the interaction with the fungal partner. The primary metabolite profile of M. truncatula was shown to be altered significantly in response to mycorrhizal colonization. Additionally, molecular mechanisms determining the progress of the interaction in the fungal partner of the AM symbiosis were investigated. The R. irregularis transcriptome in planta and in extraradical tissues gave new insight into genes that are differentially expressed in these two fungal tissues. Over 3200 fungal transcripts with a significantly altered expression level in laser capture microdissection-collected arbuscules compared to extraradical tissues were identified. Among them, six previously unknown specifically regulated potential transporter genes were found. These are likely to play a role in the nutrient exchange between plant and fungus. While the substrates of three potential MFS transporters are as yet unknown, two potential sugar transporters are might play a role in the carbohydrate flow towards the fungal partner. In summary, this study provides new insights into transport processes between plant and fungus in the course of the AM symbiosis, analysing M. truncatula on the transcript and metabolite level, and provides a dataset of the R. irregularis transcriptome in planta, providing a high amount of new information for future works. N2 - In der arbuskulären Mykorrhiza (AM) Symbiose werden die Wurzeln fast aller Landpflanzen von Pilzen der Abteilung Glomeromycota besiedelt. Der Pilz erleichtert der Pflanze die Aufnahme von Mineralien, hauptsächlich Phosphat, und Wasser. Im Gegenzug versorgt die Pflanze ihn mit Photoassimilaten. Trotz der zentralen Bedeutung der Austauschmechanismen zwischen Pilz und Pflanze ist nur wenig darüber bekannt. Um die molekularen Grundlagen der Interaktion zwischen den Wurzeln der Leguminose Medicago truncatula und dem arbuskulären Mykorrhizapilz Rhizophagus irregularis besser zu verstehen, werden hier die Transportprozesse, die zwischen den Symbiosepartnern ablaufen, näher untersucht. Die zellspezifische Regulation der Transkription potentieller M. truncatula Transporter Gene in arbuskelhaltigen und nicht-arbuskelhaltigen Zellen mykorrhizierter Wurzeln wird bestätigt. Ein Modell zur möglichen Verteilung von Kohlenhydraten in mykorrhizierten Wurzeln, nach dem Zucker in nicht-arbuskelhaltigen Zellen mobilisiert und symplastisch an arbuskelhaltige Zellen abgegeben werden, wird vorgestellt. Die Analyse eines Mykorrhiza-induzierten Hexose/H+ Symporter Gens, MtHxt1, liefert neue Einsichten in die Mechanismen der Kohlenhydratverteilung in mykorrhizierten Pflanzen. Metabolitanalysen von Wurzeln und Blättern einer knock-out Mutante dieses Gens zeigen dessen Einfluss auf den Kohlenhydrathaushalt der ganzen Pflanze und auf die Interaktion mit dem Pilz. Die Metabolitzusammensetzung von M. truncatula wird durch die Mykorrhiza Symbiose signifikant beeinflusst. Darüber hinaus werden durch Transkriptomanalysen die molekularen Grundlagen der AM Symbiose auf der Seite des Pilzes analysiert. Arbuskeln wurden mittels Laser Capture Mikrodissektion direkt aus mykorrhizierten Wurzeln isoliert. Über 3200 pilzliche Transkripte weisen in diesen Arbuskeln im Vergleich zu extraradikalen Geweben ein deutlich verändertes Expressionslevel auf. Unter diesen Transkripten sind auch sechs zuvor unbekannte Gene, die für potentielle Transporter codieren und mit großer Wahrscheinlichkeit eine Rolle im Nährstoffaustausch zwischen Pilz und Pflanze spielen. Während die Substrate von drei potentiellen MFS Transportern noch unbekannt sind, spielen zwei potentiellen Zuckertransporter möglicherweise eine Rolle im Transport von Kohlenhydraten in Richtung des Pilzes. Zusammengefasst bietet diese Arbeit neue Einsichten in Transportprozesse zwischen Pilz und Pflanze im Laufe der AM Symbiose. M. truncatula Transkript- und Metabolitlevel werden analysiert und die Transkriptomanalyse von R. irregularis liefert einen umfassenden Datensatz mit einer großen Menge an Informationen zu der noch unzureichend erforschten pilzlichen Seite der Symbiose für folgende Arbeiten. KW - arbuskuläre Mykorrhizasymbiose KW - Zuckertransporter KW - Medicago truncatula KW - Rhizophagus irregularis KW - Transkriptom Sequenzierung KW - arbuscular mycorrhizal symbiosis KW - sugar transporter KW - Medicago truncatula KW - Rhizophagus irregularis KW - transcriptome sequencing Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-68210 ER - TY - JOUR A1 - Messerschmidt, Katrin A1 - Heilmann, Katja T1 - Toxin-antigen conjugates as selection tools for antibody producing cells JF - Journal of immunological methods N2 - The generation of antibodies with designated specificity requires cost-intensive and time-consuming screening procedures. Here we present a new method by which hybridoma cells can be selected based on the specificity of the produced antibody by the use of antigen-toxin-conjugates thus eliminating the need of a screening procedure. Initial experiments were done with methotrexate as low molecular weight toxin and fluorescein as model antigen. Methotrexate and a methotrexate-fluorescein conjugate were characterized regarding their toxicity. Afterwards the effect of the fluorescein-specific antibody B13-DE1 on the toxicity of the methotrexate-fluorescein conjugate was determined. Finally, first results showed that hybridoma cells that produce fluorescein specific antibodies are able to grow in the presence of fluorescein-toxin-conjugates. KW - Monoclonal antibody KW - Hybridoma technology KW - Selection of antibody producing cells Y1 - 2013 U6 - https://doi.org/10.1016/j.jim.2012.10.010 SN - 0022-1759 VL - 387 IS - 1-2 SP - 167 EP - 172 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Leunert, Franziska A1 - Grossart, Hans-Peter A1 - Gerhardt, Volkmar A1 - Eckert, Werner T1 - Toxicant induced changes on delayed fluorescence decay kinetics of cyanobacteria and green algae a rapid and sensitive biotest JF - PLoS one N2 - Algal tests have developed into routine tools for testing toxicity of pollutants in aquatic environments. Meanwhile, in addition to algal growth rates, an increasing number of fluorescence based methods are used for rapid and sensitive toxicity measures. The present study stresses the suitability of delayed fluorescence (DF) as a promising parameter for biotests. DF is based on the recombination fluorescence at the reaction centre of photosystem II, which is emitted only by photosynthetically active cells. We analyzed the effects of three chemicals (3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), 3,5 Dichlorophenol (3,5 DCP) and copper) on the shape of the DF decay kinetics for potential use in phytoplankton toxicity tests. The short incubation tests were done with four phytoplankton species, with special emphasis on the cyanobacterium Microcystis aeruginosa. All species exhibited a high sensitivity to DCMU, but cyanobacteria were more affected by copper and less by 3,5 DCP than the tested green algae. Analyses of changes in the DF decay curve in response to the added chemicals indicated the feasibility of the DF decay approach as a rapid and sensitive testing tool. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0063127 SN - 1932-6203 VL - 8 IS - 4 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Becher, Matthias A. A1 - Osborne, Juliet L. A1 - Thorbek, Pernille A1 - Kennedy, Peter J. A1 - Grimm, Volker T1 - Towards a systems approach for understanding honeybee decline - a stocktaking and synthesis of existing models JF - Journal of applied ecology : an official journal of the British Ecological Society N2 - 1. The health of managed and wild honeybee colonies appears to have declined substantially in Europe and the United States over the last decade. Sustainability of honeybee colonies is important not only for honey production, but also for pollination of crops and wild plants alongside other insect pollinators. A combination of causal factors, including parasites, pathogens, land use changes and pesticide usage, are cited as responsible for the increased colony mortality. 2. However, despite detailed knowledge of the behaviour of honeybees and their colonies, there are no suitable tools to explore the resilience mechanisms of this complex system under stress. Empirically testing all combinations of stressors in a systematic fashion is not feasible. We therefore suggest a cross-level systems approach, based on mechanistic modelling, to investigate the impacts of (and interactions between) colony and land management. 3. We review existing honeybee models that are relevant to examining the effects of different stressors on colony growth and survival. Most of these models describe honeybee colony dynamics, foraging behaviour or honeybee - varroa mite - virus interactions. 4. We found that many, but not all, processes within honeybee colonies, epidemiology and foraging are well understood and described in the models, but there is no model that couples in-hive dynamics and pathology with foraging dynamics in realistic landscapes. 5. Synthesis and applications. We describe how a new integrated model could be built to simulate multifactorial impacts on the honeybee colony system, using building blocks from the reviewed models. The development of such a tool would not only highlight empirical research priorities but also provide an important forecasting tool for policy makers and beekeepers, and we list examples of relevant applications to bee disease and landscape management decisions. KW - Apis mellifera KW - colony decline KW - feedbacks KW - integrated model KW - multiple stressors KW - predictive systems ecology KW - review Y1 - 2013 U6 - https://doi.org/10.1111/1365-2664.12112 SN - 0021-8901 VL - 50 IS - 4 SP - 868 EP - 880 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Wissel, Jörg A1 - Manack, Aubrey A1 - Brainin, Michael T1 - Toward an epidemiology of poststroke spasticity JF - Neurology : official journal of the American Academy of Neurology N2 - Poststroke spasticity (PSS)-related disability is emerging as a significant health issue for stroke survivors. There is a need for predictors and early identification of PSS in order to minimize complications and maladaptation from spasticity. Reviewing the literature on stroke and upper motor neuron syndrome, spasticity, contracture, and increased muscle tone measured with the Modified Ashworth Scale and the Tone Assessment Scale provided data on the dynamic time course of PSS. Prevalence estimates of PSS were highly variable, ranging from 4% to 42.6%, with the prevalence of disabling spasticity ranging from 2% to 13%. Data on phases of the PSS continuum revealed evidence of PSS in 4% to 27% of those in the early time course (1-4 weeks poststroke), 19% to 26.7% of those in the postacute phase (1-3 months poststroke), and 17% to 42.6% of those in the chronic phase (>3 months poststroke). Data also identified key risk factors associated with the development of spasticity, including lower Barthel Index scores, severe degree of paresis, stroke-related pain, and sensory deficits. Although such indices could be regarded as predictors of PSS and thus enable early identification and treatment, the different measures of PSS used in those studies limit the strength of the findings. To optimize evaluation in the different phases of care, the best possible assessment of PSS would make use of a combination of indicators for clinical impairment, motor performance, activity level, quality of life, and patient-reported outcome measures. Applying these recommended measures, as well as increasing our knowledge of the physiologic predictors of PSS, will enable us to perform clinical and epidemiologic studies that will facilitate identification and early, multimodal treatment. Y1 - 2013 SN - 0028-3878 VL - 80 IS - 1 SP - S13 EP - S19 PB - Lippincott Williams & Wilkins CY - Philadelphia ER - TY - JOUR A1 - Sagolla, Kristina A1 - Löhmannsröben, Hans-Gerd A1 - Hille, Carsten T1 - Time-resolved fluorescence microscopy for quantitative Ca2+ imaging in living cells JF - Analytical & bioanalytical chemistry N2 - Calcium (Ca2+) is a ubiquitous intracellular second messenger and involved in a plethora of cellular processes. Thus, quantification of the intracellular Ca2+ concentration ([Ca2+](i)) and of its dynamics is required for a comprehensive understanding of physiological processes and potential dysfunctions. A powerful approach for studying [Ca2+](i) is the use of fluorescent Ca2+ indicators. In addition to the fluorescence intensity as a common recording parameter, the fluorescence lifetime imaging microscopy (FLIM) technique provides access to the fluorescence decay time of the indicator dye. The nanosecond lifetime is mostly independent of variations in dye concentration, allowing more reliable quantification of ion concentrations in biological preparations. In this study, the feasibility of the fluorescent Ca2+ indicator Oregon Green Bapta-1 (OGB-1) for two-photon fluorescence lifetime imaging microscopy (2P-FLIM) was evaluated. In aqueous solution, OGB-1 displayed a Ca2+-dependent biexponential fluorescence decay behaviour, indicating the presence of a Ca2+-free and Ca2+-bound dye form. After sufficient dye loading into living cells, an in situ calibration procedure has also unravelled the Ca2+-free and Ca2+-bound dye forms from a global biexponential fluorescence decay analysis, although the dye's Ca2+ sensitivity is reduced. Nevertheless, quantitative [Ca2+](i) recordings and its stimulus-induced changes in salivary gland cells could be performed successfully. These results suggest that OGB-1 is suitable for 2P-FLIM measurements, which can gain access to cellular physiology. KW - Fluorescence lifetime KW - TCSPC KW - Two-photon excitation KW - 2P cross section KW - Epithelial ion transport KW - OGB-1 Y1 - 2013 U6 - https://doi.org/10.1007/s00216-013-7290-6 SN - 1618-2642 VL - 405 IS - 26 SP - 8525 EP - 8537 PB - Springer CY - Heidelberg ER - TY - THES A1 - Fiedler, Sebastian T1 - Thermodynamic stability of the a-Helical membrane-interacting protein mistic in detergent micelles Y1 - 2013 CY - Potsdam ER - TY - JOUR A1 - Bertilsson, Stefan A1 - Burgin, Amy A1 - Carey, Cayelan C. A1 - Fey, Samuel B. A1 - Grossart, Hans-Peter A1 - Grubisic, Lorena M. A1 - Jones, Ian D. A1 - Kirillin, Georgiy A1 - Lennon, Jay T. A1 - Shade, Ashley A1 - Smyth, Robyn L. T1 - The under-ice microbiome of seasonally frozen lakes JF - Limnology and oceanography N2 - Compared to the well-studied open water of the "growing" season, under-ice conditions in lakes are characterized by low and rather constant temperature, slow water movements, limited light availability, and reduced exchange with the surrounding landscape. These conditions interact with ice-cover duration to shape microbial processes in temperate lakes and ultimately influence the phenology of community and ecosystem processes. We review the current knowledge on microorganisms in seasonally frozen lakes. Specifically, we highlight how under-ice conditions alter lake physics and the ways that this can affect the distribution and metabolism of auto-and heterotrophic microorganisms. We identify functional traits that we hypothesize are important for understanding under-ice dynamics and discuss how these traits influence species interactions. As ice coverage duration has already been seen to reduce as air temperatures have warmed, the dynamics of the under-ice microbiome are important for understanding and predicting the dynamics and functioning of seasonally frozen lakes in the near future. Y1 - 2013 U6 - https://doi.org/10.4319/lo.2013.58.6.1998 SN - 0024-3590 SN - 1939-5590 VL - 58 IS - 6 SP - 1998 EP - 2012 PB - Wiley CY - Waco ER - TY - JOUR A1 - Cheng, Shifeng A1 - van den Bergh, Erik A1 - Zeng, Peng A1 - Zhong, Xiao A1 - Xu, Jiajia A1 - Liu, Xin A1 - Hofberger, Johannes A1 - de Bruijn, Suzanne A1 - Bhide, Amey S. A1 - Kuelahoglu, Canan A1 - Bian, Chao A1 - Chen, Jing A1 - Fan, Guangyi A1 - Kaufmann, Kerstin A1 - Hall, Jocelyn C. A1 - Becker, Annette A1 - Bräutigam, Andrea A1 - Weber, Andreas P. M. A1 - Shi, Chengcheng A1 - Zheng, Zhijun A1 - Li, Wujiao A1 - Lv, Mingju A1 - Tao, Yimin A1 - Wang, Junyi A1 - Zou, Hongfeng A1 - Quan, Zhiwu A1 - Hibberd, Julian M. A1 - Zhang, Gengyun A1 - Zhu, Xin-Guang A1 - Xu, Xun A1 - Schranz, M. Eric T1 - The Tarenaya hassleriana Genome Provides insight Into Reproductive Trait and Genome Evolution of Crucifers JF - The plant cell N2 - The Brassicaceae, including Arabidopsis thaliana and Brassica crops, is unmatched among plants in its wealth of genomic and functional molecular data and has long served as a model for understanding gene, genome, and trait evolution. However, genome information from a phylogenetic outgroup that is essential for inferring directionality of evolutionary change has been lacking. We therefore sequenced the genome of the spider flower (Tarenaya hassleriana) from the Brassicaceae sister family, the Cleomaceae. By comparative analysis of the two lineages, we show that genome evolution following ancient polyploidy and gene duplication events affect reproductively important traits. We found an ancient genome triplication in Tarenaya (Th-alpha) that is independent of the Brassicaceae-specific duplication (At-alpha) and nested Brassica (Br-a) triplication. To showcase the potential of sister lineage genome analysis, we investigated the state of floral developmental genes and show Brassica retains twice as many floral MADS (for MINICHROMOSOME MAINTENANCE1, AGAMOUS, DEFICIENS and SERUM RESPONSE FACTOR) genes as Tarenaya that likely contribute to morphological diversity in Brassica. We also performed synteny analysis of gene families that confer self-incompatibility in Brassicaceae and found that the critical SERINE RECEPTOR KINASE receptor gene is derived from a lineage-specific tandem duplication. The T. hassleriana genome will facilitate future research toward elucidating the evolutionary history of Brassicaceae genomes. Y1 - 2013 U6 - https://doi.org/10.1105/tpc.113.113480 SN - 1040-4651 VL - 25 IS - 8 SP - 2813 EP - 2830 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Dahl, Jan-Ulrik A1 - Radon, Christin A1 - Bühning, Martin A1 - Nimtz, Manfred A1 - Leichert, Lars I. A1 - Denis, Yann A1 - Jourlin-Castelli, Cecile A1 - Iobbi-Nivol, Chantal A1 - Mejean, Vincent A1 - Leimkühler, Silke T1 - The Sulfur Carrier Protein TusA Has a Pleiotropic Role in Escherichia coli That Also Affects Molybdenum Cofactor Biosynthesis JF - JOURNAL OF BIOLOGICAL CHEMISTRY N2 - The Escherichia coli L-cysteine desulfurase IscS mobilizes sulfur from L-cysteine for the synthesis of several biomolecules such as iron-sulfur (FeS) clusters, molybdopterin, thiamin, lipoic acid, biotin, and the thiolation of tRNAs. The sulfur transfer from IscS to various biomolecules is mediated by different interaction partners (e.g. TusA for thiomodification of tRNAs, IscU for FeS cluster biogenesis, and ThiI for thiamine biosynthesis/tRNA thiolation), which bind at different sites of IscS. Transcriptomic and proteomic studies of a Delta tusA strain showed that the expression of genes of the moaABCDE operon coding for proteins involved in molybdenum cofactor biosynthesis is increased under aerobic and anaerobic conditions. Additionally, under anaerobic conditions the expression of genes encoding hydrogenase 3 and several molybdoenzymes such as nitrate reductase were also increased. On the contrary, the activity of all molydoenzymes analyzed was significantly reduced in the Delta tusA mutant. Characterization of the Delta tusA strain under aerobic conditions showed an overall low molybdopterin content and an accumulation of cyclic pyranopterin monophosphate. Under anaerobic conditions the activity of nitrate reductase was reduced by only 50%, showing that TusA is not essential for molybdenum cofactor biosynthesis. We present a model in which we propose that the direction of sulfur transfer for each sulfur-containing biomolecule is regulated by the availability of the interaction partner of IscS. We propose that in the absence of TusA, more IscS is available for FeS cluster biosynthesis and that the overproduction of FeS clusters leads to a modified expression of several genes. Y1 - 2013 U6 - https://doi.org/10.1074/jbc.M112.431569 SN - 0021-9258 VL - 288 IS - 8 SP - 5426 EP - 5442 PB - AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC CY - BETHESDA ER - TY - JOUR A1 - Jedrusik-Bode, Monika A1 - Studencka, Maja A1 - Smolka, Christian A1 - Baumann, Tobias A1 - Schmidt, Henning A1 - Kampf, Jan A1 - Paap, Franziska A1 - Martin, Sophie A1 - Tazi, Jamal A1 - Müller, Kristian M. A1 - Krüger, Marcus A1 - Braun, Thomas A1 - Bober, Eva T1 - The sirtuin SIRT6 regulates stress granule formation in C. elegans and mammals JF - Journal of cell science N2 - SIRT6 is a NAD(+)-dependent deacetylase that modulates chromatin structure and safeguards genomic stability. Until now, SIRT6 has been assigned to the nucleus and only nuclear targets of SIRT6 are known. Here, we demonstrate that in response to stress, C. elegans SIR-2.4 and its mammalian orthologue SIRT6 localize to cytoplasmic stress granules, interact with various stress granule components and induce their assembly. Loss of SIRT6 or inhibition of its catalytic activity in mouse embryonic fibroblasts impairs stress granule formation and delays disassembly during recovery, whereas deficiency of SIR-2.4 diminishes maintenance of P granules and decreases survival of C. elegans under stress conditions. Our findings uncover a novel, evolutionary conserved function of SIRT6 in the maintenance of stress granules in response to stress. KW - C. elegans KW - G3BP KW - SIRT6 KW - Sirtuins KW - Stress KW - Stress granules Y1 - 2013 U6 - https://doi.org/10.1242/jcs.130708 SN - 0021-9533 SN - 1477-9137 VL - 126 IS - 22 SP - 5166 EP - + PB - Company of Biologists Limited CY - Cambridge ER - TY - CHAP A1 - Ebenhöh, O. A1 - Kartal, Oe. A1 - Skupin, A. A1 - Mahlow, S. A1 - Steup, Martin T1 - The role of mixing entropy in carbohydrate metabolism T2 - European biophysics journal : with biophysics letters ; an international journal of biophysics Y1 - 2013 SN - 0175-7571 SN - 1432-1017 VL - 42 SP - S73 EP - S73 PB - Springer CY - New York ER - TY - JOUR A1 - Sharma, Tripti A1 - Dreyer, Ingo A1 - Riedelsberger, Janin T1 - The role of K+ channels in uptake and redistribution of potassium in the model plant Arabidopsis thaliana JF - Frontiers in plant science N2 - Potassium (K+) is inevitable for plant growth and development. It plays a crucial role in the regulation of enzyme activities, in adjusting the electrical membrane potential and the cellular turgor, in regulating cellular homeostasis and in the stabilization of protein synthesis. Uptake of K+ from the soil and its transport to growing organs is essential for a healthy plant development. Uptake and allocation of K+ are performed by K+ channels and transporters belonging to different protein families. In this review we summarize the knowledge on the versatile physiological roles of plant K+ channels and their behavior under stress conditions in the model plant Arabidopsis thaliana. KW - plant potassium channel KW - Shaker KW - TPK KW - K-ir-like KW - Arabidopsis thaliana KW - voltage-dependent KW - voltage-independent Y1 - 2013 U6 - https://doi.org/10.3389/fpls.2013.00224 SN - 1664-462X VL - 4 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Hartmann, Tobias A1 - Leimkühler, Silke T1 - The oxygen-tolerant and NAD+-dependent formate dehydrogenase from Rhodobacter capsulatus is able to catalyze the reduction of CO2 to formate JF - The FEBS journal N2 - The formate dehydrogenase from Rhodobactercapsulatus (RcFDH) is an oxygen-tolerant protein with an ()(2) subunit composition that is localized in the cytoplasm. It belongs to the group of metal and NAD(+)-dependent FDHs with the coordination of a molybdenum cofactor, four [Fe4S4] clusters and one [Fe2S2] cluster associated with the -subunit, one [Fe4S4] cluster and one FMN bound to the -subunit, and one [Fe2S2] cluster bound to the -subunit. RcFDH was heterologously expressed in Escherichiacoli and characterized. Cofactor analysis showed that the bis-molybdopterin guanine dinucleotide cofactor is bound to the FdsA subunit containing a cysteine ligand at the active site. A turnover rate of 2189min(-1) with formate as substrate was determined. The back reaction for the reduction of CO2 was catalyzed with a k(cat) of 89min(-1). The preference for formate oxidation shows an energy barrier for CO2 reduction of the enzyme. Furthermore, the FMN-containing and [Fe4S4]-containing -subunit together with the [Fe2S2]-containing -subunit forms a diaphorase unit with activities for both NAD(+) reduction and NADH oxidation. In addition to the structural genes fdsG, fdsB, and fdsA, the fds operon in R.capsulatus contains the fdsC and fdsD genes. Expression studies showed that RcFDH is only active when both FdsC and FdsD are present. Both proteins are proposed to be involved in bis-molybdopterin guanine dinucleotide modification and insertion into RcFDH. KW - FeS cluster KW - FMN KW - formate dehydrogenase KW - molybdenum cofactor (Moco)-binding chaperone KW - molybdoenzyme Y1 - 2013 U6 - https://doi.org/10.1111/febs.12528 SN - 1742-464X SN - 1742-4658 VL - 280 IS - 23 SP - 6083 EP - 6096 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Lukas, Marcus A1 - Frost, Paul C. A1 - Wacker, Alexander T1 - The neonate nutrition hypothesis - early feeding affects the body stoichiometry of Daphnia offspring JF - Freshwater biology N2 - Aquatic herbivores consume variable quantities and qualities of food. In freshwater systems, where phosphorus (P) is often a primary limiting element, inadequate dietary P can slow maternal growth and reduce body P content. There remains uncertainty about whether and how dietary effects on mothers are transferred to offspring by way of egg provisioning. Using the keystone herbivore Daphnia, we tested a novel explanation (the neonate nutrition hypothesis') to determine whether the early nutrition of newborns affects their elemental composition and whether the indications of differences in maternal P nutrition found previously might be overestimated. We thus examined the P content of mothers and their eggs from deposition through development to the birth of neonates. We examined further whether very short periods of ingestion (3h) by the offspring alter the overall P content of juvenile Daphnia. We showed that strong dietary P effects on mothers were not directly transferred to their eggs. Irrespective of the supply of P in the maternal diet, the P content of eggs in different developmental stages and in (unfed) neonates did not differ. This indicates that Daphnia mothers do not reduce the quality (in terms of P) of newly produced offspring after intermittent periods (i.e. several days) of poor nutrition. In contrast, the P content of neonates reflected that of their food after brief periods of feeding, indicating that even temporary exposure to nutrient poor food immediately after birth may strongly affect the elemental composition of neonates. Our results thus support the neonate nutrition hypothesis, which, like differential maternal provisioning, is a possible explanation for the variable elemental quality of young Daphnia. KW - ecological stoichiometry KW - food quality KW - maternal effects KW - nutrient limitation KW - zooplankton Y1 - 2013 U6 - https://doi.org/10.1111/fwb.12213 SN - 0046-5070 VL - 58 IS - 11 SP - 2333 EP - 2344 PB - Wiley-Blackwell CY - Hoboken ER - TY - CHAP A1 - Smith, Mychal Daijon A1 - Mattos, Carla A1 - Barbirz, Stefanie T1 - The multiple solvent crystal structures method of P22TSP T2 - The FASEB journal : the official journal of the Federation of American Societies for Experimental Biology Y1 - 2013 SN - 0892-6638 VL - 27 IS - 11 PB - Federation of American Societies for Experimental Biology CY - Bethesda ER - TY - JOUR A1 - Sengupta, Saswati A1 - Chattopadhyay, Madhab K. A1 - Grossart, Hans-Peter T1 - The multifaceted roles of antibiotics and antibiotic resistance in nature JF - Frontiers in microbiology N2 - Antibiotics are chemotherapeutic agents, which have been a very powerful tool in the clinical management of bacterial diseases since the 1940s. However, benefits offered by these magic bullets have been substantially lost in subsequent days following the widespread emergence and dissemination of antibiotic-resistant strains. While it is obvious that excessive and imprudent use of antibiotics significantly contributes to the emergence of resistant strains, antibiotic resistance is also observed in natural bacteria of remote places unlikely to be impacted by human intervention. Both antibiotic biosynthetic genes and resistance-conferring genes have been known to evolve billions of years ago, long before clinical use of antibiotics. Hence it appears that antibiotics and antibiotics resistance determinants have some other roles in nature, which often elude our attention because of overemphasis on the therapeutic importance of antibiotics and the crisis imposed by the antibiotic resistance in pathogens. In the natural milieu, antibiotics are often found to be present in sub-inhibitory concentrations acting as signaling molecules supporting the process of quorum sensing and biofilm formation. They also play an important role in the production of virulence factors and influence host-parasite interactions (e.g., phagocytosis, adherence to the target cell, and so on). The evolutionary and ecological aspects of antibiotics and antibiotic resistance in the naturally occurring microbial community are little understood. Therefore, the actual role of antibiotics in nature warrants in-depth investigations. Studies on such an intriguing behavior of the microorganisms promise insight into the intricacies of the microbial physiology and are likely to provide some lead in controlling the emergence and subsequent dissemination of antibiotic resistance. This article highlights some of the recent findings on the role of antibiotics and the genes that confer resistance to antibiotics in nature. KW - antibiotics KW - sub-inhibitory concentration KW - quorum sensing KW - virulence KW - stress response KW - antibiotic resistance KW - antibiotic paradox Y1 - 2013 U6 - https://doi.org/10.3389/fmicb.2013.00047 SN - 1664-302X VL - 4 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Marelja, Zvonimir A1 - Chowdhury, Mita Mullick A1 - Dosche, Carsten A1 - Hille, Carsten A1 - Baumann, Otto A1 - Löhmannsröben, Hans-Gerd A1 - Leimkühler, Silke T1 - The L-cysteine desulfurase NFS1 is localized in the cytosol where it provides the sulfur for molybdenum cofactor biosynthesis in humans JF - PLoS one N2 - In humans, the L-cysteine desulfurase NFS1 plays a crucial role in the mitochondrial iron-sulfur cluster biosynthesis and in the thiomodification of mitochondrial and cytosolic tRNAs. We have previously demonstrated that purified NFS1 is able to transfer sulfur to the C-terminal domain of MOCS3, a cytosolic protein involved in molybdenum cofactor biosynthesis and tRNA thiolation. However, no direct evidence existed so far for the interaction of NFS1 and MOCS3 in the cytosol of human cells. Here, we present direct data to show the interaction of NFS1 and MOCS3 in the cytosol of human cells using Forster resonance energy transfer and a split-EGFP system. The colocalization of NFS1 and MOCS3 in the cytosol was confirmed by immunodetection of fractionated cells and localization studies using confocal fluorescence microscopy. Purified NFS1 was used to reconstitute the lacking molybdoenzyme activity of the Neurospora crassa nit-1 mutant, giving additional evidence that NFS1 is the sulfur donor for Moco biosynthesis in eukaryotes in general. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0060869 SN - 1932-6203 VL - 8 IS - 4 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Snijman, Deirdre A. A1 - Kocyan, Alexander T1 - The genus Pauridia (Hypoxidaceae) amplified to include Hypoxis sect. Ianthe, Saniella and Spiloxene, with revised nomenclature and typification JF - Phytotaxa : a rapid international journal for accelerating the publication of botanical taxonomy N2 - Recent phylogenetic analyses show that the species of the southern African genera Pauridia, Saniella and Spiloxene and the Australian, Tasmanian and New Zealand Hypoxis sect. Ianthe form a highly supported, monophyletic clade. In keeping with earlier suggestions that these taxa doubtfully warrant separate status, and to avoid the recognition of Hypoxis and Spiloxene as paraphyletic, we expand the circumscription of Pauridia to include Saniella, Spiloxene and Hypoxis sect. Ianthe. As a result 33 new combinations at specific and infraspecific level are proposed and one epitype, two neotypes and 30 lectotypes are newly designated. Three basionyms, of which Linnaeus, Linnaeus filius and Lamarck are the authors, are also typified (Amaryllis capensis, Hypoxis aquatica, and Hypoxis pumila). KW - Hypoxidaceae KW - Hypoxis KW - new combination KW - Pauridia KW - Saniella KW - Spiloxene KW - taxonomy KW - typification Y1 - 2013 U6 - https://doi.org/10.11646/phytotaxa.116.1.2 SN - 1179-3155 VL - 116 IS - 1 SP - 19 EP - 33 PB - Magnolia Press CY - Auckland ER - TY - JOUR A1 - Speck, Janina A1 - Räuber, Christina A1 - Kükenshöner, Tim A1 - Niemöller, Christoph A1 - Mueller, Katelyn J. A1 - Schleberger, Paula A1 - Dondapati, Padmarupa A1 - Hecky, Jochen A1 - Arndt, Katja Maren A1 - Müller, Kristian M. T1 - TAT hitchhiker selection expanded to folding helpers, multimeric interactions and combinations with protein fragment complementation JF - Protein engineering design & selection N2 - The twin-arginine translocation (TAT) pathway of the bacterial cytoplasmic membrane mediates translocation only of proteins that accomplished a native-like conformation. We deploy this feature in modular selection systems for directed evolution, in which folding helpers as well as dimeric or oligomeric proteinprotein interactions enable TAT-dependent translocation of the resistance marker TEM -lactamase (L). Specifically, we demonstrate and analyze selection of (i) enhancers for folding by direct TAT translocation selection of a target protein interposed between the TorA signal sequence and L, (ii) dimeric or oligomeric proteinprotein interactions by hitchhiker translocation (HiT) selection of proteins fused to the TorA signal sequence and to the L, respectively and (iii) heterotrimeric proteinprotein interactions by combining HiT with protein fragment complementation selection of proteins fused to two split L fragments and TorA, respectively. The lactamase fragments were additionally engineered for improved activity and stability. Applicability was benchmarked with interaction partners of known affinity and multimerization whereby cellular fitness correlated well with biophysical protein properties. Ultimately, the HiT selection was employed to identify peptides, which specifically bind to leukemia- and melanoma-relevant target proteins (MITF and ETO) by coiled-coil or tetra-helix-bundle formation with high affinity. The various versions of TAT selection led to inhibiting peptides (iPEPs) of disease-promoting interactions and enabled so far difficult to achieve selections. KW - HiT selection KW - NHR2 KW - TAT selection KW - three hybrid KW - two hybrid Y1 - 2013 U6 - https://doi.org/10.1093/protein/gzs098 SN - 1741-0126 VL - 26 IS - 3 SP - 225 EP - 242 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Müller, Sara A1 - Windhof, Indra M. A1 - Maximov, Vladimir A1 - Jurkowski, Tomasz A1 - Jeltsch, Albert A1 - Förstner, Konrad U. A1 - Sharma, Cynthia M. A1 - Gräf, Ralph A1 - Nellen, Wolfgang T1 - Target recognition, RNA methylation activity and transcriptional regulation of the dictyostelium discoideum Dnmt2-homologue (DnmA) JF - Nucleic acids research N2 - Although the DNA methyltransferase 2 family is highly conserved during evolution and recent reports suggested a dual specificity with stronger activity on transfer RNA (tRNA) than DNA substrates, the biological function is still obscure. We show that the Dictyostelium discoideum Dnmt2-homologue DnmA is an active tRNA methyltransferase that modifies C38 in tRNA(Asp(GUC)) in vitro and in vivo. By an ultraviolet-crosslinking and immunoprecipitation approach, we identified further DnmA targets. This revealed specific tRNA fragments bound by the enzyme and identified tRNA(Glu(CUC/UUC)) and tRNA(Gly(GCC)) as new but weaker substrates for both human Dnmt2 and DnmA in vitro but apparently not in vivo. Dnmt2 enzymes form transient covalent complexes with their substrates. The dynamics of complex formation and complex resolution reflect methylation efficiency in vitro. Quantitative PCR analyses revealed alterations in dnmA expression during development, cell cycle and in response to temperature stress. However, dnmA expression only partially correlated with tRNA methylation in vivo. Strikingly, dnmA expression in the laboratory strain AX2 was significantly lower than in the NC4 parent strain. As expression levels and binding of DnmA to a target in vivo are apparently not necessarily accompanied by methylation, we propose an additional biological function of DnmA apart from methylation. Y1 - 2013 U6 - https://doi.org/10.1093/nar/gkt634 SN - 0305-1048 SN - 1362-4962 VL - 41 IS - 18 SP - 8615 EP - 8627 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Weisse, Thomas A1 - Moser, Michael A1 - Scheffel, Ulrike A1 - Stadler, Peter A1 - Berendonk, Thomas U. A1 - Weithoff, Guntram A1 - Berger, Helmut T1 - Systematics and species-specific response to pH of Oxytricha acidotolerans sp nov and Urosomoida sp (Ciliophora, Hypotricha) from acid mining lakes JF - European journal of protistology N2 - We investigated the morphology, phylogeny of the 18S rDNA, and pH response of Oxytricha acidotolerans sp. nov. and Urosomoida sp. (Ciliophora, Hypotricha) isolated from two chemically similar acid mining lakes (pH similar to 2.6) located at Langau, Austria, and in Lusatia, Germany. Oxytricha acidotolerans sp. nov. from Langau has 18 frontal-ventral-transverse cirri but a very indistinct kinety 3 fragmentation so that the assignment to Oxytricha is uncertain. The somewhat smaller species from Lusatia has a highly variable cirral pattern and the dorsal kineties arranged in the Urosomoida pattern and is, therefore, preliminary designated as Urosomoida sp. The pH response was measured as ciliate growth rates in laboratory experiments at pH ranging from 2.5 to 7.0. Our hypothesis was that the shape of the pH reaction norm would not differ between these closely related (3% difference in their SSU rDNA) species. Results revealed a broad pH niche for O. acidotolerans, with growth rates peaking at moderately acidic conditions (pH 5.2). Cyst formation was positively and linearly related to pH. Urosomoida sp. was more sensitive to pH and did not survive at circumneutral pH. Accordingly, we reject our hypothesis that similar habitats would harbour ciliate species with virtually identical pH reaction norm. KW - Acid mining lakes KW - Growth rates KW - pH response KW - Oxytricha KW - SSU rDNA KW - Urosomoida Y1 - 2013 U6 - https://doi.org/10.1016/j.ejop.2012.08.001 SN - 0932-4739 VL - 49 IS - 2 SP - 255 EP - 271 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Sachse, Rita A1 - Wüstenhagen, Doreen Anja A1 - Samalikova, Maria A1 - Gerrits, Michael A1 - Bier, Frank Fabian A1 - Kubick, Stefan T1 - Synthesis of membrane proteins in eukaryotic cell-free systems JF - Engineering in life sciences : Industry, Environment, Plant, Food N2 - Cell-free protein synthesis (CFPS) is a valuable method for the fast expression of difficult-to-express proteins as well as posttranslationally modified proteins. Since cell-free systems circumvent possible cytotoxic effects caused by protein overexpression in living cells, they significantly enlarge the scale and variety of proteins that can be characterized. We demonstrate the high potential of eukaryotic CFPS to express various types of membrane proteins covering a broad range of structurally and functionally diverse proteins. Our eukaryotic cell-free translation systems are capable to provide high molecular weight membrane proteins, fluorescent-labeled membrane proteins, as well as posttranslationally modified proteins for further downstream analysis. KW - Cell-free protein expression KW - In vitro protein synthesis KW - Labeled membrane proteins KW - Synthetic glycoprotein Y1 - 2013 U6 - https://doi.org/10.1002/elsc.201100235 SN - 1618-0240 VL - 13 IS - 1 SP - 39 EP - 48 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Reim, Tina A1 - Thamm, Markus A1 - Rolke, Daniel A1 - Blenau, Wolfgang A1 - Scheiner, Ricarda T1 - Suitability of three common reference genes for quantitative real-time PCR in honey bees JF - Apidologie : a quality journal in bee science N2 - Honey bees are important model organisms for neurobiology, because they display a large array of behaviors. To link behavior with individual gene function, quantitative polymerase chain reaction is frequently used. Comparing gene expression of different individuals requires data normalization using adequate reference genes. These should ideally be expressed stably throughout lifetime. Unfortunately, this is frequently not the case. We studied how well three commonly used reference genes are suited for this purpose and measured gene expression in the brains of honey bees differing in age and social role. Although rpl32 is used most frequently, it only remains stable in expression between newly emerged bees, nurse-aged bees, and pollen foragers but shows a peak at the age of 12 days. The genes gapdh and ef1 alpha-f1, in contrast, are expressed stably in the brain throughout all age groups except newly emerged bees. According to stability software, gapdh was expressed most stably, followed by rpl32 and ef1 alpha-f1. KW - gene expression KW - quantitative PCR KW - reference gene KW - stability program KW - Apis mellifera Y1 - 2013 U6 - https://doi.org/10.1007/s13592-012-0184-3 SN - 0044-8435 VL - 44 IS - 3 SP - 342 EP - 350 PB - Springer CY - Paris ER - TY - JOUR A1 - Scheiner, Ricarda A1 - Abramson, Charles I. A1 - Brodschneider, Robert A1 - Crailsheim, Karl A1 - Farina, Walter M. A1 - Fuchs, Stefan A1 - Grünewald, Bernd A1 - Hahshold, Sybille A1 - Karrer, Marlene A1 - Koeniger, Gudrun A1 - Königer, Niko A1 - Menzel, Randolf A1 - Mujagic, Samir A1 - Radspieler, Gerald A1 - Schmickl, Thomas A1 - Schneider, Christof A1 - Siegel, Adam J. A1 - Szopek, Martina A1 - Thenius, Ronald T1 - Standard methods for behavioural studies of Apis mellifera JF - Journal of apicultural research N2 - In this BEEBOOK paper we present a set of established methods for quantifying honey bee behaviour. We start with general methods for preparing bees for behavioural assays. Then we introduce assays for quantifying sensory responsiveness to gustatory, visual and olfactory stimuli. Presentation of more complex behaviours like appetitive and aversive learning under controlled laboratory conditions and learning paradigms under free-flying conditions will allow the reader to investigate a large range of cognitive skills in honey bees. Honey bees are very sensitive to changing temperatures. We therefore present experiments which aim at analysing honey bee locomotion in temperature gradients. The complex flight behaviour of honey bees can be investigated under controlled conditions in the laboratory or with sophisticated technologies like harmonic radar or RFID in the field. These methods will be explained in detail in different sections. Honey bees are model organisms in behavioural biology for their complex yet plastic division of labour. To observe the daily behaviour of individual bees in a colony, classical observation hives are very useful. The setting up and use of typical observation hives will be the focus of another section. The honey bee dance language has important characteristics of a real language and has been the focus of numerous studies. We here discuss the background of the honey bee dance language and describe how it can be studied. Finally, the mating of a honey bee queen with drones is essential to survival of the entire colony. We here give detailed and structured information how the mating behaviour of drones and queens can be observed and experimentally manipulated. The ultimate goal of this chapter is to provide the reader with a comprehensive set of experimental protocols for detailed studies on all aspects of honey bee behaviour including investigation of pesticide and insecticide effects. KW - COLOSS KW - BEEBOOK KW - honey bee KW - behaviour KW - gustatory responsiveness KW - olfactory responsiveness KW - phototaxis KW - non-associative learning KW - associative learning KW - appetitive learning KW - aversive learning KW - locomotion KW - temperature sensing KW - honey bee flight KW - observation hive KW - honey bee dance KW - honey bee navigation KW - harmonic radar KW - BeeScan KW - RFID KW - honey bee mating KW - free-flying honey bees Y1 - 2013 U6 - https://doi.org/10.3896/IBRA.1.52.4.04 SN - 0021-8839 SN - 2078-6913 VL - 52 IS - 4 PB - International Bee Research Association CY - Cardiff ER - TY - THES A1 - Baumann, Tobias T1 - Stability and Interconnected protein properties studied with TEM ß-lactamase Y1 - 2013 CY - Potsdam ER - TY - JOUR A1 - Drygala, Frank A1 - Zoller, Hinrich T1 - Spatial use and interaction of the invasive raccoon dog and the native red fox in Central Europe - competition or coexistence? JF - European journal of wildlife research N2 - The main objective was to discover extent of interference and/or exploitative competition between the native red fox (Vulpes vulpes) and the introduced, invasive raccoon dog (Nyctereues proconoides) in the intensively used, agricultural landscape of northeast Germany (Mecklenburg-Western Pomerania) using very high frequency (VHF) radio telemetry. We recorded location data for 12 foxes and 16 raccoon dogs between July 2004 and December 2006. Species had similar average home range sizes estimated in each season (K95). Home ranges of adjacent raccoon dogs and foxes overlapped from 0.5 to 74.5 % with a mean of 26.4 %. We found a significantly different home range overlap index between the species showing that raccoon dog ranges shifted between seasons to a greater extent than red fox ranges. The raccoon dog differed significantly from the red fox in its use of habitat types, preferring dense vegetation cover and avoiding open areas. The red fox displayed less preference for or avoidance of specific habitat types. Moreover, an almost neutral inter-specific interaction index ranging from -0.12 to 0.12 indicates that raccoon dogs and red foxes ignored each other. It is concluded that widespread and available resources and differences in spatial use patterns prevent competition between red foxes and raccoon dogs in the agricultural landscape of northeast Germany. KW - Vulpes vulpes KW - Nyctereutes procyonoides KW - Space use KW - Habitat use KW - Invasive species Y1 - 2013 U6 - https://doi.org/10.1007/s10344-013-0722-y SN - 1612-4642 SN - 1439-0574 VL - 59 IS - 5 SP - 683 EP - 691 PB - Springer CY - New York ER - TY - THES A1 - May, Felix T1 - Spatial models of plant diversity and plant functional traits : towards a better understanding of plant community dynamics in fragmented landscapes T1 - Räumliche Modelle der Diversität und der funktionellen Eigenschaften von Pflanzen : für ein besseres Verständnis der Dynamik von Pflanzengemeinschaften in fragmentierten Landschaften N2 - The fragmentation of natural habitat caused by anthropogenic land use changes is one of the main drivers of the current rapid loss of biodiversity. In face of this threat, ecological research needs to provide predictions of communities' responses to fragmentation as a prerequisite for the effective mitigation of further biodiversity loss. However, predictions of communities' responses to fragmentation require a thorough understanding of ecological processes, such as species dispersal and persistence. Therefore, this thesis seeks an improved understanding of community dynamics in fragmented landscapes. In order to approach this overall aim, I identified key questions on the response of plant diversity and plant functional traits to variations in species' dispersal capability, habitat fragmentation and local environmental conditions. All questions were addressed using spatially explicit simulations or statistical models. In chapter 2, I addressed scale-dependent relationships between dispersal capability and species diversity using a grid-based neutral model. I found that the ratio of survey area to landscape size is an important determinant of scale-dependent dispersal-diversity relationships. With small ratios, the model predicted increasing dispersal-diversity relationships, while decreasing dispersal-diversity relationships emerged, when the ratio approached one, i.e. when the survey area approached the landscape size. For intermediate ratios, I found a U-shaped pattern that has not been reported before. With this study, I unified and extended previous work on dispersal-diversity relationships. In chapter 3, I assessed the type of regional plant community dynamics for the study area in the Southern Judean Lowlands (SJL). For this purpose, I parameterised a multi-species incidence-function model (IFM) with vegetation data using approximate Bayesian computation (ABC). I found that the type of regional plant community dynamics in the SJL is best characterized as a set of isolated “island communities” with very low connectivity between local communities. Model predictions indicated a significant extinction debt with 33% - 60% of all species going extinct within 1000 years. In general, this study introduces a novel approach for combining a spatially explicit simulation model with field data from species-rich communities. In chapter 4, I first analysed, if plant functional traits in the SJL indicate trait convergence by habitat filtering and trait divergence by interspecific competition, as predicted by community assembly theory. Second, I assessed the interactive effects of fragmentation and the south-north precipitation gradient in the SJL on community-mean plant traits. I found clear evidence for trait convergence, but the evidence for trait divergence fundamentally depended on the chosen null-model. All community-mean traits were significantly associated with the precipitation gradient in the SJL. The trait associations with fragmentation indices (patch size and connectivity) were generally weaker, but statistically significant for all traits. Specific leaf area (SLA) and plant height were consistently associated with fragmentation indices along the precipitation gradient. In contrast, seed mass and seed number were interactively influenced by fragmentation and precipitation. In general, this study provides the first analysis of the interactive effects of climate and fragmentation on plant functional traits. Overall, I conclude that the spatially explicit perspective adopted in this thesis is crucial for a thorough understanding of plant community dynamics in fragmented landscapes. The finding of contrasting responses of local diversity to variations in dispersal capability stresses the importance of considering the diversity and composition of the metacommunity, prior to implementing conservation measures that aim at increased habitat connectivity. The model predictions derived with the IFM highlight the importance of additional natural habitat for the mitigation of future species extinctions. In general, the approach of combining a spatially explicit IFM with extensive species occupancy data provides a novel and promising tool to assess the consequences of different management scenarios. The analysis of plant functional traits in the SJL points to important knowledge gaps in community assembly theory with respect to the simultaneous consequences of habitat filtering and competition. In particular, it demonstrates the importance of investigating the synergistic consequences of fragmentation, climate change and land use change on plant communities. I suggest that the integration of plant functional traits and of species interactions into spatially explicit, dynamic simulation models offers a promising approach, which will further improve our understanding of plant communities and our ability to predict their dynamics in fragmented and changing landscapes. N2 - Die Fragmentierung von Landschaften umfasst die Zerschneidung und den Verlust von Flächen mit natürlicher Vegetationsentwicklung und ist eine der Hauptursachen für den gegenwärtigen drastischen Verlust an Biodiversität. Diese Dissertation soll zu einem besseren Verständnis der Vegetationsdynamik in fragmentierten Landschaften beitragen. Damit verbunden ist das Ziel, Vorhersagen über die Reaktion von Pflanzengemeinschaften auf Fragmentierung zu verbessern. Diese Vorhersagen sind notwendig, um gezielte Naturschutzmaßnahmen zur Verminderung eines weiteren Verlustes an Biodiversität umsetzen zu können. In Kapitel 2 der Dissertation wird mit einem Simulationsmodell untersucht, wie sich die Ausbreitungsdistanz von Samen auf die lokale Artenzahl von Pflanzengemeinschaften auswirkt. Dabei zeigte sich, dass längere Ausbreitungsdistanzen die lokale Artenvielfalt sowohl erhöhen, als auch verringern können. Der wichtigste Einflussfaktor war dabei die Artenvielfalt der über-geordneten Pflanzengemeinschaft, in der die betrachtete lokale Gemeinschaft eingebettet war. Im dritten Kapitel wird die Konnektivität zwischen Pflanzengemeinschaften in Habitat-fragmenten, d.h. der Austausch von Arten und Individuen durch Samenausbreitung, im Unter-suchungsgebiet in Israel analysiert. Dafür wurde ein zweites räumliches Simulationsmodell mit statistischen Verfahren an Felddaten angepasst. Der Vergleich des Modells mit den Daten wies auf eine sehr geringe Konnektivität zwischen den Habitatfragmenten hin. Das Modell sagte vorher, dass innerhalb von 1000 Jahren 33% - 60% der Arten aussterben könnten. In Kapitel 4 wird zuerst analysiert, welche Prozesse die Verteilung von funktionellen Eigenschaften in Pflanzengemeinschaften bestimmen. In einem zweiten Schritt wird dann unter-sucht, wie sich funktionelle Eigenschaften von Pflanzengemeinschaften mit dem Niederschlag und der Fragmentierung im Untersuchungsgebiet in Israel verändern. Der Zusammenhang zwischen den Eigenschaften Pflanzenhöhe, sowie spezifischer Blattfläche und der Fragmentierung änderte sich nicht entlang des Niederschlagsgradienten. Im Gegensatz dazu, änderte sich der Zusammenhang zwischen der Samenmasse bzw. der Samenzahl und der Fragmentierung mit dem Niederschlag. Aus den Ergebnissen der ersten Teilstudie wird deutlich, dass Naturschutzmaßnahmen, die natürliche Habitate stärker vernetzen sollen, die Diversität, sowie die Zusammensetzung der übergeordneten Artengemeinschaft berücksichtigen müssen, um Verluste an Biodiversität zu vermeiden. Die Verknüpfung eines räumlichen Simulationsmodells mit Felddaten in der zweiten Teilstudie stellt einen neuen und vielversprechenden Ansatz für die Untersuchung der Auswirkungen verschiedener Management-Szenarien dar. Die dritte Teilstudie ist die erste Analyse der gemeinsamen Auswirkungen von Klima und Fragmentierung auf funktionelle Pflanzen-eigenschaften und zeigt die hohe Bedeutung der Untersuchung von Synergie-Effekten verschiedener Umweltfaktoren. Für zukünftige Forschung legt diese Dissertation nahe, funktionelle Eigenschaften und Konkurrenz zwischen Arten in räumlichen Simulationsmodellen zu berücksichtigen, um das Verständnis von Artengemeinschaften in fragmentierten Landschaften noch weiter zu verbessern. KW - Diversität KW - Ausbreitung KW - Pflanzengemeinschaften KW - Fragmentierung KW - ökologische Modellierung KW - diversity KW - dispersal KW - plant communities KW - fragmentation KW - ecological modelling Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-68444 ER - TY - JOUR A1 - Leuschner, Christoph A1 - Wulf, Monika A1 - Bäuchler, Patricia A1 - Hertel, Dietrich T1 - Soil C and nutrient stores under Scots pine afforestations compared to ancient beech forests in the German Pleistocene - the role of tree species and forest history JF - Forest ecology and management N2 - In the diluvial lowlands of northern Germany, the Netherlands and northern Poland, an estimated similar to 5 Mio ha of Scots pine plantations (Pinus sylvestris) has been established on sandy soil in the last 250 years replacing the former temperate broad-leaved forests after extended periods of cultivation in the Middle Ages. We examined the effect of variable stand continuity of pine plantations (recent vs. ancient: 51-128 vs. >230 years) on the soil organic carbon (SOC) store and soil nutrient capital in comparison to ancient beech forests (>230 years of continuity) which represent the potential natural forest vegetation. Recent and ancient pine stands had c. 75% larger organic layer C stores than ancient beech forests, while the total C stock in the soil (organic layer and mineral soil to 100 cm) was similar to 25% larger in the beech forests due to higher C concentrations in 0-50 cm depth of the mineral soil. The soil stores of N-tot were similar to 50% and the exchangeable Ca, K and Mg pools about three times larger under beech than under the pine stands. Resin-exchangeable P was enriched in the soils under ancient pine stands probably due to manuring in the past. After clear-cut and long cultivation, it may take >230 years of forest presence to restore the greatly reduced mineral soil C and N pools. The C and N sequestration potential of the soils appeared to be particularly small under pine indicating a pronounced tree species (pine vs. beech) effect on soil C and N dynamics. We conclude that, in the face of rising greenhouse gas emissions, the limited soil C and nutrient storage potential of Scots pine plantations on sandy soils needs consideration when selecting suitable tree species for future forestry. (C) 2013 Elsevier B.V. All rights reserved. KW - Sandy soil KW - Pinus sylvestris KW - Fagus sylvatica KW - Forest continuity KW - Historic land use KW - Nitrogen Y1 - 2013 U6 - https://doi.org/10.1016/j.foreco.2013.08.043 SN - 0378-1127 SN - 1872-7042 VL - 310 IS - 6 SP - 405 EP - 415 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Bröker, Nina Kristin A1 - Gohlke, Ulrich A1 - Müller, Jürgen J. A1 - Uetrecht, Charlotte A1 - Heinemann, Udo A1 - Seckler, Robert A1 - Barbirz, Stefanie T1 - Single amino acid exchange in bacteriophage HK620 tailspike protein results in thousand-fold increase of its oligosaccharide affinity JF - Glycobiology N2 - Bacteriophage HK620 recognizes and cleaves the O-antigen polysaccharide of Escherichia coli serogroup O18A1 with its tailspike protein (TSP). HK620TSP binds hexasaccharide fragments with low affinity, but single amino acid exchanges generated a set of high-affinity mutants with submicromolar dissociation constants. Isothermal titration calorimetry showed that only small amounts of heat were released upon complex formation via a large number of direct and solvent-mediated hydrogen bonds between carbohydrate and protein. At room temperature, association was both enthalpy- and entropy-driven emphasizing major solvent rearrangements upon complex formation. Crystal structure analysis showed identical protein and sugar conformers in the TSP complexes regardless of their hexasaccharide affinity. Only in one case, a TSP mutant bound a different hexasaccharide conformer. The extended sugar binding site could be dissected in two regions: first, a hydrophobic pocket at the reducing end with minor affinity contributions. Access to this site could be blocked by a single aspartate to asparagine exchange without major loss in hexasaccharide affinity. Second, a region where the specific exchange of glutamate for glutamine created a site for an additional water molecule. Side-chain rearrangements upon sugar binding led to desolvation and additional hydrogen bonding which define this region of the binding site as the high-affinity scaffold. KW - bacterial O-antigen KW - carbohydrate interaction KW - site-directed mutagenesis KW - structural thermodynamics KW - tailspike protein Y1 - 2013 U6 - https://doi.org/10.1093/glycob/cws126 SN - 0959-6658 VL - 23 IS - 1 SP - 59 EP - 68 PB - Oxford Univ. Press CY - Cary ER - TY - THES A1 - Razzaq, Muhammad Yasar T1 - Shape-memory investigations of magneto-sensitive polymer nanocomposites Y1 - 2013 CY - Potsdam ER - TY - CHAP A1 - Funkeu, A. D. M. A1 - Gouado, I. A1 - Schweigert, Florian J. A1 - Tchounguep, F. T1 - Serum response to a single dose of dietary carotenoids from steamed, fried and steam-dried squashes pulp (Cucurbita spp) T2 - Annals of nutrition & metabolism : journal of nutrition, metabolic diseases and dietetics ; an official journal of International Union of Nutritional Sciences (IUNS) KW - Squashes pulp KW - steamed KW - fried KW - steam-dried KW - carotenoids bioavailability Y1 - 2013 SN - 0250-6807 SN - 1421-9697 VL - 63 IS - 3 SP - 1501 EP - 1501 PB - Karger CY - Basel ER - TY - JOUR A1 - Hüttl, Christine A1 - Hettrich, Cornelia A1 - Miller, Reinhard A1 - Paulke, Bernd-Reiner A1 - Henklein, Petra A1 - Rawel, Harshadrai Manilal A1 - Bier, Frank Fabian T1 - Self-assembled peptide amphiphiles function as multivalent binder with increased hemagglutinin affinity JF - BMC biotechnology N2 - Background: A promising way in diagnostic and therapeutic applications is the development of peptide amphiphiles (PAs). Peptides with a palmitic acid alkylchain were designed and characterized to study the effect of the structure modifications on self-assembling capabilities and the multiple binding capacity to hemagglutinin (HA), the surface protein of influenza virus type A. The peptide amphiphiles consists of a hydrophilic headgroup with a biological functionality of the peptide sequence and a chemically conjugated hydrophobic tail. In solution they self-assemble easily to micelles with a hydrophobic core surrounded by a closely packed peptide-shell. Results: In this study the effect of a multiple peptide binding partner to the receptor binding site of HA could be determined with surface plasmon resonance measurements. The applied modification of the peptides causes signal amplification in relationship to the unmodified peptide wherein the high constant specificity persists. The molecular assembly of the peptides was characterized by the determination of critical micelle concentration (CMC) with concentration of 10(-5) M and the colloidal size distribution. Conclusion: The modification of the physico-chemical parameters by producing peptide amphiphiles form monomeric structures which enhances the binding affinity and allows a better examination of the interaction with the virus surface protein hemagglutinin. KW - CMC KW - Influenza virus detection KW - Micelle KW - PAs KW - Surface plasmon resonance Y1 - 2013 U6 - https://doi.org/10.1186/1472-6750-13-51 SN - 1472-6750 VL - 13 IS - 22 PB - BioMed Central CY - London ER - TY - JOUR A1 - Eccard, Jana A1 - Herde, Antje T1 - Seasonal variation in the behaviour of a short-lived rodent Y1 - 2013 UR - http://download.springer.com/static/pdf/700/art%253A10.1186%252F1472-6785-13- 43.pdf?auth66=1394893257_fb87cace3b247b85c3038fc43e5d93de&ext=.pdf U6 - https://doi.org/10.1186/1472-6785-13-43 ER - TY - GEN A1 - Eccard, Jana A1 - Herde, Antje T1 - Seasonal variation in the behaviour of a short-lived rodent N2 - Background: Short lived, iteroparous animals in seasonal environments experience variable social and environmental conditions over their lifetime. Animals can be divided into those with a "young-of-the-year" life history (YY, reproducing and dying in the summer of birth) and an "overwinter" life history (OW, overwintering in a subadult state before reproducing next spring). We investigated how behavioural patterns across the population were affected by season and sex, and whether variation in behaviour reflects the variation in life history patterns of each season. Applications of pace-of-life (POL) theory would suggest that long-lived OW animals are shyer in order to increase survival, and YY are bolder in order to increase reproduction. Therefore, we expected that in winter and spring samples, when only OW can be sampled, the animals should be shyer than in summer and autumn, when both OW and YY animals can be sampled. We studied common vole (Microtus arvalis) populations, which express typical, intra-annual density fluctuation. We captured a total of 492 voles at different months over 3 years and examined boldness and activity level with two standardised behavioural experiments. Results: Behavioural variables of the two tests were correlated with each other. Boldness, measured as short latencies in both tests, was extremely high in spring compared to other seasons. Activity level was highest in spring and summer, and higher in males than in females. Conclusion: Being bold in laboratory tests may translate into higher risk-taking in nature by being more mobile while seeking out partners or valuable territories. Possible explanations include asset-protection, with OW animals being rather old with low residual reproductive value in spring. Therefore, OW may take higher risks during this season. Offspring born in spring encounter a lower population density and may have higher reproductive value than offspring of later cohorts. A constant connection between life history and animal personality, as suggested by the POL theory, however, was not found. Nevertheless, correlations of traits suggest the existence of animal personalities. In conclusion, complex patterns of population dynamics, seasonal variation in life histories, and variability of behaviour due to asset-protection may cause complex seasonal behavioural dynamics in a population. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 403 KW - animal personalities KW - boldness KW - life history KW - pace-of-life KW - POL KW - phenotypic plasticity KW - common vole Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-401370 ER - TY - JOUR A1 - Hartwich, Melanie A1 - Martin-Creuzburg, Dominik A1 - Wacker, Alexander T1 - Seasonal changes in the accumulation of polyunsaturated fatty acids in zooplankton JF - Journal of plankton research N2 - In aquatic food webs, consumers, such as daphnids and copepods, differ regarding their accumulation of polyunsaturated fatty acids (PUFAs). We tested if the accumulation of PUFAs in a seston size fraction containing different consumers and in Daphnia as a separate consumer is subject to seasonal changes in a large deep lake due to changes in the dietary PUFA supply and specific demands of different consumers. We found that the accumulation of arachidonic acid (ARA) in Daphnia increased from early summer to late summer and autumn. However, ARA requirements of Daphnia appeared to be constant throughout the year, because the accumulation of ARA increased when the dietary ARA supply decreased. In the size fraction 140 m, we found an increased accumulation of docosahexaenoic acid (DHA) during late summer and autumn. These seasonal changes in DHA accumulation were linked to changes in the proportion of copepods in this size fraction, which may have increasingly accumulated DHA for active overwintering. We show that consumer-specific PUFA demands can result in seasonal changes in PUFA accumulation, which may influence the trophic transfer of PUFAs within the food web. KW - accumulation KW - Daphnia KW - copepods KW - ARA KW - DHA Y1 - 2013 U6 - https://doi.org/10.1093/plankt/fbs078 SN - 0142-7873 VL - 35 IS - 1 SP - 121 EP - 134 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Schmidt, Romy A1 - Mieulet, Delphine A1 - Hubberten, Hans-Michael A1 - Obata, Toshihiro A1 - Höfgen, Rainer A1 - Fernie, Alisdair R. A1 - Fisahn, Joachim A1 - Segundo, Blanca San A1 - Guiderdoni, Emmanuel A1 - Schippers, Jos H. M. A1 - Müller-Röber, Bernd T1 - Salt-responsive ERF1 regulates reactive oxygen species-dependent signaling during the initial response to salt stress in rice JF - The plant cell N2 - Early detection of salt stress is vital for plant survival and growth. Still, the molecular processes controlling early salt stress perception and signaling are not fully understood. Here, we identified SALT-RESPONSIVE ERF1 (SERF1), a rice (Oryza sativa) transcription factor (TF) gene that shows a root-specific induction upon salt and hydrogen peroxide (H2O2) treatment. Loss of SERF1 impairs the salt-inducible expression of genes encoding members of a mitogen-activated protein kinase (MAPK) cascade and salt tolerance-mediating TFs. Furthermore, we show that SERF1-dependent genes are H2O2 responsive and demonstrate that SERF1 binds to the promoters of MAPK KINASE KINASE6 (MAP3K6), MAPK5, DEHYDRATION-RESPONSIVE ELEMENT BINDING2A (DREB2A), and ZINC FINGER PROTEIN179 (ZFP179) in vitro and in vivo. SERF1 also directly induces its own gene expression. In addition, SERF1 is a phosphorylation target of MAPK5, resulting in enhanced transcriptional activity of SERF1 toward its direct target genes. In agreement, plants deficient for SERF1 are more sensitive to salt stress compared with the wild type, while constitutive overexpression of SERF1 improves salinity tolerance. We propose that SERF1 amplifies the reactive oxygen species-activated MAPK cascade signal during the initial phase of salt stress and translates the salt-induced signal into an appropriate expressional response resulting in salt tolerance. Y1 - 2013 U6 - https://doi.org/10.1105/tpc.113.113068 SN - 1040-4651 VL - 25 IS - 6 SP - 2115 EP - 2131 PB - American Society of Plant Physiologists CY - Rockville ER - TY - THES A1 - Verhounig, Andreas T1 - Riboswitche für die konditionale Genexpression in Bakterien und Plastiden Y1 - 2013 CY - Potsdam ER - TY - JOUR A1 - Arnison, Paul G. A1 - Bibb, Mervyn J. A1 - Bierbaum, Gabriele A1 - Bowers, Albert A. A1 - Bugni, Tim S. A1 - Bulaj, Grzegorz A1 - Camarero, Julio A. A1 - Campopiano, Dominic J. A1 - Challis, Gregory L. A1 - Clardy, Jon A1 - Cotter, Paul D. A1 - Craik, David J. A1 - Dawson, Michael A1 - Dittmann-Thünemann, Elke A1 - Donadio, Stefano A1 - Dorrestein, Pieter C. A1 - Entian, Karl-Dieter A1 - Fischbach, Michael A. A1 - Garavelli, John S. A1 - Goeransson, Ulf A1 - Gruber, Christian W. A1 - Haft, Daniel H. A1 - Hemscheidt, Thomas K. A1 - Hertweck, Christian A1 - Hill, Colin A1 - Horswill, Alexander R. A1 - Jaspars, Marcel A1 - Kelly, Wendy L. A1 - Klinman, Judith P. A1 - Kuipers, Oscar P. A1 - Link, A. James A1 - Liu, Wen A1 - Marahiel, Mohamed A. A1 - Mitchell, Douglas A. A1 - Moll, Gert N. A1 - Moore, Bradley S. A1 - Mueller, Rolf A1 - Nair, Satish K. A1 - Nes, Ingolf F. A1 - Norris, Gillian E. A1 - Olivera, Baldomero M. A1 - Onaka, Hiroyasu A1 - Patchett, Mark L. A1 - Piel, Jörn A1 - Reaney, Martin J. T. A1 - Rebuffat, Sylvie A1 - Ross, R. Paul A1 - Sahl, Hans-Georg A1 - Schmidt, Eric W. A1 - Selsted, Michael E. A1 - Severinov, Konstantin A1 - Shen, Ben A1 - Sivonen, Kaarina A1 - Smith, Leif A1 - Stein, Torsten A1 - Suessmuth, Roderich D. A1 - Tagg, John R. A1 - Tang, Gong-Li A1 - Truman, Andrew W. A1 - Vederas, John C. A1 - Walsh, Christopher T. A1 - Walton, Jonathan D. A1 - Wenzel, Silke C. A1 - Willey, Joanne M. A1 - van der Donk, Wilfred A. T1 - Ribosomally synthesized and post-translationally modified peptide natural products overview and recommendations for a universal nomenclature JF - Natural product reports : a journal of current developments in bio-organic chemistry N2 - This review presents recommended nomenclature for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), a rapidly growing class of natural products. The current knowledge regarding the biosynthesis of the >20 distinct compound classes is also reviewed, and commonalities are discussed. Y1 - 2013 U6 - https://doi.org/10.1039/c2np20085f SN - 0265-0568 VL - 30 IS - 1 SP - 108 EP - 160 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Czech, Andreas A1 - Wende, Sandra A1 - Moerl, Mario A1 - Pan, Tao A1 - Ignatova, Zoya T1 - Reversible and rapid transfer-RNA deactivation as a mechanism of translational repression in stress JF - PLoS Genetics : a peer-reviewed, open-access journal N2 - Stress-induced changes of gene expression are crucial for survival of eukaryotic cells. Regulation at the level of translation provides the necessary plasticity for immediate changes of cellular activities and protein levels. In this study, we demonstrate that exposure to oxidative stress results in a quick repression of translation by deactivation of the aminoacylends of all transfer-RNA (tRNA). An oxidative-stress activated nuclease, angiogenin, cleaves first within the conserved single-stranded 3'-CCA termini of all tRNAs, thereby blocking their use in translation. This CCA deactivation is reversible and quickly repairable by the CCA-adding enzyme [ATP(CTP): tRNA nucleotidyltransferase]. Through this mechanism the eukaryotic cell dynamically represses and reactivates translation at low metabolic costs. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pgen.1003767 SN - 1553-7404 VL - 9 IS - 8 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Sibly, Richard M. A1 - Grimm, Volker A1 - Martin, Benjamin T. A1 - Johnston, Alice S. A. A1 - Kulakowska, Katarzyna A1 - Topping, Christopher J. A1 - Calow, Peter A1 - Nabe-Nielsen, Jacob A1 - Thorbek, Pernille A1 - DeAngelis, Donald L. T1 - Representing the acquisition and use of energy by individuals in agent-based models of animal populations JF - Methods in ecology and evolution : an official journal of the British Ecological Society N2 - Agent-based models (ABMs) are widely used to predict how populations respond to changing environments. As the availability of food varies in space and time, individuals should have their own energy budgets, but there is no consensus as to how these should be modelled. Here, we use knowledge of physiological ecology to identify major issues confronting the modeller and to make recommendations about how energy budgets for use in ABMs should be constructed. Our proposal is that modelled animals forage as necessary to supply their energy needs for maintenance, growth and reproduction. If there is sufficient energy intake, an animal allocates the energy obtained in the order: maintenance, growth, reproduction, energy storage, until its energy stores reach an optimal level. If there is a shortfall, the priorities for maintenance and growth/reproduction remain the same until reserves fall to a critical threshold below which all are allocated to maintenance. Rates of ingestion and allocation depend on body mass and temperature. We make suggestions for how each of these processes should be modelled mathematically. Mortality rates vary with body mass and temperature according to known relationships, and these can be used to obtain estimates of background mortality rate. If parameter values cannot be obtained directly, then values may provisionally be obtained by parameter borrowing, pattern-oriented modelling, artificial evolution or from allometric equations. The development of ABMs incorporating individual energy budgets is essential for realistic modelling of populations affected by food availability. Such ABMs are already being used to guide conservation planning of nature reserves and shell fisheries, to assess environmental impacts of building proposals including wind farms and highways and to assess the effects on nontarget organisms of chemicals for the control of agricultural pests. KW - bioenergetics KW - energy budget KW - individual-based models KW - population dynamics Y1 - 2013 U6 - https://doi.org/10.1111/2041-210x.12002 SN - 2041-210X VL - 4 IS - 2 SP - 151 EP - 161 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Eccard, Jana A1 - Klemme, Ines T1 - Reducing mortality of shrews in rodent live trapping - a method increasing live-trap selectivity with shrew exits JF - Annales zoologici Fennici : descriptive, analytic and experimental zoology from the boreal region N2 - Shrews have very high metabolic rates and are often unintentionally starved in rodent live-traps during capture mark recapture (CMR) studies. Here, we suggest a shrew exit as a modification to rodent traps. To test whether this modification is (1) saving shrews and (2) not jeopardizing results of rodent captures, we compared captures in Ugglan traps with and without shrew exits, studying bank voles (Myodes glareolus) in a spruce forest in central Finland. Numbers of captured bank voles and body size of smallest juvenile bank voles were not affected by the shrew exit, while the number of captured common shrews (Sorex araneus) was reduced from 31 to 0 individuals per 100 trap nights. However, rare larger shrew species (> 8 g body weight) could not escape through the exit. A shrew exit can, therefore, save smaller shrew species in standard live-trapping of vole-sized rodents without affecting CMR data of the rodent. Y1 - 2013 SN - 0003-455X SN - 1797-2450 VL - 50 IS - 6 SP - 371 EP - 376 PB - Finnish Zoological and Botanical Publishing Board CY - Helsinki ER - TY - JOUR A1 - Milinkovitch, Michel C. A1 - Kanitz, Ricardo A1 - Tiedemann, Ralph A1 - Tapia, Washington A1 - Llerena, Fausto A1 - Caccone, Adalgisa A1 - Gibbs, James P. A1 - Powell, Jeffrey R. T1 - Recovery of a nearly extinct Galapagos tortoise despite minimal genetic variation JF - Evolutionary applications N2 - A species of Galapagos tortoise endemic to Espanola Island was reduced to just 12 females and three males that have been bred in captivity since 1971 and have produced over 1700 offspring now repatriated to the island. Our molecular genetic analyses of juveniles repatriated to and surviving on the island indicate that none of the tortoises sampled in 1994 had hatched on the island versus 3% in 2004 and 24% in 2007, which demonstrates substantial and increasing reproduction in situ once again. This recovery occurred despite the parental population having an estimated effective population size <8 due to a combination of unequal reproductive success of the breeders and nonrandom mating in captivity. These results provide guidelines for adapting breeding regimes in the parental captive population and decreasing inbreeding in the repatriated population. Using simple morphological data scored on the sampled animals, we also show that a strongly heterogeneous distribution of tortoise sizes on Espanola Island observed today is due to a large variance in the number of animals included in yearly repatriation events performed in the last 40years. Our study reveals that, at least in the short run, some endangered species can recover dramatically despite a lack of genetic variation and irregular repatriation efforts. KW - captive populations KW - conservation biology KW - conservation genetics Y1 - 2013 U6 - https://doi.org/10.1111/eva.12014 SN - 1752-4571 VL - 6 IS - 2 SP - 377 EP - 383 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Hoppe, Sebastian A1 - Bier, Frank Fabian A1 - von Nickisch-Rosenegk, Markus T1 - Rapid identification of novel immunodominant proteins and characterization of a specific linear epitope of campylobacter jejuni JF - PLoS one N2 - Campylobacter jejuni remains one of the major gut pathogens of our time. Its zoonotic nature and wide-spread distribution in industrialized countries calls for a quick and reliable diagnostic tool. Antibody-based detection presents a suitable means to identify pathogenic bacteria. However, the knowledge about immunodominant targets is limited. Thus, an approach is presented, which allows for the rapid screening of numerous cDNA derived expression clones to identify novel antigens. The deeper understanding of immunodominant proteins assists in the design of diagnostic tools and furthers the insight into the bacterium's pathogenicity as well as revealing potential candidates for vaccination. We have successfully screened 1536 clones of an expression library to identify 22 proteins that have not been described as immunodominant before. After subcloning the corresponding 22 genes and expression of full-length proteins, we investigated the immunodominant character by microarrays and ELISA. Subsequently, seven proteins were selected for epitope mapping. For cj0669 and cj0920c linear epitopes were identified. For cj0669, specificity assays revealed a specific linear epitope site. Consequently, an eleven amino acid residue sequence TLIKELKRLGI was analyzed via alanine scan, which revealed the glycine residue to be significant for binding of the antibody. The innovative approach presented herein of generating cDNAs of prokaryotes in combination with a microarray platform rendering time-consuming purification steps obsolete has helped to illuminate novel immunodominant proteins of C. jejuni. The findings of a specific linear epitope pave the way for a plethora of future research and the potential use in diagnostic applications such as serological screenings. Moreover, the current approach is easily adaptable to other highly relevant bacteria making it a formidable tool for the future discovery of antigens and potential biomarkers. Consequently, it is desirable to simplify the identification of structural epitopes, as this would extend the spectrum of novel epitopes to be detected. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0065837 SN - 1932-6203 VL - 8 IS - 5 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Franz, Kamila W. A1 - Romanowski, Jerzy A1 - Johst, Karin A1 - Grimm, Volker T1 - Ranking landscape development scenarios affecting natterjack toad (Bufo calamita) population dynamics in Central Poland JF - PLoS one N2 - When data are limited it is difficult for conservation managers to assess alternative management scenarios and make decisions. The natterjack toad (Bufo calamita) is declining at the edges of its distribution range in Europe and little is known about its current distribution and abundance in Poland. Although different landscape management plans for central Poland exist, it is unclear to what extent they impact this species. Based on these plans, we investigated how four alternative landscape development scenarios would affect the total carrying capacity and population dynamics of the natterjack toad. To facilitate decision-making, we first ranked the scenarios according to their total carrying capacity. We used the software RAMAS GIS to determine the size and location of habitat patches in the landscape. The estimated carrying capacities were very similar for each scenario, and clear ranking was not possible. Only the reforestation scenario showed a marked loss in carrying capacity. We therefore simulated metapopulation dynamics with RAMAS taking into account dynamical processes such as reproduction and dispersal and ranked the scenarios according to the resulting species abundance. In this case, we could clearly rank the development scenarios. We identified road mortality of adults as a key process governing the dynamics and separating the different scenarios. The renaturalisation scenario clearly ranked highest due to its decreased road mortality. Taken together our results suggest that road infrastructure development might be much more important for natterjack toad conservation than changes in the amount of habitat in the semi-natural river valley. We gained these insights by considering both the resulting metapopulation structure and dynamics in the form of a PVA. We conclude that the consideration of dynamic processes in amphibian conservation management may be indispensable for ranking management scenarios. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0064852 SN - 1932-6203 VL - 8 IS - 5 PB - PLoS CY - San Fransisco ER - TY - THES A1 - Mahro, Martin T1 - Purification and characterization of mouse aldehyde oxidase homologue 1 Y1 - 2013 CY - Potsdam ER - TY - CHAP A1 - Holzlöhner, Pamela A1 - Schliebs, Erik A1 - Maier, Natalia A1 - Füner, Jonas A1 - Micheel, Burkhard A1 - Heilmann, Katja T1 - Production of monoclonal camelid antibodies by means of hybridoma technology T2 - The journal of immunology Y1 - 2013 SN - 0022-1767 VL - 190 PB - American Assoc. of Immunologists CY - Bethesda ER - TY - JOUR A1 - Martin, Benjamin T. A1 - Jager, Tjalling A1 - Nisbet, Roger M. A1 - Preuss, Thomas G. A1 - Grimm, Volker T1 - Predicting population dynamics from the properties of individuals - a cross-level test of dynamic energy budget theory JF - The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences N2 - Individual-based models (IBMs) are increasingly used to link the dynamics of individuals to higher levels of biological organization. Still, many IBMs are data hungry, species specific, and time-consuming to develop and analyze. Many of these issues would be resolved by using general theories of individual dynamics as the basis for IBMs. While such theories have frequently been examined at the individual level, few cross-level tests exist that also try to predict population dynamics. Here we performed a cross-level test of dynamic energy budget (DEB) theory by parameterizing an individual-based model using individual-level data of the water flea, Daphnia magna, and comparing the emerging population dynamics to independent data from population experiments. We found that DEB theory successfully predicted population growth rates and peak densities but failed to capture the decline phase. Further assumptions on food-dependent mortality of juveniles were needed to capture the population dynamics after the initial population peak. The resulting model then predicted, without further calibration, characteristic switches between small-and large-amplitude cycles, which have been observed for Daphnia. We conclude that cross-level tests help detect gaps in current individual-level theories and ultimately will lead to theory development and the establishment of a generic basis for individual-based models and ecology. KW - population dynamics KW - dynamic energy budget theory KW - bioenergetics KW - individual-based model Y1 - 2013 U6 - https://doi.org/10.1086/669904 SN - 0003-0147 VL - 181 IS - 4 SP - 506 EP - 519 PB - Univ. of Chicago Press CY - Chicago ER - TY - JOUR A1 - Häring, Tim A1 - Reger, Birgit A1 - Ewald, Jörg A1 - Hothorn, Torsten A1 - Schröder-Esselbach, Boris T1 - Predicting Ellenberg's soil moisture indicator value in the Bavarian Alps using additive georegression JF - Applied vegetation science : official organ of the International Association for Vegetation Science N2 - Questions Can forest site characteristics be used to predict Ellenberg indicator values for soil moisture? Which is the best averaged mean value for modelling? Does the distribution of soil moisture depend on spatial information? Location Bavarian Alps, Germany. Methods We used topographic, climatic and edaphic variables to model the mean soil moisture value as found on 1505 forest plots from the database WINALPecobase. All predictor variables were taken from area-wide geodata layers so that the model can be applied to some 250 000 ha of forest in the target region. We adopted methods developed in species distribution modelling to regionalize Ellenberg indicator values. Therefore, we use the additive georegression framework for spatial prediction of Ellenberg values with the R-library mboost, which is a feasible way to consider environmental effects, spatial autocorrelation, predictor interactions and non-stationarity simultaneously in our data. The framework is much more flexible than established statistical and machine-learning models in species distribution modelling. We estimated five different mboost models reflecting different model structures on 50 bootstrap samples in each case. Results Median R2 values calculated on independent test samples ranged from 0.28 to 0.45. Our results show a significant influence of interactions and non-stationarity in addition to environmental covariates. Unweighted mean indicator values can be modelled better than abundance-weighted values, and the consideration of bryophytes did not improve model performance. Partial response curves indicate meaningful dependencies between moisture indicator values and environmental covariates. However, mean indicator values <4.5 and >6.0 could not be modelled correctly, since they were poorly represented in our calibration sample. The final map represents high-resolution information of site hydrological conditions. Conclusions Indicator values offer an effect-oriented alternative to physically-based hydrological models to predict water-related site conditions, even at landscape scale. The presented approach is applicable to all kinds of Ellenberg indicator values. Therefore, it is a significant step towards a new generation of models of forest site types and potential natural vegetation. KW - Boosting KW - Mboost KW - Non-stationarity KW - Predictive vegetation mapping KW - Site ecology KW - Species distribution modelling Y1 - 2013 U6 - https://doi.org/10.1111/j.1654-109X.2012.01210.x SN - 1402-2001 VL - 16 IS - 1 SP - 110 EP - 121 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Sauter, Tilman A1 - Kratz, Karl A1 - Lendlein, Andreas T1 - Pore-size distribution controls shape-memory properties on the macro- and microscale of polymeric foams JF - Macromolecular chemistry and physics N2 - Open porous foams with identical foam density but different pore-size distributions (bimodal or monomodal) are prepared from a shape-memory polyetherurethane (PEU) by thermally induced phase separation. The shape-memory effect of the two PEU foams is explored by cyclic thermomechanical compression tests and microstructural analysis. The obtained results reveal that the PEU foam with a bimodal pore-size distribution exhibits an increased shape-recovery under stress-free conditions, both on the macro- (foam level) as well as the microscale (pore level). While bimodal pore-size distributions induce microscale bending during compression, buckling occurs in foams with monomodal pore-size distributions, leading to both a reduced and delayed shape recovery. KW - microstructure KW - morphology KW - polymer foams KW - pore-size distribution KW - shape-memory polymers Y1 - 2013 U6 - https://doi.org/10.1002/macp.201300062 SN - 1022-1352 VL - 214 IS - 11 SP - 1184 EP - 1188 PB - Wiley-VCH CY - Weinheim ER - TY - CHAP A1 - Sauter, Tilman A1 - Lützow, Karola A1 - Schossig, Michael A1 - Kosmella, Hans A1 - Weigel, Thomas A1 - Kratz, Karl A1 - Lendlein, Andreas T1 - Pore morphology as structural parameter to tailor the shape-memory effect of polyuetherurethane foams T2 - Abstracts of papers : joint conference / The Chemical Institute of Cananda, CIC, American Chemical Society, ACS Y1 - 2013 SN - 0065-7727 VL - 245 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Meli, Mattia A1 - Auclerc, Apolline A1 - Palmqvist, Annemette A1 - Forbes, Valery E. A1 - Grimm, Volker T1 - Population-level consequences of spatially heterogeneous exposure to heavy metals in soil an individual-based model of springtails JF - Ecological modelling : international journal on ecological modelling and engineering and systems ecolog N2 - Contamination of soil with toxic heavy metals poses a major threat to the environment and human health. Anthropogenic sources include smelting of ores, municipal wastes, fertilizers, and pesticides. In assessing soil quality and the environmental and ecological risk of contamination with heavy metals, often homogeneous contamination of the soil is assumed. However, soils are very heterogeneous environments. Consequently, both contamination and the response of soil organisms can be assumed to be heterogeneous. This might have consequences for the exposure of soil organisms and for the extrapolation of risk from the individual to the population level. Therefore, to explore how soil contamination of different spatial heterogeneity affects population dynamics of soil invertebrates, we developed a spatially explicit individual-based model of the springtail, Folsomia candida, a standard test species for ecotoxicological risk assessment. In the model, individuals were assumed to sense and avoid contaminated habitat with a certain probability that depends on contamination level. Avoidance of contaminated areas thus influenced the individuals' movement and feeding, their exposure, and in turn all other biological processes underlying population dynamics. Model rules and parameters were based on data from the literature, or were determined via pattern-oriented modelling. The model correctly predicted several patterns that were not used for model design and calibration. Simulation results showed that the ability of the individuals to detect and avoid the toxicant, combined with the presence of clean habitat patches which act as "refuges", made equilibrium population size due to toxic effects less sensitive to increases in toxicant concentration. Additionally, the level of heterogeneity among patches of soil (i.e. the difference in concentration) was important: at the same average concentration, a homogeneously contaminated scenario was the least favourable habitat, while higher levels of heterogeneity corresponded to higher population growth rate and equilibrium size. Our model can thus be used as a tool for extrapolating from short-term effects at the individual level to long-term effects at the population level under more realistic conditions. It can thus be used to develop and extrapolate from standard ecotoxicological tests in the laboratory to ecological risk assessments. KW - Avoidance KW - Folsomia candida KW - Copper KW - Heterogeneity KW - Pattern-oriented modelling KW - Soil ecology Y1 - 2013 U6 - https://doi.org/10.1016/j.ecolmodel.2012.11.010 SN - 0304-3800 VL - 250 IS - 1 SP - 338 EP - 351 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Breitkopf, Hendrik A1 - Schlüter, P. M. A1 - Xu, S. A1 - Schiestl, Florian P. A1 - Cozzolino, S. A1 - Scopece, G. T1 - Pollinator shifts between Ophrys sphegodes populations: might adaptation to different pollinators drive population divergence? JF - Journal of evolutionary biology N2 - Local adaptation to different pollinators is considered one of the possible initial stages of ecological speciation as reproductive isolation is a by-product of the divergence in pollination systems. However, pollinator-mediated divergent selection will not necessarily result in complete reproductive isolation, because incipient speciation is often overcome by gene flow. We investigated the potential of pollinator shift in the sexually deceptive orchids Ophrys sphegodes and Ophrys exaltata and compared the levels of floral isolation vs. genetic distance among populations with contrasting predominant pollinators. We analysed floral hydrocarbons as a proxy for floral divergence between populations. Floral adoption of pollinators and their fidelity was tested using pollinator choice experiments. Interpopulation gene flow and population differentiation levels were estimated using AFLP markers. The Tyrrhenian O.sphegodes population preferentially attracted the pollinator bee Andrena bimaculata, whereas the Adriatic O.sphegodes population exclusively attracted A.nigroaenea. Significant differences in scent component proportions were identified in O.sphegodes populations that attracted different preferred pollinators. High interpopulation gene flow was detected, but populations were genetically structured at species level. The high interpopulation gene flow levels independent of preferred pollinators suggest that local adaptation to different pollinators has not (yet) generated detectable genome-wide separation. Alternatively, despite extensive gene flow, few genes underlying floral isolation remain differentiated as a consequence of divergent selection. Different pollination ecotypes in O.sphegodes might represent a local selective response imposed by temporal variation in a geographical mosaic of pollinators as a consequence of the frequent disturbance regimes typical of Ophrys habitats. KW - adaptation KW - ecotypes KW - floral scent KW - gene flow KW - Ophrys KW - orchids KW - pollinator shift KW - sexual deception KW - speciation Y1 - 2013 U6 - https://doi.org/10.1111/jeb.12216 SN - 1010-061X SN - 1420-9101 VL - 26 IS - 10 SP - 2197 EP - 2208 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Pedersen, Henrik AE. A1 - Watthana, Santi A1 - Kocyan, Alexander A1 - Srimuang, Kanok-orn T1 - Pollination biology of Luisia curtisii (Orchidaceae) indications of a deceptive system operated by beetles JF - Plant systematics and evolution N2 - A population of Luisia curtisii (Orchidaceae: Aeridinae) in northern Thailand was studied with regard to pollination biology. Although a high level of self-compatibility was demonstrated experimentally, the very low natural fruit set (1.4-1.9 %) clearly indicated that the species depends on external agents for pollination. Our observations suggest that L. curtisii is pollinated by beetles, as Lema unicolor (Chrysomelidae) and Clinteria ducalis (Scarabaeidae) were the only flower visitors observed to carry pollinaria of this species. The hypothesis of specialised cantharophily is further supported by 2-methylbutyric acid and caproic acid being striking components of the floral scent. Judging from the lack of nectar and the behaviour of visiting beetles, the pollination system seems to rely on food or brood site deception. Retention of the anther on the pollinarium for some time after pollinarium removal probably reduces the frequency of insect-mediated autogamy and geitonogamy in Luisia curtisii-a possibility that was supported by comparative data on (1) the anther retention time and inflorescence visitation time of Lema unicolor and (2) stigma and anther length in the orchid. Existing reports of specialised beetle pollination in orchids are reviewed, and we conclude that there is accumulating evidence that specialised cantharophily is more common in the Orchidaceae than previously assumed. KW - Allogamy KW - Anther retention KW - Cantharophily KW - Floral scent KW - Fruit set KW - Outcrossing Y1 - 2013 U6 - https://doi.org/10.1007/s00606-012-0713-6 SN - 0378-2697 VL - 299 IS - 1 SP - 177 EP - 185 PB - Springer CY - Wien ER - TY - JOUR A1 - Lin, Yue A1 - Berger, Uta A1 - Grimm, Volker A1 - Huth, Franka A1 - Weiner, Jacob T1 - Plant interactions alter the predictions of metabolic scaling theory JF - PLoS one N2 - Metabolic scaling theory (MST) is an attempt to link physiological processes of individual organisms with macroecology. It predicts a power law relationship with an exponent of -4/3 between mean individual biomass and density during density-dependent mortality (self-thinning). Empirical tests have produced variable results, and the validity of MST is intensely debated. MST focuses on organisms' internal physiological mechanisms but we hypothesize that ecological interactions can be more important in determining plant mass-density relationships induced by density. We employ an individual-based model of plant stand development that includes three elements: a model of individual plant growth based on MST, different modes of local competition (size-symmetric vs. -asymmetric), and different resource levels. Our model is consistent with the observed variation in the slopes of self-thinning trajectories. Slopes were significantly shallower than -4/3 if competition was size-symmetric. We conclude that when the size of survivors is influenced by strong ecological interactions, these can override predictions of MST, whereas when surviving plants are less affected by interactions, individual-level metabolic processes can scale up to the population level. MST, like thermodynamics or biomechanics, sets limits within which organisms can live and function, but there may be stronger limits determined by ecological interactions. In such cases MST will not be predictive. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0057612 SN - 1932-6203 VL - 8 IS - 2 PB - PLoS CY - San Fransisco ER - TY - INPR A1 - Kaufmann, Kerstin A1 - Busch, Wolfgang T1 - Plant genomics from weed to wheat T2 - Genome biology : biology for the post-genomic era N2 - A report on the first 'Plant Genomics Congress' meeting, held in London, UK, 12-13 May 2013. Y1 - 2013 U6 - https://doi.org/10.1186/gb-2013-14-6-308 SN - 1465-6906 SN - 1474-760X VL - 14 IS - 6 PB - BioMed Central CY - London ER - TY - JOUR A1 - May, Felix A1 - Giladi, Itamar A1 - Ristow, Michael A1 - Ziv, Yaron A1 - Jeltsch, Florian T1 - Plant functional traits and community assembly along interacting gradients of productivity and fragmentation JF - Perspectives in plant ecology, evolution and systematics N2 - Quantifying the association of plant functional traits to environmental gradients is a promising approach for understanding and projecting community responses to land use and climatic changes. Although habitat fragmentation and climate are expected to affect plant communities interactively, there is a lack of empirical studies addressing trait associations to fragmentation in different climatic regimes. In this study, we analyse data on the key functional traits: specific leaf area (SLA), plant height, seed mass and seed number. First, we assess the evidence for the community assembly mechanisms habitat filtering and competition at different spatial scales, using several null-models and a comprehensive set of community-level trait convergence and divergence indices. Second, we analyse the association of community-mean traits with patch area and connectivity along a south-north productivity gradient. We found clear evidence for trait convergence due to habitat filtering. In contrast, the evidence for trait divergence due to competition fundamentally depended on the null-model used. When the null-model controlled for habitat filtering, there was only evidence for trait divergence at the smallest sampling scale (0.25 m x 0.25 m). All traits varied significantly along the S-N productivity gradient. While plant height and SLA were consistently associated with fragmentation, the association of seed mass and seed number with fragmentation changed along the S-N gradient. Our findings indicate trait convergence due to drought stress in the arid sites and due to higher productivity in the mesic sites. The association of plant traits to fragmentation is likely driven by increased colonization ability in small and/or isolated patches (plant height, seed number) or increased persistence ability in isolated patches (seed mass). Our study provides the first empirical test of trait associations with fragmentation along a productivity gradient. We conclude that it is crucial to study the interactive effects of different ecological drivers on plant functional traits. KW - Connectivity KW - Drought-stress KW - Habitat filtering KW - Limiting similarity KW - Null models KW - Plant height KW - Seed mass KW - Seed number KW - Specific leaf area (SLA) Y1 - 2013 U6 - https://doi.org/10.1016/j.ppees.2013.08.002 SN - 1433-8319 VL - 15 IS - 6 SP - 304 EP - 318 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Brothers, Soren M. A1 - Hilt, Sabine A1 - Meyer, Stephanie A1 - Köhler, Jan T1 - Plant community structure determines primary productivity in shallow, eutrophic lakes JF - Freshwater biology N2 - Regime shifts are commonly associated with the loss of submerged macrophytes in shallow lakes; yet, the effects of this on whole-lake primary productivity remain poorly understood. This study compares the annual gross primary production (GPP) of two shallow, eutrophic lakes with different plant community structures but similar nutrient concentrations. Daily GPP rates were substantially higher in the lake containing submerged macrophytes (58623gCm(-2)year(-1)) than in the lake featuring only phytoplankton and periphyton (40823gCm(-2)year(-1); P<0.0001). Comparing lake-centre diel oxygen curves to compartmental estimates of GPP confirmed that single-site oxygen curves may provide unreliable estimates of whole-lake GPP. The discrepancy between approaches was greatest in the macrophyte-dominated lake during the summer, with a high proportion of GPP occurring in the littoral zone. Our empirical results were used to construct a simple conceptual model relating GPP to nutrient availability for these alternative ecological regimes. This model predicted that lakes featuring submerged macrophytes may commonly support higher rates of GPP than phytoplankton-dominated lakes, but only within a moderate range of nutrient availability (total phosphorus ranging from 30 to 100gL(-1)) and with mean lake depths shallower than 3 or 4m. We conclude that shallow lakes with a submerged macrophyte-epiphyton complex may frequently support a higher annual primary production than comparable lakes that contain only phytoplankton and periphyton. We thus suggest that a regime shift involving the loss of submerged macrophytes may decrease the primary productivity of many lakes, with potential consequences for the entire food webs of these ecosystems. KW - macrophytes KW - oxygen curves KW - periphyton KW - regime shift KW - trophic status Y1 - 2013 U6 - https://doi.org/10.1111/fwb.12207 SN - 0046-5070 VL - 58 IS - 11 SP - 2264 EP - 2276 PB - Wiley-Blackwell CY - Hoboken ER - TY - THES A1 - Nitschke, Felix T1 - Phosphorylation of polyglycans, especially glycogen and starch T1 - Phosphorylierung von Polysacchariden, insbesondere bei Glykogen und Stärke N2 - Functional metabolism of storage carbohydrates is vital to plants and animals. The water-soluble glycogen in animal cells and the amylopectin which is the major component of water-insoluble starch granules residing in plant plastids are chemically similar as they consist of α-1,6 branched α-1,4 glucan chains. Synthesis and degradation of transitory starch and of glycogen are accomplished by a set of enzymatic activities that to some extend are also similar in plants and animals. Chain elongation, branching, and debranching are achieved by synthases, branching enzymes, and debranching enzymes, respectively. Similarly, both types of polyglucans contain low amounts of phosphate esters whose abundance varies depending on species and organs. Starch is selectively phosphorylated by at least two dikinases (GWD and PWD) at the glucosyl carbons C6 and C3 and dephosphorylated by the phosphatase SEX4 and SEX4-like enzymes. In Arabidopsis insufficiency in starch phosphorylation or dephosphorylation results in largely impaired starch turnover, starch accumulation, and often in retardation of growth. In humans the progressive neurodegenerative epilepsy, Lafora disease, is the result of a defective enzyme (laforin) that is functional equivalent to the starch phosphatase SEX4 and capable of glycogen dephosphorylation. Patients lacking laforin progressively accumulate unphysiologically structured insoluble glycogen-derived particles (Lafora bodies) in many tissues including brain. Previous results concerning the carbon position of glycogen phosphate are contradictory. Currently it is believed that glycogen is esterified exclusively at the carbon positions C2 and C3 and that the monophosphate esters, being incorporated via a side reaction of glycogen synthase (GS), lack any specific function but are rather an enzymatic error that needs to be corrected. In this study a versatile and highly sensitive enzymatic cycling assay was established that enables quantification of very small G6P amounts in the presence of high concentrations of non-target compounds as present in hydrolysates of polysaccharides, such as starch, glycogen, or cytosolic heteroglycans in plants. Following validation of the G6P determination by analyzing previously characterized starches G6P was quantified in hydrolysates of various glycogen samples and in plant heteroglycans. Interestingly, glucosyl C6 phosphate is present in all glycogen preparations examined, the abundance varying between glycogens of different sources. Additionally, it was shown that carbon C6 is severely hyperphosphorylated in glycogen of Lafora disease mouse model and that laforin is capable of removing C6 phosphate from glycogen. After enrichment of phosphoglucans from amylolytically degraded glycogen, several techniques of two-dimensional NMR were applied that independently proved the existence of 6-phosphoglucosyl residues in glycogen and confirmed the recently described phosphorylation sites C2 and C3. C6 phosphate is neither Lafora disease- nor species-, or organ-specific as it was demonstrated in liver glycogen from laforin-deficient mice and in that of wild type rabbit skeletal muscle. The distribution of 6-phosphoglucosyl residues was analyzed in glycogen molecules and has been found to be uneven. Gradual degradation experiments revealed that C6 phosphate is more abundant in central parts of the glycogen molecules and in molecules possessing longer glucan chains. Glycogen of Lafora disease mice consistently contains a higher proportion of longer chains while most short chains were reduced as compared to wild type. Together with results recently published (Nitschke et al., 2013) the findings of this work completely unhinge the hypothesis of GS-mediated phosphate incorporation as the respective reaction mechanism excludes phosphorylation of this glucosyl carbon, and as it is difficult to explain an uneven distribution of C6 phosphate by a stochastic event. Indeed the results rather point to a specific function of 6-phosphoglucosyl residues in the metabolism of polysaccharides as they are present in starch, glycogen, and, as described in this study, in heteroglycans of Arabidopsis. In the latter the function of phosphate remains unclear but this study provides evidence that in starch and glycogen it is related to branching. Moreover a role of C6 phosphate in the early stages of glycogen synthesis is suggested. By rejecting the current view on glycogen phosphate to be a stochastic biochemical error the results permit a wider view on putative roles of glycogen phosphate and on alternative biochemical ways of glycogen phosphorylation which for many reasons are likely to be mediated by distinct phosphorylating enzymes as it is realized in starch metabolism of plants. Better understanding of the enzymology underlying glycogen phosphorylation implies new possibilities of Lafora disease treatment. N2 - Pflanzen und Tiere speichern Glukose in hochmolekularen Kohlenhydraten, um diese bei Bedarf unter anderem zur Gewinnung von Energie zu nutzen. Amylopectin, der größte Bestandteil des pflanzlichen Speicherkohlenhydrats Stärke, und das tierische Äquivalent Glykogen sind chemisch betrachtet ähnlich, denn sie bestehen aus verzweigten Ketten, deren Bausteine (Glukosylreste) auf identische Weise miteinander verbunden sind. Zudem kommen in beiden Kohlenhydraten kleine aber ähnliche Mengen von Phosphatgruppen vor, die offenbar eine tragende Rolle in Pflanzen und Tieren spielen. Ist in Pflanzen der Einbau oder die Entfernung von Phosphatgruppen in bzw. aus Stärke gestört, so ist oft der gesamte Stärkestoffwechsel beeinträchtigt. Dies zeigt sich unter anderem in der übermäßigen Akkumulation von Stärke und in Wachstumsverzögerungen der gesamten Pflanze. Beim Menschen und anderen Säugern beruht eine schwere Form der Epilepsie (Lafora disease) auf einer Störung des Glykogenstoffwechsels. Sie wird durch das erblich bedingte Fehlen eines Enzyms ausgelöst, das Phosphatgruppen aus dem Glykogen entfernt. Während die Enzyme, die für die Entfernung des Phosphats aus Stärke und Glykogen verantwortlich sind, hohe Ähnlichkeit aufweisen, ist momentan die Ansicht weit verbreitet, dass der Einbau von Phosphat in beide Speicherkohlenhydrate auf höchst unterschiedliche Weise erfolgt. In Pflanzen sind zwei Enzyme bekannt, die Phosphatgruppen an unterschiedlichen Stellen in Glukosylreste einbauen (Kohlenstoffatome 6 und 3). In Tieren soll eine seltene, unvermeidbare und zufällig auftretende Nebenreaktion eines Enzyms, das eigentlich die Ketten des Glykogens verlängert (Glykogen-Synthase), den Einbau von Phosphat bewirken, der somit als unwillkürlich gilt und weithin als „biochemischer Fehler“ (mit fatalen Konsequenzen bei ausbleibender Korrektur) betrachtet wird. In den Glukosylresten des Glykogens sollen ausschließlich die C-Atome 2 und 3 phosphoryliert sein. Die Ergebnisse dieser Arbeit zeigen mittels zweier unabhängiger Methoden, dass Glykogen auch am Glukosyl-Kohlenstoff 6 phosphoryliert ist, der Phosphatposition, die in der Stärke am häufigsten vorkommt. Die Tatsache, dass in dieser Arbeit Phosphat neben Stärke auch erstmals an Glukosylresten von anderen pflanzlichen Kohlenhydraten (wasserlösliche Heteroglykane) nachgewiesen werden konnte, lässt vermuten, dass Phosphorylierung ein generelles Phänomen bei Polysacchariden ist. Des Weiteren wiesen die Ergebnisse darauf hin, dass Phosphat im Glykogen, wie auch in der Stärke, einem bestimmten Zweck dient, der im Zusammenhang mit der Regulation von Kettenverzweigung steht, und dass kein zufälliges biochemisches Ereignis für den Einbau verantwortlich sein kann. Aufgrund der grundlegenden Ähnlichkeiten im Stärke- und Glykogenstoffwechsel, liegt es nahe, dass die Phosphorylierung von Glykogen, ähnlich der von Stärke, ebenfalls durch spezifische Enzyme bewirkt wird. Ein besseres Verständnis der Mechanismen, die der Glykogen-Phosphorylierung zugrunde liegen, kann neue Möglichkeiten der Behandlung von Lafora disease aufzeigen. KW - Stärke KW - Glykogen KW - Phosphorylierung KW - NMR KW - Lafora disease KW - starch KW - glycogen KW - phosphorylation KW - NMR KW - Lafora disease Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-67396 ER - TY - JOUR A1 - Sultanow, Eldar A1 - Weber, Edzard T1 - Pharmataxigraphie Model of a Hybrid System of RFID Technology and optical Methods JF - Die pharmazeutische Industrie Y1 - 2013 SN - 0031-711X VL - 75 IS - 7 SP - 1197 EP - + PB - Editio-Cantor-Verl. für Medizin und Naturwiss. CY - Aulendorf ER - TY - JOUR A1 - Pavesi, Laura A1 - Ketmaier, Valerio T1 - Patterns of genetics structuring and levels of differentiation in supralittoral talitrid amphipods - an overview JF - Crustaceana : international journal of crustacean research N2 - Talitrids are the only family within the order Amphipoda to have colonised supralittoral and terrestrial environments. They live in a variety of settings, from sandy to rocky and pebble beaches, to river and lake banks, and to leaf litter and caves. A common feature is the absence of a planktonic larval stage to facilitate passive dispersal over long-distances. However, some species have broad distributions. Genetic studies over the past 25 years have tried to explain this apparent contradiction by assessing patterns of species genetic structuring on different geographical scales. Here, we review the molecular studies available to date and focus on the population genetics of talitrids. Most of these studies considered populations in the Mediterranean area, but also along the Atlantic coast and in Canary Island caves. From this review, the group emerges as a potential model to understand processes of dispersal and divergence in non-highly-vagile supralittoral organisms. At the same time, studies on these issues are still too restricted geographically: a worldwide scale including different regions would provide us with a better perspective on these problems. KW - Supralittoral talitrids KW - dispersal KW - gene flow KW - allozymes KW - mitochondrial DNA KW - microsatellites Y1 - 2013 U6 - https://doi.org/10.1163/15685403-00003212 SN - 0011-216X VL - 86 IS - 7-8 SP - 890 EP - 907 PB - Brill CY - Leiden ER - TY - JOUR A1 - Einarsson, Jon M. A1 - Bahrke, Sven A1 - Sigurdsson, Bjarni Thor A1 - Ng, Chuen-How A1 - Petersen, Petur Henry A1 - Sigurjonsson, Olafur E. A1 - Jonsson, Halldor A1 - Gislason, Johannes A1 - Thormodsson, Finnbogi R. A1 - Peter, Martin G. T1 - Partially acetylated chitooligosaccharides bind to YKL-40 and stimulate growth of human osteoarthritic chondrocytes JF - Biochemical and biophysical research communications N2 - Recent evidences indicating that cellular kinase signaling cascades are triggered by oligomers of N-acetylglucosamine (ChOS) and that condrocytes of human osteoarthritic cartilage secrete the inflammation associated chitolectin YKL-40, prompted us to study the binding affinity of partially acetylated ChOS to YKL-40 and their effect on primary chondrocytes in culture. Extensive chitinase digestion and filtration of partially deacetylated chitin yielded a mixture of ChOS (Oligomin(TM)) and further ultrafiltration produced T-ChOS(TM), with substantially smaller fraction of the smallest sugars. YKL-40 binding affinity was determined for the different sized homologues, revealing micromolar affinities of the larger homologues to YKL-40. The response of osteoarthritic chondrocytes to Oligomin(TM) and T-ChOS(TM) was determined, revealing 2- to 3-fold increases in cell number. About 500 mu g/ml was needed for Oligomin(TM) and around five times lower concentration for T-ChOS(TM), higher concentrations abolished this effect for both products. Addition of chitotriose inhibited cellular responses mediated by larger oligosaccharides. These results, and the fact that the partially acetylated T-ChOS(TM) homologues should resist hydrolysis, point towards a new therapeutic concept for treating inflammatory joint diseases. KW - Cell culture KW - Chitolectin KW - Chitooligosaccharides KW - Chondrocytes KW - High affinity binding KW - Rheumatoid arthritis KW - YKL-40 Y1 - 2013 U6 - https://doi.org/10.1016/j.bbrc.2013.02.122 SN - 0006-291X VL - 434 IS - 2 SP - 298 EP - 304 PB - Elsevier CY - San Diego ER - TY - JOUR A1 - Read, Betsy A. A1 - Kegel, Jessica A1 - Klute, Mary J. A1 - Kuo, Alan A1 - Lefebvre, Stephane C. A1 - Maumus, Florian A1 - Mayer, Christoph A1 - Miller, John A1 - Monier, Adam A1 - Salamov, Asaf A1 - Young, Jeremy A1 - Aguilar, Maria A1 - Claverie, Jean-Michel A1 - Frickenhaus, Stephan A1 - Gonzalez, Karina A1 - Herman, Emily K. A1 - Lin, Yao-Cheng A1 - Napier, Johnathan A1 - Ogata, Hiroyuki A1 - Sarno, Analissa F. A1 - Shmutz, Jeremy A1 - Schroeder, Declan A1 - de Vargas, Colomban A1 - Verret, Frederic A1 - von Dassow, Peter A1 - Valentin, Klaus A1 - Van de Peer, Yves A1 - Wheeler, Glen A1 - Dacks, Joel B. A1 - Delwiche, Charles F. A1 - Dyhrman, Sonya T. A1 - Glöckner, Gernot A1 - John, Uwe A1 - Richards, Thomas A1 - Worden, Alexandra Z. A1 - Zhang, Xiaoyu A1 - Grigoriev, Igor V. A1 - Allen, Andrew E. A1 - Bidle, Kay A1 - Borodovsky, M. A1 - Bowler, C. A1 - Brownlee, Colin A1 - Cock, J. Mark A1 - Elias, Marek A1 - Gladyshev, Vadim N. A1 - Groth, Marco A1 - Guda, Chittibabu A1 - Hadaegh, Ahmad A1 - Iglesias-Rodriguez, Maria Debora A1 - Jenkins, J. A1 - Jones, Bethan M. A1 - Lawson, Tracy A1 - Leese, Florian A1 - Lindquist, Erika A1 - Lobanov, Alexei A1 - Lomsadze, Alexandre A1 - Malik, Shehre-Banoo A1 - Marsh, Mary E. A1 - Mackinder, Luke A1 - Mock, Thomas A1 - Müller-Röber, Bernd A1 - Pagarete, Antonio A1 - Parker, Micaela A1 - Probert, Ian A1 - Quesneville, Hadi A1 - Raines, Christine A1 - Rensing, Stefan A. A1 - Riano-Pachon, Diego Mauricio A1 - Richier, Sophie A1 - Rokitta, Sebastian A1 - Shiraiwa, Yoshihiro A1 - Soanes, Darren M. A1 - van der Giezen, Mark A1 - Wahlund, Thomas M. A1 - Williams, Bryony A1 - Wilson, Willie A1 - Wolfe, Gordon A1 - Wurch, Louie L. T1 - Pan genome of the phytoplankton Emiliania underpins its global distribution JF - Nature : the international weekly journal of science N2 - Coccolithophores have influenced the global climate for over 200 million years(1). These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems(2). They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space(3). Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean(4). Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions. Y1 - 2013 U6 - https://doi.org/10.1038/nature12221 SN - 0028-0836 SN - 1476-4687 VL - 499 IS - 7457 SP - 209 EP - 213 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Rauf, Mamoona A1 - Arif, Muhammad A1 - Dortay, Hakan A1 - Matallana-Ramirez, Lilian P. A1 - Waters, Mark T. A1 - Nam, Hong Gil A1 - Lim, Pyung-Ok A1 - Müller-Röber, Bernd A1 - Balazadeh, Salma T1 - ORE1 balances leaf senescence against maintenance by antagonizing G2-like-mediated transcription JF - EMBO reports N2 - Leaf senescence is a key physiological process in all plants. Its onset is tightly controlled by transcription factors, of which NAC factor ORE1 (ANAC092) is crucial in Arabidopsis thaliana. Enhanced expression of ORE1 triggers early senescence by controlling a downstream gene network that includes various senescence-associated genes. Here, we report that unexpectedly ORE1 interacts with the G2-like transcription factors GLK1 and GLK2, which are important for chloroplast development and maintenance, and thereby for leaf maintenance. ORE1 antagonizes GLK transcriptional activity, shifting the balance from chloroplast maintenance towards deterioration. Our finding identifies a new mechanism important for the control of senescence by ORE1. KW - transcription factor KW - senescence KW - chloroplast KW - protein-protein interaction Y1 - 2013 U6 - https://doi.org/10.1038/embor.2013.24 SN - 1469-221X VL - 14 IS - 4 SP - 382 EP - 388 PB - Nature Publ. Group CY - London ER - TY - THES A1 - Coroca Cáceres, Rodrigo Sebastian T1 - Optimazion of expression casettes for high-level gene activity in chromopalast and study of the essential gene accD in tobacco Y1 - 2013 CY - Potsdam ER - TY - JOUR A1 - Neigenfind, Jost A1 - Grimbs, Sergio A1 - Nikoloski, Zoran T1 - On the relation between reactions and complexes of (bio)chemical reaction networks JF - Journal of theoretical biology N2 - Robustness of biochemical systems has become one of the central questions in systems biology although it is notoriously difficult to formally capture its multifaceted nature. Maintenance of normal system function depends not only on the stoichiometry of the underlying interrelated components, but also on the multitude of kinetic parameters. Invariant flux ratios, obtained within flux coupling analysis, as well as invariant complex ratios, derived within chemical reaction network theory, can characterize robust properties of a system at steady state. However, the existing formalisms for the description of these invariants do not provide full characterization as they either only focus on the flux-centric or the concentration-centric view. Here we develop a novel mathematical framework which combines both views and thereby overcomes the limitations of the classical methodologies. Our unified framework will be helpful in analyzing biologically important system properties. KW - Metabolic network KW - Mass action system KW - Flux coupling analysis KW - Chemical reaction network theory Y1 - 2013 U6 - https://doi.org/10.1016/j.jtbi.2012.10.016 SN - 0022-5193 VL - 317 IS - 2 SP - 359 EP - 365 PB - Elsevier CY - London ER - TY - THES A1 - Picchi, Douglas Gatte T1 - On the characterisation of biosynthetic pathways and functional metagenomic approaches of cyanobacterial peptides Y1 - 2013 CY - Potsdam ER - TY - JOUR A1 - Burgold, Julia A1 - Rolfes, Manfred T1 - Of voyeuristic safari tours and responsible tourism with educational value observing moral communication in slum and township tourism in Cape Town and Mumbai JF - Die Erde : journal of the Geographical Society of Berlin ; Zeitschrift der Gesellschaft für Erdkunde zu Berlin N2 - Sightseeing in the poorest quarters of southern hemisphere cities has been observed occurring in Cape Town, Rio de Janeiro, Mumbai and many other cities. The increasing global interest in touring poor urban environments is accompanied by a strong morally charged debate; so far, this debate has not been critically addressed. This article avoids asking if slum tourism is good or bad, but instead seeks a second-order observation, i.e. to investigate under what conditions the social praxis of slum tourism is considered as good or bad, by processing information on esteem or dis-esteem among tourists and tour providers. Special attention is given to any relation between morality and place, and the thesis posited is that the moral charging of slum tourism is dependent on the presence of specific preconceived notions of slums and poverty. This shall be clarified by means of references to two empirical case studies carried out in (1) Cape Town in 2007 and 2008 and (2) Mumbai in 2009. KW - Slum tourism KW - township tourism KW - morality KW - place Y1 - 2013 SN - 0013-9998 VL - 144 IS - 2 SP - 161 EP - 174 PB - Gesellschaft für Erdkunde CY - Berlin ER - TY - JOUR A1 - Wagner, Nicole D. A1 - Hillebrand, Helmut A1 - Wacker, Alexander A1 - Frost, Paul C. T1 - Nutritional indicators and their uses in ecology JF - Ecology letters N2 - The nutrition of animal consumers is an important regulator of ecological processes due to its effects on their physiology, life-history and behaviour. Understanding the ecological effects of poor nutrition depends on correctly diagnosing the nature and strength of nutritional limitation. Despite the need to assess nutritional limitation, current approaches to delineating nutritional constraints can be non-specific and imprecise. Here, we consider the need and potential to develop new complementary approaches to the study of nutritional constraints on animal consumers by studying and using a suite of established and emerging biochemical and molecular responses. These nutritional indicators include gene expression, transcript regulators, protein profiling and activity, and gross biochemical and elemental composition. The potential applications of nutritional indicators to ecological studies are highlighted to demonstrate the value that this approach would have to future studies in community and ecosystem ecology. KW - Ecological stoichiometry KW - lipid profiling KW - metabolism KW - nutrient-stress KW - nutrition KW - proteomics KW - transcriptomics Y1 - 2013 U6 - https://doi.org/10.1111/ele.12067 SN - 1461-023X VL - 16 IS - 4 SP - 535 EP - 544 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Gläser, Stefanie P. A1 - Bolte, Kathrin A1 - Martin, Karin A1 - Busse, Hans-Jürgen A1 - Grossart, Hans-Peter A1 - Kämpfer, Peter A1 - Gläser, Jens T1 - Novosphingobium fuchskuhlense sp nov., isolated from the north-east basin of Lake Grosse Fuchskuhle JF - International journal of systematic and evolutionary microbiology N2 - A yellow pigmented, Gram-negative, rod-shaped bacterium designated FNE08-7(T) was isolated from subsurface water of the north-east basin of the bog lake Grosse Fuchskuhle (Brandenburg, Germany). A first analysis of the nearly full-length 16S rRNA gene sequence analysis including environmental 16S rRNA gene sequences derived from freshwater ecosystems showed that strain FNE08-7(T) is the first cultured representative, to our knowledge, of the freshwater tribe Novo-A2. Further analysis indicates highest 16S rRNA gene sequence similarities to the type strains of Novosphingobium stygium (98.0%) and Novosphingobium taihuense (97.4%) and between 94.0% and 96.9% sequence similarity to other members of the genus Novosphingobium. Reconstruction of phylogenetic trees showed that strain FNE08-7(T) formed a distinct cluster with the type strains of N. stygium and N. taihuense supported by high bootstrap values. DNA DNA hybridization of strain FNE08-7(T) with N. stygium SMCC B0712(T) and N. taihuense DSM 17507(T) revealed low similarity values of 18.4% (reciprocal: 11.4%) and 23.1% (reciprocal: 54.2%), respectively. The predominant fatty acid of the isolate is C-18:1 omega 7c (56.4%) and two characteristic 2-hydroxy fatty acids, C-14:0 2-OH (16.5%) and C-15:0 2-OH (3.3%) occur. Ubiquinone Q-10 is the major respiratory quinone. The predominant polar lipids are phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, sphingoglycolipid, phosphatidylcholine and minor amounts of diphosphatidylglycerol. Spermidine is the predominant polyamine. Characterization by genotypic, chemotaxonomic and phenotypic analysis indicate that strain FNE08-7(T) represents a novel species of the genus Novosphingobium within the Alphaproteobacteria. Therefore, we propose the species Novosphingobium fuchskuhlense sp. nov., with FNE08-7(T) (=DSM 25065(T)=CCM 7978(T)=CCUG 61508(T)) as the type strain. Y1 - 2013 U6 - https://doi.org/10.1099/ijs.0.043083-0 SN - 1466-5026 VL - 63 SP - 586 EP - 592 PB - Society for General Microbiology CY - Reading ER - TY - CHAP A1 - Memczak, Henry A1 - Lauster, Daniel A1 - Herrmann, Andreas A1 - Stöcklein, Walter F. M. A1 - Bier, Frank Fabian T1 - Novel hemagglutinin-binding peptides for biosensing and inhibition of Influenza Viruses T2 - Biopolymers Y1 - 2013 SN - 0006-3525 SN - 1097-0282 VL - 100 IS - 3 SP - 255 EP - 255 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Tanentzap, Andrew J. A1 - Lee, William G. A1 - Schulz, Katharina A. C. T1 - Niches drive peaked and positive relationships between diversity and disturbance in natural ecosystems JF - Ecosphere : the magazine of the International Ecology University N2 - A unified understanding of the relationship between disturbance and biodiversity is needed to predict biotic responses to global change. Recent advances have identified the need to deconstruct traditional models of disturbance into intensity and frequency to reconcile empirical studies that appear to generate contradictory associations between species diversity and disturbance. We integrate results from theoretical simulation modelling, field-based surveys of 5176 vegetation plots from 48 transects across 6 sites, and experimental pot-based manipulations of flooding to identify how disturbance drives species diversity within ephemeral wetlands in South Island, New Zealand. We find empirical, hump-shaped and positive relationships between species diversity and both disturbance intensity and frequency, mirroring patterns from a simulation model in which species differed in their demographic responses to disturbance. More generally, our simulations show that the relationships between diversity and disturbance shift from positive to hump-shaped to negative as species that are favored at low disturbance because of their resistance strategies, defined by low mortality and recruitment, decline within communities relative to resilient species. Resilient species with higher mortality and recruitment rates are instead favored as disturbance intensity and frequency intensify. Our theoretical findings suggest that sites must also have a third group of unique species with intermediate resilience and resistance. Analyses of community composition along our disturbance gradients support this prediction, emphasizing that shifts in community-level resistance and resilience drive empirical associations between diversity and disturbance. Overall, terrestrial plants may be unable to resist intense and frequent flooding, even with specialized traits. Only fast-growing species with high regeneration from seed may respond once flooding subsides and dominate community composition in these situations, especially on nutrient-rich soils. However, different strategies can co-occur at intermediate disturbance, ultimately increasing species richness. As disturbances become more pervasive globally, our results suggest that differences in the niches of species, rather than demographic stochasticity, drive biodiversity patterns. These niche-based processes may especially prevail, without accompanying losses in species richness, where sites are initially dominated by resistant taxa or life history strategies that balance resistance and resilience. KW - beta-diversity KW - coexistence KW - community structure KW - functional traits KW - intermediate disturbance hypothesis KW - neutral theory KW - trade-offs Y1 - 2013 U6 - https://doi.org/10.1890/ES13-00102.1 SN - 2150-8925 VL - 4 IS - 11 PB - Wiley CY - Washington ER - TY - JOUR A1 - Omranian, Nooshin A1 - Klie, Sebastian A1 - Müller-Röber, Bernd A1 - Nikoloski, Zoran T1 - Network-based segmentation of biological multivariate time series JF - PLoS one N2 - Molecular phenotyping technologies (e.g., transcriptomics, proteomics, and metabolomics) offer the possibility to simultaneously obtain multivariate time series (MTS) data from different levels of information processing and metabolic conversions in biological systems. As a result, MTS data capture the dynamics of biochemical processes and components whose couplings may involve different scales and exhibit temporal changes. Therefore, it is important to develop methods for determining the time segments in MTS data, which may correspond to critical biochemical events reflected in the coupling of the system's components. Here we provide a novel network-based formalization of the MTS segmentation problem based on temporal dependencies and the covariance structure of the data. We demonstrate that the problem of partitioning MTS data into k segments to maximize a distance function, operating on polynomially computable network properties, often used in analysis of biological network, can be efficiently solved. To enable biological interpretation, we also propose a breakpoint-penalty (BP-penalty) formulation for determining MTS segmentation which combines a distance function with the number/length of segments. Our empirical analyses of synthetic benchmark data as well as time-resolved transcriptomics data from the metabolic and cell cycles of Saccharomyces cerevisiae demonstrate that the proposed method accurately infers the phases in the temporal compartmentalization of biological processes. In addition, through comparison on the same data sets, we show that the results from the proposed formalization of the MTS segmentation problem match biological knowledge and provide more rigorous statistical support in comparison to the contending state-of-the-art methods. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0062974 SN - 1932-6203 VL - 8 IS - 5 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Rauf, Mamoona A1 - Arif, Muhammad A1 - Fisahn, Joachim A1 - Xue, Gang-Ping A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd T1 - NAC transcription factor speedy hyponastic growth regulates flooding-induced leaf movement in arabidopsis JF - The plant cell N2 - In rosette plants, root flooding (waterlogging) triggers rapid upward (hyponastic) leaf movement representing an important architectural stress response that critically determines plant performance in natural habitats. The directional growth is based on localized longitudinal cell expansion at the lower (abaxial) side of the leaf petiole and involves the volatile phytohormone ethylene (ET). We report the existence of a transcriptional core unit underlying directional petiole growth in Arabidopsis thaliana, governed by the NAC transcription factor SPEEDY HYPONASTIC GROWTH (SHYG). Overexpression of SHYG in transgenic Arabidopsis thaliana enhances waterlogging-triggered hyponastic leaf movement and cell expansion in abaxial cells of the basal petiole region, while both responses are largely diminished in shyg knockout mutants. Expression of several EXPANSIN and XYLOGLUCAN ENDOTRANSGLYCOSYLASE/HYDROLASE genes encoding cell wall-loosening proteins was enhanced in SHYG overexpressors but lowered in shyg. We identified ACC OXIDASE5 (ACO5), encoding a key enzyme of ET biosynthesis, as a direct transcriptional output gene of SHYG and found a significantly reduced leaf movement in response to root flooding in aco5 T-DNA insertion mutants. Expression of SHYG in shoot tissue is triggered by root flooding and treatment with ET, constituting an intrinsic ET-SHYG-ACO5 activator loop for rapid petiole cell expansion upon waterlogging. Y1 - 2013 U6 - https://doi.org/10.1105/tpc.113.117861 SN - 1040-4651 SN - 1532-298X VL - 25 IS - 12 SP - 4941 EP - 4955 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Matallana-Ramirez, Lilian P. A1 - Rauf, Mamoona A1 - Farage-Barhom, Sarit A1 - Dortay, Hakan A1 - Xue, Gang-Ping A1 - Droege-Laser, Wolfgang A1 - Lers, Amnon A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd T1 - NAC Transcription Factor ORE1 and Senescence-Induced BIFUNCTIONAL NUCLEASE1 (BFN1) Constitute a Regulatory Cascade in Arabidopsis JF - Molecular plant N2 - The NAC transcription factor ORE1 is a key regulator of senescence in Arabidopsis thaliana. Here, we demonstrate that senescence-induced and cell death-associated BIFUNCTIONAL NUCLEASE1 (BFN1) is a direct downstream target of ORE1, revealing a previously unknown regulatory cascade.Senescence is a highly regulated process that involves the action of a large number of transcription factors. The NAC transcription factor ORE1 (ANAC092) has recently been shown to play a critical role in positively controlling senescence in Arabidopsis thaliana; however, no direct target gene through which it exerts its molecular function has been identified previously. Here, we report that BIFUNCTIONAL NUCLEASE1 (BFN1), a well-known senescence-enhanced gene, is directly regulated by ORE1. We detected elevated expression of BFN1 already 2 h after induction of ORE1 in estradiol-inducible ORE1 overexpression lines and 6 h after transfection of Arabidopsis mesophyll cell protoplasts with a 35S:ORE1 construct. ORE1 and BFN1 expression patterns largely overlap, as shown by promoterreporter gene (GUS) fusions, while BFN1 expression in senescent leaves and the abscission zones of maturing flower organs was virtually absent in ore1 mutant background. In vitro binding site assays revealed a bipartite ORE1 binding site, similar to that of ORS1, a paralog of ORE1. A bipartite ORE1 binding site was identified in the BFN1 promoter; mutating the cis-element within the context of the full-length BFN1 promoter drastically reduced ORE1-mediated transactivation capacity in transiently transfected Arabidopsis mesophyll cell protoplasts. Furthermore, chromatin immunoprecipitation (ChIP) demonstrates in vivo binding of ORE1 to the BFN1 promoter. We also demonstrate binding of ORE1 in vivo to the promoters of two other senescence-associated genes, namely SAG29/SWEET15 and SINA1, supporting the central role of ORE1 during senescence. KW - Arabidopsis thaliana KW - senescence KW - transcription factor KW - ORE1 KW - BFN1 KW - promoter Y1 - 2013 U6 - https://doi.org/10.1093/mp/sst012 SN - 1674-2052 VL - 6 IS - 5 SP - 1438 EP - 1452 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Lim, Sze Chern A1 - Friemel, Martin A1 - Marum, Justine E. A1 - Tucker, Elena J. A1 - Bruno, Damien L. A1 - Riley, Lisa G. A1 - Christodoulou, John A1 - Kirk, Edwin P. A1 - Boneh, Avihu A1 - DeGennaro, Christine M. A1 - Springer, Michael A1 - Mootha, Vamsi K. A1 - Rouault, Tracey A. A1 - Leimkühler, Silke A1 - Thorburn, David R. A1 - Compton, Alison G. T1 - Mutations in LYRM4, encoding ironsulfur cluster biogenesis factor ISD11, cause deficiency of multiple respiratory chain complexes JF - Human molecular genetics N2 - Ironsulfur clusters (ISCs) are important prosthetic groups that define the functions of many proteins. Proteins with ISCs (called ironsulfur or FeS proteins) are present in mitochondria, the cytosol, the endoplasmic reticulum and the nucleus. They participate in various biological pathways including oxidative phosphorylation (OXPHOS), the citric acid cycle, iron homeostasis, heme biosynthesis and DNA repair. Here, we report a homozygous mutation in LYRM4 in two patients with combined OXPHOS deficiency. LYRM4 encodes the ISD11 protein, which forms a complex with, and stabilizes, the sulfur donor NFS1. The homozygous mutation (c.203GT, p.R68L) was identified via massively parallel sequencing of 1000 mitochondrial genes (MitoExome sequencing) in a patient with deficiency of complexes I, II and III in muscle and liver. These three complexes contain ISCs. Sanger sequencing identified the same mutation in his similarly affected cousin, who had a more severe phenotype and died while a neonate. Complex IV was also deficient in her skeletal muscle. Several other FeS proteins were also affected in both patients, including the aconitases and ferrochelatase. Mutant ISD11 only partially complemented for an ISD11 deletion in yeast. Our in vitro studies showed that the l-cysteine desulfurase activity of NFS1 was barely present when co-expressed with mutant ISD11. Our findings are consistent with a defect in the early step of ISC assembly affecting a broad variety of FeS proteins. The differences in biochemical and clinical features between the two patients may relate to limited availability of cysteine in the newborn period and suggest a potential approach to therapy. Y1 - 2013 U6 - https://doi.org/10.1093/hmg/ddt295 SN - 0964-6906 SN - 1460-2083 VL - 22 IS - 22 SP - 4460 EP - 4473 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Weisse, Thomas A1 - Laufenstein, Nicole A1 - Weithoff, Guntram T1 - Multiple environmental stressors confine the ecological niche of the rotifer Cephalodella acidophila JF - Freshwater biology N2 - 1The planktonic food web in extremely acidic mining lakes is restricted to a few species that are either acidophilic or acidotolerant. Common metazoans inhabiting acidic mining lakes with a pH below 3 include rotifers in the genera Cephalodella and Elosa. 2The life history response of Cephalodella acidophila to three environmental key factors, pH (2, 3.5, 5.0 and 7.0), temperature (10, 17.5 and 25 degrees C) and food concentration (10000, 35000 and 50000algal cells per mL), was investigated in a full factorial design using life-table experiments. 3The effect of each of the three environmental variables investigated on the rotifer life cycle parameters (life span, fecundity and population growth rate) differed. C.acidophila is a stenoecious species with a pH optimum in the range 34 and a comparably high food threshold. Combining the laboratory results with field data, we conclude that C.acidophila is severely growth limited in its natural habitat. However, low pH alone is not harmful as long as temperatures are moderate to warm and food is abundant. 4The population of C.acidophila in the field is maintained mainly due to release from competitors and predators. KW - acid lakes KW - Cephalodella acidophila KW - life-table experiments KW - pH KW - rotifers Y1 - 2013 U6 - https://doi.org/10.1111/fwb.12104 SN - 0046-5070 VL - 58 IS - 5 SP - 1008 EP - 1015 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Schmidt, Romy A1 - Schippers, Jos H. M. A1 - Mieulet, Delphine A1 - Obata, Toshihiro A1 - Fernie, Alisdair R. A1 - Guiderdoni, Emmanuel A1 - Müller-Röber, Bernd T1 - Multipass, a rice R2R3-type MYB transcription factor, regulates adaptive growth by integrating multiple hormonal pathways JF - The plant journal N2 - Growth regulation is an important aspect of plant adaptation during environmental perturbations. Here, the role of MULTIPASS (OsMPS), an R2R3-type MYB transcription factor of rice, was explored. OsMPS is induced by salt stress and expressed in vegetative and reproductive tissues. Over-expression of OsMPS reduces growth under non-stress conditions, while knockdown plants display increased biomass. OsMPS expression is induced by abscisic acid and cytokinin, but is repressed by auxin, gibberellin and brassinolide. Growth retardation caused by OsMPS over-expression is partially restored by auxin application. Expression profiling revealed that OsMPS negatively regulates the expression of EXPANSIN (EXP) and cell-wall biosynthesis as well as phytohormone signaling genes. Furthermore, the expression of OsMPS-dependent genes is regulated by auxin, cytokinin and abscisic acid. Moreover, we show that OsMPS is a direct upstream regulator of OsEXPA4, OsEXPA8, OsEXPB2, OsEXPB3, OsEXPB6 and the endoglucanase genes OsGLU5 and OsGLU14. The multiple responses of OsMPS and its target genes to various hormones suggest an integrative function of OsMPS in the cross-talk between phytohormones and the environment to regulate adaptive growth. KW - development KW - expansin KW - transcription KW - Oryza sativa KW - hormone KW - abiotic stress Y1 - 2013 U6 - https://doi.org/10.1111/tpj.12286 SN - 0960-7412 SN - 1365-313X VL - 76 IS - 2 SP - 258 EP - 273 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Schmitz-Hertzberg, Sebastian-Tim A1 - Mak, Wing Cheung A1 - Lai, Kwok Kei A1 - Teller, Carsten A1 - Bier, Frank Fabian T1 - Multifactorial design of Poly(D, L-lactic-co-glycolic acid) capsules with various release properties for differently sized filling agents JF - Journal of applied polymer science N2 - The hydrolytic degradation and corresponding content release of capsules made of poly(d,l-lactic-co-glycolic acid) (PLGA) strongly depends on the composition and material properties of the initially applied copolymer. Consecutive or simultaneous release from capsule batches of combinable material compositions, therefore, offers high control over the bioavailability of an encapsulated drug. The keynote of this study was the creation of a superordinated database that addressed the correlation between the release kinetics of filling agents with different molecular weights from PLGA capsules of alternating composition. Fluorescein isothiocyanate (FITC)-dextran (with molecular weights of 4, 40, and 2000 kDa) was chosen as a model analyte, whereas the copolymers were taken from various 50:50 PLGA, 75:25 PLGA, and polylactide blends. With reference to recent publications, the capsule properties, such as the size, morphology, and encapsulation efficiency, were further modified during production. Hence, uniform microdisperse and polydisperse submicrometer nanocapsules were prepared by two different water-in-oil-in-water emulsification techniques, and additional effects on the size and morphology were achieved by capsule solidification in two different sodium salt buffers. The qualitative and quantitative examination of the physical capsule properties was performed by confocal laser scanning microscopy, scanning electron microscopy, and Coulter counting techniques to evaluate the capsule size distribution and the morphological appearance of the different batches. The corresponding agent release was quantified by fluorescence measurement of the FITC-dextran in the incubation media and by the direct measurement of the capsule brightness via fluorescence microscopy. In summary, the observed agent release showed a highly controllable flexibility depending on the PLGA blends, preparation methods, and molecular weight of the used filling substances. (c) 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 130: 4219-4228, 2013 KW - biodegradable copolymers (PLGA) KW - microcapsules KW - submicrometer KW - nanocapsules KW - FITC-dextran release KW - drug delivery system KW - biomedical applications Y1 - 2013 U6 - https://doi.org/10.1002/app.39537 SN - 0021-8995 SN - 1097-4628 VL - 130 IS - 6 SP - 4219 EP - 4228 PB - Wiley-Blackwell CY - Hoboken ER - TY - CHAP A1 - Sapir, N. A1 - Rotics, S. A1 - Kaatz, M. A1 - Davidson, S. A1 - Zurell, Damaris A1 - Eggers, U. A1 - Jeltsch, Florian A1 - Nathan, R. A1 - Wikelski, M. T1 - Multi-year tracking of white storks (Ciconia ciconia) how the environment shapes the movement and behavior of a soaring-gliding inter-continental migrant T2 - Integrative and comparative biology Y1 - 2013 SN - 1540-7063 VL - 53 IS - 3 SP - E189 EP - E189 PB - Oxford Univ. Press CY - Cary ER - TY - JOUR A1 - Zhang, Hucai A1 - Paijmans, Johanna L. A. A1 - Chang, Fengqin A1 - Wu, Xiaohong A1 - Chen, Guangjie A1 - Lei, Chuzhao A1 - Yang, Xiujuan A1 - Wei, Zhenyi A1 - Bradley, Daniel G. A1 - Orlando, Ludovic A1 - O'Connor, Terry A1 - Hofreiter, Michael T1 - Morphological and genetic evidence for early Holocene cattle management in northeastern China JF - Nature Communications N2 - The domestication of cattle is generally accepted to have taken place in two independent centres: around 10,500 years ago in the Near East, giving rise to modern taurine cattle, and two millennia later in southern Asia, giving rise to zebu cattle. Here we provide firmly dated morphological and genetic evidence for early Holocene management of taurine cattle in northeastern China. We describe conjoining mandibles from this region that show evidence of oral stereotypy, dated to the early Holocene by two independent C-14 dates. Using Illumina high-throughput sequencing coupled with DNA hybridization capture, we characterize 15,406 bp of the mitogenome with on average 16.7-fold coverage. Phylogenetic analyses reveal a hitherto unknown mitochondrial haplogroup that falls outside the known taurine diversity. Our data suggest that the first attempts to manage cattle in northern China predate the introduction of domestic cattle that gave rise to the current stock by several thousand years. Y1 - 2013 U6 - https://doi.org/10.1038/ncomms3755 SN - 2041-1723 VL - 4 IS - 6 PB - Nature Publ. Group CY - London ER - TY - CHAP A1 - Bilitewski, Ursula A1 - Kaba, H. A1 - Heilmann, Katja A1 - Mayer, Yvonne A1 - Hofmann, B. A1 - Mueller, P. A1 - van den Heuvel, J. T1 - Monoclonal antibodies against specific peptides derived from the 1,3-beta-glucosyltransferase Bgl2p allow detection of Candida albicans cells T2 - Mycoses : diagnosis, therapy and prophylaxis of fungal diseases Y1 - 2013 SN - 0933-7407 VL - 56 IS - 1 SP - 27 EP - 27 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Iobbi-Nivol, Chantal A1 - Leimkühler, Silke T1 - Molybdenum enzymes, their maturation and molybdenum cofactor biosynthesis in Escherichia coli JF - Biochimica et biophysica acta : Bioenergetics N2 - Molybdenum cofactor (Moco) biosynthesis is an ancient, ubiquitous, and highly conserved pathway leading to the biochemical activation of molybdenum. Moco is the essential component of a group of redox enzymes, which are diverse in terms of their phylogenetic distribution and their architectures, both at the overall level and in their catalytic geometry. A wide variety of transformations are catalyzed by these enzymes at carbon, sulfur and nitrogen atoms, which include the transfer of an oxo group or two electrons to or from the substrate. More than 50 molybdoenzymes were identified in bacteria to date. In molybdoenzymes Mo is coordinated to a dithiolene group on the 6-alkyl side chain of a pterin called molybdopterin (MPT). The biosynthesis of Moco can be divided into four general steps in bacteria: I) formation of the cyclic pyranopterin monophosphate, 2) formation of MPT, 3) insertion of molybdenum into molybdopterin to form Moco, and 4) additional modification of Moco with the attachment of GMP or CMP to the phosphate group of MPT, forming the dinucleotide variant of Moco. This review will focus on molybdoenzymes, the biosynthesis of Moco, and its incorporation into specific target proteins focusing on Escherichia coli. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems. KW - Molybdenum cofactor KW - Molybdenum KW - Dithiolene KW - Molybdopterin KW - Bis-MGD KW - Moco Y1 - 2013 U6 - https://doi.org/10.1016/j.bbabio.2012.11.007 SN - 0005-2728 VL - 1827 IS - 8-9 SP - 1086 EP - 1101 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Taylan, Mehmet Sait A1 - Di Russo, Claudio A1 - Rampini, Mauro A1 - Ketmaier, Valerio T1 - Molecular systematics of the genus Troglophilus (Rhaphidophoridae, Orthoptera) in Turkey mitochondrial 16S rDNA evidences JF - ZooKeys N2 - This study focuses on the evolutionary relationships among Turkish species of the cave cricket genus Troglophilus. Fifteen populations were studied for sequence variation in a fragment (543 base pairs) of the mitochondrial DNA (mtDNA) 16S rDNA gene (16S) to reconstruct their phylogenetic relationships and biogeographic history. Genetic data retrieved three main clades and at least three divergent lineages that could not be attributed to any of the taxa known for the area. Molecular time estimates suggest that the diversification of the group took place between the Messinian and the Plio-Pleistocene. KW - Troglophilus KW - Rhaphidophoridae KW - Orthoptera KW - 16S rDNA KW - mitochondrial DNA KW - molecular systematics KW - cave crickets Y1 - 2013 U6 - https://doi.org/10.3897/zookeys.257.4133 SN - 1313-2989 IS - 257 SP - 33 EP - 46 PB - Pensoft Publ. CY - Sofia ER -