TY - JOUR A1 - Zuppinger-Dingley, D. A1 - Schmid, Bernhard A1 - Chen, Y. A1 - Brandl, H. A1 - van der Heijden, M. G. A. A1 - Joshi, Jasmin Radha T1 - In their native range, invasive plants are held in check by negative soil-feedbacks JF - Ecosphere : the magazine of the International Ecology University N2 - The ability of some plant species to dominate communities in new biogeographical ranges has been attributed to an innate higher competitive ability and release from co-evolved specialist enemies. Specifically, invasive success in the new range might be explained by release from biotic negative soil-feedbacks, which control potentially dominant species in their native range. To test this hypothesis, we grew individuals from sixteen phylogenetically paired European grassland species that became either invasive or naturalized in new ranges, in either sterilized soil or in sterilized soil with unsterilized soil inoculum from their native home range. We found that although the native members of invasive species generally performed better than those of naturalized species, these native members of invasive species also responded more negatively to native soil inoculum than did the native members of naturalized species. This supports our hypothesis that potentially invasive species in their native range are held in check by negative soil-feedbacks. However, contrary to expectation, negative soil-feedbacks in potentially invasive species were not much increased by interspecific competition. There was no significant variation among families between invasive and naturalized species regarding their feedback response (negative vs. neutral). Therefore, we conclude that the observed negative soil feedbacks in potentially invasive species may be quite widespread in European families of typical grassland species. KW - biotic interactions KW - enemy release KW - invasive species KW - native range KW - naturalized species KW - plant invasions KW - plant-soil feedbacks KW - soil inoculation KW - soil sterilization Y1 - 2011 U6 - https://doi.org/10.1890/ES11-00061.1 SN - 2150-8925 VL - 2 IS - 5 PB - Wiley CY - Washington ER - TY - JOUR A1 - Zude, Manuela A1 - Pflanz, Michael A1 - Spinelli, Lorenzo A1 - Dosche, Carsten A1 - Torricelli, Alessandro T1 - Non-destructive analysis of anthocyanins in cherries by means of Lambert-Beer and multivariate regression based on spectroscopy and scatter correction using time-resolved analysis JF - Journal of food engineering N2 - In high-value sweet cherry (Prunus avium), the red coloration - determined by the anthocyanins content - is correlated with the fruit ripeness stage and market value. Non-destructive spectroscopy has been introduced in practice and may be utilized as a tool to assess the fruit pigments in the supply chain processes. From the fruit spectrum in the visible (Vis) wavelength range, the pigment contents are analyzed separately at their specific absorbance wavelengths. A drawback of the method is the need for re-calibration due to varying optical properties of the fruit tissue. In order to correct for the scattering differences, most often the spectral intensity in the visible spectrum is normalized by wavelengths in the near infrared (NIR) range, or pre-processing methods are applied in multivariate calibrations. In the present study, the influence of the fruit scattering properties on the Vis/NIR fruit spectrum were corrected by the effective pathlength in the fruit tissue obtained from time-resolved readings of the distribution of time-of-flight (DTOF). Pigment analysis was carried out according to Lambert-Beer law, considering fruit spectral intensities, effective pathlength, and refractive index. Results were compared to commonly applied linear color and multivariate partial least squares (PLS) regression analysis. The approaches were validated on fruits at different ripeness stages, providing variation in the scattering coefficient and refractive index exceeding the calibration sample set. In the validation, the measuring uncertainty of non-destructively analyzing fruits with Vis/NIR spectra by means of PLS or Lambert-Beer in comparison with combined application of Vis/NIR spectroscopy and DTOF measurements showed a dramatic bias reduction as well as enhanced coefficients of determination when using both, the spectral intensities and apparent information on the scattering influence by means of DTOF readings. Corrections for the refractive index did not render improved results. KW - Cherry KW - DTOF KW - Effective pathlength KW - Fruit maturity KW - Lambert-Beer KW - NIR KW - Non-invasive KW - Pigments KW - PLS KW - Ripeness KW - Sensor fusion KW - Spectroscopy KW - Time-resolved spectroscopy KW - TIRF KW - Vis KW - Scattering Y1 - 2011 U6 - https://doi.org/10.1016/j.jfoodeng.2010.09.021 SN - 0260-8774 VL - 103 IS - 1 SP - 68 EP - 75 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Zilliges, Yvonne A1 - Kehr, Jan-Christoph A1 - Meissner, Sven A1 - Ishida, Keishi A1 - Mikkat, Stefan A1 - Hagemann, Martin A1 - Kaplan, Aaron A1 - Börner, Thomas A1 - Dittmann-Thünemann, Elke T1 - The cyanobacterial hepatotoxin microcystin binds to proteins and increases the fitness of microcystis under oxidative stress conditions JF - PLoS one N2 - Microcystins are cyanobacterial toxins that represent a serious threat to drinking water and recreational lakes worldwide. Here, we show that microcystin fulfils an important function within cells of its natural producer Microcystis. The microcystin deficient mutant Delta mcyB showed significant changes in the accumulation of proteins, including several enzymes of the Calvin cycle, phycobiliproteins and two NADPH-dependent reductases. We have discovered that microcystin binds to a number of these proteins in vivo and that the binding is strongly enhanced under high light and oxidative stress conditions. The nature of this binding was studied using extracts of a microcystin-deficient mutant in vitro. The data obtained provided clear evidence for a covalent interaction of the toxin with cysteine residues of proteins. A detailed investigation of one of the binding partners, the large subunit of RubisCO showed a lower susceptibility to proteases in the presence of microcystin in the wild type. Finally, the mutant defective in microcystin production exhibited a clearly increased sensitivity under high light conditions and after hydrogen peroxide treatment. Taken together, our data suggest a protein-modulating role for microcystin within the producing cell, which represents a new addition to the catalogue of functions that have been discussed for microbial secondary metabolites. Y1 - 2011 U6 - https://doi.org/10.1371/journal.pone.0017615 SN - 1932-6203 VL - 6 IS - 3 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Zhang, Gong A1 - Lukoszek, Radoslaw A1 - Müller-Röber, Bernd A1 - Ignatova, Zoya T1 - Different sequence signatures in the upstream regions of plant and animal tRNA genes shape distinct modes of regulation JF - Nucleic acids research N2 - In eukaryotes, the transcription of tRNA genes is initiated by the concerted action of transcription factors IIIC (TFIIIC) and IIIB (TFIIIB) which direct the recruitment of polymerase III. While TFIIIC recognizes highly conserved, intragenic promoter elements, TFIIIB binds to the non-coding 5'-upstream regions of the tRNA genes. Using a systematic bioinformatic analysis of 11 multicellular eukaryotic genomes we identified a highly conserved TATA motif followed by a CAA-motif in the tRNA upstream regions of all plant genomes. Strikingly, the 5'-flanking tRNA regions of the animal genomes are highly heterogeneous and lack a common conserved sequence signature. Interestingly, in the animal genomes the tRNA species that read the same codon share conserved motifs in their upstream regions. Deep-sequencing analysis of 16 human tissues revealed multiple splicing variants of two of the TFIIIB subunits, Bdp1 and Brf1, with tissue-specific expression patterns. These multiple forms most likely modulate the TFIIIB-DNA interactions and explain the lack of a uniform signature motif in the tRNA upstream regions of animal genomes. The anticodon-dependent 5'-flanking motifs provide a possible mechanism for independent regulation of the tRNA transcription in various human tissues. Y1 - 2011 U6 - https://doi.org/10.1093/nar/gkq1257 SN - 0305-1048 VL - 39 IS - 8 SP - 3331 EP - 3339 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Zhang, Gong A1 - Ignatova, Zoya T1 - Folding at the birth of the nascent chain: coordinating translation with co-translational folding JF - Current opinion in structural biology : review of all advances ; evaluation of key references ; comprehensive listing of papers N2 - In the living cells, the folding of many proteins is largely believed to begin co-translationally, during their biosynthesis at the ribosomes. In the ribosomal tunnel, the nascent peptide may establish local interactions and stabilize alpha-helical structures. Long-range contacts are more likely outside the ribosomes after release of larger segments of the nascent chain. Examples suggest that domains can attain native-like structure on the ribosome with and without population of folding intermediates. The co-translational folding is limited by the speed of the gradual extrusion of the nascent peptide which imposes conformational restraints on its folding landscape. Recent experimental and in silico modeling studies indicate that translation kinetics fine-tunes co-translational folding by providing a time delay for sequential folding of distinct portions of the nascent chain. Y1 - 2011 U6 - https://doi.org/10.1016/j.sbi.2010.10.008 SN - 0959-440X VL - 21 IS - 1 SP - 25 EP - 31 PB - Elsevier CY - London ER - TY - JOUR A1 - Zaupa, Alessandro A1 - Neffe, Axel T. A1 - Pierce, Benjamin F. A1 - Nöchel, Ulrich A1 - Lendlein, Andreas T1 - Influence of tyrosine-derived moieties and drying conditions on the formation of helices in gelatin JF - Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences N2 - The single and triple helical organization of protein chains strongly influences the mechanical properties of gelatin-based materials. A chemical method for obtaining different degrees of helical organization in gelatin is covalent functionalization, while a physical method for achieving the same goal is the variation of the drying conditions of gelatin solutions. Here we explored how the introduction of desaminotyrosine (DAT) and desaminotyrosyl tyrosine (DATT) linked to lysine residues of gelatin influenced the kinetics and thermodynamic equilibrium of the helicalization process of single and triple helices following different drying conditions. Drying at a temperature above. the helix-to-coil transition temperature of gelatin (T > T-c, called nu(short)) generally resulted in gelatins with relatively lower triple helical content (X-c,X-t = 1-2%) than lower temperature drying (T < T-c, called nu(long)) (X-c,X-t = 8-10%), where the DAT(T) functional groups generally disrupted helix formation. While different helical contents affected the thermal transition temperatures only slightly, the mechanical properties were strongly affected for swollen hydrogels (E = 4-13 kPa for samples treated by nu(long) and E = 120-700 kPa for samples treated by nu(short)). This study shows that side group functionalization and different drying conditions are viable options to control the helicalization and macroscopic properties of gelatin-based materials. Y1 - 2011 U6 - https://doi.org/10.1021/bm101029k SN - 1525-7797 VL - 12 IS - 1 SP - 75 EP - 81 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Yarman, Aysu A1 - Badalyan, Artavazd A1 - Gajovic-Eichelmann, Nenad A1 - Wollenberger, Ursula A1 - Scheller, Frieder W. T1 - Enzyme electrode for aromatic compounds exploiting the catalytic activities of microperoxidase-11 JF - Biosensors and bioelectronics : the principal international journal devoted to research, design development and application of biosensors and bioelectronics N2 - Microperoxidase-11 (MR-11) which has been immobilised in a matrix of chitosan-embedded gold nanoparticles on the surface of a glassy carbon electrode catalyzes the conversion of aromatic substances. This peroxide-dependent catalysis of microperoxidase has been applied in an enzyme electrode for the first time to indicate aromatic compounds such as aniline. 4-fluoroaniline, catechol and p-aminophenol. The electrode signal is generated by the cathodic reduction of the quinone or quinoneimine which is formed in the presence of both MP-II and peroxide from the substrate. The same sensor principle will be extended to aromatic drugs. KW - Microperoxidase-11 KW - Nanoparticles KW - p-Aminophenol KW - Aniline KW - Catechol KW - 4-Fluoroaniline KW - Biosensors Y1 - 2011 U6 - https://doi.org/10.1016/j.bios.2011.09.004 SN - 0956-5663 VL - 30 IS - 1 SP - 320 EP - 323 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Wulf, Monika A1 - Rujner, Hendrik T1 - A GIS-based method for the reconstruction of the late eighteenth century forest vegetation in the Prignitz region (NE Germany) JF - Landscape ecology N2 - Our goal was to reconstruct the late eighteenth century forest vegetation of the Prignitz region (NE Germany) at a scale of 1:50,000. We also wanted to relate the historical forest vegetation to the actual and potential natural vegetation. For these purposes, we selected 15 woody species and transferred relevant data found in historical records from various sources together with the recent localities of (very) old individuals belonging to these woody species into ArcView GIS. Following multi-step data processing including the generation of a point density layer using a moving window with kernel estimation and derivation of vegetation units applying Boolean algebra rules together with information on site conditions, we derived 17 forest communities corresponding to the potential natural vegetation. We were able to reconstruct the historical forest vegetation for 90% of the forest area ca. 1780. Only two of the 17 forest communities covered large parts of the forested area. The oak forest with Agrostis capillaris covered about 44% of the total forest area, and alder forests on fenland made up about 37%. Oak-hornbeam forests with Stellaria holostea comprised slightly less than 6% of the forest area, while all other forest communities comprised less than 1%. The historical forest vegetation is more similar to the potential forest vegetation and quite different from the actual forest vegetation because coniferous tree species currently cover approximately two-thirds of the actual forest area. The most beneficial result of this study is the map of high-resolution historical vegetation units that may serve as the basis for various further studies, e.g., modelling long-term changes in biodiversity at the landscape scale. KW - Boolean algebra KW - Historical ecology KW - Kernel estimation KW - Moving window KW - Point density KW - Potential natural vegetation KW - Schmettau map KW - Toponymy KW - Vegetation map Y1 - 2011 U6 - https://doi.org/10.1007/s10980-010-9555-1 SN - 0921-2973 VL - 26 IS - 2 SP - 153 EP - 168 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Wu, Yunhua A1 - Wollenberger, Ursula A1 - Hofrichter, Martin A1 - Ullrich, Rene A1 - Scheibner, Katrin A1 - Scheller, Frieder W. T1 - Direct electron transfer of Agrocybe aegerita peroxygenase at electrodes modified with chitosan-capped Au nanoparticles and its bioelectrocatalysis to aniline JF - Sensors and actuators : B, Chemical N2 - Three different sizes of chitosan-capped Au nanoparticles were synthesized and were used to incorporate Agrocybe aegerita peroxygenase (AaeAPO) onto the surface of glassy carbon electrode. The direct electron transfer of AaeAPO was achieved in all films. The highest amount of electroactive enzyme and highest electron transfer rate constant k(s) of AaeAPO were obtained in the film with the smallest size of chitosan-capped Au nanoparticles. In anaerobic solutions, quasi-reversible oxidation and reduction are obtained with a formal potential of -0.280V vs. Ag/AgCl 1 M KCl in 100 mM (pH 7.0) PBS at scan rate of 1 V s(-1). Bioelectrocatalytic reduction currents can be obtained with the AaeAPO-modified electrode on addition of hydrogen peroxide. This reaction was suppressed when sodium azide, an inhibitor of AaeAPO, was present. Furthermore, the peroxide-dependent conversion of aniline was characterized and it was found that a polymer product via p-aminophenol is formed. And the AaeAPO biosensor was applied to determine aniline and p-aminophenol. KW - Agrocybe aegerita peroxygenase KW - Au nanoparticles KW - Direct electron transfer KW - Aniline biosensor KW - Bioelectrocatalysis Y1 - 2011 U6 - https://doi.org/10.1016/j.snb.2011.09.090 SN - 0925-4005 VL - 160 IS - 1 SP - 1419 EP - 1426 PB - Elsevier CY - Lausanne ER - TY - JOUR A1 - Winck, Flavia Vischi A1 - Kwasniewski, Miroslaw A1 - Wienkoop, Stefanie A1 - Müller-Röber, Bernd T1 - An optimized method for the isolation of nuclei from chlamydomas Reinhardtii (Chlorophyceae) JF - Journal of phycology N2 - The cell nucleus harbors a large number of proteins involved in transcription, RNA processing, chromatin remodeling, nuclear signaling, and ribosome assembly. The nuclear genome of the model alga Chlamydomonas reinhardtii P. A. Dang. was recently sequenced, and many genes encoding nuclear proteins, including transcription factors and transcription regulators, have been identified through computational discovery tools. However, elucidating the specific biological roles of nuclear proteins will require support from biochemical and proteomics data. Cellular preparations with enriched nuclei are important to assist in such analyses. Here, we describe a simple protocol for the isolation of nuclei from Chlamydomonas, based on a commercially available kit. The modifications done in the original protocol mainly include alterations of the differential centrifugation parameters and detergent-based cell lysis. The nuclei-enriched fractions obtained with the optimized protocol show low contamination with mitochondrial and plastid proteins. The protocol can be concluded within only 3 h, and the proteins extracted can be used for gel-based and non-gel-based proteomic approaches. KW - 2D gel electrophoresis KW - algae KW - Chlamydomonas KW - nuclear proteins KW - nucleus KW - proteomics Y1 - 2011 U6 - https://doi.org/10.1111/j.1529-8817.2011.00967.x SN - 0022-3646 VL - 47 IS - 2 SP - 333 EP - 340 PB - Wiley-Blackwell CY - Malden ER - TY - THES A1 - Winck, Flavia Vischi T1 - Nuclear proteomics and transcription factor profiling in Chlamydomonas reinhardtii T1 - Nukleare Proteomics und Transkriptionsfaktoren : Profiling in Chlamydomonas reinhardtii N2 - The transcriptional regulation of the cellular mechanisms involves many different components and different levels of control which together contribute to fine tune the response of cells to different environmental stimuli. In some responses, diverse signaling pathways can be controlled simultaneously. One of the most important cellular processes that seem to possess multiple levels of regulation is photosynthesis. A model organism for studying photosynthesis-related processes is the unicellular green algae Chlamydomonas reinhardtii, due to advantages related to culturing, genetic manipulation and availability of genome sequence. In the present study, we were interested in understanding the regulatory mechanisms underlying photosynthesis-related processes. To achieve this goal different molecular approaches were followed. In order to indentify protein transcriptional regulators we optimized a method for isolation of nuclei and performed nuclear proteome analysis using shotgun proteomics. This analysis permitted us to improve the genome annotation previously published and to discover conserved and enriched protein motifs among the nuclear proteins. In another approach, a quantitative RT-PCR platform was established for the analysis of gene expression of predicted transcription factor (TF) and other transcriptional regulator (TR) coding genes by transcript profiling. The gene expression profiles for more than one hundred genes were monitored in time series experiments under conditions of changes in light intensity (200 µE m-2 s-1 to 700 µE m-2 s-1), and changes in concentration of carbon dioxide (5% CO2 to 0.04% CO2). The results indicate that many TF and TR genes are regulated in both environmental conditions and groups of co-regulated genes were found. Our findings also suggest that some genes can be common intermediates of light and carbon responsive regulatory pathways. These approaches together gave us new insights about the regulation of photosynthesis and revealed new candidate regulatory genes, helping to decipher the gene regulatory networks in Chlamydomonas. Further experimental studies are necessary to clarify the function of the candidate regulatory genes and to elucidate how cells coordinately regulate the assimilation of carbon and light responses. N2 - Pflanzen nutzen das Sonnenlicht um Substanzen, sogenannte Kohlenhydrate, zu synthetisieren. Diese können anschließend als Energielieferant für das eigene Wachstum genutzt werden. Der aufbauende Prozess wird als Photosynthese bezeichnet. Ein wichtiges Anliegen ist deshalb zu verstehen, wie Pflanzen äußere Einflüsse wahrnehmen und die Photosynthese dementsprechend regulieren. Ihre Zellen tragen diese Informationen in den Genen. Die Pflanzen nutzen aber in der Regel nicht alle ihre Gene gleichzeitig, die sie zur Anpassung an Umwelteinflüsse besitzen. Zu meist wird nur eine Teilfraktion der gesamten Information benötigt. Wir wollten der Frage nachgehen, welche Gene die Zellen für welche Situation regulieren. Im Zellkern gibt es Proteine, sogenannte Transkriptionsfaktoren, die spezifische Gene finden können und deren Transkription modulieren. Wenn ein Gen gebraucht wird, wird seine Information in andere Moleküle übersetzt (transkribiert), sogenannte Transkripte. Die Information dieser Transkripte wird benutzt um Proteine, Makromoleküle aus Aminsäuren, zu synthetisieren. Aus der Transkription eines Gens kann eine große Zahl des Transkripts entstehen. Es ist wahrscheinlich, dass ein Gen, dass gerade gebraucht wird, mehr Transkriptmoleküle hat als andere Gene. Da die Transkriptionsfaktoren mit der Transkription der Gene interferieren können, entwickelten wir in der vorliegenden Arbeit Strategien zur Identifikation dieser im Zellkern zu findenden Proteine mittels eines „Proteomics“-Ansatzes. Wir entwickelten weiterhin eine Strategie zur Identififikation von Transkripten Transkriptionsfaktor-codierender Gene in der Zelle und in welche Menge sie vorkommen. Dieser Ansatz wird als „Transcript-Profiling“ bezeichnet. Wir fanden Zellkern-lokalisierte Proteine, die als Signalmoleküle funktionieren könnten und Transkripte, die bei unterschiedlichen Umweltbedingungen in der Zelle vorhanden waren. Wir benutzten, die oben genannten Ansätze um die einzellige Grünalge Chlamydomonas zu untersuchen. Die Informationen, die wir erhielten, halfen zu verstehen welche Transkriptionsfaktoren notwendig sind, damit Chlamydomonas bei unterschiedlichen Umweltbedingungen, wie z.B. unterschiedliche Lichtintensitäten und unterschiedlicher Konzentration von Kohlenstoffdioxid, überlebt. KW - Proteomics KW - Transkriptionsfaktoren KW - Pflanzen KW - Chlamydomonas KW - Transcriptomics KW - Proteomics KW - Transcription factors KW - Plants KW - Chlamydomonas KW - Transcriptomics Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-53909 ER - TY - JOUR A1 - Wiesner, Kerstin R. A1 - Loxdale, Hugh D. A1 - Köhler, Günter A1 - Schneider, Anja R. R. A1 - Tiedemann, Ralph A1 - Weisser, Wolfgang W. T1 - Patterns of local and regional genetic structuring in the meadow grasshopper, Chorthippus parallelus (Orthoptera: Acrididae), in Central Germany revealed using microsatellite markers JF - Biological journal of the Linnean Society : a journal of evolution N2 - The meadow grasshopper, Chorthippus parallelus (Zetterstedt), is common and widespread in Central Europe, with a low dispersal range per generation. A population study in Central Germany (Frankenwald and Thuringer Schiefergebirge) showed strong interpopulation differences in abundance and individual fitness. We examined genetic variability using microsatellite markers within and between 22 populations in a short-to long-distance sampling (19 populations, Frankenwald, Schiefergebirge, as well as a southern transect), and in the Erzgebirge region (three populations), with the latter aiming to check for effects as a result of historical forest cover. Of the 671 C. parallelus captured, none was macropterous (functionally winged). All populations showed a high level of expected and observed heterozygosity (mean 0.80-0.90 and 0.60-0.75, respectively), whereas there was evidence of inbreeding (F(IS) values all positive). Allelic richness for all locus-population combinations was high (mean 9.3-11.2), whereas alleles per locus ranged from 15-62. At a local level, genic and genotypic differences were significant. Pairwise F(ST) values were in the range 0.00-0.04, indicating little interpopulation genetic differentiation. Similarly, the calculated gene flow was very high, based on the respective F(ST) (19.5) and using private alleles (7.7). A Neighbour-joining tree using Nei's D(A) and principal coordinate analysis separated two populations that were collected in the Erzgebirge region. Populations from this region may have escaped the effects of the historical forest cover. The visualization of the spatial arrangement of genotypes revealed one geographical barrier to gene flow in the short-distance sampling. KW - adaptation KW - gene flow KW - diversity KW - landscape structure KW - wing polyphenism Y1 - 2011 U6 - https://doi.org/10.1111/j.1095-8312.2011.01698.x SN - 0024-4066 VL - 103 IS - 4 SP - 875 EP - 890 PB - Wiley-Blackwell CY - Malden ER - TY - THES A1 - Weiß, Julia T1 - Computer assisted proteomics in a systems biology context Y1 - 2011 CY - Potsdam ER - TY - JOUR A1 - Weiz, Annika R. A1 - Ishida, Keishi A1 - Makower, Katharina A1 - Ziemert, Nadine A1 - Hertweck, Christian A1 - Dittmann-Thünemann, Elke T1 - Leader Peptide and a Membrane Protein Scaffold Guide the Biosynthesis of the Tricyclic Peptide Microviridin JF - Chemistry & biology N2 - Microviridins are unique protease inhibitors from bloom-forming cyanobacteria that have both ecological and pharmacological relevance. Their peptide backbones are produced ribosomally, and ATP grasp ligases introduce omega-ester and omega-amide bonds to yield rare cage-like structures. Bioinformatic analysis of the microviridin biosynthesis gene cluster suggests a novel type of processing machinery, which could rationalize the challenging in vivo/in vitro reconstitution of the pathway. In this work, we report the establishment of a minimal expression system for microviridins. Through bioinformatics and mutational analysis of the MdnA leader peptide we identified and characterized a strictly conserved binding motif that is specific for microviridin ligases. Furthermore, we showed that the ABC transporter MdnE is crucial for cyclization and processing of microviridins and demonstrated that MdnE is essential for stability of the microviridin biosynthesis complex. Y1 - 2011 U6 - https://doi.org/10.1016/j.chembiol.2011.09.011 SN - 1074-5521 VL - 18 IS - 11 SP - 1413 EP - 1421 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Weisse, Thomas A1 - Berendonk, Thomas U. A1 - Kamjunke, Norbert A1 - Moser, Michael A1 - Scheffel, U. A1 - Stadler, P. A1 - Weithoff, Guntram T1 - Significant habitat effects influence protist fitness evidence for local adaptation from acidic mining lakes JF - Ecosphere : the magazine of the International Ecology University N2 - It is currently controversially discussed if the same freshwater microorganisms occur worldwide wherever their required habitats are realized, i.e., without any adaptation to local conditions below the species level. We performed laboratory experiments with flagellates and ciliates from three acidic mining lakes (AML, pH similar to 2.7) to investigate if similar habitats may affect similar organisms differently. Such man-made lakes provide suitable ecosystem models to test for the significance of strong habitat selection. To this end, we analyzed the growth response of three protist taxa (three strains of the phytoflagellate Chlamydomonas acidophila, two isolates of the phytoflagellate Ochromonas and two species of the ciliate genus Oxytricha) by exposing them to lake water of their origin and from the two other AML in a cross-factorial design. Population growth rates were measured as a proxy for their fitness. Results revealed significant effects of strain, lake (= habitat), and strain X habitat interaction. In the environmentally most adverse AML, all three protist taxa were locally adapted. In conclusion, our study demonstrates that (1) the same habitat may affect strains of the same species differently and that (2) similar habitats may harbor ecophysiologically different strains or species. These results contradict the 'everything is everywhere' paradigm. KW - allopatric speciation KW - Chlamydomonas acidophila KW - ciliates KW - everything is everywhere KW - flagellates KW - freshwater microbes KW - habitat-species interaction KW - local adaptation KW - Ochromonas spp. KW - Oxytricha spp. Y1 - 2011 U6 - https://doi.org/10.1890/ES11-00157.1 SN - 2150-8925 VL - 2 IS - 12 PB - Wiley CY - Washington ER - TY - JOUR A1 - Weber, Ewald T1 - Strong regeneration ability from rhizome fragments in two invasive clonal plants (Solidago canadensis and S. gigantea) JF - Biological invasions : unique international journal uniting scientists in the broad field of biological invasions N2 - The two rhizomatous perennials Solidago canadensis and S. gigantea belong to the most widespread alien plants in Europe. Anecdotal observations suggest that they disperse also by rhizome fragments. For testing their resprouting ability, rhizome fragments of different sizes from both species were buried at four different soil depths (0, 5, 10 and 20 cm, respectively) in a common garden. Rhizome fragments of S. canadensis ranged 3-6 cm in length, those of S. gigantea 5-20 cm in length. Resprouting plants were harvested after 3 months and growth related traits measured to assess their vitality. Resprouting rate in S. gigantea was far higher than in S. canadensis (85 and 19%, respectively). In S. gigantea, fragments of all sizes resprouted from all soil depths whereas none rhizome of S. canadensis emerged from 20 cm burial depth. In S. gigantea, size related traits showed significant interactions between fragment size and burial depth, but not relative shoot growth rate. At all burial depths, vitality of plants emerging from small rhizomes was lower than plants emerging from large rhizomes. Effects of rhizome size became stronger with increasing burial depth. The results show that both species are able to resprout from buried rhizome fragments, and that succesful regeneration is more likely to occur in S. gigantea. Managing these species should avoid any activities promoting rhizome fragmentation and dispersal of fragments. KW - Clonal growth KW - Dispersal KW - Establishment KW - Goldenrod KW - Invasive plant species KW - Vegetative regeneration Y1 - 2011 U6 - https://doi.org/10.1007/s10530-011-9977-y SN - 1387-3547 VL - 13 IS - 12 SP - 2947 EP - 2955 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Wand, Inga A1 - Holzlöhner, Pamela A1 - Neupert, Steffi A1 - Micheel, Burkhard A1 - Heilmann, Katja T1 - Cooperation of dendritic cells with naive lymphocyte populations to induce the generation of antigen-specific antibodies in vitro JF - Journal of biotechnology N2 - The production of monoclonal antibodies by hybridoma technology is dependent on lymphocytes taken from vertebrates which have to be immunized against the corresponding antigen. We present here our first experiments which should allow the replacement of this in vivo immunization step by an in vitro immunization procedure. This work provides new possibilities for the specific activation of immune cells in order to use them for the generation of antibodies which are not of murine origin. Bone marrow-derived dendritic cells were loaded with antigen and co-cultured with naive T and B lymphocytes of non-immunized mice. The interaction and activation of the different cell types were investigated by measuring the expression of specific cell surface markers, the release of activation-dependent interleukins and the secretion of antigen-specific antibodies. We could demonstrate that dendritic cells process and present antigen fragments and activate T cells, that T cells proliferate and release activation-induced interleukins, and that B cells maturate under the influence of activated T cells and secrete antigen-specific antibodies. KW - In vitro immunization KW - Activation of dendritic cells KW - Interaction of T and B cells with antigen-presenting cells KW - Induction of antibody responses Y1 - 2011 U6 - https://doi.org/10.1016/j.jbiotec.2011.09.002 SN - 0168-1656 VL - 156 IS - 3 SP - 173 EP - 181 PB - Elsevier CY - Amsterdam ER - TY - INPR A1 - Walz, Norbert A1 - Adrian, Rita A1 - Gilbert, John J. A1 - Monaghan, Michael T. A1 - Weithoff, Guntram A1 - Zimmermann-Timm, Heike T1 - Preface T2 - Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica Y1 - 2011 U6 - https://doi.org/10.1007/s10750-010-0514-2 SN - 0018-8158 VL - 662 IS - 1 SP - 1 EP - 4 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Wagner, Viktoria A1 - Antunes, Pedro M. A1 - Ristow, Michael A1 - Lechner, Ute A1 - Hensen, Isabell T1 - Prevailing negative soil biota effect and no evidence for local adaptation in a widespread eurasian grass JF - PLoS one N2 - Background: Soil biota effects are increasingly accepted as an important driver of the abundance and distribution of plants. While biogeographical studies on alien invasive plant species have indicated coevolution with soil biota in their native distribution range, it is unknown whether adaptation to soil biota varies among populations within the native distribution range. The question of local adaptation between plants and their soil biota has important implications for conservation of biodiversity and may justify the use of seed material from local provenances in restoration campaigns. Methodology/Principal Findings: We studied soil biota effects in ten populations of the steppe grass Stipa capillata from two distinct regions, Europe and Asia. We tested for local adaptation at two different scales, both within (ca. 10-80 km) and between (ca. 3300 km) regions, using a reciprocal inoculation experiment in the greenhouse for nine months. Generally, negative soil biota effects were consistent. However, we did not find evidence for local adaptation: both within and between regions, growth of plants in their 'home soil' was not significantly larger relative to that in soil from other, more distant, populations. Conclusions/Significance: Our study suggests that negative soil biota effects can prevail in different parts of a plant species' range. Absence of local adaptation points to the possibility of similar rhizosphere biota composition across populations and regions, sufficient gene flow to prevent coevolution, selection in favor of plasticity, or functional redundancy among different soil biota. From the point of view of plant - soil biota interactions, our findings indicate that the current practice of using seeds exclusively from local provenances in ecosystem restoration campaigns may not be justified. Y1 - 2011 U6 - https://doi.org/10.1371/journal.pone.0017580 SN - 1932-6203 VL - 6 IS - 3 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Voss, Martin A1 - Nimtz, Manfred A1 - Leimkühler, Silke T1 - Elucidation of the dual role of Mycobacterial MoeZR in Molybdenum Cofactor Biosynthesis and Cysteine Biosynthesis JF - PLoS one N2 - The pathway of molybdenum cofactor biosynthesis has been studied in detail by using proteins from Mycobacterium species, which contain several homologs associated with the first steps of Moco biosynthesis. While all Mycobacteria species contain a MoeZR, only some strains have acquired an additional homolog, MoeBR, by horizontal gene transfer. The role of MoeBR and MoeZR was studied in detail for the interaction with the two MoaD-homologs involved in Moco biosynthesis, MoaD1 and MoaD2, in addition to the CysO protein involved in cysteine biosynthesis. We show that both proteins have a role in Moco biosynthesis, while only MoeZR, but not MoeBR, has an additional role in cysteine biosynthesis. MoeZR and MoeBR were able to complement an E. coli moeB mutant strain, but only in conjunction with the Mycobacterial MoaD1 or MoaD2 proteins. Both proteins were able to sulfurate MoaD1 and MoaD2 in vivo, while only MoeZR additionally transferred the sulfur to CysO. Our in vivo studies show that Mycobacteria have acquired several homologs to maintain Moco biosynthesis. MoeZR has a dual role in Moco- and cysteine biosynthesis and is involved in the sulfuration of MoaD and CysO, whereas MoeBR only has a role in Moco biosynthesis, which is not an essential function for Mycobacteria. Y1 - 2011 U6 - https://doi.org/10.1371/journal.pone.0028170 SN - 1932-6203 VL - 6 IS - 11 PB - PLoS CY - San Fransisco ER - TY - THES A1 - Vosloh, Daniel T1 - Subcellular compartmentation of primary carbon metabolism in mesophyll cells of Arabidopsis thaliana T1 - Subzelluläre Kompartimentierung des primären Kohlenstoffmetabolismus in Mesophyllzellen von Arabidopsis thaliana N2 - Metabolismus in Pflanzenzellen ist stark kompartimentiert. Viele Stoffwechselwege haben Reaktionen in mehr als einem Kompartiment. Zum Beispiel wird während der Photosynthese in pflanzlichen Mesophyllzellen Kohlenstoff in Form von Stärke in den Chloroplasten synthetisiert, während es im Zytosol in Form von Sacharose gebildet und in der Vakuole gespeichert wird. Diese Reaktionen sind strikt reguliert um ein Gleichgewicht der Kohlenstoffpools der verschiedenen Kompartimente aufrecht zu erhalten und die Energieversorgung aller Teile der Zelle für anabolische Reaktionen sicher zu stellen. Ich wende eine Methode an, bei der die Zellen unter nicht-wässrigen Bedingungen fraktioniert werden und daher der metabolische Status der während der Ernte herrschte über den ganzen Zeitraum der Auftrennung beibehalten wird. Durch die Kombination von nichtwässriger Fraktionierung und verschiedener Massenspektrometrietechniken (Flüssigchromotagraphie- und Gaschromotagraphie basierende Massenspekrometrie) ist es möglich die intrazelluläre Verteilung der meisten Intermediate des photosynthetischen Kohlenstoffstoffwechsels und der Produkte der nachgelagerten metabolischen Reaktionen zu bestimmen. Das Wissen über die in vivo Konzentrationen dieser Metabolite wurde genutzt um die Änderung der freien Gibbs Energie in vivo zu bestimmen. Mit Hilfe dessen kann bestimmt werden, welche Reaktion sich in einem Gleichgewichtszustand befinden und welche davon entfernt sind. Die Konzentration der Enzyme und der Km Werte wurden mit den Konzentrationen der Metabolite in vivo verglichen, um festzustellen, welche Enzyme substratlimitiert sind und somit sensitiv gegenüber Änderungen der Substratkonzentration sind. Verschiedene Intermediate des Calvin-Benson Zyklus sind gleichzeitig Substrate für andere Stoffwechselwege, als da wären Dihyroxyaceton-phosphat (DHAP, Saccharosesynthese), Fructose 6-phosphat (Fru6P, Stärkesynthese), Erythrose 4-phosphat (E4P, Shikimat Stoffwechselweg) und Ribose 5-phosphat (R5P, Nukleotidbiosynthese). Die Enzyme, die diese Intermediate verstoffwechseln, liegen an den Abzweigungspunkten zu diesen Stoffwechselwegen. Diese sind Trisose phosphat isomerase (DHAP), Transketolase (E4P), Sedoheptulose-1,7 biphosphat aldolase (E4P) und Ribose-5-phosphat isomerase (R5P), welche nicht mit ihren Substraten gesättigt sind, da die jeweilige Substratkonzentration geringer als der zugehörige Km Wert ist. Für metabolische Kontrolle bedeutet dies, dass diese Schritte am sensitivsten gegenüber Änderungen der Substratkonzentrationen sind. Im Gegensatz dazu sind die regulierten irreversiblen Schritte von Fructose-1,6.biphosphatase und Sedoheptulose-1,7-biphosphatase relativ insensitiv gegenüber Änderungen der Substratkonzentration. Für den Stoffwechselweg der Saccharosesynthese konnte gezeigt werden, dass die zytosolische Aldolase eine geringer Bindeseitenkonzentration als Substratkonzentration (DHAP) aufweist, und dass die Konzentration von Saccharose-6-phosphat geringer als der Km Wert des synthetisierenden Enzyms Saccharose-phosphatase ist. Sowohl die Saccharose-phosphat-synthase, also auch die Saccharose-phosphatase sind in vivo weit von einem Gleichgewichtszustand entfernt. In Wildtyp Arabidopsis thaliana Columbia-0 Blättern wurde der gesamte Pool von ADPGlc im Chloroplasten gefunden. Das Enzyme ADPGlc pyrophosphorylase ist im Chloroplasten lokalisiert und synthetisiert ADPGlc aus ATP und Glc1P. Dieses Verteilungsmuster spricht eindeutig gegen die Hypothese von Pozueta-Romero und Kollegen, dass ADPGlc im Zytosol durch ADP vermittelte Spaltung von Saccharose durch die Saccharose Synthase erzeugt wird. Basierend auf dieser Beobachtung und anderen veröffentlichten Ergebnissen wurde geschlußfolgert, dass der generell akzeptierte Stoffwechselweg der Stärkesynthese durch ADPGlc Produktion via ADPGlc pyrophosphorylase in den Chloroplasten korrekt ist, und die Hypothese des alternativen Stoffwechselweges unhaltbar ist. Innerhalb des Stoffwechselweges der Saccharosesynthsese wurde festgestellt, dass die Konzentration von ADPGlc geringer als der Km Wert des Stärkesynthase ist, was darauf hindeutet, dass das Enzym substratlimitiert ist. Eine generelle Beobachtung ist, dass viele Enzmye des Calvin-Benson Zyklus ähnliche Bindeseitenkonzentrationen wie Metabolitkonzentrationen aufweisen, wohingegen in den Synthesewegen von Saccharose und Stärke die Bindeseitenkonzentrationen der Enzyme viel geringer als die Metabolitkonzentrationen sind. N2 - Metabolism in plant cells is highly compartmented, with many pathways involving reactions in more than one compartment. For example, during photosynthesis in leaf mesophyll cells, primary carbon fixation and starch synthesis take place in the chloroplast, whereas sucrose is synthesized in the cytosol and stored in the vacuole. These reactions are tightly regulated to keep a fine balance between the carbon pools of the different compartments and to fulfil the energy needs of the organelles. I applied a technique which fractionates the cells under non-aqueous conditions, whereby the metabolic state is frozen at the time of harvest and held in stasis throughout the fractionation procedure. With the combination of non-aqueous fractionation and mass spectrometry based metabolite measurements (LC-MS/MS, GC-MS) it was possible to investigate the intracellular distributions of the intermediates of photosynthetic carbon metabolism and its products in subsequent metabolic reactions. With the knowledge about the in vivo concentrations of these metabolites under steady state photosynthesis conditions it was possible to calculate the mass action ratio and change in Gibbs free energy in vivo for each reaction in the pathway, to determine which reactions are near equilibrium and which are far removed from equilibrium. The Km value and concentration of each enzyme were compared with the concentrations of its substrates in vivo to assess which reactions are substrate limited and so sensitive to changes in substrate concentration. Several intermediates of the Calvin-Benson cycle are substrates for other pathways, including dihydroxyacetone-phosphate (DHAP,sucrose synthesis), fructose 6-phosphate (Fru6P, starch synthesis), erythrose 4-phosphate (E4P,shikimate pathway) and ribose 5-phosphate (R5P, nucleotide synthesis). Several of the enzymes that metabolise these intermediates, and so lie at branch points in the pathway, are triose-phosphate isomerase (DHAP), transketolase (E4P, Fru6P), sedoheptulose-1,7-bisphosphate aldolase (E4P) and ribose-5-phosphate isomerase (R5P) are not saturated with their respective substrate as the metabolite concentration is lower than the respective Km value. In terms of metabolic control these are the steps that are most sensitive to changes in substrate availability, while the regulated irreversible reactions of fructose-1,6-bisphosphatase and sedoheptulose-1,7-bisphosphatase are relatively insensitive to changes in the concentrations of their substrates. In the pathway of sucrose synthesis it was shown that the concentration of the catalytic binding site of the cytosolic aldolase is lower than the substrate concentration of DHAP, and that the concentration of Suc6P is lower than the Km of sucrose-phosphatase for this substrate. Both the sucrose-phosphate synthase and sucrose-phosphatase reactions are far removed from equilibrium in vivo. In wild type A. thaliana Columbia-0 leaves, all of the ADPGlc was found to be localised in the chloroplasts. ADPglucose pyrophosphorylase is localised to the chloroplast and synthesises ADPGlc from ATP and Glc1P. This distribution argues strongly against the hypothesis proposed by Pozueta-Romero and colleagues that ADPGlc for starch synthesis is produced in the cytosol via ADP-mediated cleavage of sucrose by sucrose synthase. Based on this observation and other published data it was concluded that the generally accepted pathway of starch synthesis from ADPGlc produced by ADPglucose pyrophosphorylase in the chloroplasts is correct, and that the alternative pathway is untenable. Within the pathway of starch synthesis the concentration of ADPGlc was found to be well below the Km value of starch synthase for ADPGlc, indicating that the enzyme is substrate limited. A general finding in the comparison of the Calvin-Benson cycle with the synthesis pathways of sucrose and starch is that many enzymes in the Calvin Benson cycle have active binding site concentrations that are close to the metabolite concentrations, while for nearly all enzymes in the synthesis pathways the active binding site concentrations are much lower than the metabolite concentrations. KW - Pflanze KW - Kohlenstoffmetabolismus KW - Mesophyll KW - Zelle KW - plant KW - carbon metabolism KW - mesophyll KW - cell Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-55534 ER - TY - JOUR A1 - Voigt, Andrea A1 - Scheffler, Christiane T1 - Manual abilities of the elderly - handgrip strength, finger and thumb push strength and opening strength in age comparison Y1 - 2011 SN - 0003-5548 ER - TY - JOUR A1 - Voigt, Andrea A1 - Scheffler, Christiane T1 - Manual abilities of the elderly - handgrip strength, finger and thumb push strength and opening strength in age comparison JF - Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft für Anthropologie N2 - The purpose of this paper is to display the static strength capacities of healthy adults in different age categories. A total of 279 healthy German adults at the ages of 20 to 29 years, 50 to 59 years and 60 to 69 years generated their maximum static handgrip, index finger and thumb push strength, as well as their maximum opening strength on a smooth jar lid of 85 mm diameter and on a knurled bottle lid of 31 mm with their right hand. The results show larger male strength than female strength. Significant age-induced differences appear primarily in opening strengths between the age groups 20 to 29 and 50 to 59 years in male subjects and in female opening strengths between the age groups 20 to 29 and 60 to 69 years as well as between the age groups 50 to 59 and 60 to 69 years. Of greatest interest is that elderly men show the largest opening strengths. KW - elderly KW - torque KW - handgrip strength KW - opening strength Y1 - 2011 U6 - https://doi.org/10.1127/0003-5548/2011/0090 SN - 0003-5548 VL - 68 IS - 2 SP - 167 EP - 173 PB - Schweizerbart CY - Stuttgart ER - TY - JOUR A1 - Vater, Marianne A1 - Koessl, Manfred T1 - Comparative aspects of cochlear functional organization in mammals JF - Hearing research N2 - This review addresses the functional organization of the mammalian cochlea under a comparative and evolutionary perspective. A comparison of the monotreme cochlea with that of marsupial and placental mammals highlights important evolutionary steps towards a hearing organ dedicated to process higher frequencies and a larger frequency range than found in non-mammalian vertebrates. Among placental mammals, there are numerous cochlear specializations which relate to hearing range in adaptation to specific habitats that are superimposed on a common basic design. These are illustrated by examples of specialist ears which evolved excellent high frequency hearing and echolocation (bats and dolphins) and by the example of subterranean rodents with ears devoted to processing low frequencies. Furthermore, structural functional correlations important for tonotopic cochlear organization and predictions of hearing capabilities are discussed. Y1 - 2011 U6 - https://doi.org/10.1016/j.heares.2010.05.018 SN - 0378-5955 VL - 273 IS - 1-2 SP - 89 EP - 99 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Van Donk, Ellen A1 - Ianora, Adrianna A1 - Vos, Matthijs T1 - Induced defences in marine and freshwater phytoplankton a review JF - Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica N2 - Many organisms have developed defences to avoid predation by species at higher trophic levels. The capability of primary producers to defend themselves against herbivores affects their own survival, can modulate the strength of trophic cascades and changes rates of competitive exclusion in aquatic communities. Algal species are highly flexible in their morphology, growth form, biochemical composition and production of toxic and deterrent compounds. Several of these variable traits in phytoplankton have been interpreted as defence mechanisms against grazing. Zooplankton feed with differing success on various phytoplankton species, depending primarily on size, shape, cell wall structure and the production of toxins and deterrents. Chemical cues associated with (i) mechanical damage, (ii) herbivore presence and (iii) grazing are the main factors triggering induced defences in both marine and freshwater phytoplankton, but most studies have failed to disentangle the exact mechanism(s) governing defence induction in any particular species. Induced defences in phytoplankton include changes in morphology (e.g. the formation of spines, colonies and thicker cell walls), biochemistry (such as production of toxins, repellents) and in life history characteristics (formation of cysts, reduced recruitment rate). Our categorization of inducible defences in terms of the responsible induction mechanism provides guidance for future work, as hardly any of the available studies on marine or freshwater plankton have performed all the treatments that are required to pinpoint the actual cue(s) for induction. We discuss the ecology of inducible defences in marine and freshwater phytoplankton with a special focus on the mechanisms of induction, the types of defences, their costs and benefits, and their consequences at the community level. KW - Defenses KW - Algae KW - Review KW - Plankton community KW - Cyanobacteria KW - Toxins Y1 - 2011 U6 - https://doi.org/10.1007/s10750-010-0395-4 SN - 0018-8158 SN - 1573-5117 VL - 668 IS - 1 SP - 3 EP - 19 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Tschöpe, Okka A1 - Wallschläger, Hans-Dieter A1 - Burkart, Michael A1 - Tielbörger, Katja T1 - Managing open habitats by wild ungulate browsing and grazing a case-study in North-Eastern Germany JF - Applied vegetation science : official organ of the International Association for Vegetation Science N2 - Question: Can wild ungulates efficiently maintain and restore open habitats? Location: Brandenburg, NE Germany. Methods: The effect of wild ungulate grazing and browsing was studied in three successional stages: (1) Corynephorus canescens-dominated grassland; (2) ruderal tall forb vegetation dominated by Tanacetum vulgare; and (3) Pinus sylvestris-pioneer forest. The study was conducted over 3 yr. In each successional stage, six paired 4 m(2)-monitoring plots of permanently grazed versus ungrazed plots were arranged in three random blocks. Removal of grazing was introduced de novo for the study. In each plot, percentage cover of each plant and lichen species and total cover of woody plants was recorded. Results: Wild ungulates considerably affected successional pathways and species composition in open habitats but this influence became evident in alteration of abundances of only a few species. Grazing effects differed considerably between successional stages: species richness was higher in grazed versus ungrazed ruderal and pioneer forest plots, but not in the Corynephorus sites. Herbivory affected woody plant cover only in the Pioneer forest sites. Although the study period was too short to observe drastic changes in species richness and woody plant cover, notable changes in species composition were still detected in all successional stages. Conclusion: Wild ungulate browsing is a useful tool to inhibit encroachment of woody vegetation and to conserve a species-rich, open landscape. KW - Conservation KW - Red deer KW - Fallow deer KW - Succession KW - Species richness KW - Woody plant Y1 - 2011 U6 - https://doi.org/10.1111/j.1654-109X.2010.01119.x SN - 1402-2001 VL - 14 IS - 2 SP - 200 EP - 209 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Tirok, Katrin A1 - Bauer, Barbara A1 - Wirtz, Kai A1 - Gaedke, Ursula T1 - Predator-Prey Dynamics Driven by Feedback between Functionally Diverse Trophic Levels JF - PLoS one N2 - Neglecting the naturally existing functional diversity of communities and the resulting potential to respond to altered conditions may strongly reduce the realism and predictive power of ecological models. We therefore propose and study a predator-prey model that describes mutual feedback via species shifts in both predator and prey, using a dynamic trait approach. Species compositions of the two trophic levels were described by mean functional traits-prey edibility and predator food-selectivity- and functional diversities by the variances. Altered edibility triggered shifts in food-selectivity so that consumers continuously respond to the present prey composition, and vice versa. This trait-mediated feedback mechanism resulted in a complex dynamic behavior with ongoing oscillations in the mean trait values, reflecting continuous reorganization of the trophic levels. The feedback was only possible if sufficient functional diversity was present in both trophic levels. Functional diversity was internally maintained on the prey level as no niche existed in our system, which was ideal under any composition of the predator level due to the trade-offs between edibility, growth and carrying capacity. The predators were only subject to one trade-off between food-selectivity and grazing ability and in the absence of immigration, one predator type became abundant, i.e., functional diversity declined to zero. In the lack of functional diversity the system showed the same dynamics as conventional models of predator-prey interactions ignoring the potential for shifts in species composition. This way, our study identified the crucial role of trade-offs and their shape in physiological and ecological traits for preserving diversity. Y1 - 2011 U6 - https://doi.org/10.1371/journal.pone.0027357 SN - 1932-6203 VL - 6 IS - 11 PB - PLoS CY - San Fransisco ER - TY - THES A1 - Tiller, Nadine T1 - Plastid translation : functions of plastid-specific ribosomal proteins and identification of a factor mediating plastid-to-nucleus retrograde sifnalling Y1 - 2011 CY - Potsdam ER - TY - CHAP A1 - Tikhonenko, I. A1 - Magidson, V. A1 - Gräf, Ralph A1 - Khodjakov, A. A1 - Koonce, M. T1 - A kinesin-mediated linkage between centrosomes and the nuclear envelope T2 - Molecular biology of the cell : the official publication of the American Society for Cell Biology Y1 - 2011 SN - 1059-1524 VL - 22 IS - 1 PB - American Society for Cell Biology CY - Bethesda ER - TY - JOUR A1 - Tiedemann, Ralph A1 - Paulus, Kirsten B. A1 - Havenstein, Katja A1 - Thorstensen, Sverrir A1 - Petersen, Aevar A1 - Lyngs, Peter A1 - Milinkovitch, Michel C. T1 - Alien eggs in duck nests brood parasitism or a help from Grandma? JF - Molecular ecology N2 - Intraspecific brood parasitism (IBP) is a remarkable phenomenon by which parasitic females can increase their reproductive output by laying eggs in conspecific females' nests in addition to incubating eggs in their own nest. Kin selection could explain the tolerance, or even the selective advantage, of IBP, but different models of IBP based on game theory yield contradicting predictions. Our analyses of seven polymorphic autosomal microsatellites in two eider duck colonies indicate that relatedness between host and parasitizing females is significantly higher than the background relatedness within the colony. This result is unlikely to be a by-product of relatives nesting in close vicinity, as nest distance and genetic identity are not correlated. For eider females that had been ring-marked during the decades prior to our study, our analyses indicate that (i) the average age of parasitized females is higher than the age of nonparasitized females, (ii) the percentage of nests with alien eggs increases with the age of nesting females, (iii) the level of IBP increases with the host females' age, and (iv) the number of own eggs in the nest of parasitized females significantly decreases with age. IBP may allow those older females unable to produce as many eggs as they can incubate to gain indirect fitness without impairing their direct fitness: genetically related females specialize in their energy allocation, with young females producing more eggs than they can incubate and entrusting these to their older relatives. Intraspecific brood parasitism in ducks may constitute cooperation among generations of closely related females. KW - eider duck KW - indirect fitness KW - intraspecific brood parasitism KW - microsatellites KW - relatedness KW - Somateria mollissima Y1 - 2011 U6 - https://doi.org/10.1111/j.1365-294X.2011.05158.x SN - 0962-1083 VL - 20 IS - 15 SP - 3237 EP - 3250 PB - Wiley-Blackwell CY - Hoboken ER - TY - THES A1 - Szecówka, Marek T1 - Metabolic fluxes in photosynthetic and heterotrophic plant tissues Y1 - 2011 CY - Potsdam ER - TY - THES A1 - Sun, Xiaoliang T1 - Towards understanding the dynamics of biological systems from -Omics data Y1 - 2011 CY - Potsdam ER - TY - JOUR A1 - Struck, Torsten H. A1 - Paul, Christiane A1 - Hill, Natascha A1 - Hartmann, Stefanie A1 - Hoesel, Christoph A1 - Kube, Michael A1 - Lieb, Bernhard A1 - Meyer, Achim A1 - Tiedemann, Ralph A1 - Purschke, Guenter A1 - Bleidorn, Christoph T1 - Phylogenomic analyses unravel annelid evolution JF - Nature : the international weekly journal of science N2 - Annelida, the ringed worms, is a highly diverse animal phylum that includes more than 15,000 described species and constitutes the dominant benthic macrofauna from the intertidal zone down to the deep sea. A robust annelid phylogeny would shape our understanding of animal body-plan evolution and shed light on the bilaterian ground pattern. Traditionally, Annelida has been split into two major groups: Clitellata (earthworms and leeches) and polychaetes (bristle worms), but recent evidence suggests that other taxa that were once considered to be separate phyla (Sipuncula, Echiura and Siboglinidae (also known as Pogonophora)) should be included in Annelida(1-4). However, the deep-level evolutionary relationships of Annelida are still poorly understood, and a robust reconstruction of annelid evolutionary history is needed. Here we show that phylogenomic analyses of 34 annelid taxa, using 47,953 amino acid positions, recovered a well-supported phylogeny with strong support for major splits. Our results recover chaetopterids, myzostomids and sipunculids in the basal part of the tree, although the position of Myzostomida remains uncertain owing to its long branch. The remaining taxa are split into two clades: Errantia (which includes the model annelid Platynereis), and Sedentaria (which includes Clitellata). Ancestral character trait reconstructions indicate that these clades show adaptation to either an errant or a sedentary lifestyle, with alteration of accompanying morphological traits such as peristaltic movement, parapodia and sensory perception. Finally, life history characters in Annelida seem to be phylogenetically informative. Y1 - 2011 U6 - https://doi.org/10.1038/nature09864 SN - 0028-0836 VL - 471 IS - 7336 SP - 95 EP - U113 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Junginger, Annett A1 - Olaka, Lydia A. A1 - Tiedemann, Ralph A1 - Trauth, Martin H. T1 - Environmental variability in Lake Naivasha, Kenya, over the last two centuries JF - Journal of paleolimnolog N2 - Lake Naivasha, Kenya, is one of a number of freshwater lakes in the East African Rift System. Since the beginning of the twentieth century, it has experienced greater anthropogenic influence as a result of increasingly intensive farming of coffee, tea, flowers, and other horticultural crops within its catchment. The water-level history of Lake Naivasha over the past 200 years was derived from a combination of instrumental records and sediment data. In this study, we analysed diatoms in a lake sediment core to infer past lacustrine conductivity and total phosphorus concentrations. We also measured total nitrogen and carbon concentrations in the sediments. Core chronology was established by (210)Pb dating and covered a similar to 186-year history of natural (climatic) and human-induced environmental changes. Three stratigraphic zones in the core were identified using diatom assemblages. There was a change from littoral/epiphytic diatoms such as Gomphonema gracile and Cymbella muelleri, which occurred during a prolonged dry period from ca. 1820 to 1896 AD, through a transition period, to the present planktonic Aulacoseira sp. that favors nutrient-rich waters. This marked change in the diatom assemblage was caused by climate change, and later a strong anthropogenic overprint on the lake system. Increases in sediment accumulation rates since 1928, from 0.01 to 0.08 g cm(-2) year(-1) correlate with an increase in diatom-inferred total phosphorus concentrations since the beginning of the twentieth century. The increase in phosphorus accumulation suggests increasing eutrophication of freshwater Lake Naivasha. This study identified two major periods in the lake's history: (1) the period from 1820 to 1950 AD, during which the lake was affected mainly by natural climate variations, and (2) the period since 1950, during which the effects of anthropogenic activity overprinted those of natural climate variation. KW - Lake sediments KW - Diatoms KW - Conductivity KW - Lake Naivasha KW - Human impact KW - Eutrophication Y1 - 2011 U6 - https://doi.org/10.1007/s10933-011-9502-4 SN - 0921-2728 VL - 45 IS - 3 SP - 353 EP - 367 PB - Springer CY - Dordrecht ER - TY - THES A1 - Stoof-Leichsenring, Kathleen Rosemarie T1 - Genetic analysis of diatoms and rotifers in tropical Kenyan lake sediments Y1 - 2011 CY - Potsdam ER - TY - JOUR A1 - Stanke, Sandra A1 - Bier, Frank Fabian A1 - Hoezel, Ralph T1 - Fluid streaming above interdigitated electrodes in dielectrophoresis experiments JF - Electrophoresis : microfluidics, nanoanalysis & proteomics N2 - For the investigation of alternating current electrokinetic effects, a system is presented that allows for the simultaneous observation of fluid flow above and around microelectrodes in all three directions in space. Beside the usual microscopical view from top, lateral observation through the same objective is made possible by two small mirrors that are placed next to the electrodes. Fluid flow and movement of fluorescent nanoparticles above interdigitated electrodes are monitored by fluorescence microscopy and digital imaging and are further analysed by image processing. Field frequencies are varied from 10 Hz to 1 GHz at up to 10V(rms). Electrical conductivity of the fluid is monitored in situ in the actual measuring chamber. KW - Dielectrophoresis KW - Fluid streaming KW - Nanobead Y1 - 2011 U6 - https://doi.org/10.1002/elps.201100096 SN - 0173-0835 VL - 32 IS - 18 SP - 2448 EP - 2455 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Spijkerman, Elly A1 - Wacker, Alexander T1 - Interactions between P-limitation and different C conditions on the fatty acid composition of an extremophile microalga JF - Extremophiles : life under extreme conditions N2 - The extremophilic microalga Chlamydomonas acidophila inhabits very acidic waters (pH 2-3.5), where its growth is often limited by phosphorus (P) or colimited by P and inorganic carbon (CO(2)). Because this alga is a major food source for predators in acidic habitats, we studied its fatty acid content, which reflects their quality as food, grown under a combination of P-limited and different carbon conditions (either mixotrophically with light + glucose or at high or low CO(2), both without glucose). The fatty acid composition largely depended on the cellular P content: stringent P-limited cells had a higher total fatty acid concentration and had a lower percentage of polyunsaturated fatty acids. An additional limitation for CO(2) inhibited this decrease, especially reflected in enhanced concentrations of 18:3(9,12,15) and 16:4(3,7,10,13), resulting in cells relatively rich in polyunsaturated fatty acids under colimiting growth conditions. The percentage of polyunsaturated to total fatty acid content was positively related with maximum photosynthesis under all conditions applied. The two factors, P and CO(2), thus interact in their effect on the fatty acid composition in C. acidophila, and colimited cells P-limited algae can be considered a superior food source for herbivores because of the high total fatty acid content and relative richness in polyunsaturated fatty acids. KW - Acidophilic algae KW - Cellular P quota KW - Chlamydomonas acidophila KW - Chlorophyceae KW - Colimitation KW - CO(2) KW - Fatty acid composition KW - Food quality KW - Glucose KW - Mixotrophy KW - Photosynthesis KW - Phytoplankton KW - Phosphorus limitation Y1 - 2011 U6 - https://doi.org/10.1007/s00792-011-0390-3 SN - 1431-0651 VL - 15 IS - 5 SP - 597 EP - 609 PB - Springer CY - Tokyo ER - TY - JOUR A1 - Spijkerman, Elly A1 - de Castro, Francisco A1 - Gaedke, Ursula T1 - Independent Colimitation for Carbon Dioxide and Inorganic Phosphorus JF - PLoS one N2 - Simultaneous limitation of plant growth by two or more nutrients is increasingly acknowledged as a common phenomenon in nature, but its cellular mechanisms are far from understood. We investigated the uptake kinetics of CO(2) and phosphorus of the algae Chlamydomonas acidophila in response to growth at limiting conditions of CO(2) and phosphorus. In addition, we fitted the data to four different Monod-type models: one assuming Liebigs Law of the minimum, one assuming that the affinity for the uptake of one nutrient is not influenced by the supply of the other (independent colimitation) and two where the uptake affinity for one nutrient depends on the supply of the other (dependent colimitation). In addition we asked whether the physiological response under colimitation differs from that under single nutrient limitation. We found no negative correlation between the affinities for uptake of the two nutrients, thereby rejecting a dependent colimitation. Kinetic data were supported by a better model fit assuming independent uptake of colimiting nutrients than when assuming Liebigs Law of the minimum or a dependent colimitation. Results show that cell nutrient homeostasis regulated nutrient acquisition which resulted in a trade-off in the maximum uptake rates of CO(2) and phosphorus, possibly driven by space limitation on the cell membrane for porters for the different nutrients. Hence, the response to colimitation deviated from that to a single nutrient limitation. In conclusion, responses to single nutrient limitation cannot be extrapolated to situations where multiple nutrients are limiting, which calls for colimitation experiments and models to properly predict growth responses to a changing natural environment. These deviations from single nutrient limitation response under colimiting conditions and independent colimitation may also hold for other nutrients in algae and in higher plants. Y1 - 2011 U6 - https://doi.org/10.1371/journal.pone.0028219 SN - 1932-6203 VL - 6 IS - 12 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Spijkerman, Elly T1 - The expression of a carbon concentrating mechanism in Chlamydomonas acidophila under variable phosphorus, iron, and CO2 concentrations JF - Photosynthesis research N2 - The CO2 acquisition was analyzed in Chlamydomonas acidophila at pH 2.4 in a range of medium P and Fe concentrations and at high and low CO2 condition. The inorganic carbon concentrating factor (CCF) was related to cellular P quota (Q(p)), maximum CO2-uptake rate by photosynthesis (V-max; O-2), half saturation constant for CO2 uptake (K-0.5), and medium Fe concentration. There was no effect of the medium Fe concentration on the CCF. The CCF increased with increasing Q(p) in both high and low CO2 grown algae, but maximum Q(p) was 6-fold higher in the low CO2 cells. In high CO2 conditions, the CCF was low, ranging between 0.8 and 3.5. High CCF values up to 9.1 were only observed in CO2-limited cells, but P- and CO2-colimited cells had a low CCF. High CCF did not relate with a low K-0.5 as all CO2-limited cells had a low K-0.5 (<4 mu M CO2). High Ci-pools in cells with high Qp suggested the presence of an active CO2-uptake mechanism. The CCF also increased with increasing V-max; O-2 which reflect an adaptation to the nutrient in highest demand (CO2) under balanced growth conditions. It is proposed that the size of the CCF in C. acidophila is more strongly related to porter density for CO2 uptake (reflected in V-max; O-2) and less- to high-affinity CO2 uptake (low K-0.5) at balanced growth. In addition, high CCF can only be realized with high Q(p). KW - C3 photosynthesis KW - Micro-algae KW - Carbon concentrating mechanism KW - Phosphorus limitation KW - Iron toxicity Y1 - 2011 U6 - https://doi.org/10.1007/s11120-010-9607-z SN - 0166-8595 VL - 109 IS - 1-3 SP - 179 EP - 189 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Sperfeld, Erik A1 - Wacker, Alexander T1 - Temperature- and cholesterol-induced changes in eicosapentaenoic acid limitation of Daphnia magna determined by a promising method to estimate growth saturation thresholds JF - Limnology and oceanography N2 - We present data on eicosapentaenoic acid (EPA)-limited growth responses of Daphnia magna under different temperatures and different dietary cholesterol availabilities to assess how EPA growth saturation thresholds depend on changing environmental conditions. D. magna was raised on gradients of dietary EPA at 15 degrees C and 20 degrees C with high cholesterol supply and at 20 degrees C with low and high cholesterol supply in laboratory experiments. A new method was applied to estimate EPA growth saturation thresholds on the basis of fitted saturation curves using bootstrapped data. The EPA threshold at which 75% and 90% of maximum growth was reached ranged from 0.7 to 1.6 mu g EPA (mg dietary C)(-1) and 2.0 to 4.9 mu g EPA (mg dietary C)(-1), respectively. Previously reported EPA concentrations in natural seston of many different lakes suggest that the thresholds measured here indicate a frequent potential for at least moderate EPA limitation in nature. Furthermore, the calculated EPA thresholds were higher in treatments of low compared with high temperature and higher in treatments of low compared with high cholesterol availability. The EPA-dependent growth responses were more strongly affected by temperature than by cholesterol availability. Our results suggest that EPA growth saturation thresholds for a particular Daphnia species probably vary in nature under different environmental conditions. Y1 - 2011 U6 - https://doi.org/10.4319/lo.2011.56.4.1273 SN - 0024-3590 VL - 56 IS - 4 SP - 1273 EP - 1284 PB - Wiley CY - Waco ER - TY - THES A1 - Sperfeld, Erik T1 - Effects of temperature and co-limiting nutritional components on life history traits of Daphnia magna and its biochemical composition Y1 - 2011 CY - Potsdam ER - TY - JOUR A1 - Speck, Janina A1 - Arndt, Katja Maren A1 - Müller, Kristian M. T1 - Efficient phage display of intracellularly folded proteins mediated by the TAT pathway JF - Protein engineering design & selection N2 - Phage display with filamentous phages is widely applied and well developed, yet proteins requiring a cytoplasmic environment for correct folding still defy attempts at functional display. To extend applicability of phage display, we employed the twin-arginine translocation (TAT) pathway to incorporate proteins fused to the C-terminal domain of the geneIII protein into phage particles. We investigated functionality and display level of fluorescent proteins depending on the translocation pathway, which was the TAT, general secretory (SEC) or signal recognition particle (SRP) pathway mediated by the TorA, PelB or DsbA signal sequences, respectively. Importantly, for green fluorescent protein, yellow fluorescent protein and cyan fluorescent protein, only TAT, but not SEC or SRP, translocation led to fluorescence of purified phage particles, although all three proteins could be displayed regardless of the translocation pathway. In contrast, the monomeric red fluorescent protein mCherry was functionally displayed regardless of the translocation pathway. Hence, correct folding and fluorophor formation of mCherry is not limited to the cytosol. Furthermore, we successfully displayed firefly luciferase as well as an 83 kDa argonaute protein, both containing free cysteines. This demonstrates broad applicability of the TAT-mediated phagemid system for the display of proteins requiring cytoplasmic factors for correct folding and should prove useful for the display of proteins requiring incorporation of co-factors or oligomerization to gain function. KW - g3p KW - phagemid display KW - protein design KW - protein engineering KW - selection Y1 - 2011 U6 - https://doi.org/10.1093/protein/gzr001 SN - 1741-0126 VL - 24 IS - 6 SP - 473 EP - 484 PB - Oxford Univ. Press CY - Oxford ER - TY - CHAP A1 - Smith, Mychal Daijon A1 - Mattos, Carla A1 - Barbiz, Stefanie T1 - The multiple solvent crystal structures of P22TSP T2 - The FASEB journal : the official journal of the Federation of American Societies for Experimental Biology Y1 - 2011 SN - 0892-6638 VL - 25 IS - 2 PB - Federation of American Societies for Experimental Biology CY - Bethesda ER - TY - THES A1 - Siewert, Katharina T1 - Autoaggressive human t cell receptorrs and their antigen specificities Y1 - 2011 CY - Potsdam ER - TY - JOUR A1 - Sicard, Adrien A1 - Stacey, Nicola A1 - Hermann, Katrin A1 - Dessoly, Jimmy A1 - Neuffer, Barbara A1 - Bäurle, Isabel A1 - Lenhard, Michael T1 - Genetics, evolution, and adaptive significance of the selfing syndrome in the genus Capsella JF - The plant cell N2 - The change from outbreeding to selfing is one of the most frequent evolutionary transitions in flowering plants. It is often accompanied by characteristic morphological and functional changes to the flowers (the selfing syndrome), including reduced flower size and opening. Little is known about the developmental and genetic basis of the selfing syndrome, as well as its adaptive significance. Here, we address these issues using the two closely related species Capsella grandiflora (the ancestral outbreeder) and red shepherd's purse (Capsella rubella, the derived selfer). In C. rubella, petal size has been decreased by shortening the period of proliferative growth. Using interspecific recombinant inbred lines, we show that differences in petal size and flower opening between the two species each have a complex genetic basis involving allelic differences at multiple loci. An intraspecific cross within C. rubella suggests that flower size and opening have been decreased in the C. rubella lineage before its extensive geographical spread. Lastly, by generating plants that likely resemble the earliest ancestors of the C. rubella lineage, we provide evidence that evolution of the selfing syndrome was at least partly driven by selection for efficient self-pollination. Thus, our studies pave the way for a molecular dissection of selfing-syndrome evolution. Y1 - 2011 U6 - https://doi.org/10.1105/tpc.111.088237 SN - 1040-4651 VL - 23 IS - 9 SP - 3156 EP - 3171 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Sicard, Adrien A1 - Lenhard, Michael T1 - The selfing syndrome a model for studying the genetic and evolutionary basis of morphological adaptation in plants JF - Annals of botany N2 - Background In angiosperm evolution, autogamously selfing lineages have been derived from outbreeding ancestors multiple times, and this transition is regarded as one of the most common evolutionary tendencies in flowering plants. In most cases, it is accompanied by a characteristic set of morphological and functional changes to the flowers, together termed the selfing syndrome. Two major areas that have changed during evolution of the selfing syndrome are sex allocation to male vs. female function and flower morphology, in particular flower (mainly petal) size and the distance between anthers and stigma. Scope A rich body of theoretical, taxonomic, ecological and genetic studies have addressed the evolutionary modification of these two trait complexes during or after the transition to selfing. Here, we review our current knowledge about the genetics and evolution of the selfing syndrome. Conclusions We argue that because of its frequent parallel evolution, the selfing syndrome represents an ideal model for addressing basic questions about morphological evolution and adaptation in flowering plants, but that realizing this potential will require the molecular identification of more of the causal genes underlying relevant trait variation. KW - Evolution KW - selfing syndrome KW - autogamy KW - pollen-to-ovule ratio KW - flower size KW - herkogamy KW - quantitative trait loci KW - self-incompatibility Y1 - 2011 U6 - https://doi.org/10.1093/aob/mcr023 SN - 0305-7364 SN - 1095-8290 VL - 107 IS - 9 SP - 1433 EP - 1443 PB - Oxford Univ. Press CY - Oxford ER - TY - THES A1 - Sharma, Tripti T1 - Regulation of potassium channels in plants : biophysical mechanisms and physiological implacations Y1 - 2011 CY - Potsdam ER - TY - JOUR A1 - Sharma, Reeta A1 - Stuckas, Heiko A1 - Bhaskar, Ranjana A1 - Khan, Imran A1 - Goyal, Surendra Prakash A1 - Tiedemann, Ralph T1 - Genetically distinct population of Bengal tiger (Panthera tigris tigris) in Terai Arc Landscape (TAL) of India JF - Mammalian biology = Zeitschrift für Säugetierkunde N2 - We analyzed mtDNA polymorphisms (a total of 741 bp from a part of conserved control region, ND5, ND2, Cyt b and 12S) in 91 scats and 12 tissue samples of Bengal tiger (Panthera tigris tigris) populations across Terai Arc Landscape (TAL) located at the foothills of Himalayas in North Western India, Buxa Tiger Reserve (BTR), and North East India. In TAL and BTR, we found a specific haplotype at high frequency, which was absent elsewhere, indicating a genetically distinct population in these regions. Within the TAL region, there is some evidence for genetic isolation of the tiger populations west of river Ganges, i.e., in the western part of Rajaji National Park (RNP). Although the river itself might not constitute a significant barrier for tigers, recent human-induced changes in habitat and degradation of the Motichur-Chilla Corridor connecting the two sides of the tiger habitat of RNP might effectively prevent genetic exchange. A cohesive population is observed for the rest of the TAL. Even the more eastern BTR belongs genetically to this unit, despite the present lack of a migration corridor between BTR and TAL. In spite of a close geographic proximity, Chitwan (Nepal) constitutes a tiger population genetically different from TAL. Moreover, it is observed that the North East India tiger populations are genetically different from TAL and BTR, as well as from the other Bengal tiger populations in India. KW - Bengal tiger KW - Population genetics KW - mtDNA haplotype KW - Terai Arc Y1 - 2011 U6 - https://doi.org/10.1016/j.mambio.2010.10.005 SN - 1616-5047 VL - 76 IS - 4 SP - 484 EP - 490 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Scott, James A1 - Muhling, Janet A1 - Fletcher, Ian A1 - Billia, Marco A1 - Palin, J. Michael A1 - Elliot, Tim A1 - Günter, Christina T1 - The relationship of Palaeozoic metamorphism and S-type magmatism on the paleo-Pacific Gondwana margin JF - Lithos : an international journal of mineralogy, petrology, and geochemistry N2 - A massive pulse of granitic magma was rapidly emplaced into the once contiguous West Antarctic and New Zealand segments of the palaeo-Pacific margin of the Gondwana supercontinent at similar to 371 Ma. In New Zealand, these Late Devonian S-type granitoids cover an areal extent of > 3400 km(2), but the tectonic setting for crustal partial melting has remained unclear because most of the exposure represents either emplacement-level, or rocks that have been reworked during Cretaceous orogenesis. New petrologic data indicate that aluminous paragneisses and orthogneisses in the Bonar Range represent a rare portion of Devonian middle crust that preserves evidence for the initiation of crustal melting. The investigated rocks outline the tail of a clockwise P-T path that involved partial melting at peak conditions (similar to 670 degrees C, 5.1 kb), deformation during the immediately following near-isothermal decompression, and then partial re-equilibration under static conditions. Syn- to post-kinematic growth of zoned monazite establishes the timing of recrystallisation to a similar to 16 Ma period that began at 373.4 +/- 4.1 Ma. This age overlaps with the initiation of regional Karamea S-type granitic magmatism. Although estimated metamorphic conditions were insufficient for large amounts of melt to have been produced from Bonar Range pelites (calculated melt volumes are <10%), they do provide evidence consistent with widespread heating and partial melting in the deeper crust. This heating episode was contemporaneous with partial melting in Fiordland (New Zealand) and West Antarctica, although Mesozoic thermal and deformational events complicate the Palaeozoic record in both those areas. Nevertheless, the apparent 1000 s km of along-strike crustal partial melting indicates that a continental-scale tectonic plate margin re-organisation took place at this time. The cause in the New Zealand segment was most likely, but not unequivocally, an extensional tectonic regime with an elevated geothermal gradient caused by conductive heating from a shallowed lithospheric mantle. KW - Geothermobarometric P-T KW - Monazite growth KW - Palaeozoic metamorphism New Zealand KW - Gondwana Y1 - 2011 U6 - https://doi.org/10.1016/j.lithos.2011.09.008 SN - 0024-4937 VL - 127 IS - 3-4 SP - 522 EP - 534 PB - Elsevier CY - Amsterdam ER - TY - THES A1 - Schütte, Moritz T1 - Evolutionary fingerprints in genome-scale networks T1 - Evolutionäre Spuren in genomskaligen Netzwerken N2 - Mathematical modeling of biological phenomena has experienced increasing interest since new high-throughput technologies give access to growing amounts of molecular data. These modeling approaches are especially able to test hypotheses which are not yet experimentally accessible or guide an experimental setup. One particular attempt investigates the evolutionary dynamics responsible for today's composition of organisms. Computer simulations either propose an evolutionary mechanism and thus reproduce a recent finding or rebuild an evolutionary process in order to learn about its mechanism. The quest for evolutionary fingerprints in metabolic and gene-coexpression networks is the central topic of this cumulative thesis based on four published articles. An understanding of the actual origin of life will probably remain an insoluble problem. However, one can argue that after a first simple metabolism has evolved, the further evolution of metabolism occurred in parallel with the evolution of the sequences of the catalyzing enzymes. Indications of such a coevolution can be found when correlating the change in sequence between two enzymes with their distance on the metabolic network which is obtained from the KEGG database. We observe that there exists a small but significant correlation primarily on nearest neighbors. This indicates that enzymes catalyzing subsequent reactions tend to be descended from the same precursor. Since this correlation is relatively small one can at least assume that, if new enzymes are no "genetic children" of the previous enzymes, they certainly be descended from any of the already existing ones. Following this hypothesis, we introduce a model of enzyme-pathway coevolution. By iteratively adding enzymes, this model explores the metabolic network in a manner similar to diffusion. With implementation of an Gillespie-like algorithm we are able to introduce a tunable parameter that controls the weight of sequence similarity when choosing a new enzyme. Furthermore, this method also defines a time difference between successive evolutionary innovations in terms of a new enzyme. Overall, these simulations generate putative time-courses of the evolutionary walk on the metabolic network. By a time-series analysis, we find that the acquisition of new enzymes appears in bursts which are pronounced when the influence of the sequence similarity is higher. This behavior strongly resembles punctuated equilibrium which denotes the observation that new species tend to appear in bursts as well rather than in a gradual manner. Thus, our model helps to establish a better understanding of punctuated equilibrium giving a potential description at molecular level. From the time-courses we also extract a tentative order of new enzymes, metabolites, and even organisms. The consistence of this order with previous findings provides evidence for the validity of our approach. While the sequence of a gene is actually subject to mutations, its expression profile might also indirectly change through the evolutionary events in the cellular interplay. Gene coexpression data is simply accessible by microarray experiments and commonly illustrated using coexpression networks where genes are nodes and get linked once they show a significant coexpression. Since the large number of genes makes an illustration of the entire coexpression network difficult, clustering helps to show the network on a metalevel. Various clustering techniques already exist. However, we introduce a novel one which maintains control of the cluster sizes and thus assures proper visual inspection. An application of the method on Arabidopsis thaliana reveals that genes causing a severe phenotype often show a functional uniqueness in their network vicinity. This leads to 20 genes of so far unknown phenotype which are however suggested to be essential for plant growth. Of these, six indeed provoke such a severe phenotype, shown by mutant analysis. By an inspection of the degree distribution of the A.thaliana coexpression network, we identified two characteristics. The distribution deviates from the frequently observed power-law by a sharp truncation which follows after an over-representation of highly connected nodes. For a better understanding, we developed an evolutionary model which mimics the growth of a coexpression network by gene duplication which underlies a strong selection criterion, and slight mutational changes in the expression profile. Despite the simplicity of our assumption, we can reproduce the observed properties in A.thaliana as well as in E.coli and S.cerevisiae. The over-representation of high-degree nodes could be identified with mutually well connected genes of similar functional families: zinc fingers (PF00096), flagella, and ribosomes respectively. In conclusion, these four manuscripts demonstrate the usefulness of mathematical models and statistical tools as a source of new biological insight. While the clustering approach of gene coexpression data leads to the phenotypic characterization of so far unknown genes and thus supports genome annotation, our model approaches offer explanations for observed properties of the coexpression network and furthermore substantiate punctuated equilibrium as an evolutionary process by a deeper understanding of an underlying molecular mechanism. N2 - Die biologische Zelle ist ein sehr kompliziertes Gebilde. Bei ihrer Betrachtung gilt es, das Zusammenspiel von Tausenden bis Millionen von Genen, Regulatoren, Proteinen oder Molekülen zu beschreiben und zu verstehen. Durch enorme Verbesserungen experimenteller Messgeräte gelingt es mittlerweile allerdings in geringer Zeit enorme Datenmengen zu messen, seien dies z.B. die Entschlüsselung eines Genoms oder die Konzentrationen der Moleküle in einer Zelle. Die Systembiologie nimmt sich dem Problem an, aus diesem Datenmeer ein quantitatives Verständnis für die Gesamtheit der Wechselwirkungen in der Zelle zu entwickeln. Dabei stellt die mathematische Modellierung und computergestützte Analyse ein eminent wichtiges Werkzeug dar, lassen sich doch am Computer in kurzer Zeit eine Vielzahl von Fällen testen und daraus Hypothesen generieren, die experimentell verifiziert werden können. Diese Doktorarbeit beschäftigt sich damit, wie durch mathematische Modellierung Rückschlüsse auf die Evolution und deren Mechanismen geschlossen werden können. Dabei besteht die Arbeit aus zwei Teilen. Zum Einen wurde ein Modell entwickelt, dass die Evolution des Stoffwechsels nachbaut. Der zweite Teil beschäftigt sich mit der Analyse von Genexpressionsdaten, d.h. der Stärke mit der ein bestimmtes Gen in ein Protein umgewandelt, "exprimiert", wird. Der Stoffwechsel bezeichnet die Gesamtheit der chemischen Vorgänge in einem Organismus; zum Einen werden Nahrungsstoffe für den Organismus verwertbar zerlegt, zum Anderen aber auch neue Stoffe aufgebaut. Da für nahezu jede chemische Reaktion ein katalysierendes Enzym benötigt wird, ist davon auszugehen, dass sich der Stoffwechsel parallel zu den Enzymen entwickelt hat. Auf dieser Annahme basiert das entwickelte Modell zur Enzyme-Stoffwechsel-Koevolution. Von einer Anfangsmenge von Enzymen und Molekülen ausgehend, die etwa in einer primitiven Atmosphäre vorgekommen sind, werden sukzessive Enzyme und die nun katalysierbaren Reaktionen hinzugefügt, wodurch die Stoffwechselkapazität anwächst. Die Auswahl eines neuen Enzyms geschieht dabei in Abhängigkeit von der Ähnlichkeit mit bereits vorhandenen und ist so an den evolutionären Vorgang der Mutation angelehnt: je ähnlicher ein neues Enzym zu den vorhandenen ist, desto schneller kann es hinzugefügt werden. Dieser Vorgang wird wiederholt, bis der Stoffwechsel die heutige Form angenommen hat. Interessant ist vor allem der zeitliche Verlauf dieser Evolution, der mittels einer Zeitreihenanalyse untersucht wird. Dabei zeigt sich, dass neue Enzyme gebündelt in Gruppen kurzer Zeitfolge auftreten, gefolgt von Intervallen relativer Stille. Dasselbe Phänomen kennt man von der Evolution neuer Arten, die ebenfalls gebündelt auftreten, und wird Punktualismus genannt. Diese Arbeit liefert somit ein besseres Verständnis dieses Phänomens durch eine Beschreibung auf molekularer Ebene. Im zweiten Projekt werden Genexpressionsdaten von Pflanzen analysiert. Einerseits geschieht dies mit einem eigens entwickelten Cluster-Algorithmus. Hier läßt sich beobachten, dass Gene mit einer ähnlichen Funktion oft auch ein ähnliches Expressionsmuster aufweisen. Das Clustering liefert einige Genkandidaten, deren Funktion bisher unbekannt war, von denen aber nun vermutet werden konnte, dass sie enorm wichtig für das Wachstum der Pflanze sind. Durch Experimente von Pflanzen mit und ohne diese Gene zeigte sich, dass sechs neuen Genen dieses essentielle Erscheinungsbild zugeordnet werden kann. Weiterhin wurden Netzwerke der Genexpressionsdaten einer Pflanze, eines Pilzes und eines Bakteriums untersucht. In diesen Netzwerken werden zwei Gene verbunden, falls sie ein sehr ähnliches Expressionsprofil aufweisen. Nun zeigten diese Netzwerke sehr ähnliche und charakteristische Eigenschaften auf. Im Rahmen dieser Arbeit wurde daher ein weiteres evolutionäres Modell entwickelt, das die Expressionsprofile anhand von Duplikation, Mutation und Selektion beschreibt. Obwohl das Modell auf sehr simplen Eigenschaften beruht, spiegelt es die beobachteten Eigenschaften sehr gut wider, und es läßt sich der Schluss ziehen, dass diese als Resultat der Evolution betrachtet werden können. Die Ergebnisse dieser Arbeiten sind als Doktorarbeit in kumulativer Form bestehend aus vier veröffentlichten Artikeln vereinigt. KW - Systembiologie KW - Modellierung KW - Evolution KW - Stoffwechsel KW - Gen-Koexpression KW - Systems Biology KW - Modeling KW - Evolution KW - Metabolism KW - Gene co-expression Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-57483 ER - TY - THES A1 - Schönheit, Jörg T1 - A phagocyte-specific Irf8 gene enhancer establishes early conventional dendritic cell commitment T1 - Ein Phagozyten spezifischer Enhancer des Irf8 Gens steuert die Entwicklung konventioneller dendritischer Zellen N2 - Haematopoietic development is a complex process that is strictly hierarchically organized. Here, the phagocyte lineages are a very heterogeneous cell compartment with specialized functions in innate immunity and induction of adaptive immune responses. Their generation from a common precursor must be tightly controlled. Interference within lineage formation programs for example by mutation or change in expression levels of transcription factors (TF) is causative to leukaemia. However, the molecular mechanisms driving specification into distinct phagocytes remain poorly understood. In the present study I identify the transcription factor Interferon Regulatory Factor 8 (IRF8) as the specification factor of dendritic cell (DC) commitment in early phagocyte precursors. Employing an IRF8 reporter mouse, I showed the distinct Irf8 expression in haematopoietic lineage diversification and isolated a novel bone marrow resident progenitor which selectively differentiates into CD8α+ conventional dendritic cells (cDCs) in vivo. This progenitor strictly depends on Irf8 expression to properly establish its transcriptional DC program while suppressing a lineage-inappropriate neutrophile program. Moreover, I demonstrated that Irf8 expression during this cDC commitment-step depends on a newly discovered myeloid-specific cis-enhancer which is controlled by the haematopoietic transcription factors PU.1 and RUNX1. Interference with their binding leads to abrogation of Irf8 expression, subsequently to disturbed cell fate decisions, demonstrating the importance of these factors for proper phagocyte cell development. Collectively, these data delineate a transcriptional program establishing cDC fate choice with IRF8 in its center. N2 - Die Differenzierung von hämatopoietischen Zellen ist ein komplexer Prozess, der strikt hierarchisch organisiert ist. Dabei stellen die Phagozyten eine sehr heterogene Zellpopulation dar, mit hochspezialisierten Funktionen im angeborenen Immunsystem sowie während der Initialisierung der adaptiven Immunreaktion. Ihre Entwicklung, ausgehend von einer gemeinsamen Vorläuferzelle, unterliegt einer strikten Kontrolle. Die Beeinträchtigung dieser Linienentscheidungsprogramme, z.B. durch Mutationen oder Änderungen der Expressionslevel von Transkriptionsfaktoren kann Leukämie auslösen. Die molekularen Mechanismen, welche die linienspezifische Entwicklung steuern, sind allerdings noch nicht im Detail bekannt. In dieser Arbeit zeige ich den maßgeblichen Einfluss des Transkriptionsfaktors Interferon Regulierender Faktor 8 (IRF8) auf die Entwicklung von dendritischen Zellen (DC) innerhalb der Phagozyten. Mittels einer IRF8-Reporter Maus stellte ich die sehr differenziellen Expressionsmuster von Irf8 in der hämatopoietischen Entwicklung dar. Dabei konnte ich eine neue, im Knochenmark lokalisierte, Vorläuferpopulation isolieren, die in vivo spezifisch Differenzierung in CD8α+ konventionelle dendritische Zellen (cDC) steuert. Dieser Vorläufer ist dabei absolut von der Expression von Irf8 abhängig und etabliert auf transkriptioneller Ebene die dendritische Zellentwicklung, während gleichzeitig die Entwicklung neutrophiler Zellen unterdrückt wird. Darüber hinaus zeigte ich, dass Irf8 Expression während der cDC Entwicklung von einem neu charakterisierten cis-regulatorischen Enhancer abhängt, der spezifisch in myeloiden Zellen agiert. Ich konnte zeigen, dass die hämatopoietischen Transkriptionfaktoren PU.1 und RUNX1 mittels dieses Enhancers die Irf8 Expression steuern. Können diese beiden Faktoren nicht mit dem Enhancer interagieren, führt das zu stark verminderter Irf8 Expression, damit zu Veränderungen in den Differnzierungsprogrammen der Zellen, was die Bedeutung dieses regulatorischen Mechanismus unterstreicht. Zusammengefasst beschreiben diese Daten die Etablierung der frühen cDC Entwicklung, in der IRF8 die zentrale Rolle spielt. KW - Hämatopoiese KW - dendritische Zelle KW - Immunologie KW - Transkiptionsfaktor KW - Genregulation KW - haematopoiesis KW - dendritic cell KW - immunology KW - transcription factor KW - gene regulation Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-55482 ER - TY - CHAP A1 - Schweigert, Florian J. A1 - Raila, Jens A1 - Mothes, Ralf A1 - Frey, S. T1 - Point of care measurements of Vitamin A in blood and breast milk for low resource settings T2 - Annals of nutrition & metabolism : journal of nutrition, metabolic diseases and dietetics ; an official journal of International Union of Nutritional Sciences (IUNS) KW - Blood KW - Milk KW - Point of Care Assay and Vitamin A Y1 - 2011 SN - 0250-6807 VL - 58 IS - 2 SP - 382 EP - 382 PB - Karger CY - Basel ER - TY - JOUR A1 - Schwarte, Sandra A1 - Tiedemann, Ralph T1 - A Gene Duplication/Loss Event in the Ribulose-1,5-Bisphosphate-Carboxylase/Oxygenase (Rubisco) Small Subunit Gene Family among Accessions of Arabidopsis thaliana JF - Molecular biology and evolution N2 - Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39), the most abundant protein in nature, catalyzes the assimilation of CO(2) (worldwide about 10(11) t each year) by carboxylation of ribulose-1,5-bisphosphate. It is a hexadecamer consisting of eight large and eight small subunits. Although the Rubisco large subunit (rbcL) is encoded by a single gene on the multicopy chloroplast genome, the Rubisco small subunits (rbcS) are encoded by a family of nuclear genes. In Arabidopsis thaliana, the rbcS gene family comprises four members, that is, rbcS-1a, rbcS-1b, rbcS-2b, and rbcS-3b. We sequenced all Rubisco genes in 26 worldwide distributed A. thaliana accessions. In three of these accessions, we detected a gene duplication/loss event, where rbcS-1b was lost and substituted by a duplicate of rbcS-2b (called rbcS-2b*). By screening 74 additional accessions using a specific polymerase chain reaction assay, we detected five additional accessions with this duplication/loss event. In summary, we found the gene duplication/loss in 8 of 100 A. thaliana accessions, namely, Bch, Bu, Bur, Cvi, Fei, Lm, Sha, and Sorbo. We sequenced an about 1-kb promoter region for all Rubisco genes as well. This analysis revealed that the gene duplication/loss event was associated with promoter alterations (two insertions of 450 and 850 bp, one deletion of 730 bp) in rbcS-2b and a promoter deletion (2.3 kb) in rbcS-2b* in all eight affected accessions. The substitution of rbcS-1b by a duplicate of rbcS-2b (i.e., rbcS-2b*) might be caused by gene conversion. All four Rubisco genes evolve under purifying selection, as expected for central genes of the highly conserved photosystem of green plants. We inferred a single positive selected site, a tyrosine to aspartic acid substitution at position 72 in rbcS-1b. Exactly the same substitution compromises carboxylase activity in the cyanobacterium Anacystis nidulans. In A. thaliana, this substitution is associated with an inferred recombination. Functional implications of the substitution remain to be evaluated. KW - Arabidopsis thaliana KW - Arabidopsis lyrata KW - Rubisco KW - gene duplication KW - positive selection Y1 - 2011 U6 - https://doi.org/10.1093/molbev/msr008 SN - 0737-4038 VL - 28 IS - 6 SP - 1861 EP - 1876 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Schudoma, Christian A1 - Larhlimi, Abdelhalim A1 - Walther, Dirk T1 - The influence of the local sequence environment on RNA loop structures JF - RNA : a publication of the RNA Society N2 - RNA folding is assumed to be a hierarchical process. The secondary structure of an RNA molecule, signified by base-pairing and stacking interactions between the paired bases, is formed first. Subsequently, the RNA molecule adopts an energetically favorable three-dimensional conformation in the structural space determined mainly by the rotational degrees of freedom associated with the backbone of regions of unpaired nucleotides (loops). To what extent the backbone conformation of RNA loops also results from interactions within the local sequence context or rather follows global optimization constraints alone has not been addressed yet. Because the majority of base stacking interactions are exerted locally, a critical influence of local sequence on local structure appears plausible. Thus, local loop structure ought to be predictable, at least in part, from the local sequence context alone. To test this hypothesis, we used Random Forests on a nonredundant data set of unpaired nucleotides extracted from 97 X-ray structures from the Protein Data Bank (PDB) to predict discrete backbone angle conformations given by the discretized eta/theta-pseudo-torsional space. Predictions on balanced sets with four to six conformational classes using local sequence information yielded average accuracies of up to 55%, thus significantly better than expected by chance (17%-25%). Bases close to the central nucleotide appear to be most tightly linked to its conformation. Our results suggest that RNA loop structure does not only depend on long-range base-pairing interactions; instead, it appears that local sequence context exerts a significant influence on the formation of the local loop structure. KW - RNA KW - 3D structure KW - structure prediction KW - Random Forests KW - machine learning KW - backbone conformation Y1 - 2011 U6 - https://doi.org/10.1261/rna.2550211 SN - 1355-8382 VL - 17 IS - 7 SP - 1247 EP - 1257 PB - Cold Spring Harbor Laboratory Press CY - Cold Spring Harbor, NY ER - TY - THES A1 - Schudoma, Christian T1 - Bioinformatic approaches to sequence-structure relationships in RNA loops Y1 - 2011 CY - Potsdam ER - TY - JOUR A1 - Schröder, Florian A1 - Lisso, Janina A1 - Muessig, Carsten T1 - Exordium-Like1 promotes growth during low carbon availability in arabidopsis JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - Little is known about genes that control growth and development under low carbon (C) availability. The Arabidopsis (Arabidopsis thaliana) EXORDIUM-LIKE1 (EXL1) gene (At1g35140) was identified as a brassinosteroid-regulated gene in a previous study. We show here that the EXL1 protein is required for adaptation to C-and energy-limiting growth conditions. In-depth analysis of EXL1 transcript levels under various environmental conditions indicated that EXL1 expression is controlled by the C and energy status. Sugar starvation, extended night, and anoxia stress induced EXL1 gene expression. The C status also determined EXL1 protein levels. These results suggested that EXL1 is involved in the C-starvation response. Phenotypic changes of an exl1 loss-of-function mutant became evident only under corresponding experimental conditions. The mutant showed diminished biomass production in a short-day/low-light growth regime, impaired survival during extended night, and impaired survival of anoxia stress. Basic metabolic processes and signaling pathways are presumed to be barely impaired in exl1, because the mutant showed wild-type levels of major sugars, and transcript levels of only a few genes such as QUA-QUINE STARCH were altered. Our data suggest that EXL1 is part of a regulatory pathway that controls growth and development when C and energy supply is poor. Y1 - 2011 U6 - https://doi.org/10.1104/pp.111.177204 SN - 0032-0889 VL - 156 IS - 3 SP - 1620 EP - 1630 PB - American Society of Plant Physiologists CY - Rockville ER - TY - THES A1 - Schröder, Florian T1 - Funktionelle Charakterisierung der EXO/EXL-Proteinfamilie und NFXL2-Isoformen in Arabidopsis thaliana Y1 - 2011 CY - Potsdam ER - TY - JOUR A1 - Schmidt, Bernd A1 - Staude, Lucia T1 - Desymmetrization of (R,R)-Hexa-1,5-diene-3,4-diol via Monofunctionallization and Rhodium-Catalyzed Allylic Substitution JF - The journal of organic chemistry N2 - A sequence of selective monoprotection and Rh-catalyzed enantioconservative allylic subEtitution is established as a desymmetrization strategy for C-2-symmetric hexa-1,5-diene-3,4-diol. A benzyl protecting group and ethyl carbonate as a leaving group emerged as the most useful combination with respect to reproducibility, stereoselectivity, and yield: A remarkable deviation from the normally observed regiospecificity of Rh-catalyzed allylic alkylations was observed for unprotected carbonates. In this case, a linear, rather than a branched alkylation product was obtained exclusively. Y1 - 2011 U6 - https://doi.org/10.1021/jo2001337 SN - 0022-3263 VL - 76 IS - 7 SP - 2220 EP - 2226 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Schmidt, Bernd A1 - Hölter, Frank A1 - Kelling, Alexandra A1 - Schilde, Uwe T1 - Pd-Catalyzed arylation reactions with phenol diazonium salts application in the synthesis of diarylheptanoids JF - The journal of organic chemistry N2 - The first total synthesis of the natural product (3S,7R)-5,6-dehydro-de-O-methyl centrolobine and various analogues is reported, using a highly regio- and diastereoselective Mizoroki-Heck reaction of phenol diazonium salts and enantiopure dihydropyrans. The assigned relative configuration was confirmed by single-crystal X-ray structure analysis, but a revision of the absolute configuration is proposed based on polarimetric measurement. Y1 - 2011 U6 - https://doi.org/10.1021/jo2002787 SN - 0022-3263 SN - 1520-6904 VL - 76 IS - 9 SP - 3357 EP - 3365 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Schleuning, Matthias A1 - Templin, Mathias A1 - Huaman, Vicky A1 - Vadillo, Giovana P. A1 - Becker, Thomas A1 - Durka, Walter A1 - Fischer, Markus A1 - Matthies, Diethart T1 - Effects of inbreeding, outbreeding, and supplemental pollen on the reproduction of a hummingbird-pollinated clonal amazonian herb JF - Biotropica : a publication of the Association for Tropical Biology N2 - Understory herbs are an essential part of tropical rain forests, but little is known about factors limiting their reproduction. Many of these herbs are clonal, patchily distributed, and produce large floral displays of nectar-rich 1-d flowers to attract hummingbird pollinators that may transport pollen over long distances. The aim of this study was to investigate the effects of clonality, cross-proximity, and patchy distribution on the reproduction of the hummingbird-pollinated Amazonian herb Heliconia metallica. We experimentally pollinated flowers within populations with self-pollen and with pollen of different diversity, crossed flowers between populations, and added supplemental pollen to ramets growing solitarily or in conspecific patches. Only flowers pollinated early in the morning produced seeds. Selfed flowers produced seeds, but seed number and mass were strongly reduced, suggesting partial sterility and inbreeding depression after selfing. Because of pollen competition, flowers produced more seeds after crosses with several than with single donor plants. Crosses between populations mostly resulted in lower seed production than those within populations, suggesting outbreeding depression. Ramets in patches produced fewer seeds than solitary ramets and were more pollen-limited, possibly due to geitonogamy and biparental inbreeding in patches. We conclude that high rates of geitonogamy due to clonality and pollen limitation due to the short receptivity of flowers and patchy distribution constrain the reproduction of this clonal herb. Even in unfragmented rain forests with highly mobile pollinators, outbreeding depression may be a widespread phenomenon in plant reproduction. KW - clonality KW - geitonogamy KW - Heliconiaceae KW - hummingbird pollination KW - Peru KW - pollen limitation KW - pollination experiment KW - rain forest understory Y1 - 2011 U6 - https://doi.org/10.1111/j.1744-7429.2010.00663.x SN - 0006-3606 VL - 43 IS - 2 SP - 183 EP - 191 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Schleicher, Jana A1 - Meyer, Katrin M. A1 - Wiegand, Kerstin A1 - Schurr, Frank Martin A1 - Ward, David T1 - Disentangling facilitation and seed dispersal from environmental heterogeneity as mechanisms generating associations between savanna plants JF - Journal of vegetation science N2 - Question: How can we disentangle facilitation and seed dispersal from environmental heterogeneity as mechanisms causing spatial associations of plant species? Location: Semi-arid savanna in the Kimberley Thorn Bushveld, South Africa. Methods: We developed a two-step protocol for the statistical differentiation of association-promoting mechanisms in plants based on the Acacia erioloba-Grewia flava association. Individuals of the savanna shrub G. flava and the tree A. erioloba were mapped on four study plots. Disentangling the mechanism causing the association of G. flava and A. erioloba involved tests of three spatial and one non-spatial null model. The spatial null models include homogeneous and heterogeneous Poisson processes for spatial randomness based on the bivariate spatial point patterns of the four plots. With the non-spatial analysis, we determined the relationship between the canopy diameter of A. erioloba trees and presence or absence of G. flava shrubs in the tree understorey to find whether shrub presence requires a minimum tree canopy diameter. Results: We first showed a significant positive spatial association of the two species. Thereafter, the non-spatial analysis supported an exclusion of environmental heterogeneity as the sole cause of this positive association. We found a minimum tree size under which no G. flava shrubs occurred. Conclusions: Our two-step analysis showed that it is unlikely that heterogeneous environmental conditions caused the spatial association of A. erioloba and G. flava. Instead, this association may have been caused by seed dispersal and/or facilitation (e.g. caused by hydraulic lift and/or nitrogen fixation by the host tree). KW - Acacia erioloba KW - Grewia flava KW - Plant interactions KW - Spatial association KW - Wiegand-Moloney O-ring statistics Y1 - 2011 U6 - https://doi.org/10.1111/j.1654-1103.2011.01310.x SN - 1100-9233 VL - 22 IS - 6 SP - 1038 EP - 1048 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Schiffers, Katja A1 - Tielboerger, Katja A1 - Tietjen, Britta A1 - Jeltsch, Florian T1 - Root plasticity buffers competition among plants theory meets experimental data JF - Ecology : a publication of the Ecological Society of America N2 - Morphological plasticity is a striking characteristic of plants in natural communities. In the context of foraging behavior particularly, root plasticity has been documented for numerous species. Root plasticity is known to mitigate competitive interactions by reducing the overlap of the individuals' rhizospheres. But despite its obvious effect on resource acquisition, plasticity has been generally neglected in previous empirical and theoretical studies estimating interaction intensity among plants. In this study, we developed a semi-mechanistic model that addresses this shortcoming by introducing the idea of compensatory growth into the classical-zone-of influence (ZOI) and field-of-neighborhood (FON) approaches. The model parameters describing the belowground plastic sphere of influence (PSI) were parameterized using data from an accompanying field experiment. Measurements of the uptake of a stable nutrient analogue at distinct distances to the neighboring plants showed that the study species responded plastically to belowground competition by avoiding overlap of individuals' rhizospheres. An unexpected finding was that the sphere of influence of the study species Bromus hordeaceus could be best described by a unimodal function of distance to the plant's center and not with a continuously decreasing function as commonly assumed. We employed the parameterized model to investigate the interplay between plasticity and two other important factors determining the intensity of competitive interactions: overall plant density and the distribution of individuals in space. The simulation results confirm that the reduction of competition intensity due to morphological plasticity strongly depends on the spatial structure of the competitive environment. We advocate the use of semi-mechanistic simulations that explicitly consider morphological plasticity to improve our mechanistic understanding of plant interactions. KW - Bromus hordeaceus KW - competition intensity KW - morphological plasticity KW - nutrient analogues KW - plant density KW - PSI (plastic sphere of influence) KW - zone-of-influence model Y1 - 2011 SN - 0012-9658 VL - 92 IS - 3 SP - 610 EP - 620 PB - Wiley CY - Washington ER - TY - JOUR A1 - Scheffler, Ingo T1 - Artenspektren und Wirtsbindung von Ektoparasiten der Fledermäuse aus Nordbulgarien : Bewertung des Zusammenhangs von Körperkondition und Ektoparasitenlast N2 - Waehrend der herbstlichen Schwaermpase wurden im Norden Bulgariens die Ektoparasiten von neun Fledermausarten untersucht. Die hoechsten Abundanzen erreichten Fledermausfliegen, von denen 6 verschiedene Arten determiniert wurden. In geringeren Dichten besiedelten auch Flughautmilben (6 Arten) sowie Macronyssidae und Ixodidae (jeweils eine Art) die Fledermaeuse. Die Bindung an den Wirt und die Verbreitung aller Ektoparasiten sind kurz zusammengefasst. Fuer die Berechnung der Parasitenlast wird ein neues Modell vorgeschlagen, dass unter Beruecksichtigung von Groessenrealtionen und Abundanzen vergleichbare Daten bei unterschiedlichen Befallsszenarien ermoeglicht. Parasitenkombinationen traten im Norden Bulgariens seltener auf, als erwartet. Mit den Werten der haeufigsten Fledermausarten wurde ueberprueft, ob es einen Zusammenhang zwischen Masse, Unterarmlaenge und Parasitierung gibt. In keinem Fall konnte eine sichere Korrelation zwischen diesen Faktoren ermittelt werden. Unter Verwendung eines adaptierten Body-Mass-Index (BMI) oder eines Body- Condition-Index (BCI) ergab sich ebenfalls kein Zusammenhang zwischen der Koerperkondition und der Parasitenlast. Im Verlaufe der Untersuchung kam es in einer Hoehle zu einer unerwarteten Zunahme der Abundanzen von Flughautmilben. Dieses Phaenomen koennte ein interessanter Ansatz weiterer Studien sein. Im Vergleich zu herbstlichen Untersuchungen in Deutschland waren die Fledermaeuse im Norden Bulgariens deutlich staerker parasitiert. Y1 - 2011 ER - TY - JOUR A1 - Scheffler, Ingo T1 - Die Ektoparasiten der Fledermäuse Europas : Teil 1 N2 - Die vorliegende Arbeit liefert eine Zusammenstellung der bisher bekannten Ektoparasitenarten europaeischer Fledermausarten. Auf der Basis eigener Untersuchungen in Deutschland erfolgt eine Analyse der Abundanz der Parasiten. Fuer jede Wirtsart wird das Artenspektrum der haeufig vorkommenden Ektoparasiten angegeben und die Spezifitaet der Wirt- Parasit-Beziehung diskutiert. Teil 1 behandelt die Ektoparasiten der Mopsfledermaus (Barbastella barbastellus), der Nordfledermaus (Eptesicus nilssonii), der Breitfluegelfledermaus (Eptesicus serotinus), der Bechsteinfledermaus (Myotis bechsteinii),der Grossen Bartfledermaus (Myotis brandtii), der Teichfledermaus (Myotis dasycneme) und der Wasserfledermaus (Myotis daubentonii). Y1 - 2011 ER - TY - JOUR A1 - Scheffler, Christiane T1 - The change of skeletal robustness of 6 - 12 years old children in Brandenburg (Germany) - Comparison of body composition 1999 - 2009 Y1 - 2011 SN - 0003-5548 ER - TY - CHAP A1 - Scheffler, Christiane T1 - How many skeletons do we need? - An evolutionary approach of the change of skeleton measures in school children in the last decade T2 - Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft für Anthropologie Y1 - 2011 SN - 0003-5548 VL - 68 IS - 4 SP - 519 EP - 519 PB - Schweizerbart CY - Stuttgart ER - TY - JOUR A1 - Scheffler, Christiane T1 - The change of skeletal robustness of 6-12 years old children in Brandenburg (Germany) - Comparison of body composition 1999-2009 JF - Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft für Anthropologie N2 - Overweight as a global problem is a challenge to the health systems today and in the future. Detailed information about the development of body composition in children can help to design preventive measures to stop this trend. In the present study 1397 German children aged 6-12 complete years were investigated with anthropometric methods (i.e. height, weight, BMI, skeleton robustness, and percentage of body fat) in 2008/09. The results were compared with a 10 years old identical study. Today, the investigated children are a little bit smaller and the range of BMI and percentage of body fat is increasing. The large decrease of the skeletal robustness especially in the 10(th) and 3(rd) percentile is important. Decrease of physical activity as the most important reason for shrinking skeletal robustness is discussed. KW - school children KW - body composition KW - skeletal robustness Y1 - 2011 U6 - https://doi.org/10.1127/0003-5548/2011/0095 SN - 0003-5548 VL - 68 IS - 2 SP - 153 EP - 165 PB - Schweizerbart CY - Stuttgart ER - TY - JOUR A1 - Sarmento, Juliano Sarmento A1 - Bond, William J. A1 - Midgley, Guy F. A1 - Rebelo, Anthony G. A1 - Thuiller, Wilfried A1 - Schurr, Frank Martin T1 - Effects of harvesting flowers from shrubs on the persistence and abundance of wild shrub populations at multiple spatial extents JF - Conservation biology : the journal of the Society for Conservation Biology N2 - Wildflower harvesting is an economically important activity of which the ecological effects are poorly understood. We assessed how harvesting of flowers affects shrub persistence and abundance at multiple spatial extents. To this end, we built a process-based model to examine the mean persistence and abundance of wild shrubs whose flowers are subject to harvest (serotinous Proteaceae in the South African Cape Floristic Region). First, we conducted a general sensitivity analysis of how harvesting affects persistence and abundance at nested spatial extents. For most spatial extents and combinations of demographic parameters, persistence and abundance of flowering shrubs decreased abruptly once harvesting rate exceeded a certain threshold. At larger extents, metapopulations supported higher harvesting rates before their persistence and abundance decreased, but persistence and abundance also decreased more abruptly due to harvesting than at smaller extents. This threshold rate of harvest varied with species' dispersal ability, maximum reproductive rate, adult mortality, probability of extirpation or local extinction, strength of Allee effects, and carrying capacity. Moreover, spatial extent interacted with Allee effects and probability of extirpation because both these demographic properties affected the response of local populations to harvesting more strongly than they affected the response of metapopulations. Subsequently, we simulated the effects of harvesting on three Cape Floristic Region Proteaceae species and found that these species reacted differently to harvesting, but their persistence and abundance decreased at low rates of harvest. Our estimates of harvesting rates at maximum sustainable yield differed from those of previous investigations, perhaps because researchers used different estimates of demographic parameters, models of population dynamics, and spatial extent than we did. Good demographic knowledge and careful identification of the spatial extent of interest increases confidence in assessments and monitoring of the effects of harvesting. Our general sensitivity analysis improved understanding of harvesting effects on metapopulation dynamics and allowed qualitative assessment of the probability of extirpation of poorly studied species. KW - Allee effects KW - metapopulation dynamics KW - process-based models KW - serotinous Proteaceae KW - South African Cape Floristic Region KW - spatial scales KW - threshold behavior Y1 - 2011 U6 - https://doi.org/10.1111/j.1523-1739.2010.01628.x SN - 0888-8892 VL - 25 IS - 1 SP - 73 EP - 84 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Sangoro, J. R. A1 - Iacob, C. A1 - Naumov, S. A1 - Valiullin, R. A1 - Rexhausen, Hans A1 - Hunger, J. A1 - Buchner, R. A1 - Strehmel, Veronika A1 - Kaerger, J. A1 - Kremer, F. T1 - Diffusion in ionic liquids the interplay between molecular structure and dynamics JF - Soft matter N2 - Diffusion in a series of ionic liquids is investigated by a combination of Broadband Dielectric Spectroscopy (BDS) and Pulsed Field Gradient Nuclear Magnetic Resonance (PFG NMR). It is demonstrated that the mean jump lengths increase with the molecular volumes determined from quantum-chemical calculations. This provides a direct means-via Einstein-Smoluchowski relation-to determine the diffusion coefficient by BDS over more than 8 decades unambiguously and in quantitative agreement with PFG NMR measurements. New possibilities in the study of charge transport and dynamic glass transition in ionic liquids are thus opened. Y1 - 2011 U6 - https://doi.org/10.1039/c0sm01404d SN - 1744-683X VL - 7 IS - 5 SP - 1678 EP - 1681 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Samuel, Prinson P. A1 - Horn, Sebastian A1 - Döring, Alexander A1 - Havelius, Kajsa G. V. A1 - Reschke, Stefan A1 - Leimkühler, Silke A1 - Haumann, Michael A1 - Schulzke, Carola T1 - A Crystallographic and Mo K-Edge XAS Study of Molybdenum Oxo Bis-,Mono-, and Non-Dithiolene Complexes - First-Sphere Coordination Geometry and Noninnocence of Ligands JF - European journal of inorganic chemistry : a journal of ChemPubSoc Europe N2 - Ten square-based pyramidal molybdenum complexes with different sulfur donor ligands, that is, a variety of dithiolenes and sulfides, were prepared, which mimic coordination motifs of the molybdenum cofactors of molybdenum-dependent oxidoreductases. The model compounds were investigated by Mo K-edge X-ray absorption spectroscopy (XAS) and (with one exception) their molecular structures were analyzed by X-ray diffraction to derive detailed information on bond lengths and geometries of the first coordination shell of molybdenum. Only small variations in Mo=O and Mo-S bond lengths and their respective coordination angles were observed for all complexes including those containing Mo(CO)(2) or Mo(mu-S)(2)Mo motifs. XAS analysis (edge energy) revealed higher relative oxidation levels in the molybdenum ion in compounds with innocent sulfur-based ligands relative to those in dithiolene complexes, which are known to exhibit noninnocence, that is, donation of substantial electron density from ligand to metal. In addition, longer average Mo-S and Mo=O bonds and consequently lower.(Mo=O) stretching frequencies in the IR spectra were observed for complexes with dithiolene-derived ligands. The results emphasize that the noninnocent character of the dithiolene ligand influences the electronic structure of the model compounds, but does not significantly affect their metal coordination geometry, which is largely determined by the Mo(IV) or (V) ion itself. The latter conclusion also holds for the molybdenum site geometries in the oxidized Mo-VI cofactor of DMSO reductase and the reduced Mo-IV cofactor of arsenite oxidase. The innocent behavior of the dithiolene molybdopterin ligands observed in the enzymes is likely to be related to cofactor-protein interactions. KW - Molybdenum KW - Enzyme models KW - X-ray absorption spectroscopy KW - Noninnocence KW - Bioinorganic chemistry Y1 - 2011 U6 - https://doi.org/10.1002/ejic.201100331 SN - 1434-1948 IS - 28 SP - 4387 EP - 4399 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Sammler, Svenja A1 - Bleidorn, Christoph A1 - Tiedemann, Ralph T1 - Full mitochondrial genome sequences of two endemic Philippine hornbill species (Aves: Bucerotidae) provide evidence for pervasive mitochondrial DNA recombination JF - BMC genomics N2 - Background: Although nowaday it is broadly accepted that mitochondrial DNA (mtDNA) may undergo recombination, the frequency of such recombination remains controversial. Its estimation is not straightforward, as recombination under homoplasmy (i.e., among identical mt genomes) is likely to be overlooked. In species with tandem duplications of large mtDNA fragments the detection of recombination can be facilitated, as it can lead to gene conversion among duplicates. Although the mechanisms for concerted evolution in mtDNA are not fully understood yet, recombination rates have been estimated from "one per speciation event" down to 850 years or even "during every replication cycle". Results: Here we present the first complete mt genome of the avian family Bucerotidae, i.e., that of two Philippine hornbills, Aceros waldeni and Penelopides panini. The mt genomes are characterized by a tandemly duplicated region encompassing part of cytochrome b, 3 tRNAs, NADH6, and the control region. The duplicated fragments are identical to each other except for a short section in domain I and for the length of repeat motifs in domain III of the control region. Due to the heteroplasmy with regard to the number of these repeat motifs, there is some size variation in both genomes; with around 21,657 bp (A. waldeni) and 22,737 bp (P. panini), they significantly exceed the hitherto longest known avian mt genomes, that of the albatrosses. We discovered concerted evolution between the duplicated fragments within individuals. The existence of differences between individuals in coding genes as well as in the control region, which are maintained between duplicates, indicates that recombination apparently occurs frequently, i. e., in every generation. Conclusions: The homogenised duplicates are interspersed by a short fragment which shows no sign of recombination. We hypothesize that this region corresponds to the so-called Replication Fork Barrier (RFB), which has been described from the chicken mitochondrial genome. As this RFB is supposed to halt replication, it offers a potential mechanistic explanation for frequent recombination in mitochondrial genomes. Y1 - 2011 U6 - https://doi.org/10.1186/1471-2164-12-35 SN - 1471-2164 VL - 12 IS - 2 PB - BioMed Central CY - London ER - TY - JOUR A1 - Samereier, Matthias A1 - Baumann, Otto A1 - Meyer, Irene A1 - Gräf, Ralph T1 - Analysis of dictyostelium TACC reveals differential interactions with CP224 and unusual dynamics of dictyostelium microtubules JF - Cellular and molecular life sciences N2 - We have localized TACC to the microtubule-nucleating centrosomal corona and to microtubule plus ends. Using RNAi we proved that Dictyostelium TACC promotes microtubule growth during interphase and mitosis. For the first time we show in vivo that both TACC and XMAP215 family proteins can be differentially localized to microtubule plus ends during interphase and mitosis and that TACC is mainly required for recruitment of an XMAP215-family protein to interphase microtubule plus ends but not for recruitment to centrosomes and kinetochores. Moreover, we have now a marker to study dynamics and behavior of microtubule plus ends in living Dictyostelium cells. In a combination of live cell imaging of microtubule plus ends and fluorescence recovery after photobleaching (FRAP) experiments of GFP-alpha-tubulin cells we show that Dictyostelium microtubules are dynamic only in the cell periphery, while they remain stable at the centrosome, which also appears to harbor a dynamic pool of tubulin dimers. KW - Dictyostelium KW - TACC KW - DdCP224 KW - XMAP215 KW - Microtubules KW - Centrosome Y1 - 2011 U6 - https://doi.org/10.1007/s00018-010-0453-0 SN - 1420-682X VL - 68 IS - 2 SP - 275 EP - 287 PB - Springer CY - Basel ER - TY - THES A1 - Samereier, Matthias T1 - Functional analyses of microtubule and centrosome-associated proteins in Dictyostelium discoideum T1 - Funktionelle Analyse von Mikrotubuli- und Centrosom-assoziierten Proteinen in Dictyostelium discoideum N2 - Understanding the role of microtubule-associated proteins is the key to understand the complex mechanisms regulating microtubule dynamics. This study employs the model system Dictyostelium discoideum to elucidate the role of the microtubule-associated protein TACC (Transforming acidic coiled-coil) in promoting microtubule growth and stability. Dictyostelium TACC was localized at the centrosome throughout the entire cell cycle. The protein was also detected at microtubule plus ends, however, unexpectedly only during interphase but not during mitosis. The same cell cycle-dependent localization pattern was observed for CP224, the Dictyostelium XMAP215 homologue. These ubiquitous MAPs have been found to interact with TACC proteins directly and are known to act as microtubule polymerases and nucleators. This work shows for the first time in vivo that both a TACC and XMAP215 family protein can differentially localize to microtubule plus ends during interphase and mitosis. RNAi knockdown mutants revealed that TACC promotes microtubule growth during interphase and is essential for proper formation of astral microtubules in mitosis. In many organisms, impaired microtubule stability upon TACC depletion was explained by the failure to efficiently recruit the TACC-binding XMAP215 protein to centrosomes or spindle poles. By contrast, fluorescence recovery after photobleaching (FRAP) analyses conducted in this study demonstrate that in Dictyostelium recruitment of CP224 to centrosomes or spindle poles is not perturbed in the absence of TACC. Instead, CP224 could no longer be detected at the tips of microtubules in TACC mutant cells. This finding demonstrates for the first time in vivo that a TACC protein is essential for the association of an XMAP215 protein with microtubule plus ends. The GFP-TACC strains generated in this work also turned out to be a valuable tool to study the unusual microtubule dynamics in Dictyostelium. Here, microtubules exhibit a high degree of lateral bending movements but, in contrast most other organisms, they do not obviously undergo any growth or shrinkage events during interphase. Despite of that they are affected by microtubuledepolymerizing drugs such as thiabendazole or nocodazol which are thought to act solely on dynamic microtubules. Employing 5D-fluorescence live cell microscopy and FRAP analyses this study suggests Dictyostelium microtubules to be dynamic only in the periphery, while they are stable at the centrosome. In the recent years, the identification of yet unknown components of the Dictyostelium centrosome has made tremendous progress. A proteomic approach previously conducted by our group disclosed several uncharacterized candidate proteins, which remained to be verified as genuine centrosomal components. The second part of this study focuses on the investigation of three such candidate proteins, Cenp68, CP103 and the putative spindle assembly checkpoint protein Mad1. While a GFP-CP103 fusion protein could clearly be localized to isolated centrosomes that are free of microtubules, Cenp68 and Mad1 were found to associate with the centromeres and kinetochores, respectively. The investigation of Cenp68 included the generation of a polyclonal anti-Cenp68 antibody, the screening for interacting proteins and the generation of knockout mutants which, however, did not display any obvious phenotype. Yet, Cenp68 has turned out as a very useful marker to study centromere dynamics during the entire cell cycle. During mitosis, GFP-Mad1 localization strongly resembled the behavior of other Mad1 proteins, suggesting the existence of a yet uncharacterized spindle assembly checkpoint in Dictyostelium. N2 - Die Kenntnis der Funktion von Mikrotubuli-assoziierenden Proteinen (MAPs) ist von grundlegender Bedeutung für das Verständnis der Mikrotubuli-Dynamik und deren Regulation. Im Rahmen dieser Arbeit wurde die Rolle des Mikrotubuli-assoziierenden Proteins TACC (Transforming acidic coiled-coil), welches in vielen Organismen an der Stabilisierung und dem Wachstum von Mikrotubuli beteiligt ist, im Modellorganismus Dictyostelium discoideum untersucht. Das Dictyostelium TACC Protein konnte während des gesamten Zellzyklus am Centrosom nachgewiesen werden. Darüber hinaus wurde es an den Mikrotubuli-Plus-Enden vorgefunden, überraschenderweise jedoch ausschließlich während der Interphase. Die gleiche Zellzyklusabhängige Lokalisation wurde für CP224 beobachtet, einem Homologen der XMAP215 Proteine in Dictyostelium. Diese ubiquitären MAPs sind konservierte, direkte Interaktionspartner der TACC Proteine und spielen eine zentrale Rolle bei der Nukleation und der Polymerisation von Mikrotubuli. Durch diese Arbeit konnte erstmals in vivo gezeigt werden, dass TACC und XMAP215 Proteine während der Interphase und Mitose unterschiedlich stark mit Mikrotubuli-Plus-Enden assoziiert sein können. Durch Untersuchungen an Knockdown-Mutanten wurde ersichtlich, dass Dictyostelium TACC eine Rolle beim Mikrotubuli-Wachstum während der Interphase spielt und über weite Strecken der Mitose essentiell für die Ausbildung von astralen Mikrotubuli ist. In anderen Organismen konnte als Ursache instabiler Mikrotubuli in TACC Mutanten häufig unzureichendes Rekrutieren des jeweiligen XMAP215 Proteins an das Centrosom ausgemacht werden. Um entsprechende Auswirkungen auf die Lokalisation von CP224 durch den Knockdown von TACC in Dictyostelium zu untersuchen, wurden Fluorescence Recovery after Photobleaching (FRAP) Experimente durchgeführt. Diese ergaben, dass CP224 auch in Abwesenheit von TACC in vollem Umfang an die Centrosomen und Spindelpole rekrutiert wird. Anders als im Wildtyp, konnte in TACC Mutanten allerdings kein CP224 an den Mikrotubuli-Plus-Enden nachgewiesen werden. Somit konnte erstmals in vivo gezeigt werden, dass ein TACC Protein essentiell für die Assoziation eines XMAP215 Proteins mit den Mikrotubuli-Plus-Enden ist. Im Laufe der genannten Experimente stellte sich heraus, dass sich die GFP-TACC Stämme aufgrund ihrer markierten Plus-Enden sehr gut für Untersuchungen zur ungewöhnlichen Mikrotubuli-Dynamik in Dictyostelium eignen. Zwar weisen Mikrotubuli hier über die gesamte Länge ausgeprägte Krümmungs- und Seitwärtsbewegungen auf, es können jedoch im Vergleich zu anderen Organismen während der Interphase kaum Wachstums- oder Verkürzungsvorgänge beobachtet werden. Dennoch können Dictyostelium Mikrotubuli unter Verwendung von Agenzien wie Thiabendazol oder Nocodazol, welche ausschließlich auf dynamische Mikrotubuli wirken, signifikant verkürzt werden. Durch FRAP Experimente und Einsatz von 5D Fluoreszenz-Mikroskopie an lebenden Zellen konnte in dieser Arbeit erstmalig nachgewiesen werden, dass Dictyostelium Mikrotubuli nur in der Zellperipherie, nicht aber im pericentrosomalen Bereich dynamisch sind. Die Identifikation bislang unbekannter Bestandteile des Dictyostelium Centrosoms erfuhr in den vergangenen Jahren große Fortschritte. Ein von unserer Gruppe durchgeführter Proteomics-Ansatz brachte eine Vielzahl potentiell centrosomaler Proteine zu Tage, von welchen bereits viele am Centrosom nachgewiesen werden konnten. Der zweite Teil dieser Arbeit befasst sich mit der Charakterisierung dreier noch unbekannter Proteine aus dem Proteomics-Ansatz, Cenp68, CP103 und dem Dictyostelium Homologen des Spindle Assembly Checkpunkt Proteins Mad1. Hierbei zeigte sich, dass lediglich CP103 Bestandteil isolierter, Mikrotubuli-freier Centrosomen ist, während Cenp68 an die Centromere und Mad1 an die Kinetochoren lokalisieren. Die Charakterisierung von Cenp68 umfasste außerdem die Herstellung eines polyklonalen anti-Cenp68 Antikörpers, das Suchen nach Interaktionspartnern und die Erzeugung eines Cenp68 Knockout-Stammes. Letzterer wies jedoch keinen offensichtlichen Phänotyp auf. Das Verhalten des Dictyostelium Mad1 Proteins während der Mitose stimmte in großen Teilen mit dem anderer Mad1 Proteine überein, was auf die Existenz eines bislang unerforschten Spindle Assembly Chekpunkts in Dictyostelium hinweisen könnte. KW - Dictyostelium KW - Mikrotubuli KW - TACC KW - Centrosom KW - Centromere KW - Dictyostelium KW - Microtubules KW - TACC KW - Centrosome KW - Centromeres Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-52835 ER - TY - JOUR A1 - Ryngajllo, Malgorzata A1 - Childs, Liam H. A1 - Lohse, Marc A1 - Giorgi, Federico M. A1 - Lude, Anja A1 - Selbig, Joachim A1 - Usadel, Björn T1 - SLocX predicting subcellular localization of Arabidopsis proteins leveraging gene expression data JF - Frontiers in plant science N2 - Despite the growing volume of experimentally validated knowledge about the subcellular localization of plant proteins, a well performing in silico prediction tool is still a necessity. Existing tools, which employ information derived from protein sequence alone, offer limited accuracy and/or rely on full sequence availability. We explored whether gene expression profiling data can be harnessed to enhance prediction performance. To achieve this, we trained several support vector machines to predict the subcellular localization of Arabidopsis thaliana proteins using sequence derived information, expression behavior, or a combination of these data and compared their predictive performance through a cross-validation test. We show that gene expression carries information about the subcellular localization not available in sequence information, yielding dramatic benefits for plastid localization prediction, and some notable improvements for other compartments such as the mito-chondrion, the Golgi, and the plasma membrane. Based on these results, we constructed a novel subcellular localization prediction engine, SLocX, combining gene expression profiling data with protein sequence-based information. We then validated the results of this engine using an independent test set of annotated proteins and a transient expression of GFP fusion proteins. Here, we present the prediction framework and a website of predicted localizations for Arabidopsis. The relatively good accuracy of our prediction engine, even in cases where only partial protein sequence is available (e.g., in sequences lacking the N-terminal region), offers a promising opportunity for similar application to non-sequenced or poorly annotated plant species. Although the prediction scope of our method is currently limited by the availability of expression information on the ATH1 array, we believe that the advances in measuring gene expression technology will make our method applicable for all Arabidopsis proteins. KW - subcellular localization KW - support vector machine KW - prediction KW - gene expression Y1 - 2011 U6 - https://doi.org/10.3389/fpls.2011.00043 SN - 1664-462X VL - 2 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Ruprecht, Colin A1 - Mutwil, Marek A1 - Saxe, Friederike A1 - Eder, Michaela A1 - Nikoloski, Zoran A1 - Persson, Staffan T1 - Large-scale co-expression approach to dissect secondary cell wall formation across plant species JF - Frontiers in plant science N2 - Plant cell walls are complex composites largely consisting of carbohydrate-based polymers, and are generally divided into primary and secondary walls based on content and characteristics. Cellulose microfibrils constitute a major component of both primary and secondary cell walls and are synthesized at the plasma membrane by cellulose synthase (CESA) complexes. Several studies in Arabidopsis have demonstrated the power of co-expression analyses to identify new genes associated with secondary wall cellulose biosynthesis. However, across-species comparative co-expression analyses remain largely unexplored. Here, we compared co-expressed gene vicinity networks of primary and secondary wall CESAsin Arabidopsis, barley, rice, poplar, soybean, Medicago, and wheat, and identified gene families that are consistently co-regulated with cellulose biosynthesis. In addition to the expected polysaccharide acting enzymes, we also found many gene families associated with cytoskeleton, signaling, transcriptional regulation, oxidation, and protein degradation. Based on these analyses, we selected and biochemically analyzed T-DNA insertion lines corresponding to approximately twenty genes from gene families that re-occur in the co-expressed gene vicinity networks of secondary wall CESAs across the seven species. We developed a statistical pipeline using principal component analysis and optimal clustering based on silhouette width to analyze sugar profiles. One of the mutants, corresponding to a pinoresinol reductase gene, displayed disturbed xylem morphology and held lower levels of lignin molecules. We propose that this type of large-scale co-expression approach, coupled with statistical analysis of the cell wall contents, will be useful to facilitate rapid knowledge transfer across plant species. KW - secondary cell wall KW - comparative co-expression analysis KW - Arabidopsis KW - cellulose Y1 - 2011 U6 - https://doi.org/10.3389/fpls.2011.00023 SN - 1664-462X VL - 2 PB - Frontiers Research Foundation CY - Lausanne ER - TY - THES A1 - Ruprecht, Colin T1 - Characterization of genetic modules involved in cellulose synthesis in Arabidopsis thaliana Y1 - 2011 CY - Potsdam ER - TY - THES A1 - Rott, Markus T1 - Die Rolle der plastidären APT Synthase in der Regulation des photosynthetischen Elektronenflusses Y1 - 2011 CY - Potsdam ER - TY - JOUR A1 - Rohrmann, Johannes A1 - Tohge, Takayuki A1 - Alba, Rob A1 - Osorio, Sonia A1 - Caldana, Camila A1 - McQuinn, Ryan A1 - Arvidsson, Samuel Janne A1 - van der Merwe, Margaretha J. A1 - Riano-Pachon, Diego Mauricio A1 - Müller-Röber, Bernd A1 - Fei, Zhangjun A1 - Nesi, Adriano Nunes A1 - Giovannoni, James J. A1 - Fernie, Alisdair R. T1 - Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development JF - The plant journal N2 - Maturation of fleshy fruits such as tomato (Solanum lycopersicum) is subject to tight genetic control. Here we describe the development of a quantitative real-time PCR platform that allows accurate quantification of the expression level of approximately 1000 tomato transcription factors. In addition to utilizing this novel approach, we performed cDNA microarray analysis and metabolite profiling of primary and secondary metabolites using GC-MS and LC-MS, respectively. We applied these platforms to pericarp material harvested throughout fruit development, studying both wild-type Solanum lycopersicum cv. Ailsa Craig and the hp1 mutant. This mutant is functionally deficient in the tomato homologue of the negative regulator of the light signal transduction gene DDB1 from Arabidopsis, and is furthermore characterized by dramatically increased pigment and phenolic contents. We choose this particular mutant as it had previously been shown to have dramatic alterations in the content of several important fruit metabolites but relatively little impact on other ripening phenotypes. The combined dataset was mined in order to identify metabolites that were under the control of these transcription factors, and, where possible, the respective transcriptional regulation underlying this control. The results are discussed in terms of both programmed fruit ripening and development and the transcriptional and metabolic shifts that occur in parallel during these processes. KW - transcription factor KW - Solanum lycopersicum KW - quantitative RT-PCR KW - microarray KW - metabolomics KW - fleshy fruit ripening Y1 - 2011 U6 - https://doi.org/10.1111/j.1365-313X.2011.04750.x SN - 0960-7412 VL - 68 IS - 6 SP - 999 EP - 1013 PB - Wiley-Blackwell CY - Malden ER - TY - THES A1 - Rocha, Marcia Rosa T1 - Time series analysis reveals links between functional traits, population dynamics and ecosystem functions in a diverse phytoplankton community Y1 - 2011 CY - Potsdam ER - TY - JOUR A1 - Rocha, Marcia R. A1 - Vasseur, David A. A1 - Hayn, Michael A1 - Holschneider, Matthias A1 - Gaedke, Ursula T1 - Variability patterns differ between standing stock and process rates JF - Oikos N2 - Standing stocks are typically easier to measure than process rates such as production. Hence, stocks are often used as indicators of ecosystem functions although the latter are generally more strongly related to rates than to stocks. The regulation of stocks and rates and thus their variability over time may differ, as stocks constitute the net result of production and losses. Based on long-term high frequency measurements in a large, deep lake we explore the variability patterns in primary and bacterial production and relate them to those of the corresponding standing stocks, i.e. chlorophyll concentration, phytoplankton and bacterial biomass. We employ different methods (coefficient of variation, spline fitting and spectral analysis) which complement each other for assessing the variability present in the plankton data, at different temporal scales. In phytoplankton, we found that the overall variability of primary production is dominated by fluctuations at low frequencies, such as the annual, whereas in stocks and chlorophyll in particular, higher frequencies contribute substantially to the overall variance. This suggests that using standing stocks instead of rate measures leads to an under- or overestimation of food shortage for consumers during distinct periods of the year. The range of annual variation in bacterial production is 8 times greater than biomass, showing that the variability of bacterial activity (e.g. oxygen consumption, remineralisation) would be underestimated if biomass is used. The P/B ratios were variable and although clear trends are present in both bacteria and phytoplankton, no systematic relationship between stock and rate measures were found for the two groups. Hence, standing stock and process rate measures exhibit different variability patterns and care is needed when interpreting the mechanisms and implications of the variability encountered. Y1 - 2011 U6 - https://doi.org/10.1111/j.1600-0706.2010.18786.x SN - 0030-1299 VL - 120 IS - 1 SP - 17 EP - 25 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Rocha, Marcia R. A1 - Gaedke, Ursula A1 - Vasseur, David A. T1 - Functionally similar species have similar dynamics JF - The journal of ecology N2 - 1. Improving the mechanistic basis of biodiversity-ecosystem function relationships requires a better understanding of how functional traits drive the dynamics of populations. For example, environmental disturbances or grazing may increase synchronization of functionally similar species, whereas functionally different species may show independent dynamics, because of different responses to the environment. Competition for resources, on the other hand, may yield a wide range of dynamic patterns among competitors and lead functionally similar and different species to display synchronized to compensatory dynamics. The mixed effect of these forces will influence the temporal fluctuations of populations and, thus, the variability of aggregate community properties. 2. To search for a relationship between functional and dynamics similarity, we studied the relationship between functional trait similarity and temporal dynamics similarity for 36 morphotypes of phytoplankton using long-term high-frequency measurements. 3. Our results show that functionally similar morphotypes exhibit dynamics that are more synchronized than those of functionally dissimilar ones. Functionally dissimilar morphotypes predominantly display independent temporal dynamics. This pattern is especially strong when short time-scales are considered. 4. Negative correlations are present among both functionally similar and dissimilar phytoplankton morphotypes, but are rarer and weaker than positive ones over all temporal scales. 5. Synthesis. We demonstrate that diversity in functional traits decreases community variability and ecosystem-level properties by decoupling the dynamics of individual morphotypes. KW - compensatory dynamics KW - competition KW - environmental forcing KW - functional diversity KW - functional traits KW - grazing KW - phytoplankton KW - plant population and community dynamics KW - synchrony KW - temporal dynamics Y1 - 2011 U6 - https://doi.org/10.1111/j.1365-2745.2011.01893.x SN - 0022-0477 VL - 99 IS - 6 SP - 1453 EP - 1459 PB - Wiley-Blackwell CY - Hoboken ER - TY - CHAP A1 - Rietsch, Katrin A1 - Scheffler, Christiane T1 - Association between skeletal robustness and physical activity in schoolchildren - First results T2 - Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft für Anthropologie Y1 - 2011 SN - 0003-5548 VL - 68 IS - 4 SP - 516 EP - 516 PB - Schweizerbart CY - Stuttgart ER - TY - JOUR A1 - Riede, Jens O. A1 - Binzer, Amrei A1 - Brose, Ulrich A1 - de Castro, Francisco A1 - Curtsdotter, Alva A1 - Rall, Bjoern C. A1 - Ekloef, Anna T1 - Size-based food web characteristics govern the response to species extinctions JF - Basic and applied ecology : Journal of the Gesellschaft für Ökologie N2 - How ecological communities react to species extinctions is a long-standing yet current question in ecology. The species constituting the basic units of ecosystems interact with each other forming complex networks of trophic relationships and the characteristics of these networks are highly important for the consequences of species extinction. Here we take a more general approach and analyze a broad range of network characteristics and their role in determining food web susceptibility to secondary extinctions. We extend previous studies, that have focused on the consequences of topological and dynamical food web parameters for food web robustness, by also defining network-wide characteristics depending on the relationships between the distribution of species body masses and other species characteristics. We use a bioenergetic dynamical model to simulate realistically structured model food webs that differ in their structural and dynamical properties as well as their size structure. In order to measure food web robustness we calculated the proportion of species going secondarily extinct. A multiple regression analysis was then used to fit a general model relating the proportion of species going secondarily extinct to the measured food web properties. Our results show that there are multiple factors from all three groups of food web characteristics that affect food web robustness. However, we find the most striking effect was related to the body mass abundance relationship which points to the importance of body mass relationships for food web stability. KW - Body mass-abundance KW - Connectance KW - Food web robustness KW - Hill exponent KW - Size structure KW - Secondary extinctions Y1 - 2011 U6 - https://doi.org/10.1016/j.baae.2011.09.006 SN - 1439-1791 VL - 12 IS - 7 SP - 581 EP - 589 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Redelberger, David A1 - Seduk, Farida A1 - Genest, Olivier A1 - Mejean, Vincent A1 - Leimkühler, Silke A1 - Iobbi-Nivol, Chantal T1 - YcdY Protein of Escherichia coli, an Atypical Member of the TorD Chaperone Family JF - Journal of bacteriology N2 - The TorD family of specific chaperones is divided into four subfamilies dedicated to molybdoenzyme biogenesis and a fifth one, exemplified by YcdY of Escherichia coli, for which no defined partner has been identified so far. We propose that YcdY is the chaperone of YcdX, a zinc protein involved in the swarming motility process of E. coli, since YcdY interacts with YcdX and increases its activity in vitro. Y1 - 2011 U6 - https://doi.org/10.1128/JB.05927-11 SN - 0021-9193 VL - 193 IS - 23 SP - 6512 EP - 6516 PB - American Society for Microbiology CY - Washington ER - TY - JOUR A1 - Raabova, Jana A1 - Muenzbergova, Zuzana A1 - Fischer, Markus T1 - The role of spatial scale and soil for local adaptation in Inula hirta JF - Basic and applied ecology : Journal of the Gesellschaft für Ökologie N2 - Many plant populations are adapted to their local environment. Reciprocal transplant experiments in the field and in the experimental garden allow for studying different aspects of local adaptation. However, usually only one of these approaches is used. We applied both experimental approaches to study the role of spatial scale and soil conditions for local adaptation in the perennial herb Inula hirta. We reciprocally sowed seeds and transplanted juvenile plants among six field sites from two regions and, in the garden, among pots with soil from each field site. We recorded germination percentage, survival percentage, number of stems and plant height in all experiments. We also recorded above- and below-ground biomass, flowering percentage and the number of flower heads in the garden. No population-specific local adaptation was detected in germination, survival, flowering percentages or in the number of flower heads. At the regional scale in the field, however, the performance of local transplants was higher than the performance of foreign transplants by 10% and 7% in the two regions, respectively. Similarly, when grown in the garden in soil from the more basic and nutrient-poorer region, plant height and aboveground biomass of local transplants were higher than the corresponding values for foreign transplants by 31% and 112%, respectively. Congruent evidence for local adaptation from the juvenile-transplant experiments in field and garden suggests that soil conditions represent an important factor of local adaptation in I. hirta. Overall, our results show that both spatial scale and soil conditions play an important role for local adaptation in I. hirta. Moreover, we underline the importance of combining field and garden experiments to reveal factors affecting local adaptation in plants. KW - Dry grasslands KW - Fitness components KW - Genotype by environment KW - Habitat fragmentation KW - Home-site advantage KW - Natural selection KW - Plant traits KW - Reciprocal transplant Y1 - 2011 U6 - https://doi.org/10.1016/j.baae.2011.01.001 SN - 1439-1791 VL - 12 IS - 2 SP - 152 EP - 160 PB - Elsevier CY - Jena ER - TY - THES A1 - Pyl, Eva-Theresa T1 - Networks and growth in Arabidopsis: two strategies to pertub a complex system Y1 - 2011 CY - Potsdam ER - TY - JOUR A1 - Popova, Antoaneta V. A1 - Hundertmark, Michaela A1 - Seckler, Robert A1 - Hincha, Dirk K. T1 - Structural transitions in the intrinsically disordered plant dehydration stress protein LEA7 upon drying are modulated by the presence of membranes JF - Biochimica et biophysica acta : Biomembranes N2 - Dehydration stress-related late embryogenesis abundant (LEA) proteins have been found in plants, invertebrates and bacteria. Most LEA proteins are unstructured in solution, but some fold into amphipathic a-helices during drying. The Pfam LEA_4 (Group 3) protein LEA7 from the higher plant Arabidopsis thaliana was predicted to be 87% alpha-helical, while CD spectroscopy showed it to be largely unstructured in solution and only 35% alpha-helical in the dry state. However, the dry protein contained 15% beta-sheets. FTIR spectroscopy revealed the (beta-sheets to be largely due to aggregation. beta-Sheet content was reduced and alpha-helix content increased when LEA7 was dried in the presence of liposomes with secondary structure apparently influenced by lipid composition. Secondary structure was also affected by the presence of membranes in the fully hydrated state. A temperature-induced increase in the flexibility of the dry protein was also only observed in the presence of membranes. Functional interactions of LEA7 with membranes in the dry state were indicated by its influence on the thermotropic phase transitions of the lipids and interactions with the lipid headgroup phosphates. KW - Desiccation KW - CD spectroscopy KW - FTIR spectroscopy KW - LEA protein KW - Protein-membrane interactions KW - Protein secondary structure Y1 - 2011 U6 - https://doi.org/10.1016/j.bbamem.2011.03.009 SN - 0005-2736 VL - 1808 IS - 7 SP - 1879 EP - 1887 PB - Elsevier CY - Amsterdam ER - TY - GEN A1 - Pokorny, Ina A1 - Sharma, Reeta A1 - Goyal, Surendra Prakash A1 - Mishra, Sudanshu A1 - Tiedemann, Ralph T1 - MHC class I and MHC class II DRB gene variability in wild and captive Bengal tigers (Panthera tigris tigris) (vol 10, pg 667, 2010) T2 - Immunogenetics Y1 - 2011 U6 - https://doi.org/10.1007/s00251-010-0496-2 SN - 0093-7711 VL - 63 IS - 2 SP - 121 EP - 121 PB - Springer CY - New York ER - TY - THES A1 - Piepho, Maike T1 - Phytoplankton lipids in a changing world : more than just water flea feed Y1 - 2011 CY - Potsdam ER - TY - JOUR A1 - Pavesi, Laura A1 - De Matthaeis, Elvira A1 - Tiedemann, Ralph A1 - Ketmaier, Valerio T1 - Temporal population genetics and COI phylogeography of the sandhopper macarorchestia remyi (Amphipoda: Talitridae) JF - Zoological studies N2 - Laura Pavesi, Elvira De Matthaeis, Ralph Tiedemann, and Valerio Ketmaier (2011) Temporal population genetics and COI phylogeography of the sandhopper Macarorchestia remyi (Amphipoda: Talitridae). Zoological Studies 50(2): 220-229. In this study we assessed levels of genetic divergence and variability in 208 individuals of the supralittoral sandhopper Macarorchestia remyi, a species strictly associated with rotted wood stranded on sand beaches, by analyzing sequence polymorphisms in a fragment of the mitochondrial DNA (mtDNA) gene coding cytochrome oxidase subunit I (COI). The geographical distribution and ecology of the species are poorly known. The study includes 1 Tyrrhenian and 2 Adriatic populations sampled along the Italian peninsula plus a single individual found on Corfu Is. (Greece). The Tyrrhenian population was sampled monthly for 1 yr. Genetic data revealed a deep phylogeographic break between the Tyrrhenian and Adriatic populations with no shared haplotypes. The single individual collected on Corfu Is. carried the most common haplotype found in the Tyrrhenian population. A mismatch analysis could not reject the hypothesis of a sudden demographic expansion in almost all but 2 monthly samples. When compared to previous genetic data centered on a variety of Mediterranean talitrids, our results place M. remyi among those species with profound intraspecific divergence (sandhoppers) and dissimilar from beachfleas, which generally display little population genetic structuring. KW - Macarorchestia remyi KW - Talitridae KW - Cytochrome oxidase I KW - Population genetics Y1 - 2011 SN - 1021-5506 VL - 50 IS - 2 SP - 220 EP - 229 PB - Institute of Zoology, Academia Sinica CY - Taipei ER - TY - JOUR A1 - Pauliuk, Franziska A1 - Müller, Jörg A1 - Heinken, Thilo T1 - Bryophyte dispersal by sheep on dry grassland JF - Nova Hedwigia : Zeitschrift für Kryptogamenkunde N2 - Many bryophytes may depend on epizoochorous dispersal by large mammals for maintaining their populations and colonizing new habitats. On dry grassland we investigated the transport of bryophyte diaspores by sheep, which are known to be effective epizoochorous dispersal vectors of seed plants. Twelve sheep of two breeds were examined by collecting gametophyte fragments from their fleece and hooves. Furthermore, microscopic diaspores from the soil adhering to the hooves were grown in a greenhouse. Species frequency and composition were compared to bryophyte vegetation on the pasture. Considerable amounts of unspecialized gametophyte fragments from 16 moss species, 40% of the species growing on the pasture, were transported by sheep, especially on the belly and the tail. Additionally, we provide first evidence of epizoochorous dispersal of thallus fragments from fruticose lichens. Sheep breeds differed in species spectrum and frequency, i.e. sheep with dense, curly fleece carried more fragments and larger species than those with smooth and fine hair. Among the dispersed bryophytes pleurocarps, certain taxa, sizes (small species) and life forms (mats) were overrepresented compared to the vegetation of the pasture, while large species, acrocarps, wefts and turfs were underrepresented, reflecting fragmentation and adhesion features of the species. In the hooves mostly acrocarpous colonist species were transported. We conclude that sheep are important dispersal vectors with the potential of long-range dispersal for bryophytes, especially for species without sexual reproduction, and that epizoochorous dispersal of microscopic diaspores might be underestimated in its importance so far. KW - Calcareous grassland KW - dispersal of cryptogams KW - epizoochory KW - shoot fragments KW - life history attributes KW - vegetative reproduction Y1 - 2011 U6 - https://doi.org/10.1127/0029-5035/2011/0092-0327 SN - 0029-5035 VL - 92 IS - 3-4 SP - 327 EP - 341 PB - Cramer CY - Stuttgart ER - TY - JOUR A1 - Parlitz, Steffi A1 - Kunze, Reinhard A1 - Müller-Röber, Bernd A1 - Balazadeh, Salma T1 - Regulation of photosynthesis and transcription factor expression by leaf shading and re-illumination in Arabidopsis thaliana leaves JF - Journal of plant physiology : biochemistry, physiology, molecular biology and biotechnology of plants N2 - Leaf senescence of annual plants is a genetically programmed developmental phase. The onset of leaf senescence is however not exclusively determined by tissue age but is modulated by various environmental factors. Shading of individual attached leaves evokes dark-induced senescence. The initiation and progression of dark-induced senescence depend on the plant and the age of the affected leaf, however. In several plant species dark-induced senescence is fully reversible upon re-illumination and the leaves can regreen, but the regreening ability depends on the duration of dark incubation. We studied the ability of Arabidopsis thaliana leaves to regreen after dark-incubation with the aim to identify transcription factors (TFs) that are involved in the regulation of early dark-induced senescence and regreening. Two days shading of individual attached leaves triggers the transition into a pre-senescence state from which the leaves can largely recover. Longer periods of darkness result in irreversible senescence. Large scale qRT-PCR analysis of 1872 TF genes revealed that 649 of them are regulated in leaves during normal development, upon shading or re-illumination. Leaf shading triggered upregulation of 150 TF genes, some of which are involved in controlling senescence. Of those, 39 TF genes were upregulated after two days in the dark and regained pre-shading expression level after two days of re-illumination. Furthermore, a larger number of 422 TF genes were down regulated upon shading. In TF gene clusters with different expression patterns certain TF families are over-represented. KW - Arabidopsis thaliana KW - Dark-induced senescence KW - Expression profiling KW - Regreening KW - Transcription factor Y1 - 2011 U6 - https://doi.org/10.1016/j.jplph.2011.02.001 SN - 0176-1617 VL - 168 IS - 12 SP - 1311 EP - 1319 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Paasche, Hendrik A1 - Eberle, Detlef T1 - Automated compilation of pseudo-lithology maps from geophysical data sets a comparison of Gustafson-Kessel and fuzzy c-means cluster algorithms JF - Exploration geophysics : the bulletin of the Australian Society of Exploration Geophysicists N2 - The fuzzy partitioning Gustafson-Kessel cluster algorithm is employed for rapid and objective integration of multi-parameter Earth-science related databases. We begin by evaluating the Gustafson-Kessel algorithm using the example of a synthetic study and compare the results to those obtained from the more widely employed fuzzy c-means algorithm. Since the Gustafson-Kessel algorithm goes beyond the potential of the fuzzy c-means algorithm by adapting the shape of the clusters to be detected and enabling a manual control of the cluster volume, we believe the results obtained from Gustafson-Kessel algorithm to be superior. Accordingly, a field database comprising airborne and ground-based geophysical data sets is analysed, which has previously been classified by means of the fuzzy c-means algorithm. This database is integrated using the Gustafson-Kessel algorithm thus minimising the amount of empirical data processing required before and after fuzzy c-means clustering. The resultant zonal geophysical map is more evenly clustered matching regional geology information available from the survey area. Even additional information about linear structures, e. g. as typically caused by the presence of dolerite dykes or faults, is visible in the zonal map obtained from Gustafson-Kessel cluster analysis. KW - cluster analysis KW - data integration KW - airborne KW - South Africa KW - Gustafson-Kessel KW - fuzzy c-means Y1 - 2011 U6 - https://doi.org/10.1071/EG11014 SN - 0812-3985 VL - 42 IS - 4 SP - 275 EP - 285 PB - CSIRO CY - Collingwood ER - TY - GEN A1 - Nikoloski, Zoran A1 - van Dongen, Joost T. T1 - Modeling alternatives for interpreting the change in oxygen-consumption rates during hypoxic conditions T2 - New phytologist : international journal of plant science KW - hypoxia KW - modeling KW - regulation KW - respiration KW - roots Y1 - 2011 U6 - https://doi.org/10.1111/j.1469-8137.2011.03674.x SN - 0028-646X VL - 190 IS - 2 SP - 273 EP - 276 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Nikoloski, Zoran A1 - Grimbs, Sergio A1 - Klie, Sebastian A1 - Selbig, Joachim T1 - Complexity of automated gene annotation JF - Biosystems : journal of biological and information processing sciences N2 - Integration of high-throughput data with functional annotation by graph-theoretic methods has been postulated as promising way to unravel the function of unannotated genes. Here, we first review the existing graph-theoretic approaches for automated gene function annotation and classify them into two categories with respect to their relation to two instances of transductive learning on networks - with dynamic costs and with constant costs - depending on whether or not ontological relationship between functional terms is employed. The determined categories allow to characterize the computational complexity of the existing approaches and establish the relation to classical graph-theoretic problems, such as bisection and multiway cut. In addition, our results point out that the ontological form of the structured functional knowledge does not lower the complexity of the transductive learning with dynamic costs - one of the key problems in modern systems biology. The NP-hardness of automated gene annotation renders the development of heuristic or approximation algorithms a priority for additional research. KW - Complexity KW - Gene function prediction KW - External structural measures KW - Transductive learning Y1 - 2011 U6 - https://doi.org/10.1016/j.biosystems.2010.12.003 SN - 0303-2647 VL - 104 IS - 1 SP - 1 EP - 8 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Ni, Jian A1 - Herzschuh, Ulrike T1 - Simulating biome distribution on the Tibetan Plateau using a modified global vegetation model JF - Arctic, antarctic, and alpine research : an interdisciplinary journal N2 - We used a regionally modified global vegetation model (BIOME4-Tibet) to simulate biome distribution on the Tibetan Plateau under current climate conditions derived from regional meteorological observations. The bioclimatic limits (mean temperatures of the coldest and warmest months, minimum temperature, growing degree-days on 5 degrees C and 0 degrees C bases) for some key alpine plant functional types (temperate deciduous and conifer trees, boreal deciduous and conifer trees, desert woody plants, tundra shrubs, cold herbaceous plants, and lichens/forbs) were redefined based on regional vegetation-climate relationships. Modern vegetation maps confirmed that the BIOME4-Tibet model does a better job of simulating biome patterns on the plateau (gridcell agreement 52%) than the original BIOME4 model (35%). This improved model enhanced our ability to simulate temperate conifer forest, cool conifer and mixed forest, evergreen taiga, temperate xerophytic shrubland, temperate grassland and desert, and steppe and shrub tundra biomes, but made a negligible or reduced difference to the prediction of temperate deciduous forest, warm-temperate mixed forest, and three tundra biomes (erect dwarf-shrub tundra, prostrate dwarf-shrub tundra, and cushion forb, lichen, and moss tundra). Future modification of the vegetation model, by increasing the number of shrub and herb plant functional types, re-parameterization of more precise bioclimatic constraints, and improved representation of soil, permafrost, and snow processes, will be needed to better characterize the distribution of alpine vegetation on the Tibetan Plateau. Y1 - 2011 U6 - https://doi.org/10.1657/1938-4246-43.3.429 SN - 1523-0430 VL - 43 IS - 3 SP - 429 EP - 441 PB - Institute of Arctic and Alpine Research, University of Colorado CY - Boulder ER - TY - THES A1 - Nguyen, Hung Minh T1 - Regulation of leaf growth and development by transcription factors in Arabidopsis thaliana Y1 - 2011 CY - Potsdam ER - TY - JOUR A1 - Neumann, Meina A1 - Seduk, Farida A1 - Iobbi-Nivol, Chantal A1 - Leimkühler, Silke T1 - Molybdopterin Dinucleotide Biosynthesis in Escherichia coli identification of amino acid residues of molybdopterin dinucleotide transferases that determine specificity for binding of guanine or cytosine nucleotides JF - The journal of biological chemistry N2 - The molybdenum cofactor is modified by the addition of GMP or CMP to the C4' phosphate of molybdopterin forming the molybdopterin guanine dinucleotide or molybdopterin cytosine dinucleotide cofactor, respectively. The two reactions are catalyzed by specific enzymes as follows: the GTP: molybdopterin guanylyltransferase MobA and the CTP: molybdopterin cytidylyltransferase MocA. Both enzymes show 22% amino acid sequence identity and are specific for their respective nucleotides. Crystal structure analysis of MobA revealed two conserved motifs in the N-terminal domain of the protein involved in binding of the guanine base. Based on these motifs, we performed site-directed mutagenesis studies to exchange the amino acids to the sequence found in the paralogue MocA. Using a fully defined in vitro system, we showed that the exchange of five amino acids was enough to obtain activity with both GTP and CTP in either MocA or MobA. Exchange of the complete N-terminal domain of each protein resulted in the total inversion of nucleotide specificity activity, showing that the N-terminal domain determines nucleotide recognition and binding. Analysis of protein-protein interactions showed that the C-terminal domain of either MocA or MobA determines the specific binding to the respective acceptor protein. Y1 - 2011 U6 - https://doi.org/10.1074/jbc.M110.155671 SN - 0021-9258 VL - 286 IS - 2 SP - 1400 EP - 1408 PB - American Society for Biochemistry and Molecular Biology CY - Bethesda ER - TY - JOUR A1 - Neffe, Axel T. A1 - Loebus, Axel A1 - Zaupa, Alessandro A1 - Stötzel, Christian A1 - Müller, Frank A. A1 - Lendlein, Andreas T1 - Gelatin functionalization with tyrosine derived moieties to increase the interaction with hydroxyapatite fillers JF - Acta biomaterialia N2 - Combining gelatins functionalized with the tyrosine-derived groups desaminotyrosine or desaminotyrosyl tyrosine with hydroxyapatite (HAp) led to the formation of composite materials with much lower swelling ratios than those of the pure matrices. Shifts of the infra-red (IR) bands related to the free carboxyl groups could be observed in the presence of HAp, which suggested a direct interaction of matrix and filler that formed additional physical cross-links in the material. In tensile tests and rheological measurements the composites equilibrated in water had increased Young's moduli (from 200 kPa up to 2 MPa) and tensile strengths (from 57 kPa up to 1.1 MPa) compared with the matrix polymers without affecting the elongation at break. Furthermore, an increased thermal stability of the networks from 40 to 85 degrees C could be demonstrated. The differences in the behaviour of the functionalized gelatins compared with pure gelatin as a matrix suggested an additional stabilizing bond between the incorporated aromatic groups and the HAp as supported by the IR results. The composites can potentially be applied as bone fillers. KW - Gelatin KW - Hydroxyapatite KW - Composite KW - Hydrogel KW - Biomaterial Y1 - 2011 U6 - https://doi.org/10.1016/j.actbio.2010.11.025 SN - 1742-7061 VL - 7 IS - 4 SP - 1693 EP - 1701 PB - Elsevier CY - Oxford ER - TY - GEN A1 - Nathan, Ran A1 - Horvitz, Nir A1 - He, Yanping A1 - Kuparinen, Anna A1 - Schurr, Frank Martin A1 - Katul, Gabriel G. T1 - Spread of North American wind-dispersed trees in future environments T2 - Ecology letters N2 - P>Despite ample research, understanding plant spread and predicting their ability to track projected climate changes remain a formidable challenge to be confronted. We modelled the spread of North American wind-dispersed trees in current and future (c. 2060) conditions, accounting for variation in 10 key dispersal, demographic and environmental factors affecting population spread. Predicted spread rates vary substantially among 12 study species, primarily due to inter-specific variation in maturation age, fecundity and seed terminal velocity. Future spread is predicted to be faster if atmospheric CO2 enrichment would increase fecundity and advance maturation, irrespective of the projected changes in mean surface windspeed. Yet, for only a few species, predicted wind-driven spread will match future climate changes, conditioned on seed abscission occurring only in strong winds and environmental conditions favouring high survival of the farthest-dispersed seeds. Because such conditions are unlikely, North American wind-dispersed trees are expected to lag behind the projected climate range shift. KW - Climate change KW - demography KW - dispersal KW - fat-tailed dispersal kernels KW - forecasting KW - forests KW - invasion by extremes KW - long-distance dispersal KW - mechanistic models KW - plant migration KW - population spread KW - range expansion KW - survival KW - wind dispersal Y1 - 2011 U6 - https://doi.org/10.1111/j.1461-0248.2010.01573.x SN - 1461-023X VL - 14 IS - 3 SP - 211 EP - 219 PB - Wiley-Blackwell CY - Malden ER -