@misc{MeyerKustererLisecetal.2009, author = {Meyer, Rhonda Christiane and Kusterer, Barbara and Lisec, Jan and Steinfath, Matthias and Becher, Martina and Scharr, Hanno and Melchinger, Albrecht E. and Selbig, Joachim and Schurr, Ulrich and Willmitzer, Lothar and Altmann, Thomas}, title = {QTL analysis of early stage heterosis for biomass in Arabidopsis}, series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1330}, issn = {1866-8372}, doi = {10.25932/publishup-43127}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431272}, pages = {11}, year = {2009}, abstract = {The main objective of this study was to identify genomic regions involved in biomass heterosis using QTL, generation means, and mode-of-inheritance classification analyses. In a modified North Carolina Design III we backcrossed 429 recombinant inbred line and 140 introgression line populations to the two parental accessions, C24 and Col-0, whose F 1 hybrid exhibited 44\% heterosis for biomass. Mid-parent heterosis in the RILs ranged from -31 to 99\% for dry weight and from -58 to 143\% for leaf area. We detected ten genomic positions involved in biomass heterosis at an early developmental stage, individually explaining between 2.4 and 15.7\% of the phenotypic variation. While overdominant gene action was prevalent in heterotic QTL, our results suggest that a combination of dominance, overdominance and epistasis is involved in biomass heterosis in this Arabidopsis cross.}, language = {en} } @article{MeyerKustererLisecetal.2009, author = {Meyer, Rhonda Christiane and Kusterer, Barbara and Lisec, Jan and Steinfath, Matthias and Becher, Martina and Scharr, Hanno and Melchinger, Albrecht E. and Selbig, Joachim and Schurr, Ulrich and Willmitzer, Lothar and Altmann, Thomas}, title = {QTL analysis of early stage heterosis for biomass in Arabidopsis}, series = {Theoretical and applied genetics}, volume = {129}, journal = {Theoretical and applied genetics}, number = {2}, publisher = {Springer Nature}, address = {Berlin}, issn = {1432-2242}, doi = {10.1007/s00122-009-1074-6}, pages = {227 -- 237}, year = {2009}, abstract = {The main objective of this study was to identify genomic regions involved in biomass heterosis using QTL, generation means, and mode-of-inheritance classification analyses. In a modified North Carolina Design III we backcrossed 429 recombinant inbred line and 140 introgression line populations to the two parental accessions, C24 and Col-0, whose F 1 hybrid exhibited 44\% heterosis for biomass. Mid-parent heterosis in the RILs ranged from -31 to 99\% for dry weight and from -58 to 143\% for leaf area. We detected ten genomic positions involved in biomass heterosis at an early developmental stage, individually explaining between 2.4 and 15.7\% of the phenotypic variation. While overdominant gene action was prevalent in heterotic QTL, our results suggest that a combination of dominance, overdominance and epistasis is involved in biomass heterosis in this Arabidopsis cross.}, language = {en} } @misc{SteinfathGaertnerLisecetal.2009, author = {Steinfath, Matthias and G{\"a}rtner, Tanja and Lisec, Jan and Meyer, Rhonda C. and Altmann, Thomas and Willmitzer, Lothar and Selbig, Joachim}, title = {Prediction of hybrid biomass in Arabidopsis thaliana by selected parental SNP and metabolic markers}, series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1324}, issn = {1866-8372}, doi = {10.25932/publishup-43111}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431115}, pages = {9}, year = {2009}, abstract = {A recombinant inbred line (RIL) population, derived from two Arabidopsis thaliana accessions, and the corresponding testcrosses with these two original accessions were used for the development and validation of machine learning models to predict the biomass of hybrids. Genetic and metabolic information of the RILs served as predictors. Feature selection reduced the number of variables (genetic and metabolic markers) in the models by more than 80\% without impairing the predictive power. Thus, potential biomarkers have been revealed. Metabolites were shown to bear information on inherited macroscopic phenotypes. This proof of concept could be interesting for breeders. The example population exhibits substantial mid-parent biomass heterosis. The results of feature selection could therefore be used to shed light on the origin of heterosis. In this respect, mainly dominance effects were detected.}, language = {en} } @article{SteinfathGaertnerLisecetal.2009, author = {Steinfath, Matthias and G{\"a}rtner, Tanja and Lisec, Jan and Meyer, Rhonda Christiane and Altmann, Thomas and Willmitzer, Lothar and Selbig, Joachim}, title = {Prediction of hybrid biomass in Arabidopsis thaliana by selected parental SNP and metabolic markers}, series = {Theoretical and applied genetics : TAG ; international journal of plant breeding research}, volume = {120}, journal = {Theoretical and applied genetics : TAG ; international journal of plant breeding research}, publisher = {Springer}, address = {Berlin}, issn = {0040-5752}, doi = {10.1007/s00122-009-1191-2}, pages = {239 -- 247}, year = {2009}, abstract = {A recombinant inbred line (RIL) population, derived from two Arabidopsis thaliana accessions, and the corresponding testcrosses with these two original accessions were used for the development and validation of machine learning models to predict the biomass of hybrids. Genetic and metabolic information of the RILs served as predictors. Feature selection reduced the number of variables (genetic and metabolic markers) in the models by more than 80\% without impairing the predictive power. Thus, potential biomarkers have been revealed. Metabolites were shown to bear information on inherited macroscopic phenotypes. This proof of concept could be interesting for breeders. The example population exhibits substantial mid-parent biomass heterosis. The results of feature selection could therefore be used to shed light on the origin of heterosis. In this respect, mainly dominance effects were detected.}, language = {en} } @phdthesis{Tschoep2009, author = {Tschoep, Hendrik}, title = {The response of growth and primary metabolism to a mild but sustained nitrogen limitation in arabidopsis thaliana}, address = {Potsdam}, pages = {176 S.}, year = {2009}, language = {en} } @article{NettelsMuellerSpaethKuesteretal.2009, author = {Nettels, Daniel and M{\"u}ller-Sp{\"a}th, Sonja and K{\"u}ster, Frank and Hofmann, Hagen and Haenni, Domminik and R{\"u}egger, Stefan and Reymond, Luc and Hoffmann, Armin S. and Kubelka, Jan and Heinz, Benjamin and Gast, Klaus and Best, Robert B. and Schuler, Benjamin}, title = {Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins}, issn = {0027-8424}, year = {2009}, abstract = {We used single-molecule FRET in combination with other biophysical methods and molecular simulations to investigate the effect of temperature on the dimensions of unfolded proteins. With singlemolecule FRET, this question can be addressed even under nearnative conditions, where most molecules are folded, allowing us to probe a wide range of denaturant concentrations and temperatures. We find a compaction of the unfolded state of a small cold shock protein with increasing temperature in both the presence and the absence of denaturant, with good agreement between the results from single-molecule FRET and dynamic light scattering. Although dissociation of denaturant from the polypeptide chain with increasing temperature accounts for part of the compaction, the results indicate an important role for additional temperaturedependent interactions within the unfolded chain. The observation of a collapse of a similar extent in the extremely hydrophilic, intrinsically disordered protein prothymosin suggests that the hydrophobic effect is not the sole source of the underlying interactions. Circular dichroism spectroscopy and replica exchange molecular dynamics simulations in explicit water show changes in secondary structure content with increasing temperature and suggest a contribution of intramolecular hydrogen bonding to unfolded state collapse.}, language = {en} } @phdthesis{Reiss2009, author = {Reiß, Edda}, title = {Erzeugung einzelstr{\"a}ngiger DNA-Ger{\"u}ststr{\"a}nge mittels Rolling-Circle-Amplifikation f{\"u}r den Einsatz in der Nanobiotechnologie}, address = {Potsdam}, pages = {X, 163 S. : Ill., graph. Darst. + 1 CD-Rom}, year = {2009}, language = {de} } @article{WalterCastroVossetal.2009, author = {Walter, Juliane K. and Castro, Victor Manuel and Voss, M. and Gast, Klaus and Rueckert, C. and Piontek, J. and Blasig, Ingolf E.}, title = {Redox sensitivity of the dimerization of occludin}, issn = {1420-682X}, year = {2009}, abstract = {Occludin is a self-associating transmembrane tight junction protein affected in oxidative stress. However, its function is unknown. The cytosolic C-terminal tail contains a coiled coil-domain forming dimers contributing to the self- association. Studying the hypothesis that the self-association is redox-sensitive, we found that the dimerization of the domain depended on the sulfhydryl concentration of the environment in low-millimolar range. Under physiological conditions, monomers and dimers were detected. Masking the sulfhydryl residues in the domain prevented the dimerization but affected neither its helical structure nor cylindric shape. Incubation of cell extracts containing full-length occludin with sulfhydryl reagents prevented the dimerization; a cysteine/alanine exchange mutant also did not show dimer formation. This demonstrates, for the first time, that disulfide bridge formation of the domain is involved in the occludin dimerization. It is concluded that the redox-dependent dimerization of occludin may play a regulatory role in the tight junction assembly under physiological and pathological conditions.}, language = {en} } @article{SchulzErleGraefetal.2009, author = {Schulz, Irene and Erle, Alexander and Gr{\"a}f, Ralph and Krueger, Anne and Putzler, Sascha and Samereier, Matthias and Weidenthaler, Sebastian}, title = {Cell cycle-dependent localization of novel centrosomal and centromeric proteins in Dictyostelium}, issn = {0171-9335}, doi = {10.1016/S0171-9335(09)00023-5}, year = {2009}, language = {en} } @phdthesis{Kierszniowska2009, author = {Kierszniowska, Sylwia}, title = {Characterization of the composition of detergent resistant domanins under nutrient limitation and resupply}, address = {Potsdam}, pages = {101 S.}, year = {2009}, language = {en} } @article{ZhangHubalewskaIgnatova2009, author = {Zhang, Gong and Hubalewska, Magdalena and Ignatova, Zoya}, title = {Transient ribosomal attenuation coordinates protein synthesis and co-translational folding}, issn = {1545-9985}, doi = {10.1038/Nsmb.1554}, year = {2009}, abstract = {Clustered codons that pair to low-abundance tRNA isoacceptors can form slow-translating regions in the mRNA and cause transient ribosomal arrest. We report that folding efficiency of the Escherichia coli multidomain protein Sufl can be severely perturbed by alterations in ribosome-mediated translational attenuation. Such alterations were achieved by global acceleration of the translation rate with tRNA excess in vitro or by synonymous substitutions to codons with highly abundant tRNAs both in vitro and in vivo. Conversely, the global slow-down of the translation rate modulated by low temperature suppresses the deleterious effect of the altered translational attenuation pattern. We propose that local discontinuous translation temporally separates the translation of segments of the peptide chain and actively coordinates their co-translational folding.}, language = {en} } @article{WronskiApioPlathetal.2009, author = {Wronski, Torsten and Apio, Ann and Plath, Martin and Averbeck, Christiane}, title = {Do ecotypes of bushbuck differ in grouping patterns?}, issn = {0873-9749}, doi = {10.1007/s10211-009-0058-5}, year = {2009}, abstract = {Grouping patterns within the genus Tragelaphus suggest that species inhabiting open areas tend to live in larger groups, while species preferring dense habitats live solitarily or in small family groups. We asked if similar variation would be concealed in the within-species variation of bushbuck (Tragelaphus scriptus). Recent molecular phylogeographic analyses revealed several locally adapted forms of bushbuck in different ecoregions on the African continent. We compared group sizes of south-eastern bushbuck (Tragelaphus sylvaticus) among six different populations ("ecotypes"). To date, most data on the social organization of bushbuck have been collected from only one population in Queen Elizabeth National Park (QENP) in Uganda. This particular population, however, inhabits an unusual-comparatively open-habitat type, while bushbuck otherwise inhabit dense habitats, leaving doubt whether data collected in QENP are representative of the entire species. We, therefore, compared grouping patterns between ecotypes inhabiting rather open habitats (e.g., dianae and haywoodi) and ecotypes occupying rather dense habitats (e.g., massaicus and ornatus). In bachelor groups and in all-female (spinster) groups, single sightings were the most frequent "group type" in all populations examined. We detected no significant difference among ecotypes in relative frequencies of group size categories in the case of bachelor groups. Spinster group sizes were slightly (albeit significantly) smaller in QENP than in all other areas. Moreover, a comparison of two areas inside (low human pursuit) and outside Lake Mburo National Park (high hunting pressure) in Uganda revealed no significant difference in grouping patterns in response to human pursuit (as reported for impala [Aepyceros melampus] inhabiting the same area). Altogether, our results suggest that group sizes in bushbuck are not dependent on the habitat type they inhabit; neither does human nuisance have an impact on grouping patterns. Hence, an "almost solitary" lifestyle appears to be a characteristic of the entire taxon.}, language = {en} } @article{WronskiApioPlath2009, author = {Wronski, Torsten and Apio, Ann and Plath, Martin}, title = {Absence of a dominance hierarchy confirms territorial organization in male bushbuck (Tragelaphus scriptus Pallas, 1766)}, issn = {0141-6707}, doi = {10.1111/j.1365-2028.2007.00876.x}, year = {2009}, abstract = {It has been suggested that all species of spiral-horned antelopes (Tragelaphini) lack territoriality. Furthermore, some authors suggested that bushbuck (Tragelpahus scriptus) males form dominance hierarchies. In this study, we investigated the dominance relationships in two groups of free-ranging bushbuck males in Queen Elizabeth National Park, Uganda. Adult males dominated young-adult bachelors and subadult males, but no distinct dominance relationships were found among adult males. Landau's index of linearity revealed no linear dominance hierarchy in the study populations. Our results support the idea that adult males are territorial, and overt aggression is directed almost exclusively towards bachelors that challenge territory holders.}, language = {en} } @article{WonkeWallschlaeger2009, author = {Wonke, Gundula and Wallschl{\"a}ger, Hans-Dieter}, title = {Song dialects in the yellowhammer Emberiza citrinella : bioacoustic variation between and within dialects}, issn = {0021-8375}, doi = {10.1007/s10336-008-0326-6}, year = {2009}, abstract = {The yellowhammer Emberiza citrinella is a common European bird that sings in dialects that for decades have been distinguished by the existence of one single element (called a "specific''). In this study we looked into other possibilities for dialect discrimination, measuring 24 different variables. For the first time, multivariate statistics were used to discriminate dialect in yellowhammer song. Two similar dialects (XlB and XsB) that are not clearly defined in the literature were studied. Statistics incorporated (1) all variables, ( 2) no variables of "specific'' elements, and (3) no variables under the influence of these "specific'' variables. Multivariate statistics support dialect discrimination by ear and confirmed that only one element in yellowhammer song characterises dialect. In addition, we looked for local differences within two dialects and found that one local observation area showed a higher separation than the other sites (Meck1). However, as yet there is insufficient evidence for the existence of a new subdialect.}, language = {en} } @article{WiethausMuellerNeumannetal.2009, author = {Wiethaus, Jessica and Mueller, Alexandra and Neumann, Meina and Neumann, Sandra and Leimk{\"u}hler, Silke and Narberhaus, Franz and Masepohl, Bernd}, title = {Specific interactions between four Molybdenum-binding proteins contribute to Mo-dependent gene regulation in Rhodobacter capsulatus}, issn = {0021-9193}, doi = {10.1128/Jb.00526-09}, year = {2009}, abstract = {The phototrophic purple bacterium Rhodobacter capsulatus encodes two transcriptional regulators, MopA and MopB, with partially overlapping and specific functions in molybdate-dependent gene regulation. Both MopA and MopB consist of an N-terminal DNA-binding helix-turn-helix domain and a C-terminal molybdate-binding di-MOP domain. They formed homodimers as apo-proteins and in the molybdate-bound state as shown by yeast two-hybrid (Y2H) studies, glutaraldehyde cross-linking, gel filtration chromatography, and copurification experiments. Y2H studies suggested that both the DNA- binding and the molybdate-binding domains contribute to dimer formation. Analysis of molybdate binding to MopA and MopB revealed a binding stoichiometry of four molybdate oxyanions per homodimer. Specific interaction partners of MopA and MopB were the molybdate transporter ATPase ModC and the molbindin-like Mop protein, respectively. Like other molbindins, the R. capsulatus Mop protein formed hexamers, which were stabilized by binding of six molybdate oxyanions per hexamer. Heteromer formation of MopA and MopB was shown by Y2H studies and copurification experiments. Reporter gene activity of a strictly MopA-dependent mop-lacZ fusion in mutant strains defective for either mopA, mopB, or both suggested that MopB negatively modulates expression of the mop promoter. We propose that depletion of the active MopA homodimer pool by formation of MopA-MopB heteromers might represent a fine-tuning mechanism controlling mop gene expression.}, language = {en} } @article{WeisshuhnPrati2009, author = {Weißhuhn, Karoline and Prati, Daniel}, title = {Activated carbon may have undesired side effects for testing allelopathy in invasive plants}, issn = {1439-1791}, doi = {10.1016/j.baae.2008.10.009}, year = {2009}, abstract = {Activated carbon has become a widely used tool to investigate root-mediated allelopathy of plants, especially in plant invasion biology, because it adsorbs and thereby neutralizes root exudates. Allelopathy has been a controversially debated phenomenon for years, which revived in plant invasion biology as one possible reason for the success of invasive plants. Noxious plant exudates may harm other plants and provide an advantage to the allelopathic plant. However, root exudates are not always toxic, but may stimulate the microbial community and change nutrient availability in the rhizosphere. In a greenhouse experiment, we investigated the interacting effects of activated carbon, arbuscular mycorrhiza and plant competition between the invasive Senecio inaequidens and the native Artemisia vulgaris. Furthermore, we tested whether activated carbon showed any undesired effects by directly affecting mycorrhiza or soil chemistry. Contrary to the expectation, S. inaequidens was a weak competitor and we could not support the idea that allelopathy was involved in the competition. Activated carbon led to a considerable increase in the aboveground biomass production and reduced the infection with arbuscular mycorrhiza of both plant species. We expected that arbuscular mycorrhiza promotes plant growth by increasing nutrient availability, but we found the contrary when activated carbon was added. Chemical analyses of the substrate showed, that adding activated carbon resulted in a strong increase in plant available phosphate and in a decrease of the C-organic/N-total ration both of which suggest stimulated microbial activity. Thus, activated carbon not only reduced potential allelopathic effects, but substantially changed the chemistry of the substrate. These results show that activated carbon should be handled with great care in ecological experiments on allelopathy because of possible confounding effects on the soil community.}, language = {en} } @article{WegerichTuranoAllegrozzietal.2009, author = {Wegerich, Franziska and Turano, Paola and Allegrozzi, Marco and Moehwald, Helmuth and Lisdat, Fred}, title = {Cytochrome c mutants for superoxide biosensors}, issn = {0003-2700}, doi = {10.1021/Ac802571h}, year = {2009}, abstract = {The effect of introducing positive charges (lysines) in human cytochrome c (cyt c) on the redox properties and reaction rates of cyt c with superoxide radicals was studied. The mutated forms of this electron-transfer protein are used as sensorial recognition elements for the amperometric detection of the reactive oxygen radical. The proteins were prepared by site-directed mutagenesis focusing on amino acids near the heme edge. The 11 mutants of human cyt c expressed in the course of this research have been characterized by UV-vis spectroscopy, circular dichroism, and NMR spectroscopy to verify overall structure integrity as well as axial coordination of the heme iron. The mutants are investigated voltammetrically using promoter-modified gold electrodes with respect to redox activity and formal redox potential. The rate constants for the reaction with superoxide have been determined spectrophotometrically. Four mutants show a higher reaction rate with the radical as compared to the wild type. These mutants are used for the construction of superoxide sensors based on thiol-modified gold electrodes and covalently fixed proteins. We found that the E66K mutant-based electrode has a clearly higher sensitivity in comparison with the wild-type-based sensor while retaining the high selectivity and showing a good storage stability.}, language = {en} } @article{Warsinke2009, author = {Warsinke, Axel}, title = {Point-of-care testing of proteins}, issn = {1618-2642}, doi = {10.1007/s00216-008-2572-0}, year = {2009}, abstract = {Point-of-care testing (POCT) is a fast developing area in clinical diagnostics that is considered to be one of the main driving forces for the future in vitro diagnostic market. POCT means decentralized testing at the site of patient care. The most important POCT devices are handheld blood glucose sensors. In some of these sensors, after the application of less than 1 A mu l whole blood, the results are displayed in less than 10 s. For protein determination, the most commonly used devices are based on lateral flow technology. Although these devices are convenient to use, the results are often only qualitative or semiquantitative. The review will illuminate some of the current methods employed in POCT for proteins and will discuss the outlook for techniques (e.g., electrochemical immunosensors) that could have a great impact on future POCT of proteins.}, language = {en} } @article{WalterRueckertVossetal.2009, author = {Walter, Juliane K. and R{\"u}ckert, Christine and Voss, Martin and M{\"u}ller, Sebastian L. and Piontek, Joerg and Gast, Klaus and Blasig, Ingolf E.}, title = {The oligomerization of the coiled coil-domain of occluddin is redox sensitive}, issn = {0077-8923}, doi = {10.1111/j.1749-6632.2009.04058.x}, year = {2009}, abstract = {The transmembrane tight junction protein occludin is sensitive to oxidative stress. Occludin oligomerizes; however, its function in the tight junction is unknown. The cytosolic C-terminal tail contains a coiled coil-domain and forms dimers contributing to the oligomerization. The regulation of the oligomerization remains unclear. As the domain area contains sulfhydryl residues, we tested the hypothesis that the dimerization of the coiled coil-domain depends on these residues. We showed that the dimerization is modulated by the thiol concentration in the low-millimolar range, which is relevant both for physiological and pathophysiological conditions. Masking the sulfhydryl residues in the fragment by covalent binding of 4-vinyl pyridine prevented the dimerization but did not affect its helical structure and cylindric shape. The data demonstrate, for the first time, that disulfide bridge formation of murine cystein 408 is involved in the dimerization. This process is redox-sensitive but the secondary structure of the domain is not. It is concluded that the dimerization of occludin may play a regulatory role in the tight junction assembly under physiological and pathological conditions.}, language = {en} } @article{WalterCastroVossetal.2009, author = {Walter, Juliane K. and Castro, Victor Manuel and Voss, Martin and Gast, Klaus and Rueckert, Christine and Piontek, J{\"o}rg and Blasig, Ingolf E.}, title = {Redox-sensitivity of the dimerization of occludin}, issn = {1420-682X}, doi = {10.1007/s00018-009-0150-z}, year = {2009}, abstract = {Occludin is a self-associating transmembrane tight junction protein affected in oxidative stress. However, its function is unknown. The cytosolic C-terminal tail contains a coiled coil-domain forming dimers contributing to the self- association. Studying the hypothesis that the self-association is redox-sensitive, we found that the dimerization of the domain depended on the sulfhydryl concentration of the environment in low-millimolar range. Under physiological conditions, monomers and dimers were detected. Masking the sulfhydryl residues in the domain prevented the dimerization but affected neither its helical structure nor cylindric shape. Incubation of cell extracts containing full-length occludin with sulfhydryl reagents prevented the dimerization; a cysteine/alanine exchange mutant also did not show dimer formation. This demonstrates, for the first time, that disulfide bridge formation of the domain is involved in the occludin dimerization. It is concluded that the redox-dependent dimerization of occludin may play a regulatory role in the tight junction assembly under physiological and pathological conditions.}, language = {en} } @article{WackerWeithoff2009, author = {Wacker, Alexander and Weithoff, Guntram}, title = {Carbon assimilation mode in mixotrophs and the fatty acid composition of their rotifer consumers}, issn = {0046-5070}, doi = {10.1111/j.1365-2427.2009.02251.x}, year = {2009}, abstract = {P>1. We examined an important ecophysiological link between the mixotrophic flagellate Chlamydomonas acidophila and its consumers, the rotifers Elosa worallii, Cephalodella sp. and Brachionus sericus, by comparing their fatty acid profiles. 2. The mixotrophic flagellate was grown under either exclusively autotrophic conditions in the light, under exclusively heterotrophic conditions in the dark with an organic carbon source (glucose), or in the light plus the organic carbon sources (=mixotrophic). 3. Under heterotrophic growth conditions, C. acidophila strongly reduced its content of the n-3 polyunsaturated fatty acid (PUFA) alpha-linolenic acid (ALA, C18:3n-3) compared with auto- and mixotrophic growth conditions. Although PUFAs with more than 18 carbon atoms were not detected in C. acidophila, significant amounts of eicosatetraenoic (ETA, 20:4n-3) and eicosapentaenoic acid (EPA, 20:5n-3) were found in three rotifer consumers. 4. Species-specific differences in the fatty acid profiles with respect to ETA, EPA and the precursor ALA were found in the rotifers: Brachionus and Cephalodella fed on the heterotrophic diets synthesised less EPA. In Elosa, smaller amounts of ALA were detected but were converted efficiently to a constant content of EPA and to an exceptionally high content of ETA. 5. Since in nature the mode of carbon assimilation among mixotrophic organisms differs, and their fatty acid composition varies depending on their mode of carbon assimilation, the availability of ALA might be critical for their consumers. An insufficient dietary supply of this precursor for the synthesis of ETA and EPA can prevent consumers from regulating their content of ETA and EPA. Therefore, observed differences in values of the latter might underly species-specific differences in the competitive capability of consumers.}, language = {en} } @article{VossSchmidtWalzetal.2009, author = {Voss, Martin and Schmidt, Ruth and Walz, Bernd and Baumann, Otto}, title = {Stimulus-induced translocation of the protein kinase A catalytic subunit to the apical membrane in blowfly salivary glands}, issn = {0302-766X}, doi = {10.1007/s00441-008-0673-x}, year = {2009}, abstract = {Secretion in blowfly (Calliphora vicina) salivary glands is regulated by the neurohormone serotonin (5-HT), which activates the InsP(3)/Ca2+ pathway and the cAMP/protein kinase A (PKA) pathway in the secretory cells. The latter signaling cascade induces the activation of a vacuolar H+-ATPase on the apical membrane. Here, we have determined the distribution of PKA by using antibodies against the PKA regulatory subunit-II (PKA-RII) and the PKA catalytic subunit (PKA-C) of Drosophila. PKA is present in high concentrations within the secretory cells. PKA-RII and PKA-C co-distribute in non-stimulated glands, being enriched in the basal portion of the secretory cells. Exposure to 8-CPT-cAMP or 5-HT induces the translocation of PKA-C to the apical membrane, whereas the PKA-RII distribution remains unchanged. The recruitment of PKA-C to the apical membrane corroborates our hypothesis that vacuolar H+-ATPase, which is enriched in this membrane domain, is a target protein for PKA.}, language = {en} } @article{VogtWarnckeMicheeletal.2009, author = {Vogt, Birgit and Warncke, Marit and Micheel, Burkhard and Sheriff, Ahmed}, title = {Lentiviral gene transfer of CTLA4 generates B cells with reduced costimulatory properties : brief definite report}, issn = {0891-6934}, doi = {10.1080/08916930902832470}, year = {2009}, abstract = {Peripheral T-cell (TC) tolerance can be induced by tolerogenic antigen-presenting cell (APC). A prerequisite is the reduction or blockade of B7 of APC. Besides dendritic cell, B cells can be used as APC. Here, we show the generation B cells with reduced B7 expression by lentiviral transduction of endoplasmic reticulum (ER)-directed CTLA4. Vectors coding for the human CTL4-Ig were used for the human B-cell line Raji. Transduction efficiency was over 90\% (MOI = 3). For the murine B-cell line A20 and for primary mouse B cells, murine CTLA4 was used. We show that B cells with reduced B7 expression reduce the antigen (Ag) specific TC proliferation in vitro. B cells expressing an ER-directed CTLA4 may reduce Ag-specific immune responses.}, language = {en} } @article{TreydteGrantJeltsch2009, author = {Treydte, Anna C. and Grant, Rina C. C. and Jeltsch, Florian}, title = {Tree size and herbivory determine below-canopy grass quality and species composition in savannahs}, issn = {0960-3115}, doi = {10.1007/s10531-009-9694-3}, year = {2009}, abstract = {Large single-standing trees are rapidly declining in savannahs, ecosystems supporting a high diversity of large herbivorous mammals. Savannah trees are important as they support both a unique flora and fauna. The herbaceous layer in particular responds to the structural and functional properties of a tree. As shrubland expands stem thickening occurs and large trees are replaced by smaller trees. Here we examine whether small trees are as effective in providing advantages for grasses growing beneath their crowns as large trees are. The role of herbivory in this positive tree- grass interaction is also investigated. We assessed soil and grass nutrient content, structural properties, and herbaceous species composition beneath trees of three size classes and under two grazing regimes in a South African savannah. We found that grass leaf content (N and P) beneath the crowns of particularly large (ca. 3.5 m) and very large trees (ca. 9 m) was as much as 40\% greater than the same grass species not growing under a tree canopy, whereas nutrient contents of grasses did not differ beneath small trees (< 2.3 m). Moderate herbivory enhanced these effects slightly. Grass species composition differed beneath and beyond the tree canopy but not between tree size classes. As large trees significantly improve the grass nutrient quality for grazers in contrast to smaller trees, the decline of the former should be halted. The presence of trees further increases grass species diversity and patchiness by favouring shade- tolerant species. Both grazing wildlife and livestock will benefit from the presence of large trees because of their structural and functional importance for savannahs.}, language = {en} } @article{TravisMustinBentonetal.2009, author = {Travis, Justin M. J. and Mustin, Karen and Benton, Tim G. and Dytham, Calvin}, title = {Accelerating invasion rates result from the evolution of density-dependent dispersal}, issn = {0022-5193}, doi = {10.1016/j.jtbi.2009.03.008}, year = {2009}, abstract = {Evolutionary processes play an important role in shaping the dynamics of range expansions, and selection on dispersal propensity has been demonstrated to accelerate rates of advance. Previous theory has considered only the evolution of unconditional dispersal rates, but dispersal is often more complex. For example, many species emigrate in response to crowding. Here, we use an individual-based model to investigate the evolution of density dependent dispersal into empty habitat, such as during an invasion. The landscape is represented as a lattice and dispersal between Populations follows a stepping-stone pattern. Individuals carry three 'genes' that determine their dispersal strategy when experiencing different population densities. For a stationary range we obtain results consistent with previous theoretical studies: few individuals emigrate from patches that are below equilibrium density. However, during the range expansion of a previously stationary population, we observe evolution towards dispersal strategies where considerable emigration occurs well below equilibrium density. This is true even for moderate costs to dispersal, and always results in accelerating rates of range expansion. Importantly, the evolution we observe at an expanding front depends upon fitness integrated over several generations and cannot be predicted by a consideration of lifetime reproductive success alone. We argue that a better understanding of the role of density dependent dispersal, and its evolution, in driving population dynamics is required especially within the context of range expansions.}, language = {en} } @article{TittelWiehleWannickeetal.2009, author = {Tittel, Joerg and Wiehle, Ines and Wannicke, Nicola and Kampe, Heike and Poerschmann, Juergen and Meier, Jutta and Kamjunke, Norbert}, title = {Utilisation of terrestrial carbon by osmotrophic algae}, issn = {1015-1621}, doi = {10.1007/s00027-008-8121-2}, year = {2009}, abstract = {Terrestrial-derived dissolved organic carbon (DOC) contributes significantly to the energetic basis of many aquatic food webs. Although heterotrophic bacteria are generally considered to be the sole consumers of DOC, algae and cyanobacteria of various taxonomic groups are also capable of exploiting this resource. We tested the hypothesis that algae can utilise DOC in the presence of bacteria if organic resources are supplied in intervals by photolysis of recalcitrant DOC. In short-term uptake experiments, we changed irradiation in the range of minutes. As model substrates, polymers of radiolabelled coumaric acid (PCA) were used, which during photolysis are known to release aromatic compounds comparable to terrestrial-derived and refractory DOC. Three cultured freshwater algae readily assimilated PCA photoproducts equivalent to a biomass-specific uptake of 5-60\% of the bacterial competitors present. Algal substrate acquisition did not depend on whether PCA was photolysed continuously or in intervals. However, the data show that photoproducts of terrestrial DOC can be a significant resource for osmotrophic algae. In long-term growth experiments, interval light was applied one hour per day. We allowed cultured Chlamydomonas to compete for ambient DOC of low concentration. We found higher abundances of Chlamydomonas when cultures were irradiated intermittently rather than continuously. These data suggest that photolysis of DOC supports algal heterotrophy, and potentially facilitates growth, when light fluctuations are large, as during the diurnal light cycle. We concluded that osmotrophic algae can efficiently convert terrestrial carbon into the biomass of larger organisms of aquatic food webs.}, language = {en} } @article{TimmermannPlath2009, author = {Timmermann, Mirna and Plath, Martin}, title = {Phototactic response and light sensitivity in an epigean and a hypogean population of a barb (Garra barreimiae, Cyprinidae)}, issn = {1386-2588}, doi = {10.1007/s10452-008-9173-z}, year = {2009}, abstract = {We investigated the response of two populations of the barb Garra barreimiae to different light intensities (0.5-2000 lx) from a light source. Adults of both the surface (epigean) and cave (hypogean) G. barreimiae populations show photophobic behavior. A photophobic response in the cave form was seen only at higher light intensities because the cavefish are eyeless and rely on extra-retinal light receptors to detect light. In contrast, juveniles (surface and cave) showed photophilic behavior, and their preference for the photic zone of the test tank decreased with increasing age. We discuss the potential role played by photophobic behavior for the colonization of caves by previously surface- dwelling fishes.}, language = {en} } @article{SulpicePylIshiharaetal.2009, author = {Sulpice, Ronan and Pyl, Eva-Theresa and Ishihara, Hirofumi and Trenkamp, Sandra and Steinfath, Matthias and Witucka-Wall, Hanna and Gibon, Yves and Usadel, Bj{\"o}rn and Poree, Fabien and Piques, Maria Conceicao and von Korff, Maria and Steinhauser, Marie Caroline and Keurentjes, Joost J. B. and Guenther, Manuela and Hoehne, Melanie and Selbig, Joachim and Fernie, Alisdair R. and Altmann, Thomas and Stitt, Mark}, title = {Starch as a major integrator in the regulation of plant growth}, issn = {0027-8424}, doi = {10.1073/pnas.0903478106}, year = {2009}, abstract = {Rising demand for food and bioenergy makes it imperative to breed for increased crop yield. Vegetative plant growth could be driven by resource acquisition or developmental programs. Metabolite profiling in 94 Arabidopsis accessions revealed that biomass correlates negatively with many metabolites, especially starch. Starch accumulates in the light and is degraded at night to provide a sustained supply of carbon for growth. Multivariate analysis revealed that starch is an integrator of the overall metabolic response. We hypothesized that this reflects variation in a regulatory network that balances growth with the carbon supply. Transcript profiling in 21 accessions revealed coordinated changes of transcripts of more than 70 carbon-regulated genes and identified 2 genes (myo-inositol-1- phosphate synthase, a Kelch-domain protein) whose transcripts correlate with biomass. The impact of allelic variation at these 2 loci was shown by association mapping, identifying them as candidate lead genes with the potential to increase biomass production.}, language = {en} } @article{StuckasStoofQuesadaetal.2009, author = {Stuckas, Heiko and Stoof, Kathleen and Quesada, Humberto and Tiedemann, Ralph}, title = {Evolutionary implications of discordant clines across the Baltic Mytilus hybrid zone (Mytilus edulis and Mytilus trossulus)}, issn = {0018-067X}, doi = {10.1038/Hdy.2009.37}, year = {2009}, abstract = {It is well established that reproductive isolation often arises from genome incompatibilities and that genes encoding reproductive traits are less prone to introgression. Hybrid zones of Mytilus trossulus and Mytilus edulis provide an intriguing model to assess reproductive isolation. Although gene flow is restricted in North America, introgression is pervasive in the Baltic. This study aimed at analyzing the shape of multilocus clines across the Baltic contact zone between M. edulis and M. trossulus to infer mechanisms of restriction to gene flow. We use maximum likelihood methods to construct the best fitting individual clines for five markers located on biparentally inherited autosomes and paternally and maternally inherited mitochondrial DNA (mtDNA). Strong cline shape differences among markers suggest that reproductive isolation arising from genome-wide incompatibilities is weak, and that these discrepancies possibly result from genetic drift, hybrid zone movement or marker-specific selection. However, the finding of a common cline center for M7 lysin (involved in fertilization) and paternally transmitted mtDNA (causing nuclear-mitochondrial incompatibilities in hybrids) suggest that these loci may play a role in incomplete reproductive isolation.}, language = {en} } @article{StuckasMesserschmidtPutzleretal.2009, author = {Stuckas, Heiko and Messerschmidt, Katrin and Putzler, Sascha and Baumann, Otto and Schenk, J{\"o}rg A. and Tiedemann, Ralph and Micheel, Burkhard}, title = {Detection and characterization of gamete-specific molecules in Mytilus edulis using selective antibody production}, issn = {1040-452X}, doi = {10.1002/Mrd.20916}, year = {2009}, abstract = {The mussel Mytilus edulis can be used as model to study the molecular basis of reproductive isolation because this species maintains its species integrity, despite of hybridizing in zones of contact with the closely related species M. trossulus or M. galloprovincialis. This study uses selective antibody production by means of hybridoma technology to identify molecules which are involved in sperm function of M. edulis. Fragmented sperm were injected into mice and 25 hybridoma cell clones were established to obtain monoclonal antibodies (mAb). Five clones were identified producing mAb targeting molecules putatively involved in sperm function based on enzyme immunoassays, dot and Western blotting as well as immunostaining of tissue sections. Specific localization of these mAb targets on sperm and partly also in somatic tissue suggests that all five antibodies bind to different molecules. The targets of the mAb obtained from clone G26-AG8 were identified using mass spectrometry (nano-LC-ESI-MS/MS) as M6 and M7 lysin. These acrosomal proteins have egg vitelline lyses function and are highly similar (76\%) which explains the cross reactivity of mAb G26- AG8. Furthermore, M7 lysin was recently shown to be under strong positive selection suggesting a role in interspecific reproductive isolation. This study shows that M6 and M7 lysin are not only found in the sperm acrosome but also in male somatic tissue of the mantle and the posterior adductor muscle, while being completely absent in females. The monoclonal antibody G26-AG8 described here will allow elucidating M7/M6 lysin function in somatic and gonad tissue of adult and developing animals.}, language = {en} } @article{SteinRissmannHempeletal.2009, author = {Stein, Claudia and Rißmann, Cornelia and Hempel, Stefan and Renker, Carsten and Buscot, Francois and Prati, Daniel and Auge, Harald}, title = {Interactive effects of mycorrhizae and a root hemiparasite on plant community productivity and diversity}, issn = {0029-8549}, doi = {10.1007/s00442-008-1192-x}, year = {2009}, abstract = {Plant communities can be affected both by arbuscular mycorrhizal fungi (AMF) and hemiparasitic plants. However, little is known about the interactive effects of these two biotic factors on the productivity and diversity of plant communities. To address this question, we set up a greenhouse study in which different AMF inocula and a hemiparasitic plant (Rhinanthus minor) were added to experimental grassland communities in a fully factorial design. In addition, single plants of each species in the grassland community were grown with the same treatments to distinguish direct AMF effects from indirect effects via plant competition. We found that AMF changed plant community structure by influencing the plant species differently. At the community level, AMF decreased the productivity by 15-24\%, depending on the particular AMF treatment, mainly because two dominant species, Holcus lanatus and Plantago lanceolata, showed a negative mycorrhizal dependency. Concomitantly, plant diversity increased due to AMF inoculation and was highest in the treatment with a combination of two commercial AM strains. AMF had a positive effect on growth of the hemiparasite, and thereby induced a negative impact of the hemiparasite on host plant biomass which was not found in non-inoculated communities. However, the hemiparasite did not increase plant diversity. Our results highlight the importance of interactions with soil microbes for plant community structure and that these indirect effects can vary among AMF treatments. We conclude that mutualistic interactions with AMF, but not antagonistic interactions with a root hemiparasite, promote plant diversity in this grassland community.}, language = {en} } @article{SpricigoDronovLisdatetal.2009, author = {Spricigo, Roberto and Dronov, Roman and Lisdat, Fred and Leimk{\"u}hler, Silke and Scheller, Frieder W. and Wollenberger, Ursula}, title = {Electrocatalytic sulfite biosensor with human sulfite oxidase co-immobilized with cytochrome c in a polyelectrolyte-containing multilayer}, issn = {1618-2642}, doi = {10.1007/s00216-008-2432-y}, year = {2009}, abstract = {An efficient electrocatalytic biosensor for sulfite detection was developed by co-immobilizing sulfite oxidase and cytochrome c with polyaniline sulfonic acid in a layer-by-layer assembly. QCM, UV-Vis spectroscopy and cyclic voltammetry revealed increasing loading of electrochemically active protein with the formation of multilayers. The sensor operates reagentless at low working potential. A catalytic oxidation current was detected in the presence of sulfite at the modified gold electrode, polarized at +0.1 V ( vs. Ag/AgCl 1 M KCl). The stability of the biosensor performance was characterized and optimized. A 17-bilayer electrode has a linear range between 1 and 60 mu M sulfite with a sensitivity of 2.19 mA M-1 sulfite and a response time of 2 min. The electrode retained a stable response for 3 days with a serial reproducibility of 3.8\% and lost 20\% of sensitivity after 5 days of operation. It is possible to store the sensor in a dry state for more than 2 months. The multilayer electrode was used for determination of sulfite in unspiked and spiked samples of red and white wine. The recovery and the specificity of the signals were evaluated for each sample.}, language = {en} } @article{Spijkerman2009, author = {Spijkerman, Elly}, title = {Physiological characteristics of co-limiting conditions for P and C in Chlamydomonas}, issn = {0031-8884}, doi = {10.2216/0031-8884-48.sp4.1}, year = {2009}, language = {en} } @article{SperfeldWacker2009, author = {Sperfeld, Erik and Wacker, Alexander}, title = {Effects of temperature and dietary sterol availability on growth and cholesterol allocation of the aquatic keystone species Daphnia}, issn = {0022-0949}, doi = {10.1242/Jeb.031401}, year = {2009}, abstract = {Enhanced water temperatures promote the occurrence of cyanobacterial blooms, which may be detrimental to aquatic herbivores. Especially, the often-dominant crustaceans could be negatively affected because cyanobacteria are deficient in phytosterols, which are required by the crustaceans to form the membrane component cholesterol, which in turn plays a role in thermal adaptation. Here, we determined the influence of temperature on growth, reproduction and the allocation of dietary sterol into somatic tissues and eggs of the keystone species Daphnia magna raised along a dietary cholesterol gradient. Mass-specific growth rates of D. magna increased with the increasing availability of dietary cholesterol up to an incipient limiting level, which increased with increasing temperature. This indicates a higher demand for cholesterol for growth at higher temperatures and may explain the consistently smaller clutch sizes of reproducing females at the highest temperature. The cholesterol content of the individuals increased with increasing dietary cholesterol; this increase was enhanced at higher temperatures, indicating a higher demand for cholesterol for tissues and probably specifically for membranes. Surprisingly, the daphnids showed different allocation strategies with regard to temperature and dietary sterol availability. The cholesterol content of eggs was enhanced at higher temperature, which suggested that females allocate more cholesterol to their offspring, presumably to ensure sufficient egg development. When dietary cholesterol was limiting, however, females did not allocate more cholesterol to their eggs. Our data suggest that during cyanobacterial blooms, a potential dietary sterol limitation of Daphnia can be intensified at higher water temperatures, which can occur with global warming.}, language = {en} } @article{SongBergstrasserRafatetal.2009, author = {Song, Hui and Bergstrasser, Claudia and Rafat, Neysan and Hoeger, Simone and Schmidt, Marc and Endres, N. and Goebeler, Matthias and Hillebrands, Jan-Luuk and Brigelius-Floh{\´e}, Regina and Banning, Antje and Beck, Grietje and Loesel, Ralf and Yard, Benito A.}, title = {The carbon monoxide releasing molecule (CORM-3) inhibits expression of vascular cell adhesion molecule-1 and E- selectin independently of haem oxygenase-1 expression}, issn = {0007-1188}, doi = {10.1111/j.1476-5381.2009.00215.x}, year = {2009}, abstract = {Background and purpose: Although carbon monoxide (CO) can modulate inflammatory processes, the influence of CO on adhesion molecules is less clear. This might be due to the limited amount of CO generated by haem degradation. We therefore tested the ability of a CO releasing molecule (CORM-3), used in supra-physiological concentrations, to modulate the expression of vascular cell adhesion molecule (VCAM)-1 and E-selectin on endothelial cells and the mechanism(s) involved. Experimental approach: Human umbilical vein endothelial cells (HUVECs) were stimulated with tumour necrosis factor (TNF)-alpha in the presence or absence of CORM-3. The influence of CORM-3 on VCAM-1 and E- selectin expression and the nuclear factor (NF)-kappa B pathway was assessed by flow cytometry, Western blotting and electrophoretic mobility shift assay. Key results: CORM-3 inhibited the expression of VCAM-1 and E-selectin on TNF-alpha- stimulated HUVEC. VCAM-1 expression was also inhibited when CORM-3 was added 24 h after TNF-alpha stimulation or when TNF-alpha was removed. This was paralleled by deactivation of NF-kappa B and a reduction in VCAM-1 mRNA. Although TNF- alpha removal was more effective in this regard, VCAM-1 protein was down-regulated more rapidly when CORM-3 was added. CORM-3 induced haem oxygenase-1 (HO-1) in a dose- and time-dependent manner, mediated by the transcription factor, Nrf2. CORM-3 was still able to down-regulate VCAM-1 expression in HUVEC transfected with siRNA for HO-1 or Nrf2. Conclusions and implications: Down-regulation of VCAM and E-selectin expression induced by CORM-3 was independent of HO-1 up- regulation and was predominantly due to inhibition of sustained NF-kappa B activation.}, language = {en} } @article{SharmaStuckasBhaskaretal.2009, author = {Sharma, Reeta and Stuckas, Heiko and Bhaskar, Ranjana and Rajput, Sandeep and Khan, Imran and Goyal, Surendra Prakash and Tiedemann, Ralph}, title = {mtDNA indicates profound population structure in Indian tiger (Panthera tigris tigris)}, issn = {1566-0621}, doi = {10.1007/s10592-008-9568-3}, year = {2009}, abstract = {We analyzed mtDNA polymorphisms (parts of control region, ND5, ND2, Cytb, 12S, together 902 bp) in 59 scat and 18 tissue samples from 13 Indian populations of the critically endangered Indian tiger (Panthera tigris tigris), along with zoo animals as reference. Northern tiger populations exhibit two unique haplotypes suggesting genetic isolation. Western populations from Sariska (extinct in 2004) and Ranthambore are genetically similar, such that Ranthambore could serve as a source for reintroduction in Sariska. Zoo populations maintain mitochondrial lineages that are rare or absent in the wild.}, language = {en} } @article{SchulzErleGraefetal.2009, author = {Schulz, Irene and Erle, Alexander and Gr{\"a}f, Ralph and Krueger, Anne and Lohmeier, Heiner and Putzler, Sascha and Samereier, Matthias and Weidenthaler, Sebastian}, title = {Identification and cell cycle-dependent localization of nine novel, genuine centrosomal components in Dictyostelium discoideum}, issn = {0886-1544}, doi = {10.1002/Cm.20384}, year = {2009}, abstract = {The centrosome is the main microtubule-organizing center and constitutes the largest protein complex in a eukaryotic cell. The Dictyostelium centrosome is an established model for acentriolar centrosomes and it consists of a layered core structure Surrounded by a so-called corona, which harbors microtubule nucleation complexes. We have identified 34 new centrosomal candidate proteins through mass spectrometrical analysis of the proteome of isolated Dictyostelium centrosomes. Here we present a characterization of 12 centrosomal candidate proteins all featuring coiled coil regions and low expression levels, which are the most common attributes of centrosomal proteins. We used GFP fusion proteins to localize the candidate proteins in whole cells and on microtubule-free, isolated centrosomes. Thus we were able to identify nine new genuine centrosomal proteins including a putative orthologue of Cep192, an interaction partner of polo-like kinase 4 in human centriole biogenesis. In this respect, centrosomal localization of the only polo-like kinase in Dictyostelium, Pik, is also shown in this work. Using confocal deconvolution microscopy, four components, CP39, CP55, CP75, and CP91 could be clearly assigned to the so far almost uncharacterized centrosomal core structure, while CP148 and Cep192 localized to a zone between that of corona marker and core proteins. Finally, CP103 and CP248 were constituents of the corona. In contrast, NE81 was localized at the nuclear envelope and three others, an orthologue of the spindle checkpoint component Mad1, the novel Cenp68, and the centrosomal CP248 were observed at the centromeres, which are clustered and linked to the centrosome throughout the entire cell cycle. Cell Motil. Cytoskeleton 66: 915-928, 2009.}, language = {en} } @article{SchulzBaumannSamereieretal.2009, author = {Schulz, Irene and Baumann, Otto and Samereier, Matthias and Zoglmeier, Christine and Gr{\"a}f, Ralph}, title = {Dictyostelium Sun1 is a dynamic membrane protein of both nuclear membranes and required for centrosomal association with clustered centromeres}, issn = {0171-9335}, doi = {10.1016/j.ejcb.2009.06.003}, year = {2009}, abstract = {Centrosomal attachment to nuclei is crucial for proper mitosis and nuclear positioning in various organisms, and generally involves Sun-family proteins located at the inner nuclear envelope. There is still no common scheme for the outer nuclear membrane proteins interacting with Sun I in centrosome/nucleus attachment. Here we propose a model in which Sun1 mediates a physical link between centrosomes and clustered centromeres through both nuclear membranes in Dictyostelium. For the first time we provide a detailed microscopic analysis of the centrosomal and nuclear envelope localization of endogenous Dictyostelium Sun1 during interphase and mitosis. By immunogold electron microscopy we show that Sun1 is a resident of both nuclear membranes. Disruption of Sun1 function by overexpression of full-length GFP-Sun1 or a GFP-Sun-domain deletion construct revealed not only the established function in centrosome/nucleus attachment and maintenance of ploidy, but also a requirement of Sun1 for the association of the centromere cluster with the centrosome. Live-cell imaging visualized the occurrence of mitotic defects, and demonstrated the requirement of microtubules for dynamic distance changes between centrosomes and nuclei. FRAP analysis revealed at least two populations of Sun1, with an immobile fraction associated with the centrosome, and a mobile fraction in the nuclear envelope.}, language = {en} } @article{SchroederBleidornHartmannetal.2009, author = {Schr{\"o}der, Christiane and Bleidorn, Christoph and Hartmann, Stefanie and Tiedemann, Ralph}, title = {Occurrence of Can-SINEs and intron sequence evolution supports robust phylogeny of pinniped carnivores and their terrestrial relatives}, issn = {0378-1119}, doi = {10.1016/j.gene.2009.06.012}, year = {2009}, abstract = {Investigating the dog genome we found 178965 introns with a moderate length of 200-1000 bp. A screening of these sequences against 23 different repeat libraries to find insertions of short interspersed elements (SINEs) detected 45276 SINEs. Virtually all of these SINEs (98\%) belong to the tRNA-derived Can-SINE family. Can-SINEs arose about 55 million years ago before Carnivora split into two basal groups, the Caniformia (doglike carnivores) and the Feliformia (cat-like carnivores). Genome comparisons of dog and cat recovered 506 putatively informative SINE loci for caniformian phylogeny. In this study we show how to use such genome information of model organisms to research the phylogeny of related non-model species of interest. Investigating a dataset including representatives of all major caniformian lineages, we analysed 24 randomly chosen loci for 22 taxa. All loci were amplifiable and revealed 17 parsimony- informative SINE insertions. The screening for informative SINE insertions yields a large amount of sequence information, in particular of introns, which contain reliable phylogenetic information as well. A phylogenetic analysis of intron- and SINE sequence data provided a statistically robust phylogeny which is congruent with the absence/presence pattern of our SINE markers. This phylogeny strongly supports a sistergroup relationship of Musteloidea and Pinnipedia. Within Pinnipedia, we see strong support from bootstrapping and the presence of a SINE insertion for a sistergroup relationship of the walrus with the Otariidae.}, language = {en} } @article{Scheller2009, author = {Scheller, Frieder W.}, title = {Tribute to Guenter Gauglitz (Editorial)}, issn = {1618-2642}, doi = {10.1007/s00216-008-2548-0}, year = {2009}, language = {en} } @article{SalaBozanoKetmaierMariani2009, author = {Sala-Bozano, Maria and Ketmaier, Valerio and Mariani, Stefano}, title = {Contrasting signals from multiple markers illuminate population connectivity in a marine fish}, issn = {0962-1083}, doi = {10.1111/j.1365-294X.2009.04404.x}, year = {2009}, abstract = {Recent advances in molecular biology and bioinformatics have helped to unveil striking and previously unrecognized patterns of geographic genetic structure in marine populations. Largely driven by the pressing needs of fisheries management and conservation, studies on marine fish populations have played a pivotal role in testing the efficiency of a range of approaches to explore connectivity and dispersal at sea. Here, we employed nuclear and mitochondrial DNA markers and parasitic infestations to examine the nature and patterns of population structure in a warm-temperate coastal marine teleost across major putative biogeographic barriers in the Mediterranean Sea and Eastern Atlantic Ocean. We detected deep genetic divergence between mitochondrial lineages, likely caused by dramatic climatic and geological transformations before and during the Pleistocene. Such long-diverged lineages later came into secondary contact and can now be found in sympatry. More importantly, microsatellite data revealed that these lineages, after millions of years of independent evolution, now interbreed extensively. By combining genetic and parasite data, we were able to identify at least five independent demographic units. While the different genetic and parasite-based methods produce notably contrasting signals and may complicate the reconstruction of connectivity dynamics, we show that by tailoring the correct interpretation to each of the descriptors used, it is possible to achieve a deeper understanding of the micro-evolutionary process and, consequently, resolve population structure.}, language = {en} } @article{RieschToblerPlathetal.2009, author = {Riesch, R{\"u}diger and Tobler, Michael and Plath, Martin and Schlupp, Ingo}, title = {Offspring number in a livebearing fish (Poecilia mexicana, Poeciliidae) : reduced fecundity and reduced plasticity in a population of cave mollies}, issn = {0378-1909}, doi = {10.1007/s10641-008-9392-0}, year = {2009}, abstract = {Life history traits within species often vary among different habitats. We measured female fecundity in mollies (Poecilia mexicana) from a H2S-rich cave and from a neighbouring surface habitat, as well as in laboratory-reared individuals of both populations raised in either light or continuous darkness. Compared to conspecifics from surface habitats, cave-dwelling P. mexicana had reduced fecundity (adjusted for size) in the field. In the laboratory, the fecundity of surface mollies was higher in light than in darkness, whereas fecundity in the cave mollies was almost unaffected by the ambient light conditions. Our results suggest a heritable component to the reduction in fecundity in female cave mollies. Moreover, the reduced plasticity in fecundity of cave mollies in response to light conditions might be an example of genetic assimilation or channelling of a life history trait in a population invading a new environment.}, language = {en} } @article{RieschDuweHerrmannetal.2009, author = {Riesch, R{\"u}diger and Duwe, Virginia and Herrmann, Nina and Padur, Lisa and Ramm, Annemarie and Scharnweber, Inga Kristin and Schulte, Matthias and Schulz-Mirbach, Tanja and Ziege, Madlen and Plath, Martin}, title = {Variation along the shy-bold continuum in extremophile fishes (Poecilia mexicana, Poecilia sulphuraria)}, issn = {0340-5443}, doi = {10.1007/s00265-009-0780-z}, year = {2009}, abstract = {One potential trade-off that bold individuals face is between increased predation risks and gains in resources. Individuals experiencing high predation and hungry individuals (or individuals with low body condition) are predicted to show increased boldness. We examined one behavioral trait previously reported to be associated with boldness (the time individual fish needed to emerge from shelter) in various populations of mollies (Poecilia spp.). Our study system included several southern Mexican surface streams with high piscine predation and high food availability, sulfidic surface streams with high avian predation, in which the inhabiting fish show reduced body condition, and a sulfidic cave, where predation and body condition are low. Our comparison revealed very short times to emerge from the start box in populations from non-sulfidic streams. In sulfidic habitats (whether surface or cave), it took individual Poecilia mexicana considerably longer to emerge from the start box, and the same difference was also found in an independent comparison between P. mexicana and the closely related, highly sulfide-adapted Poecilia sulphuraria. Fish reared under common garden conditions (in the absence of predators and hydrogen sulfide) showed intermediate boldness scores to the extremes observed in the field. Our data thus indicate that (a) boldness is shaped by environmental conditions/ experiential effects, but is not heritable, (b) predation affects boldness in the predicted direction, but (c) low body condition leads to reduced boldness. Extremophile Poecilia spp. spend most of their time surfacing to survive under sulfidic and hypoxic conditions, which exposes them to increased levels of predations, but the fish forage on the bottom. Hence, in this system, increased boldness does not increase foraging success. We argue that energy limitation favors reducing energetically costly behaviors, and exploring novel environments may be just one of them.}, language = {en} } @article{ReissHoelzelBier2009, author = {Reiss, Edda and Hoelzel, Ralph and Bier, Frank Fabian}, title = {Synthesis and stretching of rolling circle amplification products in a flow-through system}, issn = {1613-6810}, doi = {10.1002/smll.200900319}, year = {2009}, abstract = {Enzymatic isothermal rolling circle amplification (RCA) produces long concatemeric single-stranded DNA (ssDNA) molecules if a small circular ssDNA molecule is applied as the template. A method is presented here in which the RCA reaction is carried out in a flow-through system, starting from isolated surface-tethered DNA primers. This approach combines gentle fluidic handling of the single-stranded RCA products, such as staining or stretching via a receding meniscus, with the option of simultaneous (fluorescence) microscopic observation. It is shown that the stretched and surface-attached RCA products are accessible for hybridization of complementary oligonucleotides, which demonstrates their addressability by complementary base pairing. The long RCA products should be well suited to bridge the gap between biomolecular nanoscale building-blocks and structures at the micro- and macroscale, especially at the single- molecule level presented here.}, language = {en} } @article{ReichBeckerSeckleretal.2009, author = {Reich, Lothar and Becker, Marion and Seckler, Robert and Weikl, Thomas R.}, title = {In vivo folding efficiencies for mutants of the P22 tailspike beta-helix protein correlate with predicted stability changes}, issn = {0301-4622}, doi = {10.1016/j.bpc.2009.01.015}, year = {2009}, abstract = {Parallel A-helices are among the simplest repetitive structural elements in proteins. The folding behavior of A- helix proteins has been studied intensively, also to gain insight on the formation of amyloid fibrils, which share the parallel beta-helix as a central structural motif. An important system for investigating beta-helix folding is the tailspike protein from the Salmonella bacteriophage P22. The central domain of this protein is a right-handed parallel beta-helix with 13 windings. Extensive mutational analyses of the P22 tailspike protein have revealed two main phenotypes: temperature-sensitive-folding (tsf) mutations that reduce the folding efficiency at elevated temperatures, and global suppressor (su) mutations that increase the tailspike folding efficiency. A central question is whether these phenotypes can be understood from changes in the protein stability induced by the mutations. Experimental determination of the protein stability is complicated by the nearly irreversible trimerization of the folded tailspike protein. Here, we present calculations of stability changes with the program FoldX, focusing on a recently published extensive data set of 145 singe-residue alanine mutants. We find that the calculated stability changes are correlated with the experimentally measured in vivo folding efficiencies. In addition, we determine the free-energy landscape of the P22 tailspike protein in a nucleation-propagation model to explore the folding mechanism of this protein, and obtain a processive folding route on which the protein nucleates in the N-terminal region of the helix.}, language = {en} } @article{RathoreGargGarg2009, author = {Rathore, R. S. and Garg, Neha and Garg, Sarika}, title = {Starch phosphorylase : role in starch metabolism and biotechnological applications}, issn = {0738-8551}, doi = {10.1080/07388550902926063}, year = {2009}, abstract = {The alpha-glucan phosphorylases of the glycosyltransferase family are important enzymes of carbohydrate metabolism in prokaryotes and eukaryotes. The plant a-glucan phosphorylase, commonly called starch phosphorylase (EC 2.4.1.1), is largely known for the phosphorolytic degradation of starch. Starch phosphorylase catalyzes the reversible transfer of glucosyl units from glucose-1-phosphate to the nonreducing end of alpha-1,4-D-glucan chains with the release of phosphate. Two distinct forms of starch phosphorylase, plastidic phosphorylase and cytosolic phosphorylase, have been consistently observed in higher plants. Starch phosphorylase is industrially useful and a preferred enzyme among all glucan phosphorylases for phosphorolytic reactions for the production of glucose-1-phosphate and for the development of engineered varieties of glucans and starch. Despite several investigations, the precise functional mechanisms of its characteristic multiple forms and the structural details are still eluding us. Recent discoveries have shed some light on their physiological substrates, precise biological functions, and regulatory aspects. in this review, we have highlighted important developments in understanding the role of starch phosphorylases and their emerging applications in industry.}, language = {en} } @article{RaabovaMuenzbergovaFischer2009, author = {Raabov{\´a}, Jana and Muenzbergov{\´a}, Zuzana and Fischer, Markus}, title = {Consequences of near and far between-population crosses for offspring fitness in a rare herb}, issn = {1435-8603}, doi = {10.1111/j.1438-8677.2008.00186.x}, year = {2009}, abstract = {Crosses between plants from different populations may result in heterosis or outbreeding depression. However, despite its importance for conservation, little is known about the spatial scale over which these effects may arise. To investigate the consequences of between-population crosses at two distinct spatial scales, we conducted reciprocal crosses between four populations from two regions in the rare perennial herb Aster amellus. We assessed seed set and offspring fitness in a common garden experiment. Overall, between-population crosses within regions (10 km) resulted in 8\% lower seed set than within-population crosses, while between-region crosses (70 km) resulted in 17\% higher seed set than within-population crosses. Moreover, offspring from between-population crosses produced 18\% more flower heads than offspring from within-population crosses. We conclude that hybridisation between A. amellus plants from different populations did not lead to immediate outbreeding depression and, thus, could represent a valid conservation option to increase genetic diversity. Moreover, our results suggest that the distance between populations affects the outputs of between-population crosses and therefore needs to be taken into account when promoting gene flow between populations.}, language = {en} } @article{PlathKromuszczynskiTiedemann2009, author = {Plath, Martin and Kromuszczynski, Katja and Tiedemann, Ralph}, title = {Audience effect alters male but not female mating preferences}, issn = {0340-5443}, doi = {10.1007/s00265-008-0672-7}, year = {2009}, abstract = {Males often face strong mating competition by neighboring males in their social environment. A recent study by Plath et al. (Anim Behav 75:21-29, 2008a) has demonstrated that the visual presence of a male competitor (i.e., an audience male) affects the expression of male mating preferences in a poeciliid fish (Poecilia mexicana) with a weaker expression of mating preferences when an audience male observed the focal male. This may be a tactic to reduce sperm competition, since surrounding males likely share intrinsic preferences for female traits or copy mate choice decisions. Here, we examined the hypothesis that a same-sex audience would affect female mate preferences less than male mating preferences. Our hypothesis was based on the assumptions that (1) competition for mates in a fashion that would be comparable in strength to sperm competition or overt male-male aggression is absent among Poecilia females, and (2) P. mexicana females typically form female-biased shoals, such that almost any female mate choice in nature occurs in front of a female audience. Poecilia females (P. mexicana, surface and cave form, and the closely related gynogenetic Poecilia formosa) were given a choice between a large and a small male, and the tests were repeated while a conspecific, a heterospecific, or no audience female (control) was presented. Females spent more time in the neutral zone and, thus, less time near the males during the second part of a trial when an audience was presented, but-consistent with predictions-females showed only slightly weaker expression of mate preferences during the second part of the tests. This decline was not specific to the treatment involving an audience and was significantly weaker than the effect seen in the male sex.}, language = {en} } @article{Plath2009, author = {Plath, Martin}, title = {A test for conspecific cueing in two sympatric species of pupfish (Cyprinodon beltrani, C. simus)}, issn = {0378-1909}, doi = {10.1007/s10641-009-9455-x}, year = {2009}, abstract = {In many fishes, individuals prefer to associate with phenotypically similar or conspecific individuals (conspecific cueing). Such phenotypic segregation can be an important evolutionary driver, for example, in intralacustric sympatric speciation processes. I examined conspecific cueing in two species of sympatric pupfish from Laguna Chichancanab in southern Mexico: the little shoaling and highly territorial Cyprinodon beltrani and the highly shoaling but non-territorial C. simus. Females were tested for shoal species preferences in two testing scenarios: (1) a sequential choice test where shoals of four conspecific or four heterospecific (Cyprinodon sp. or Poecilia reticulata) females were presented in succession, and (2) a simultaneous choice test where female shoals of both Cyprindon species were presented concurrently. Overall, higher shoaling in C. simus was corroborated in this study. In the sequential test, no effect of the type of stimulus shoal (con- or heterospecific) on shoaling behavior was detected. In the simultaneous tests, C. beltrani, but not C. simus females showed a preference for the conspecific shoal. It seems possible that C. simus females did not evolve species recognition mechanisms because no other Cyprinodon species in the Laguna Chichancanab shows equally high shoaling, which automatically leads to the formation of single-species (i.e., C. simus-) shoals. C. simus males do not establish long-term territories, but rather spawn within shoals, whereas C. beltrani females approach males in their breeding territories to spawn. I discuss that this behavioral difference still provides a powerful reproductive isolation mechanism even in the absence of conspecific cueing in C. simus.}, language = {en} } @article{PinkernelleAbrahamSeideletal.2009, author = {Pinkernelle, Josephine and Abraham, Andreas and Seidel, Katja and Braun, Katharina}, title = {Paternal deprivation induces dendritic and synaptic changes and hemispheric asymmetry of pyramidal neurons in the somatosensory cortex}, issn = {1932-8451}, doi = {10.1002/Dneu.20726}, year = {2009}, abstract = {Similar to maternal care, paternal care is a source of neonatal sensory stimulation, which in primates and rodents has been shown to be essential for developing structure and function of sensory cortices. The aim of our study in the biparental rodent Octodon degus was to assess the impact of paternal deprivation on dendritic and synaptic development in the somatosensory cortex. We (i) quantified the amount of paternal care in relation to total parental investment and (ii) compared dendritic and synaptic development of pyramidal neurons in the somatosensory cortex of animals raised by a single mother or by both parents. On the behavioral level we show that paternal care comprises 37\% of total parent-offspring interactions, and that the somatosensory stimulation provided by the fathers primarily consists of huddling, licking/grooming, and playing. On the morphological level we found that, compared with offspring raised by both parents (mother and father), the father-deprived animals displayed significantly reduced spine numbers on the basal dendrites of pyramidal neurons. Furthermore, paternal deprivation induces hemispheric asymmetry of the dendritic morphology of somatosensory pyramidal neurons. Father-deprived animals show shorter and less complex basal dendrites in the left somatosensory cortex compared with the right hemisphere. These findings indicate that paternal deprivation results in delayed or retarded dendritic and synaptic development of somatosensory circuits.}, language = {en} } @article{PadurWedekindOeztuerketal.2009, author = {Padur, Lisa and Wedekind, Juliane and {\"O}zt{\"u}rk, {\"O}znur and Streit, Bruno and Tiedemann, Ralph and Plath, Martin}, title = {Do audience effects lead to relaxed male sexual harassment?}, issn = {0005-7959}, doi = {10.1163/000579509x12483520922124}, year = {2009}, abstract = {Several recent studies reported on so-called audience effects in male Atlantic mollies (Poecilia mexicana), in which the visual presence of a potential rival affects male sexual activity. We asked whether and how audience effects interact with male sexual harassment. Poecilia mexicana almost constantly attempt to mate, while females are mostly non- responsive to male approaches. Females flee from this sexual harassment and, thus, are more vigilant in the presence of males, so females may have hampered feeding opportunities. Do audience effects lead to altered male sexual harassment? Focal females were given an opportunity to feed in the presence of a male or a female partner and the difference in feeding times was interpreted as an effect caused by male harassment. Tests were conducted without an audience (1), or an audience male was visually presented either directly inside the test tank (2), or further away (in an adjoining compartment (3)). We found that levels of pre-mating behaviour did not vary significantly among treatments, but males exhibited more copulation attempts (thrusting) in treatment (3), suggesting that males respond to increased risk of sperm competition with higher sperm expenditure. Females fed less (and started feeding later) when a harassing partner male was around, and this effect was not dependent on the audience treatment, but, overall, females spent more time feeding (and started feeding earlier) when an audience was presented. Hence, feeding time reductions appear to be independent of audience effects, but perceived 'safety in numbers' may lead to increased foraging in larger groups.}, language = {en} } @article{NikoloskiMaySelbig2009, author = {Nikoloski, Zoran and May, Patrick and Selbig, Joachim}, title = {A new network model explains the evolution of plant-specific metabolic networks}, issn = {1095-6433}, doi = {10.1016/j.cbpa.2009.04.567}, year = {2009}, language = {en} } @article{NeumannMittelstaedtSeduketal.2009, author = {Neumann, Meina and Mittelstaedt, Gerd and Seduk, Farida and Iobbi-Nivol, Chantal and Leimk{\"u}hler, Silke}, title = {MocA is a specific cytidylyltransferase involved in molybdopterin cytosine dinucleotide biosynthesis in Escherichia coli}, issn = {0021-9258}, doi = {10.1074/jbc.M109.008565}, year = {2009}, abstract = {We have purified and characterized a specific CTP: molybdopterin cytidylyltransferase for the biosynthesis of the molybdopterin (MPT) cytosine dinucleotide (MCD) cofactor in Escherichia coli. The protein, named MocA, shows 22\% amino acid sequence identity to E. coli MobA, the specific GTP: molybdopterin guanylyltransferase for molybdopterin guanine dinucleotide biosynthesis. MocA is essential for the activity of the MCD-containing enzymes aldehyde oxidoreductase Yag-TSR and the xanthine dehydrogenases XdhABC and XdhD. Using a fully defined in vitro assay, we showed that MocA, Mo-MPT, CTP, and MgCl2 are required and sufficient for MCD biosynthesis in vitro. The activity of MocA is specific for CTP; other nucleotides such as ATP and GTP were not utilized. In the defined in vitro system a turnover number of 0.37 +/- 0.01 min(-1) was obtained. A1:1 binding ratio of MocA to Mo-MPT and CTP was determined to monomeric MocA with dissociation constants of 0.23 +/- 0.02 mu M for CTP and 1.17 +/- 0.18 mu M for Mo-MPT. We showed that MocA was also able to convert MPT to MCD in the absence of molybdate, however, with only one catalytic turnover. The addition of molybdate after one turnover gave rise to a higher MCD production, revealing that MCD remains bound to MocA in the absence of molybdate. This work presents the first characterization of a specific enzyme involved in MCD biosynthesis in bacteria.}, language = {en} } @article{NeumannMittelstaedtIobbiNivoletal.2009, author = {Neumann, Meina and Mittelstaedt, Gerd and Iobbi-Nivol, Chantal and Saggu, Miguel and Lendzian, Friedhelm and Hildebrandt, Peter and Leimk{\"u}hler, Silke}, title = {A periplasmic aldehyde oxidoreductase represents the first molybdopterin cytosine dinucleotide cofactor containing molybdo-flavoenzyme from Escherichia coli}, issn = {1742-464X}, doi = {10.1111/j.1742-4658.2009.07000.x}, year = {2009}, abstract = {Three DNA regions carrying genes encoding putative homologs of xanthine dehydrogenases were identified in Escherichia coli, named xdhABC, xdhD, and yagTSRQ. Here, we describe the purification and characterization of gene products of the yagTSRQ operon, a molybdenum-containing iron-sulfur flavoprotein from E. coli, which is located in the periplasm. The 135 kDa enzyme comprised a noncovalent (alpha beta gamma) heterotrimer with a large (78.1 kDa) molybdenum cofactor (Moco)-containing YagR subunit, a medium (33.9 kDa) FAD-containing YagS subunit, and a small (21.0 kDa) 2 x [2Fe2S]-containing YagT subunit. YagQ is not a subunit of the mature enzyme, and the protein is expected to be involved in Moco modification and insertion into YagTSR. Analysis of the form of Moco present in YagTSR revealed the presence of the molybdopterin cytosine dinucleotide cofactor. Two different [2Fe2S] clusters, typical for this class of enzyme, were identified by EPR. YagTSR represents the first example of a molybdopterin cytosine dinucleotide-containing protein in E. coli. Kinetic characterization of the enzyme revealed that YagTSR converts a broad spectrum of aldehydes, with a preference for aromatic aldehydes. Ferredoxin instead of NAD(+) or molecular oxygen was used as terminal electron acceptor. Complete growth inhibition of E. coli cells devoid of genes from the yagTSRQ operon was observed by the addition of cinnamaldehyde to a low-pH medium. This finding shows that YagTSR might have a role in the detoxification of aromatic aldehydes for E. coli under certain growth conditions.}, language = {en} } @article{NasoDreyerPedemonteetal.2009, author = {Naso, Alessia and Dreyer, Ingo and Pedemonte, Laura and Testa, Ilaria and Gomez-Porras, Judith Lucia and Usai, Cesare and M{\"u}ller-R{\"o}ber, Bernd and Diaspro, Alberto and Gambale, Franco and Picco, Cristiana}, title = {The role of the C-terminus for functional heteromerization of the plant channel KDC1}, issn = {0006-3495}, doi = {10.1016/j.bpj.2009.02.055}, year = {2009}, abstract = {Voltage-gated potassium channels are formed by the assembly of four identical (homotetramer) or different (heterotetramer) subunits. Tetramerization of plant potassium channels involves the C-terminus of the protein. We investigated the role of the C-terminus of KDC1, a Shaker-like inward-rectifying K+ channel that does not form functional homomeric channels, but participates in the formation of heteromeric complexes with other potassium alpha- subunits when expressed in Xenopus oocytes. The interaction of KDC1 with KAT1 was investigated using the yeast two- hybrid system, fluorescence and electrophysiological studies. We found that the KDC1-EGFP fusion protein is not targeted to the plasma membrane of Xenopus oocytes unless it is coexpressed with KAT1. Deletion mutants revealed that the KDC1 C- terminus is involved in heteromerization. Two domains of the C-terminus, the region downstream the putative cyclic nucleotide binding domain and the distal part of the C-terminus called K-HA domain, contributed to a different extent to channel assembly. Whereas the first interacting region of the C-terminus was necessary for channel heteromerization, the removal of the distal KHA domain decreased but did not abolish the formation of heteromeric complexes. Similar results were obtained when coexpressing KDC1 with the KAT1-homolog KDC2 from carrots, thus indicating the physiological significance of the KAT1/KDC1 characterization. Electrophysiological experiments showed furthermore that the heteromerization capacity of KDC1 was negatively influenced by the presence of the enhanced green fluorescence protein fusion.}, language = {en} } @article{MustinBentonDythametal.2009, author = {Mustin, Karen and Benton, Tim G. and Dytham, Calvin and Travis, Justin M. J.}, title = {The dynamics of climate-induced range shifting : perspectives from simulation modelling}, issn = {0030-1299}, doi = {10.1111/j.1600-0706.2008.17025.x}, year = {2009}, abstract = {Predicted future climate change will alter species' distributions as they attempt to track the most suitable 'climate window'. Climate envelope models indicate the direction of likely range changes but do not incorporate population dynamics, therefore observed responses may differ greatly from these projections. We use simulation modelling to explore the consequences of a period of environmental change for a species structured across an environmental gradient. Results indicate that a species' range may lag behind its climate envelope and demonstrate that the rate of movement of a range can accelerate during a period of climate change. We conclude that the inclusion of both population dynamics and spatial environmental variability is vital to develop models that can both predict, and be used to manage, the impact of changing climate on species' biogeography.}, language = {en} } @article{MuellerRoeberArvidsson2009, author = {M{\"u}ller-R{\"o}ber, Bernd and Arvidsson, Samuel Janne}, title = {Fertility control : the role of magnesium transporters in pollen development}, issn = {1001-0602}, doi = {10.1038/Cr.2009.82}, year = {2009}, language = {en} } @article{MartinCreuzburgSperfeldWacker2009, author = {Martin-Creuzburg, Dominik and Sperfeld, Erik and Wacker, Alexander}, title = {Colimitation of a freshwater herbivore by sterols and polyunsaturated fatty acids}, issn = {0962-8452}, doi = {10.1098/rspb.2008.1540}, year = {2009}, abstract = {Empirical data providing evidence for a colimitation of an herbivore by two or more essential nutrients are scarce, particularly in regard to biochemical resources. Here, a graphical model is presented, which describes the growth of an herbivore in a system with two potentially limiting resources. To verify this model, life-history experiments were conducted with the herbivore Daphnia magna feeding on the picocyanobacterium Synechococcus elongatus, which was supplemented with increasing amounts of cholesterol either in the presence or the absence of saturating amounts of eicosapentaenoic acid (EPA). For comparison, D. magna was raised on diets containing different proportions of S. elongatus and the cholesterol- and EPA-rich eukaryotic alga Nannochloropsis limnetica. Somatic and population growth of D. magna on a sterol- and EPA-deficient diet was initially constrained by the absence of sterols. With increased sterol availability, a colimitation by EPA became apparent and when the sterol requirements were met, the growth- limiting factor was shifted from a limitation by sterols to a limitation by EPA. These data imply that herbivores are frequently limited by two or more essential nutrients simultaneously. Hence, the concept of colimitation has to be incorporated into models assessing nutrient-limited growth kinetics of herbivores to accurately predict demographic changes and population dynamics.}, language = {en} } @article{ManaCapelliGraefLarochelle2009, author = {Mana-Capelli, Sebastian and Gr{\"a}f, Ralph and Larochelle, Denis A.}, title = {Dictyostelium discoideum CenB is a bona fide centrin essential for nuclear architecture and centrosome stability}, issn = {1535-9778}, doi = {10.1128/Ec.00025-09}, year = {2009}, abstract = {Centrins are a family of proteins within the calcium-binding EF-hand superfamily. In addition to their archetypical role at the microtubule organizing center (MTOC), centrins have acquired multiple functionalities throughout the course of evolution. For example, centrins have been linked to different nuclear activities, including mRNA export and DNA repair. Dictyostelium discoideum centrin B is a divergent member of the centrin family. At the amino acid level, DdCenB shows 51\% identity with its closest relative and only paralog, DdCenA. Phylogenetic analysis revealed that DdCenB and DdCenA form a well-supported monophyletic and divergent group within the centrin family of proteins. Interestingly, fluorescently tagged versions of DdCenB were not found at the centrosome (in whole cells or in isolated centrosomes). Instead, DdCenB localized to the nuclei of interphase cells. This localization disappeared as the cells entered mitosis, although Dictyostelium cells undergo a closed mitosis in which the nuclear envelope (NE) does not break down. DdCenB knockout cells exhibited aberrant nuclear architecture, characterized by enlarged and deformed nuclei and loss of proper centrosome-nucleus anchoring (observed as NE protrusions). At the centrosome, loss of DdCenB resulted in defects in the organization and morphology of the MTOC and supernumerary centrosomes and centrosome-related bodies. The multiple defects that the loss of DdCenB generated at the centrosome can be explained by its atypical division cycle, transitioning into the NE as it divides at mitosis. On the basis of these findings, we propose that DdCenB is required at interphase to maintain proper nuclear architecture, and before delocalizing from the nucleus, DdCenB is part of the centrosome duplication machinery.}, language = {en} } @article{LoewWollenbergerSchelleretal.2009, author = {Loew, Noya and Wollenberger, Ursula and Scheller, Frieder W. and Katterle, Martin}, title = {Direct electrochemistry and spectroelectrochemistry of osmium substituted horseradish peroxidase}, issn = {1567-5394}, doi = {10.1016/j.bioelechem.2009.03.015}, year = {2009}, abstract = {In this contribution the substitution of the central protoporphyrin IX iron complex of horseradish peroxidase by the respective osmium porphyrin complex is described. The direct electrochemical reduction of the Os containing horseradish peroxidase (OsHRP) was achieved at ITO and modified glassy carbon electrodes and in combination with spectroscopy revealed the three redox couples (OsHRP)-H-III/(OsHRP)-H-IV, (OsHRP)-H-IV/(OsHRP)-H-V and (OsHRP)-H-V/ (OsHRP)-H-VI. The midpoint potentials differ dependent on the electrode material used with E-1/2 (Os-III/IV) of -0.4 V (ITO) and -0.25 V (GC), E-1/2 (Os-IV/V) of -0.16 V (ITO) and +0.10 V (GC), and E-1/2 (Os-V/VI)of +018 V (ITO), respectively Moreover, with immobilised OsHRP the direct electrocatalytic reduction of hydrogen peroxide and tert-butyl hydroperoxide was observed. In comparison to electrodes modified with native HRP the sensitivity of the OsHRP-electrode for tert-butyl hydroperoxide is higher.}, language = {en} } @article{LisdatDronovMoehwaldetal.2009, author = {Lisdat, Fred and Dronov, Roman and M{\"o}hwald, Helmuth and Scheller, Frieder W. and Kurth, Dirk G.}, title = {Self-assembly of electro-active protein architectures on electrodes for the construction of biomimetic signal chains}, issn = {1359-7345}, doi = {10.1039/B813559b}, year = {2009}, abstract = {The layer-by-layer adsorption technique based on the consecutive deposition of oppositely charged species is for the preparation of protein multilayers with fully electro-active protein molecules. The methodology was established with cytochrome c and the polyelectrolyte sulfonated polyaniline (PASA). The technique is also useful for the construction of bi-protein architectures confining protein-protein communication to an electrode. Following natural examples of protein complexes with defined signal transfer, cytochrome c was arranged with enzymes such as xanthine oxidase, bilirubin oxidase, laccase, and sulfite oxidase in self-assembled multilayer architectures. Thus, biomimetic signal chains from the enzyme substrate via the enzyme and cytochrome c towards the electrode can be established. Communication between proteins immobilised in multiple layers on the electrode can be achieved by in situ generation of small shuttle molecules or more advantageously by direct interprotein electron transfer. This allows the construction of new sensing electrodes, the properties of which can be tuned by the number of deposited protein layers. The mechanism of electron transfer within such protein assemblies on gold electrodes will be discussed.}, language = {en} } @article{LinleyBoeseSimmonsetal.2009, author = {Linley, John E. and Boese, Stefan H. and Simmons, Nicholas L. and Gray, Michael A.}, title = {A voltage-dependent Ca2+ influx pathway regulates the Ca2+-dependent Cl- conductance of renal IMCD-3 cells}, issn = {0022-2631}, doi = {10.1007/s00232-009-9186-0}, year = {2009}, abstract = {We have previously shown that the membrane conductance of mIMCD-3 cells at a holding potential of 0 mV is dominated by a Ca2+-dependent Cl- current (I-CLCA). Here we report that I-CLCA activity is also voltage dependent and that this dependence on voltage is linked to the opening of a novel Al3+-sensitive, voltage-dependent, Ca2+ influx pathway. Using whole-cell patch-clamp recordings at a physiological holding potential (-60 mV), I-CLCA was found to be inactive and resting currents were predominantly K+ selective. However, membrane depolarization to 0 mV resulted in a slow, sigmoidal, activation of I-CLCA (T (0.5) similar to 500 s), while repolarization in turn resulted in a monoexponential decay in I-CLCA (T (0.5) similar to 100 s). The activation of I-CLCA by depolarization was reduced by lowering extracellular Ca2+ and completely inhibited by buffering cytosolic Ca2+ with EGTA, suggesting a role for Ca2+ influx in the activation of I-CLCA. However, raising bulk cytosolic Ca2+ at -60 mV did not produce sustained I-CLCA activity. Therefore I-CLCA is dependent on both an increase in intracellular Ca2+ and depolarization to be active. We further show that membrane depolarization is coupled to opening of a Ca2+ influx pathway that displays equal permeability to Ca2+ and Ba2+ ions and that is blocked by extracellular Al3+ and La3+. Furthermore, Al3+ completely and reversibly inhibited depolarization-induced activation of I-CLCA, thereby directly linking Ca2+ influx to activation of I-CLCA. We speculate that during sustained membrane depolarization, calcium influx activates I-CLCA which functions to modulate NaCl transport across the apical membrane of IMCD cells.}, language = {en} } @article{LiFranciscoZhouetal.2009, author = {Li, Jing and Francisco, Perigio and Zhou, Wenxu and Edner, Christoph and Steup, Martin and Ritte, Gerhard and Bond, Charles S. and Smith, Steven M.}, title = {Catalytically-inactive beta-amylase BAM4 required for starch breakdown in Arabidopsis leaves is a starch- binding-protein}, issn = {0003-9861}, doi = {10.1016/j.abb.2009.07.024}, year = {2009}, abstract = {Of the four chloroplast beta-amylase (BAM) proteins identified in Arabidopsis, BAM3 and BAM4 were previously shown to play the major roles in leaf starch breakdown, although BAM4 apparently lacks key active site residues and beta- amylase activity. Here we tested multiple BAM4 proteins with different N-terminal sequences with a range of glucan substrates and assay methods, but detected no alpha-1,4-glucan hydrolase activity. BAM4 did not affect BAM1, BAM2 or BAM3 activity even when added in 10-fold excess, nor the BAM3-catalysed release of maltose from isolated starch granules in the presence of glucan water dikinase. However, BAM4 binds to amylopectin and to amylose-Sepharose whereas BAM2 has very low beta-amylase activity and poor glucan binding. The low activity of BAM2 may be explained by poor glucan binding but absence of BAM4 activity is not. These results suggest that BAM4 facilitates starch breakdown by a mechanism involving direct interaction with starch or other alpha-1,4-glucan.}, language = {en} } @article{LandauLoksteinSchelleretal.2009, author = {Landau, Alejandra Mabel and Lokstein, Heiko and Scheller, Henrik Vibe and Lainez, Veronica and Maldonado, Sara and Prina, Alberto Ra{\´u}l}, title = {A cytoplasmically inherited barley mutant is defective in photosystem I assembly due to a temperature-sensitive defect in ycf3 splicing}, issn = {0032-0889}, doi = {10.1104/pp.109.147843}, year = {2009}, abstract = {A cytoplasmically inherited chlorophyll-deficient mutant of barley (Hordeum vulgare) termed cytoplasmic line 3 (CL3), displaying a viridis (homogeneously light-green colored) phenotype, has been previously shown to be affected by elevated temperatures. In this article, biochemical, biophysical, and molecular approaches were used to study the CL3 mutant under different temperature and light conditions. The results lead to the conclusion that an impaired assembly of photosystem I (PSI) under higher temperatures and certain light conditions is the primary cause of the CL3 phenotype. Compromised splicing of ycf3 transcripts, particularly at elevated temperature, resulting from a mutation in a noncoding region (intron 1) in the mutant ycf3 gene results in a defective synthesis of Ycf3, which is a chaperone involved in PSI assembly. The defective PSI assembly causes severe photoinhibition and degradation of PSII.}, language = {en} } @article{KoettingSanteliaEdneretal.2009, author = {Koetting, Oliver and Santelia, Diana and Edner, Christoph and Eicke, Simona and Marthaler, Tina and Gentry, Matthew S. and Comparot-Moss, Sylviane and Chen, Jychian and Smith, Alison M. and Steup, Martin and Ritte, Gerhard and Zeeman, Samuel C.}, title = {STARCH-EXCESS4 is a laforin-like phosphoglucan phosphatase required for starch degradation in Arabidopsis thaliana}, issn = {1040-4651}, doi = {10.1105/tpc.108.064360}, year = {2009}, abstract = {Starch is the major storage carbohydrate in plants. It is comprised of glucans that form semicrystalline granules. Glucan phosphorylation is a prerequisite for normal starch breakdown, but phosphoglucan metabolism is not understood. A putative protein phosphatase encoded at the Starch Excess 4 (SEX4) locus of Arabidopsis thaliana was recently shown to be required for normal starch breakdown. Here, we show that SEX4 is a phosphoglucan phosphatase in vivo and define its role within the starch degradation pathway. SEX4 dephosphorylates both the starch granule surface and soluble phosphoglucans in vitro, and sex4 null mutants accumulate phosphorylated intermediates of starch breakdown. These compounds are linear alpha-1,4-glucans esterified with one or two phosphate groups. They are released from starch granules by the glucan hydrolases alpha-amylase and isoamylase. In vitro experiments show that the rate of starch granule degradation is increased upon simultaneous phosphorylation and dephosphorylation of starch. We propose that glucan phosphorylating enzymes and phosphoglucan phosphatases work in synergy with glucan hydrolases to mediate efficient starch catabolism.}, language = {en} } @article{KetmaierFinamoreLargiaderetal.2009, author = {Ketmaier, Valerio and Finamore, Francesco and Largiader, Carlo Rodolfo and Milone, Marco and Bianco, Pier Giorgio}, title = {Phylogeography of bleaks Alburnus spp. (Cyprinidae) in Italy, based on cytochrome b data}, issn = {0022-1112}, doi = {10.1111/j.1095-8649.2009.02357.x}, year = {2009}, abstract = {Sequence variation of a fragment of the mitochondrial DNA encoding for the cytochrome b gene was used to reconstruct the phylogeography of the two species of bleaks occurring in Italy: the alborella Alburnus arborella in northern Italy and the vulturino Alburnus albidus in southern Italy. The study includes four populations of the alborella and 14 populations of the vulturino. A total of 57 haplotypes were identified; these could not be sorted into two reciprocally monophyletic clusters. Multiple phylogenetic methods and nested clade phylogeographical analysis consistently retrieved three well-supported clades, two of which contained both Northern and Southern Italian haplotypes. A third clade is limited to southern Italy. This clade is tentatively assigned to the vulturino. The placement in the same clade of northern and southern Italian haplotypes is explained in light of the introductions of fishes operated from northern to central and southern Italy. The origin of the vulturino dates back to the last two million years. This divergence time estimate identifies the Pleistocene confluences between adjacent river basins along the Adriatic slope of the Italian peninsula and their subsequent isolation as the cause that triggered the diversification of the genus in the area. The existence of a clade endemic to southern Italy supports the recognition of the area as a new peri-Mediterranean ichthyogeographic district, the borders of which correspond to the northern and southern edges of the vulturino range.}, language = {en} } @article{KamjunkeVogtWoelfl2009, author = {Kamjunke, Norbert and Vogt, Bernhard and Woelfl, Stefan}, title = {Trophic interactions of the pelagic ciliate Stentor spp. in North Patagonian lakes}, issn = {0075-9511}, doi = {10.1016/j.limno.2008.08.001}, year = {2009}, abstract = {The zooplankton of oligotrophic lakes in North Patagonia is often dominated by mixotrophic ciliates, particularly Stentor amethystinus and Stentor araucanus. Therefore, we tested whether Stentor spp. (i) is an important food for juvenile endemic (Cheirodon australe, Galaxias maculatus, Odontesthes mauleanum, Percichthys trucha) and introduced (Oncorhynchus mykiss) fish species, and (ii) represents a remarkable grazer of bacteria. Ingestion rates of fish estimated by disappearance of Stentor in feeding experiments ranged between 8 (G. maculatus) and 53 (C australe) ciliates per fish and day, and assimilation rates measured by using radioactively labelled Stentor ranged between 3 (P. trucha) and 52 (C australe) ciliates per fish and day. However, although we detected the consumption of Stentor by fish, the daily consumption amounted to at most 0.2\% of the fish biomass which can not cover the energy requirement of the fish. Furthermore, the daily consumption was equivalent to a maximum of 1.6\% of the Stentor standing stock so that fish predation does not seem to be an important mortality factor for the ciliates. The clearance rate of Stentor sp. on natural bacteria was on average 3.8 mu l cil(-1) h(-1). The daily ingestion (mean 3.9 ngC cil(-1) d(-1)) was about 3.5\% of the individual biomass of Stentor sp. Therefore, bacteria ingestion might explain a ciliate growth rate of appr. 1\% d(-1), which was about 17\% of the photosynthesis of endosymbiotic algae. The maximum density of Stentor sp. in the take could ingest about 1 mu g C L-1 d(-1) bacteria which is only 3\% of average bacterial production. Thus, grazing by Stentor sp. does not seem to be a main loss factor for the bacteria.}, language = {en} } @article{KamjunkeStraileGaedke2009, author = {Kamjunke, Norbert and Straile, Dietmar and Gaedke, Ursula}, title = {Response of heterotrophic bacteria, autotrophic picoplankton and heterotrophic nanoflagellates to re- oligotrophication}, issn = {0142-7873}, doi = {10.1093/plankt/fbp037}, year = {2009}, abstract = {We investigated the response of the microbial components of the pelagic food web to re-oligotrophication of large, deep Lake Constance where total phosphorus concentrations during mixing decreased from a maximum of 2.81 mu mol L- 1 in 1979 via 1.87 mu mol L-1 in 1987 to 0.26 mu mol L-1 in 2007. Measurements of heterotrophic bacteria, autotrophic picoplankton (APP) and heterotrophic nanoflagellates (HNF) in 2006 and 2007 were compared to values from 1987 to 1997. We hypothesized that the biomass and seasonal variability of all groups will decrease under more oligotrophic conditions due to reduced resource availability, particularly for APP and HNF but less for the competitively stronger bacteria. Average bacterial biomass between spring and autumn was unrelated to phosphorus, whereas the ratio of bacterial biomass to chlorophyll a concentration increased with decreasing trophy due to declining chlorophyll concentrations. In contrast, a unimodal relationship was found between APP and phosphorus with low biomass at low and high phosphorus concentrations and maximum biomass in between. Average HNF biomass decreased strongly by a factor of 10-30 with decreasing trophy, and chlorophyll-specific HNF biomass was unimodally related to phosphorus. The relative seasonal biomass variability did not change for any group during re-oligotrophication. To conclude, HNF responded much more strongly and bacteria less so than chlorophyll concentrations to oligotrophication, whereas APP exhibited a more complex pattern.}, language = {en} } @article{HuggenbergerVaterDeisz2009, author = {Huggenberger, Stefan and Vater, Marianne and Deisz, Rudolf A.}, title = {Interlaminar differences of intrinsic properties of pyramidal neurons in the auditory cortex of mice}, issn = {1047-3211}, doi = {10.1093/cercor/bhn143}, year = {2009}, abstract = {Cortical information processing depends crucially upon intrinsic neuronal properties modulating a given synaptic input, in addition to integration of excitatory and inhibitory inputs. These intrinsic mechanisms are poorly understood in sensory cortex areas. We therefore investigated neuronal properties in slices of the auditory cortex (AC) of normal hearing mice using whole-cell patch-clamp recordings of pyramidal neurons in layers II/III, IV, V, and VI in the current- and voltage clamp mode. A total of 234 pyramidal neurons were included in the analysis revealing distinct laminar differences. Regular spiking (RS) neurons in layer II/III have significantly lower resting membrane potential, higher threshold for action potential generation, and larger K-ir and I-h amplitudes compared with layer V and VI RS neurons. These currents could improve temporal resolution in the upper layers of the AC. Additionally, the presence of a T-type Ca2+ current could be an important factor of RS neurons in these upper layers to amplify temporally closely correlated inputs. Compared with upper layers, lower layers (V and VI) exhibit a higher relative abundance of intrinsic bursting neurons. These neurons may provide layer-specific transfer functions for interlaminar, intercortical, and corticofugal information processing.}, language = {en} } @article{HejaziFettkeParisetal.2009, author = {Hejazi, Mahdi and Fettke, J{\"o}rg and Paris, Oskar and Steup, Martin}, title = {The two plastidial starch-related dikinases sequentially phosphorylate glucosyl residues at the surface of both the a- and b-type allomorphs of crystallized maltodextrins but the mode of action differs}, issn = {0032-0889}, doi = {10.1104/pp.109.138750}, year = {2009}, abstract = {In this study, two crystallized maltodextrins were generated that consist of the same oligoglucan pattern but differ strikingly in the physical order of double helices. As revealed by x-ray diffraction, they represent the highly ordered A- and B-type allomorphs. Both crystallized maltodextrins were similar in size distribution and birefringence. They were used as model substrates to study the consecutive action of the two starch-related dikinases, the glucan, water dikinase and the phosphoglucan, water dikinase. The glucan, water dikinase and the phosphoglucan, water dikinase selectively esterify glucosyl residues in the C6 and C3 positions, respectively. Recombinant glucan, water dikinase phosphorylated both allomorphs with similar rates and caused complete glucan solubilization. Soluble neutral maltodextrins inhibited the glucan, water dikinase-mediated phosphorylation of crystalline particles. Recombinant phosphoglucan, water dikinase phosphorylated both the A- and B-type allomorphs only following a prephosphorylation by the glucan, water dikinase, and the activity increased with the extent of prephosphorylation. The action of the phosphoglucan, water dikinase on the prephosphorylated A- and B-type allomorphs differed. When acting on the B-type allomorph, by far more phosphoglucans were solubilized as compared with the A type. However, with both allomorphs, the phosphoglucan, water dikinase formed significant amounts of mono-phosphorylated phosphoglucans. Thus, the enzyme is capable of acting on neutral maltodextrins. It is concluded that the actual carbohydrate substrate of the phosphoglucan, water dikinase is defined by physical rather than by chemical parameters. A model is proposed that explains, at the molecular level, the consecutive action of the two starch-related dikinases.}, language = {en} } @article{HaenzelmannDahlKuperetal.2009, author = {Haenzelmann, Petra and Dahl, Jan U. and Kuper, Jochen and Urban, Alexander and Mueller-Theissen, Ursula and Leimk{\"u}hler, Silke and Schindelin, Hermann}, title = {Crystal structure of YnjE from Escherichia coli, a sulfurtransferase with three rhodanese domains}, issn = {0961-8368}, doi = {10.1002/pro.260}, year = {2009}, abstract = {Rhodaneses/sulfurtransferases are ubiquitous enzymes that catalyze the transfer of sulfane sulfur from a donor molecule to a thiophilic acceptor via an active site cysteine that is modified to a persulfide during the reaction. Here, we present the first crystal structure of a triple-domain rhodanese-like protein, namely YnjE from Escherichia coli, in two states where its active site cysteine is either unmodified or present as a persulfide. Compared to well- characterized tandem domain rhodaneses, which are composed of one inactive and one active domain, YnjE contains an extra N-terminal inactive rhodanese-like domain. Phylogenetic analysis reveals that YnjE triple-domain homologs can be found in a variety of other gamma-proteobacteria, in addition, some single-, tandem-, four and even six-domain variants exist. All YnjE rhodaneses are characterized by a highly conserved active site loop (CGTGWR) and evolved independently from other rhodaneses, thus forming their own subfamily. On the basis of structural comparisons with other rhodaneses and kinetic studies, YnjE, which is more similar to thiosulfate:cyanide sulfurtransferases than to 3- mercaptopyruvate:cyanide sulfurtransferases, has a different substrate specificity that depends not only on the composition of the active site loop with the catalytic cysteine at the first position but also on the surrounding residues. In vitro YnjE can be efficiently persulfurated by the cysteine desulfurase IscS. The catalytic site is located within an elongated cleft, formed by the central and C-terminal domain and is lined by bulky hydrophobic residues with the catalytic active cysteine largely shielded from the solvent.}, language = {en} } @article{GriessnerBroekerLehmannetal.2009, author = {Grießner, Matthias and Broeker, Patrick and Lehmann, Andr{\´e} and Ehrentreich-F{\"o}rster, Eva and Bier, Frank Fabian}, title = {Detection of angiotensin II type 1 receptor ligands by a cell-based assay}, issn = {1618-2642}, doi = {10.1007/s00216-009-3074-4}, year = {2009}, abstract = {This work describes a cell-based assay that does not depend on radioactivity or laboratory animals for the detection of ligands of angiotensin II type 1 receptor (AT(1)R). The assay makes use of stable transfected Chinese hamster ovary cells (CHO-AT(1)R) expressing the AT(1)R. A sequential saturation assay principle was used in which receptor binding sites of the CHO-AT(1)R cells are blocked by the analyte in a concentration-dependent manner. Afterwards, TAMRA-angiotensin II, a fluorescence-labeled ligand, was added to bind to the remaining free binding sites of the receptor. In consequence, the fluorescence signal determined is inversely proportional to the concentration of the analyte.}, language = {en} } @article{GajdanowiczGarciaMataGonzalezetal.2009, author = {Gajdanowicz, Pawel and Garcia-Mata, Carlos and Gonzalez, Wendy and Morales-Navarro, Samuel El{\"i}as and Sharma, Tripti and Gonzalez-Nilo, Fernando Danilo and Gutowicz, Jan and M{\"u}ller-R{\"o}ber, Bernd and Blatt, Michael R. and Dreyer, Ingo}, title = {Distinct roles of the last transmembrane domain in controlling Arabidopsis K+ channel activity}, issn = {0028-646X}, doi = {10.1111/j.1469-8137.2008.02749.x}, year = {2009}, abstract = {The family of voltage-gated potassium channels in plants presumably evolved from a common ancestor and includes both inward-rectifying (K-in) channels that allow plant cells to accumulate K+ and outward-rectifying (K-out) channels that mediate K+ efflux. Despite their close structural similarities, the activity of Kin channels is largely independent of K+ and depends only on the transmembrane voltage, whereas that of K-out channels responds to the membrane voltage and the prevailing extracellular K+ concentration. Gating of potassium channels is achieved by structural rearrangements within the last transmembrane domain (S6). Here we investigated the functional equivalence of the S6 helices of the Kin channel KAT1 and the K-out channel SKOR by domain-swapping and site-directed mutagenesis. Channel mutants and chimeras were analyzed after expression in Xenopus oocytes. We identified two discrete regions that influence gating differently in both channels, demonstrating a lack of functional complementarity between KAT1 and SKOR. Our findings are supported by molecular models of KAT1 and SKOR in the open and closed states. The role of the S6 segment in gating evolved differently during specialization of the two channel subclasses, posing an obstacle for the transfer of the K+-sensor from K-out to K-in channels.}, language = {en} } @article{FeulnerPlathEngelmannetal.2009, author = {Feulner, Philine G. D. and Plath, Martin and Engelmann, Jacob and Kirschbaum, Frank and Tiedemann, Ralph}, title = {Electrifying love : electric fish use species-specific discharge for mate recognition}, issn = {1744-9561}, doi = {10.1098/rsbl.2008.0566}, year = {2009}, abstract = {Mate choice is mediated by a range of sensory cues, and assortative mating based on these cues can drive reproductive isolation among diverging populations. A specific feature of mormyrid fish, the electric organ discharge (EOD), is used for electrolocation and intraspecific communication. We hypothesized that the EOD also facilitates assortative mating and ultimately promotes prezygotic reproductive isolation in African weakly electric fishes. Our behavioural experiments using live males as well as EOD playback demonstrated that female mate recognition is influenced by EOD signals and that females are attracted to EOD characteristics of conspecific males. The dual function of the EOD for both foraging and social communication (including mate recognition leading to assortative mating) underlines the importance of electric signal differentiation for the divergence of African weakly electric fishes. Thus, the EOD provides an intriguing mechanism promoting trophic divergence and reproductive isolation between two closely related Campylomormyrus species occurring in sympatry in the lower Congo rapids.}, language = {en} } @article{FettkeMalinovaEckermannetal.2009, author = {Fettke, J{\"o}rg and Malinova, Irina and Eckermann, Nora and Steup, Martin}, title = {Cytosolic heteroglycans in photoautotrophic and in heterotrophic plant cells}, issn = {0031-9422}, doi = {10.1016/j.phytochem.2009.03.016}, year = {2009}, abstract = {In plants several 'starch-related' enzymes exist as plastid- and cytosol-specific isoforms and in some cases the extraplastidial isoforms represent the majority of the enzyme activity. Due to the compartmentation of the plant cells, these extraplastidial isozymes have no access to the plastidial starch granules and, therefore, their in vivo function remained enigmatic. Recently, cytosolic heteroglycans have been identified that possess a complex pattern of the monomer composition and glycosidic bonds. The glycans act both as acceptors and donors for cytosolic glucosyl transferases. In autotrophic tissues the heteroglycans are essential for the nocturnal starch-sucrose conversion. In this review we summarize the current knowledge of these glycans, their interaction with glucosyl transferases and their possible cellular functions. We include data on the heteroglycans in heterotrophic plant tissues and discuss their role in intracellular carbon fluxes that originate from externally supplied carbohydrates.}, language = {en} } @article{FettkeHejaziSmirnovaetal.2009, author = {Fettke, J{\"o}rg and Hejazi, Mahdi and Smirnova, Julia and Hoechel, Erik and Stage, Marion and Steup, Martin}, title = {Eukaryotic starch degradation : integration of plastidial and cytosolic pathways}, issn = {0022-0957}, doi = {10.1093/Jxb/Erp054}, year = {2009}, abstract = {Starch is an important plant product widely used as a nutrient, as a source of renewable energy, and for many technological applications. In plants, starch is the almost ubiquitous storage carbohydrate whereas most heterotrophic prokaryotes and eukaryotes rely on glycogen. Despite close similarities in basic chemical features, starch and glycogen differ in both structural and physicochemical properties. Glycogen is a hydrosoluble macromolecule with evenly distributed branching points. Starch exists as a water-insoluble particle having a defined (and evolutionary conserved) internal structure. The biochemistry of starch requires the co-operation of up to 40 distinct (iso)enzymes whilst approximately 10 (iso)enzymes permit glycogen metabolism. The biosynthesis and degradation of native starch include the transition of carbohydrates from the soluble to the solid phase and vice versa. In this review, two novel aspects of the eukaryotic plastidial starch degradation are discussed: Firstly, biochemical reactions that take place at the surface of particulate glucans and mediate the phase transition of carbohydrates. Secondly, processes that occur downstream of the export of starch-derived sugars into the cytosol. Degradation of transitory starch mainly results in the formation of neutral sugars, such as glucose and maltose, that are transported into the cytosol via the respective translocators. The cytosolic metabolism of the neutral sugars includes the action of a hexokinase, a phosphoglucomutase, and a transglucosidase that utilizes high molecular weight glycans as a transient glucosyl acceptor or donor. Data are included on the transglucosidase (disproportionating isozyme 2) in Cyanophora paradoxa that accumulates storage carbohydrates in the cytosol rather than in the plastid.}, language = {en} } @article{EccardWolf2009, author = {Eccard, Jana and Wolf, Jochen B. W.}, title = {Effects of brood size on multiple-paternity rates : a case for 'paternity share' as an offspring- based estimate}, issn = {0003-3472}, doi = {10.1016/j.anbehav.2009.04.008}, year = {2009}, language = {en} } @article{DreyerBlatt2009, author = {Dreyer, Ingo and Blatt, Michael R.}, title = {What makes a gate? : the ins and outs of Kv-like K+ channels in plants}, issn = {1360-1385}, doi = {10.1016/j.tplants.2009.04.001}, year = {2009}, abstract = {Gating of K+ and other ion channels is 'hard-wired' within the channel protein. So it remains a puzzle how closely related channels in plants can show an unusually diverse range of biophysical properties. Gating of these channels lies at the heart of K+ mineral nutrition, signalling, abiotic and biotic stress responses in plants. Thus, our knowledge of the molecular mechanics underpinning K+ channel gating will be important for rational engineering of related traits in agricultural crops. Several key studies have added significantly to our understanding of channel gating in plants and have challenged current thinking about analogous processes found in animal K+ channels. Such studies highlight how much of K+ channel gating remains to be explored in plants.}, language = {en} } @article{DietzelKuperDoebbleretal.2009, author = {Dietzel, Uwe and Kuper, Jochen and Doebbler, Jennifer A. and Schulte, Antje and Truglio, James J. and Leimk{\"u}hler, Silke and Kisker, Caroline}, title = {Mechanism of substrate and inhibitor binding of Rhodobacter capsulatus xanthine dehydrogenase}, issn = {0021-9258}, doi = {10.1074/jbc.M808114200}, year = {2009}, abstract = {Rhodobacter capsulatus xanthine dehydrogenase (XDH) is an (alpha beta)(2) heterotetrameric cytoplasmic enzyme that resembles eukaryotic xanthine oxidoreductases in respect to both amino acid sequence and structural fold. To obtain a detailed understanding of the mechanism of substrate and inhibitor binding at the active site, we solved crystal structures of R. capsulatus XDH in the presence of its substrates hypoxanthine, xanthine, and the inhibitor pterin-6- aldehyde using either the inactive desulfo form of the enzyme or an active site mutant (E(B)232Q) to prevent substrate turnover. The hypoxanthine-and xanthine-bound structures reveal the orientation of both substrates at the active site and show the importance of residue GluB-232 for substrate positioning. The oxygen atom at the C-6 position of both substrates is oriented toward Arg(B)-310 in the active site. Thus the substrates bind in an orientation opposite to the one seen in the structure of the reduced enzyme with the inhibitor oxypurinol. The tightness of the substrates in the active site suggests that the intermediate products must exit the binding pocket to allow first the attack of the C-2, followed by oxidation of the C-8 atom to form the final product uric acid. Structural studies of pterin-6-aldehyde, a potent inhibitor of R. capsulatus XDH, contribute further to the understanding of the relative positioning of inhibitors and substrates in the binding pocket. Steady state kinetics reveal a competitive inhibition pattern with a K-i of 103.57 +/- 18.96 nM for pterin-6-aldehyde.}, language = {en} } @article{DepuydtTrenkampFernieetal.2009, author = {Depuydt, Stephen and Trenkamp, Sandra and Fernie, Alisdair R. and Elftieh, Samira and Renou, Jean-Pierre and Vuylsteke, Marnik and Holsters, Marcelle and Vereecke, Danny}, title = {An integrated genomics approach to define niche establishment by Rhodococcus fascians}, issn = {0032-0889}, doi = {10.1104/pp.108.131805}, year = {2009}, abstract = {Rhodococcus fascians is a Gram-positive phytopathogen that induces shooty hyperplasia on its hosts through the secretion of cytokinins. Global transcriptomics using microarrays combined with profiling of primary metabolites on infected Arabidopsis (Arabidopsis thaliana) plants revealed that this actinomycete modulated pathways to convert its host into a niche. The transcript data demonstrated that R. fascians leaves a very characteristic mark on Arabidopsis with a pronounced cytokinin response illustrated by the activation of cytokinin perception, signal transduction, and homeostasis. The microarray data further suggested active suppression of an oxidative burst during the R. fascians pathology, and comparison with publicly available transcript data sets implied a central role for auxin in the prevention of plant defense activation. Gene Ontology categorization of the differentially expressed genes hinted at a significant impact of infection on the primary metabolism of the host, which was confirmed by subsequent metabolite profiling. The much higher levels of sugars and amino acids in infected plants are presumably accessed by the bacteria as carbon and nitrogen sources to support epiphytic and endophytic colonization. Hexoses, accumulating from a significantly increased invertase activity, possibly inhibited the expression of photosynthesis genes and photosynthetic activity in infected leaves. Altogether, these changes are indicative of sink development in symptomatic tissues. The metabolomics data furthermore point to the possible occurrence of secondary signaling during the interaction, which might contribute to symptom development. These data are placed in the context of regulation of bacterial virulence gene expression, suppression of defense, infection phenotype, and niche establishment.}, language = {en} } @article{ChristianMayKempaetal.2009, author = {Christian, Nils and May, Patrick and Kempa, Stefan and Handorf, Thomas and Ebenhoeh, Oliver}, title = {An integrative approach towards completing genome-scale metabolic networks}, issn = {1742-206X}, doi = {10.1039/B915913b}, year = {2009}, abstract = {Genome-scale metabolic networks which have been automatically derived through sequence comparison techniques are necessarily incomplete. We propose a strategy that incorporates genomic sequence data and metabolite profiles into modeling approaches to arrive at improved gene annotations and more complete genome-scale metabolic networks. The core of our strategy is an algorithm that computes minimal sets of reactions by which a draft network has to be extended in order to be consistent with experimental observations. A particular strength of our approach is that alternative possibilities are suggested and thus experimentally testable hypotheses are produced. We carefully evaluate our strategy on the well-studied metabolic network of Escherichia coli, demonstrating how the predictions can be improved by incorporating sequence data. Subsequently, we apply our method to the recently sequenced green alga Chlamydomonas reinhardtii. We suggest specific genes in the genome of Chlamydomonas which are the strongest candidates for coding the responsible enzymes.}, language = {en} } @article{ChengHartmannGuptaetal.2009, author = {Cheng, Fuxia and Hartmann, Stefanie and Gupta, Mayetri and Ibrahim, Joseph G. and Vision, Todd J.}, title = {A hierarchical model for incomplete alignments in phylogenetic inference}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btp015}, year = {2009}, abstract = {Motivation: Full-length DNA and protein sequences that span the entire length of a gene are ideally used for multiple sequence alignments (MSAs) and the subsequent inference of their relationships. Frequently, however, MSAs contain a substantial amount of missing data. For example, expressed sequence tags (ESTs), which are partial sequences of expressed genes, are the predominant source of sequence data for many organisms. The patterns of missing data typical for EST-derived alignments greatly compromise the accuracy of estimated phylogenies. Results: We present a statistical method for inferring phylogenetic trees from EST-based incomplete MSA data. We propose a class of hierarchical models for modeling pairwise distances between the sequences, and develop a fully Bayesian approach for estimation of the model parameters. Once the distance matrix is estimated, the phylogenetic tree may be constructed by applying neighbor-joining (or any other algorithm of choice). We also show that maximizing the marginal likelihood from the Bayesian approach yields similar results to a pro. le likelihood estimation. The proposed methods are illustrated using simulated protein families, for which the true phylogeny is known, and one real protein family.}, language = {en} } @article{BulikGrimbsHuthmacheretal.2009, author = {Bulik, Sascha and Grimbs, Sergio and Huthmacher, Carola and Selbig, Joachim and Holzhutter, Hermann G.}, title = {Kinetic hybrid models composed of mechanistic and simplified enzymatic rate laws : a promising method for speeding up the kinetic modelling of complex metabolic networks}, issn = {1742-464X}, doi = {10.1111/j.1742-4658.2008.06784.x}, year = {2009}, abstract = {Kinetic modelling of complex metabolic networks - a central goal of computational systems biology - is currently hampered by the lack of reliable rate equations for the majority of the underlying biochemical reactions and membrane transporters. On the basis of biochemically substantiated evidence that metabolic control is exerted by a narrow set of key regulatory enzymes, we propose here a hybrid modelling approach in which only the central regulatory enzymes are described by detailed mechanistic rate equations, and the majority of enzymes are approximated by simplified (nonmechanistic) rate equations (e.g. mass action, LinLog, Michaelis-Menten and power law) capturing only a few basic kinetic features and hence containing only a small number of parameters to be experimentally determined. To check the reliability of this approach, we have applied it to two different metabolic networks, the energy and redox metabolism of red blood cells, and the purine metabolism of hepatocytes, using in both cases available comprehensive mechanistic models as reference standards. Identification of the central regulatory enzymes was performed by employing only information on network topology and the metabolic data for a single reference state of the network [Grimbs S, Selbig J, Bulik S, Holzhutter HG \& Steuer R (2007) Mol Syst Biol3, 146, doi:10.1038/msb4100186]. Calculations of stationary and temporary states under various physiological challenges demonstrate the good performance of the hybrid models. We propose the hybrid modelling approach as a means to speed up the development of reliable kinetic models for complex metabolic networks.}, language = {en} } @article{BleidornLanterbecqEeckhautetal.2009, author = {Bleidorn, Christoph and Lanterbecq, Deborah and Eeckhaut, Igor and Tiedemann, Ralph}, title = {A PCR survey of Hox genes in the myzostomid Myzostoma cirriferum}, issn = {0949-944X}, doi = {10.1007/s00427-009-0282-z}, year = {2009}, abstract = {Using degenerate primers, we were able to identify seven Hox genes for the myzostomid Myzostoma cirriferum. The recovered fragments belong to anterior class (Mci_lab, Mci_pb), central class (Mci_Dfd, Mci_Lox5, Mci_Antp, Mci_Lox4), and posterior class (Mci_Post2) paralog groups. Orthology assignment was verified by phylogenetic analyses and presence of diagnostic regions in the homeodomain as well as flanking regions. The presence of Lox5, Lox4, and Post2 supports the inclusion of Myzostomida within Lophotrochozoa. We found signature residues within flanking regions of Lox5, which are also found in annelids, but not in Platyhelminthes. As such the available Hox genes data of myzostomids support an annelid relationship.}, language = {en} } @article{BleidornHillErseusetal.2009, author = {Bleidorn, Christoph and Hill, Natascha and Ers{\´e}us, Christer and Tiedemann, Ralph}, title = {On the role of character loss in orbiniid phylogeny (Annelida) : molecules vs. morphology}, issn = {1055-7903}, doi = {10.1016/j.ympev.2009.03.022}, year = {2009}, abstract = {Orbiniid phylogeny is matter of debate and incongruence between hypothesis based on molecules and morphology has been repeatedly reported. Moreover, the phylogenetic position of the "oligochaetoid polychaetes" of the taxon Questa varies between morphological and molecular cladistic analyses. Here, we present a nearly complete mitochondrial genome of Questa ersei. The mitochondrial gene order is roughly identical to known orbiniid taxa. Several translocations of tRNAs are unique to Orbiniidae and Questa when compared to other annelid mitochondrial genomes. Additionally, we assembled sequence data of six genes (18S, 16S, cox1, cox3, nad1, nad4) for a representative orbiniid taxon sampling and analysed all data in concatenation using Maximum Likelihood and Bayesian inference. For comparison with morphology we compiled a morphological data matrix for all taxa included in our molecular analyses. Our results strongly support a close relationship of Questa with orbiniids (sequence data, gene order, an 18 bp indel, morphology), and a position nested within orbiniids is recovered in our sequence based analyses. We demonstrate remarkable incongruence of most included morphological characters with the recovered best ML tree and suppose that repeated independent character loss might be an explanation.}, language = {en} } @article{BarbirzBeckerFreibergetal.2009, author = {Barbirz, Stefanie and Becker, Marion and Freiberg, Alexander and Seckler, Robert}, title = {Phage tailspike proteins with beta-solenoid fold as thermostable carbohydrate binding materials}, issn = {1616-5187}, doi = {10.1002/mabi.200800278}, year = {2009}, abstract = {We have investigated the stability of three tailspike proteins (TSPs) from bacteriophages Sf6, P22, and HK620. Tailspikes are rod-like homotrimers with comparable beta-solenoid folds and similarly high kinetic stability in spite of different amino acid sequences. As tailspikes bind polysaccharides to recognize the bacterial host cell, their stability is required for maintenance of bacteriophage infectivity under harsh extracellular conditions. They resist denaturation by SDS at ambient temperature and their unfolding is slow even in 6 m guanidinium hydrochloride (GdmHCl). This makes them interesting candidates for very stable carbohydrate binding protein materials.}, language = {en} } @article{AverbeckApioPlathetal.2009, author = {Averbeck, Christiane and Apio, Ann and Plath, Martin and Wronski, Torsten}, title = {Environmental parameters and anthropogenic effects predicting the spatial distribution of wild ungulates in the Akagera savannah ecosystem}, issn = {0141-6707}, doi = {10.1111/j.1365-2028.2009.01076.x}, year = {2009}, abstract = {Savannah areas affected by human activities such as livestock keeping and agriculture are often characterized by shifts in landscape structuring, with a predominance of few(er) habitat types. This is typically accompanied by pronounced changes in the communities of ungulates. The aim of this study was to find out whether shifts in ungulate communities in Lake Mburo National Park (LMNP) are primarily predicted by an alteration in the composition of the preferred habitat types or if more complex interactions between habitat changes and the prevalence of ungulates occur. Monthly road counts were used to establish the number of eleven ungulate species in LMNP and adjacent unprotected Ankole Ranching Scheme. The common duiker (Sylvicapra grimmia campbelliae Gray, 1843) was found in more abundance in disturbed areas, while showing a significant change in habitat use. Common duiker tended to use the vegetation type otherwise used by the bushbuck (Tragelaphus scriptus dama Neumann, 1902). Our results support the claim that the occurrence of ungulates is not only directly affected by the availability of 'suitable' habitats, but behavioural plasticity and competitive exclusion also need to be considered.}, language = {en} } @article{ApioMuwanikaPlathetal.2009, author = {Apio, Ann and Muwanika, Vincent B. and Plath, Martin and Wronski, Torsten}, title = {Seasonal variation in reproductive behaviour of bushbuck (Tragelaphus scriptus Pallas, 1766) in an equatorial savannah ecosystem}, issn = {0141-6707}, doi = {10.1111/j.1365-2028.2008.01000.x}, year = {2009}, abstract = {While several authors suggest that bushbuck (Tragelaphus scriptus Pallas) from tropical areas with an approximately bimodal rainfall pattern breed throughout the year, there is also a report of seasonal breeding in this species. In this study, we provide indirect evidence of seasonality in reproduction by analysing behavioural data (e.g. rates of mixed-sex sightings) in a population of bushbuck inhabiting an equatorial savannah ecosystem in western Uganda. Observation rates of mixed-sex sightings were correlated with rainfall patterns. We suggest that peaks in reproductive behaviour following the wet season may be advantageous if calves are born during the next wet season, when fresh vegetation is available.}, language = {en} } @article{AndresenvonNickischRosenegkBier2009, author = {Andresen, Dennie and von Nickisch-Rosenegk, Markus and Bier, Frank Fabian}, title = {Helicase-dependent amplification : use in OnChip amplification and potential for point-of-care diagnostics}, issn = {1473-7159}, doi = {10.1586/erm.09.46}, year = {2009}, abstract = {Isothermal amplification technologies are emerging on the horizon that could have the potential to pose as alternatives to PCR in terms of sensitivity and ease of use. One of the most recent isothermal technologies is helicase- dependent amplification (HDA). This technology uses the helicase's capability to disrupt the hydrogen bonds of a Watson-Crick base pair in order to separate dsDNA. A denaturation step, as is used in PCR, is no longer required. This gives rise to new, less expensive and less complicated designs for point-of-care devices and 'Lab on Chip' systems. Helicase-dependent OnChip-amplification (OnChip-HDA) is a further step into this direction as it integrates the HDA technology with microarray technology and its power of multiplexing. This special report will give an overview on the HDA and OnChip-HDA technology, and its potential for point-of-care diagnostics.}, language = {en} } @article{AndresenvonNickischRosenegkBier2009, author = {Andresen, Dennie and von Nickisch-Rosenegk, Markus and Bier, Frank Fabian}, title = {Helicase dependent OnChip-amplification and its use in multiplex pathogen detection}, issn = {0009-8981}, doi = {10.1016/j.cca.2009.03.021}, year = {2009}, abstract = {Background: The need for fast, specific and sensitive multiparametric detection methods is an ever growing demand in molecular diagnostics. Here we report on a newly developed method, the helicase dependent Onchip amplification (OnChip-HDA). This approach integrates the analysis and detection in one single reaction thus leading to time and cost savings in multiparametric analysis. Methods: HDA is an isothermal amplification method that is not depending on thermocycling as known from PCR due to the helicases' ability to unwind DNA double-strands. We have combined the HDA with microarray based detection, making it suitable for multiplex detection. As an example we used the Onchip HDA in single and multiplex amplifications for the detection of the two pathogens N. gonorrhoeae and S. aureus directly on surface bound primers. Results: We have successfully shown the OnChip-HDA and applied it for single- and duplex- detection of the pathogens N. gonorrhoeae and S. aureus. Conclusion: We have developed a new method, the OnChip-HDA for the multiplex detection of pathogens. Its simplicity in reaction setup and potential for miniaturization and multiparametric analysis is advantageous for the integration in miniaturized Lab on Chip systems, e.g. needed in point of care diagnostics.}, language = {en} } @article{AbercrombieAndersonBaldwinetal.2009, author = {Abercrombie, Laura Good and Anderson, Cynthia M. and Baldwin, Bruce G. and Bang, In-Chul and Beldade, Ricardo and Bernardi, Giacomo and Boubou, Angham and Branca, Antoine and Bretagnolle, Francois and Bruford, Michael W. and Buonamici, Anna and Burnett, Robert K. and Canal, D. and Cardenas, H. and Caullet, Coraline and Chen, S. Y. and Chun, Y. J. and Cossu, C. and Crane, Charles F. and Cros-Arteil, Sandrine and Cudney-Bueno, Richard and Danti, Roberto and Davila, Jos{\´e} Antonio and Della Rocca, Gianni and Dobata, Shigeto and Dunkle, Larry D. and Dupas, Stephane and others}, title = {Permanent genetic resources added to molecular ecology resources database 1 January 2009-30 April 2009}, issn = {1755-098X}, doi = {10.1111/j.1755-0998.2009.02746.x}, year = {2009}, abstract = {This article documents the addition of 283 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Agalinis acuta; Ambrosia artemisiifolia; Berula erecta; Casuarius casuarius; Cercospora zeae-maydis; Chorthippus parallelus; Conyza canadensis; Cotesia sesamiae; Epinephelus acanthistius; Ficedula hypoleuca; Grindelia hirsutula; Guadua angustifolia; Leucadendron rubrum; Maritrema novaezealandensis; Meretrix meretrix; Nilaparvata lugens; Oxyeleotris marmoratus; Phoxinus neogaeus; Pristomyrmex punctatus; Pseudobagrus brevicorpus; Seiridium cardinale; Stenopsyche marmorata; Tetranychus evansi and Xerus inauris. These loci were cross-tested on the following species: Agalinis decemloba; Agalinis tenella; Agalinis obtusifolia; Agalinis setacea; Agalinis skinneriana; Cercospora zeina; Cercospora kikuchii; Cercospora sorghi; Mycosphaerella graminicola; Setosphaeria turcica; Magnaporthe oryzae; Cotesia flavipes; Cotesia marginiventris; Grindelia Xpaludosa; Grindelia chiloensis; Grindelia fastigiata; Grindelia lanceolata; Grindelia squarrosa; Leucadendron coniferum; Leucadendron salicifolium; Leucadendron tinctum; Leucadendron meridianum; Laodelphax striatellus; Sogatella furcifera; Phoxinus eos; Phoxinus rigidus; Phoxinus brevispinosus; Phoxinus bicolor; Tetranychus urticae; Tetranychus turkestani; Tetranychus ludeni; Tetranychus neocaledonicus; Tetranychus amicus; Amphitetranychus viennensis; Eotetranychus rubiphilus; Eotetranychus tiliarium; Oligonychus perseae; Panonychus citri; Bryobia rubrioculus; Schizonobia bundi; Petrobia harti; Xerus princeps; Spermophilus tridecemlineatus and Sciurus carolinensis.}, language = {en} } @phdthesis{Zbierzak2009, author = {Zbierzak, Anna Maria}, title = {Isolation and characterization of the chilling sensitive 1 gene from Arabidopsis}, address = {Potsdam}, pages = {iii, 131 Bl. : Ill., graph. Darst.}, year = {2009}, language = {en} } @phdthesis{Schurr2009, author = {Schurr, Frank Martin}, title = {From genes to species ranges : demographic studies of plant dynamics at multiple scales}, address = {Potsdam}, pages = {277 S. : Ill., graph. Darst. + 1 CD-Rom}, year = {2009}, language = {en} } @article{WasiolkaBlaumJeltschetal.2009, author = {Wasiolka, Bernd and Blaum, Niels and Jeltsch, Florian and Henschel, Joh}, title = {Behavioural responses of the lizard "Pedioplanis l. lineoocellata" to overgrazing}, issn = {1146-609X}, doi = {10.1016/j.actao.2008.09.009}, year = {2009}, abstract = {We studied the effects of overgrazing on the foraging behaviour of the lizard Pedioplanis l. lineoocellata (Spotted Sand Lizard), a sit-and-wait forager, in habitats of differing vegetation states to determine the effects of habitat degradation on this species. At high grazing intensity where vegetation cover and diversity is low, the lizard P. lineoocellata moves more frequently, spends more time moving and covers larger distances than in habitats where vegetation cover and diversity is high. These behavioural changes in movement patterns can be explained by less abundant prey in habitats with low vegetation cover and diversity. Although morphology, phylogeny and physiology of P. lineoocellata should constrain the change in foraging behaviour, the species has modified its foraging strategy from sit- and-wait to actively foraging. We assume that this behavioural flexibility of P. lineoocellata is a buffer mechanism enabling the species to use and survive in degraded (unfavourable) habitats.}, language = {en} } @article{SchefflerSchueler2009, author = {Scheffler, Christiane and Sch{\"u}ler, Grit}, title = {Analysis of BMI of preschool children : results of longitudinal studies}, issn = {0003-5548}, doi = {10.1127/0003-5548/2009/0007}, year = {2009}, abstract = {Exceeding weight gain in childhood is a prevailing issue in industrialised countries, such as in Germany. The aim of this study was to detect a critical age for exceeding weight gain. It is assumed that especially in the early years of life, the years of nursery school age, the individual development of weight is fundamental for the prediction of obesity. The data of 638 children (324 boys and 314 girls) and the data of additional 1390 children of a preceding longitudinal study were analysed. The results show that overweight newborns are not at higher risk of becoming overweight children later, in the first place. But the results identify a high risk of becoming overweight for children 4.5 years old through a BMI rebound. In addition, this comparably earlier BMI rebound is linked with an increasing percentage of body fat. This leads to the assumption, that a comparably early BMI rebound is remarkably atypical for healthy child development. The results are also interrelated with the test person's sex. Endangered girls are of pyknomorphic body type. In contrast, the boys' results are independent of the body type. Obesity of boys therefore is strongly assumed to be caused by environmental factors.}, language = {en} } @article{RossmanithBlaumHoentschetal.2009, author = {Rossmanith, Eva and Blaum, Niels and H{\"o}ntsch, Kerstin and Jeltsch, Florian}, title = {Sex-related parental care strategies in the lesser spotted woodpecker "Picoides minor" : of flexible mothers and dependable fathers}, issn = {0908-8857}, doi = {10.1111/j.1600-048X.2008.04353.x}, year = {2009}, abstract = {We investigated sex-specific parental care behaviour of lesser spotted woodpeckers Picoides minor in the low mountain range Taunus, Germany. Observed parental care included incubation, nest sanitation as well as brooding and feeding of nestlings. Contributions of the two sexes to parental care changed in progress of the breeding period. During incubation and the first half of the nestling period, parental care was divided equally between partners. However, in the late nestling stage, we found males to feed their nestlings irrespective of brood size while females considerably decreased feeding rate with the number of nestlings. This behaviour culminated in desertion of small broods by females shortly before fledging. The fact that even deserted nests were successful indicates that males were able to compensate for the females' absence. Interestingly, the mating of one female with two males with separate nests could be found in the population, which confirms earlier findings of polyandry in the lesser spotted woodpecker. We conclude that biparental care is not essential in the later stage and one partner can reduce effort and thus costs of parental care, at least in small broods where the mate is able to compensate for that behaviour. Reduced care and desertion appears only in females, which might be caused by a combination of two traits: First, females might suffer higher costs of investment in terms of mortality and secondly, male-biased sex ratio in the population generally leads to higher mating probabilities for females in the following breeding season. The occurrence of polyandry seems to be a result of these conditions.}, language = {en} } @article{MoloneyHolzapfelTielboergeretal.2009, author = {Moloney, Kirk A. and Holzapfel, Claus and Tielb{\"o}rger, Katja and Jeltsch, Florian and Schurr, Frank Martin}, title = {Rethinking the common garden in invasion research}, issn = {1433-8319}, doi = {10.1016/j.ppees.2009.05.002}, year = {2009}, abstract = {In common garden experiments, a number of genotypes are raised in a common environment in order to quantify the genetic component of phenotypic variation. Common gardens are thus ideally suited for disentangling how genetic and environmental factors contribute to the success of invasive species in their new non-native range. Although common garden experiments are increasingly employed in the study of invasive species, there has been little discussion about how these experiments should be designed for greatest utility. We argue that this has delayed progress in developing a general theory of invasion biology. We suggest a minimum optimal design (MOD) for common garden studies that target the ecological and evolutionary processes leading to phenotypic differentiation between native and invasive ranges. This involves four elements: (A) multiple, strategically sited garden locations, involving at the very least four gardens (2 in the native range and 2 in the invaded range); (B) careful consideration of the genetic design of the experiment; (C) standardization of experimental protocols across all gardens; and (D) care to ensure the biosafety of the experiment. Our understanding of the evolutionary ecology of biological invasions will be greatly enhanced by common garden studies, if and only if they are designed in a more systematic fashion, incorporating at the very least the MOD suggested here.}, language = {en} } @article{BlaumTietjenRossmanith2009, author = {Blaum, Niels and Tietjen, Britta and Rossmanith, Eva}, title = {The impact of livestock husbandry on small- and medium-sized carnivores in Kalahari savannah rangelands}, issn = {0022-541X}, doi = {10.2193/2008-034}, year = {2009}, abstract = {We analyzed relative sensitivities of small- and medium-sized carnivores to livestock husbandry (stocking rates and predator control) in Kalahari, South Africa, rangelands at a regional scale. We monitored small carnivores using track counts on 22 Kalahari farms across a land-use gradient ranging from low to high stocking rates and also interviewed each farm manager to identify farmers" perception of small carnivores as potential predators for livestock. We recorded 12 species of small- and medium-sized carnivores across 22 Kalahari farms. Stocking rate was the most important driving variable for local carnivore abundance. Abundance of all species was lowest on farms where stocking rate was high. Most farm managers perceived medium-sized carnivores, in particular, African wildcat (Felis silvestris lybica), black-backed jackal (Canis mesomelas), and caracal (Caracal caracal), as potential predators of livestock. Multiple regression analysis shows that black-backed jackal, African wildcat, and caracal were negatively affected by predator control measures, whereas bat-eared fox (Otocyon megalotis), cape fox (Vulpes chama), and small-spotted genet (Genetta genetta) were positively affected. Our results show a need for expanding research and conservation activities toward small- and medium-sized carnivores in southern African savannah rangelands. We, therefore, suggest developing a monitoring program combining passive tracking with indigenous knowledge of local Khoisan Bushmen to monitor carnivore populations, and we recommend additional predator removal experiments that manipulate predator densities.}, language = {en} } @phdthesis{Riegler2009, author = {Riegler, Heike}, title = {Der Nukleosidmetabolismus in Arabidopsis}, address = {Potsdam}, pages = {95 S.}, year = {2009}, language = {de} } @article{Scheffler2009, author = {Scheffler, Ingo}, title = {Ektoparasiten der Flederm{\"a}use in Deutschland - neue Erkenntnisse zur Verbreitung, {\"O}kologie und Bedeutung}, year = {2009}, abstract = {Der Artikel liefert eine Zusammenstellung der aktuellen Ektoparasitenfauna der Flederm{\"a}use (Fl{\"o}he, Fledermausfliegen, Wanzen, Zecken und Milben). Die Beziehung zwischen den Flederm{\"a}usen und ihren Ektoparasiten eignet sich in besonderem Maße als Modell {\"o}kologischer und evolution{\"a}rer Prozesse, wie das {\"U}berleben seltener Arten, die K{\"o}volution zwischen Wirten und Parasiten, die {\"U}bertragung von Parasiten, die Wirtswahl und die Verbreitung von Krankheiten. Der gegenw{\"a}rtige Stand der {\"o}kologischen Forschung auf diesen Gebieten wird zusammengefaßt und die Notwendigkeit und die Ziele weiterer Forschung werden angegeben.}, language = {de} }