@article{PoerschmannSpijkermanLanger2004, author = {Poerschmann, J{\"u}rgen and Spijkerman, Elly and Langer, Uwe}, title = {Fatty acid patterns in chlamydomonas sp as a marker for nutritional regimes and temperature under extremely acidic conditions}, year = {2004}, abstract = {Fatty acid profiles were used to characterize nutritional pathways in Chlamydomonas sp. isolated from an acidic mining lake (pH 2.7). Surprisingly, profiles of Chlamydomonas sp. grown in the lab under photoautotrophic, mixotrophic, and heterotrophic conditions at in situ deep strata lake water temperatures (8C) were very similar, polyunsaturated fatty acids including a-linolenic acid (18:3x3) and 16:4x3 along with palmitic acid (16:0) being most abundant. Therefore, heterotrophic growth of Chlamydomonas sp. at low temperatures can result in high concentrations of polyunsaturated fatty acids, as previously only described for some psychrophilic bacteria. By contrast, the cultivation of isolated Chlamydomonas sp. at 20C, reflecting surface water temperatures, provided fatty acid patterns characteristic of the nutrition strategy applied: the concentration of polyunsaturated fatty acids decreased when the growth pathway changed from photoautotrophic via mixotrophic to heterotrophic. Total fatty acid concentration also diminished in this order. Principal component analysis confirmed the significance of FA profiling to mirror nutritional pathways. Lake- water analysis revealed low concentrations of dissolved organic carbon, mainly consisting of polymeric fulvic acids that are unable to support heterotrophic growth of Chlamydomonas sp. Polymeric fulvic acids present in the deeper strata of the lake turned out to be formed in situ on the basis of organic monomers including reduced sulfur-containing ones, as revealed by thermochemolysis and pyrolysis. Growth of Chlamydomonas sp. in the deep chlorophyll maximum is therefore assumed to mainly result from photosynthesis, despite very low photon densities. Phytol-including metabolites proved to be significant biomarkers to indicate the nutritional pathway of Chlamydomonas sp. a, x-Dicarboxylic acids{\`u}light- induced degradation products of unsaturated fatty acids{\`u}appeared to be good indicators of photooxidative alterations to the algal species under study.}, language = {en} } @article{CleggMaberlyJones2004, author = {Clegg, Mark R. and Maberly, Stephen C. and Jones, Roger I.}, title = {Dominance and compromise in freshwater phytoplanktonic flagellates : the interaction of behavioural preferences for conflicting environmental gradients}, year = {2004}, language = {en} } @article{KoechyWilson2004, author = {K{\"o}chy, Martin and Wilson, Scott D.}, title = {Semiarid grassland responses to short-term variation in water availability}, issn = {1385-0237}, year = {2004}, abstract = {Standing crop and species composition in semiarid grassland are linked to long-term patterns of water availability, but grasslands are characterized by large single-season variability in rainfall. We tested whether a single season of altered water availability influenced the proportions of grasses and shrubs in a semiarid grassland near the northern edge of the North American Great Plains. We studied stands of the clonal shrub snowberry (Symphoricarpos occidentalis) and adjacent grassland dominated by the native grasses Stipa spartea and Bouteloua gracilis. Rain was excluded and water supplied in amounts corresponding to years of low, medium, and high rainfall, producing a 2 - 4-fold range in monthly precipitation among water supply treatments. There were ten replicate plots of each water treatment in both snowberry stands and grassland. Grass standing crop increased significantly with water availability in grassland but not inside snowberry stands. Total standing crop and shrub stem density increased significantly with water supply, averaged across both communities. In contrast, water had no effect on shrub standing crop or light penetration. In summary, our finding that water has significant effects on a subset of components of grassland vegetation is consistent with long-term, correlational studies, but we also found that a single season of altered water supply had no effect on other important aspects of the ecosystem.}, language = {en} } @article{SpijkermanGarciaMendozaMatthijsetal.2004, author = {Spijkerman, Elly and Garcia-Mendoza, E. and Matthijs, H. C. P. and Van Hunnik, E. and Coesel, P. F. M.}, title = {Negative effects of P-buffering and pH on photosynthetic activity of planktonic desmid species}, year = {2004}, abstract = {The photosynthetic activities of three planktonic desmid species (Staurastrum brachiatum, Staurodesmus cuspidatus var. curvatus, and Staurastrum chaetoceras) were compared after adaptation to medium enriched with either a 20 mM Na+- phosphate (P) or HEPES buffer. Incubations up to 2 d were carried out at pH 6 or 8 under normal air or air enriched with 5 \% CO2. Gross maximum photosynthetic rate (Pmax) and growth rate were decreased in both S. brachiatum and Std. cuspidatus at higher pH when using the HEPES buffer and this effect was independent of CO2 concentration, indicating that pH had an inhibitory effect on photosynthesis and growth in these species. The P-buffer at pH 8 caused a large decrease in Pmax and quantum yield for charge separation in photosystem 2 (PS2), compared to HEPES-buffered algae. This effect was very large in both S. brachiatum and Std. cuspidatus, two species characteristic of soft water lakes, but also significant in S. chaetoceras, a species dominant in eutrophic, hard water lakes. The decreased Pmax in P- buffer could not be related to a significant increase in cellular P content known to be responsible for inhibition in isolated chloroplasts. Experiments at pH 6 and 8 showed that two conditions, high pH and high Na+ concentration, both contributed to the decreased Pmax and quantum yield in the desmids. Effects of a P-buffer were less pronounced by using K+-P buffer. The use of P-buffer at pH 8 possibly resulted in high irradiance stress in all species, indicated by damage in the PS2 core complex. In the soft water species pH 8 resulted in increased non-photochemical quenching together with a high de-epoxidation state of the xanthophyll cycle pigments.}, language = {en} } @article{FischerPfistererJoshietal.2004, author = {Fischer, Markus and Pfisterer, A. and Joshi, Jasmin Radha and Schmid, Bernhard}, title = {Rapid decay of diversity-productivity relationships after invasion of experimental plant communities}, year = {2004}, language = {en} } @article{RohdeHinchaHeyer2004, author = {Rohde, P. and Hincha, Dirk K. and Heyer, Arnd G.}, title = {Heterosis in the freezing tolerance of crosses between two Arabidopsis thaliana accessions (Columbia-0 and C24) that show differences in non-acclimated and acclimated freezing tolerance}, issn = {0960-7412}, year = {2004}, language = {en} } @article{VerginFreierGzik2004, author = {Vergin, Anika and Freier, B. and Gzik, Axel}, title = {Investigations on effects of plant strengthening products to tri-trophic system field bean (Vicia faba (L.)) - black bean aphid (Aphis fabae Scop.) - lacewing larva (Chrysoperla carnea Steph.)}, year = {2004}, language = {en} } @article{JeltschWichmannDean2004, author = {Jeltsch, Florian and Wichmann, Matthias and Dean, W. R. J.}, title = {Global change challenges the Tawny Eagle (Aquila rapax) : modelling extinction risk with respect to predicted climate and land use changes}, year = {2004}, language = {en} } @article{ObelUsadelChooetal.2004, author = {Obel, Nicolai and Usadel, Bj{\"o}rn and Choo, Tze Siang and Pauly, Markus}, title = {Analysing cell wall biosynthesis to study its role in biotic and abiotic stress reactions}, isbn = {3-00-011587-0}, year = {2004}, language = {en} } @article{RhoadesCohenGussakovskyetal.2004, author = {Rhoades, E. and Cohen, M. and Gussakovsky, E. and Schuler, Benjamin and Haran, G.}, title = {Single molecule protein folding}, issn = {0006-3495}, year = {2004}, language = {en} } @article{SauerWartenbergSachinidisetal.2004, author = {Sauer, Heinrich and Wartenberg, Maria and Sachinidis, A. and Hescheler, J{\"u}rgen}, title = {The development of the cardiovascular system in embryoid bodies deriverd from embryonic stem cells}, isbn = {1-588- 29113-8}, year = {2004}, language = {en} } @article{SchellerWagener2004, author = {Scheller, Frieder W. and Wagener, C.}, title = {From gene to life}, year = {2004}, language = {en} } @article{SchellerBier2004, author = {Scheller, Frieder W. and Bier, Frank Fabian}, title = {Analytical Biochemistry (Editorial)}, year = {2004}, language = {en} } @article{BeissenhirtzSchellerStoeckleinetal.2004, author = {Beissenhirtz, Moritz Karl and Scheller, Frieder W. and St{\"o}cklein, Walter F. M. and Kurth, D. and M{\"o}hwald, Helmuth and Lisdat, Fred}, title = {Electroactive cytochrome c multilayers within a polyelectrolyte assembly}, year = {2004}, language = {en} } @article{KroeningSchellerWollenbergeretal.2004, author = {Kr{\"o}ning, Steffen and Scheller, Frieder W. and Wollenberger, Ursula and Lisdat, Fred}, title = {Myoglobin-Clay Electrode for Nitric Oxide (NO) Detection in Solution}, year = {2004}, language = {en} } @article{LieckfeldtSimonRosinZoelleretal.2004, author = {Lieckfeldt, Elke and Simon-Rosin, Ulrike and Z{\"o}ller, Daniela and Ebert, Berit and Kehr, Julia and Fisahn, Joachim}, title = {Spatio/temporal analysis of gene exression profiles within single cells and specific tissue types of developing Arabidopsis plants}, isbn = {3-00-011587-0}, year = {2004}, language = {en} } @article{SchurrDeanMiltonetal.2004, author = {Schurr, Frank Martin and Dean, W. R. J. and Milton, Sue J. and Jeltsch, Florian}, title = {A conceptual model linking demography of the shrub species Grewia flava to the dynamics of Kalahari savannas}, year = {2004}, abstract = {Environmental heterogeneity is a major determinant of plant population dynamics. In semi-arid Kalahari savannas, heterogeneity is created by savanna structure, i.e. by the spatial arrangement and temporal dynamics of woody plant and open grassland microsites. We formulate a conceptual model describing the effects of savanna dynamics on the population dynamics of the animal-dispersed shrub Grewia flava. From empirical results we derive model rules describing effects of savanna structure on several processes in Grewia's life cycle. By formulating the model, we summarise existing information on Grewia demography and identify gaps in this knowledge. Despite a number of such gaps, the model can be used to make certain quantitative predictions. As an example, we apply the model to investigate the role of seed dispersal in Grewia encroachment on rangelands. Model results show that cattle promote encroachment by depositing substantial numbers of seeds in open areas, where Grewia is otherwise dispersal-limited. Finally, we draw some general conclusions about Grewia's life history and population dynamics. Under natural conditions, concentrated seed deposition under woody plants appears to be a key process causing the observed association between Grewia and other woody plants. Furthermore, low rates of recruitment and high adult survival result in slow-motion dynamics of Grewia populations. As a consequence, Grewia populations interact with savanna dynamics on long temporal and short to intermediate spatial scales.}, language = {en} } @article{SchurrBossdorfMiltonetal.2004, author = {Schurr, Frank Martin and Bossdorf, Oliver and Milton, Sue J. and Schumacher, J.}, title = {Spatial pattern formation in semi-arid shrubland : a priori predicted versus observed pattern characteristics}, year = {2004}, abstract = {Ecologists increasingly use spatial statistics to study vegetation patterns. Mostly, however, these techniques are applied in a purely descriptive fashion without a priori statements on the pattern characteristics expected. We formulated such a priori predictions in a study of spatial pattern in a semi-arid Karoo shrubland, South Africa. Both seed dispersal and root competition have been discussed as processes shaping the spatial structure of this community. If either of the two processes dominates pattern formation, patterns within and between shrub functional groups are expected to show distinct deviations from null models. We predicted the type and scale of these deviations and compared predicted to observed pattern characteristics. As predicted by the seed dispersal hypothesis, small-scale co-occurrence within and between groups of colonisers and successors was increased as compared to complete spatially random arrangement of shrubs. The root competition predictions, however, were not met as shrubs of similar rooting depth co- occurred more frequently than expected under random shrub arrangement. Since the distribution of rooting groups to the given shrub locations also failed to match the root competition predictions, there was little evidence for dominance of root competition in pattern formation. Although other processes may contribute to small-scale plant co-occurrence, the sufficient and most parsimonious explanation for the observed pattern is that its formation was dominated by seed dispersal. To characterise point patterns we applied both cumulative (uni- and bivariate K-function) and local (pair- and mark-correlation function) techniques. Based on our results we recommend that future studies of vegetation patterns include local characteristics as they independently describe a pattern at different scales and can be easily related to processes changing with interplant distance in a predictable fashion.}, language = {en} } @article{WarnckeVogtUlrichetal.2004, author = {Warncke, Max and Vogt, Birgit and Ulrich, Jacqueline and von Laer, Meike Dorothee and Beyer, Winfried and Klump, Hannes and Micheel, Burkhard and Sheriff, Ahmed}, title = {Efficient in vitro transduction of naive murine B cells with lentiviral vectors}, year = {2004}, abstract = {The aim of this study was to determine the impact of lentiviral transduction on primary murine B cells. Studying B cell activities in vivo or using them for tolerance induction requires that the cells remain unaltered in their biological behavior except for expression of the transgene. As we show here, murine B cells can efficiently be transduced by lentiviral, VSV-G-pseudotyped vectors without the necessity of prior activation. Culture with LPS gave enhanced transduction efficiencies but led to the upregulation of CD86 and proliferation of the cells. Transduction of naive B cells by lentiviral vectors was dependent on multiplicity of infection and did not lead to a concomitant activation. Furthermore, the transduced cells could be used for studies in the NOD mouse system without altering the onset of diabetes. We conclude that lentiviral gene transfer into naive B cells is a powerful tool for manipulation of B cells for therapeutic applications.}, language = {en} } @article{SchenkMatyssekMicheel2004, author = {Schenk, J{\"o}rg A. and Matyssek, Franziska and Micheel, Burkhard}, title = {Interleukin 4 increases the antibody response against Rubisco in mice}, year = {2004}, abstract = {The influence of interleukin 4 (IL-4) on antibody titer in serum and spleen culture supernatant in mice immunized with spinach (Spinacia oleracea L.) Rubisco was investigated. Therefore, we boosted one mouse additionally to the antigen with recombinant mouse IL-4. We found that the Rubisco-specific antibody titer in serum as well as in spleen cell culture supernatant was significantly enhanced in the IL-4 mouse. Most of the antibodies were of the IgG1 subclass. After hybridoma generation, Rubisco-specific antibodies were found in more than 95\% of the wells tested compared to about 12\% of the control mouse.}, language = {en} } @article{AleAghaBolayBraunetal.2004, author = {Ale-Agha, Nosratollah and Bolay, Adrien and Braun, Uwe and Jage, Horst and Kummer, Volker and Lebeda, Ales and Piatek, Marcin and Shin, Hyeon-Dong and Zimmermannova-Pastircakova, Katarina}, title = {Erysiphe catalpae and E. elevata in Europe}, year = {2004}, language = {en} } @article{vanKleunenRitland2005, author = {van Kleunen, Mark and Ritland, K.}, title = {Estimating heritabilities and genetic correlations with marker-based methods : an experimental test in Mimulus guttatus}, year = {2005}, abstract = {The calculation of heritabilities and genetic correlations, which are necessary for predicting evolutionary responses, requires knowledge about the relatedness between individuals. This information is often not directly available, especially not for natural populations, but can be inferred by using molecular markers such as allozymes. Several methods based on inferred relatedness from marker data have been developed to estimate heritabilities and genetic correlations in natural populations. Most methods use maximum-likelihood procedures to assign pairs or groups of individuals to predefined discrete relatedness classes (e.g., half sibs and unrelated individuals). The Ritland method, on the other hand, uses method of moments estimators to estimate pairwise relatedness among individuals as continuous values. We tested both the Ritland method and a maximum-likelihood method by applying them to a greenhouse population consisting of seed families of the herb Mimulus guttatus and comparing the results to the ones from a frequently used standard method based on half-sib families. Estimates of genetic correlations were far from accurate, especially when we used the Ritland method. However, this study shows that even with a few variable allozyme loci, it is possible to get qualitatively good indications about the presence of heritable genetic variation from marker-based methods, even though both methods underestimated it}, language = {en} } @article{VirtaKochRoslundetal.2005, author = {Virta, P. and Koch, Andreas and Roslund, M. U. and Mattjus, P. and Kleinpeter, Erich and Kronberg, L. and Sjoholm, R. and Klika, Karel D.}, title = {Synthesis, characterisation and theoretical calculations of 2,6-diaminopurine etheno derivatives}, issn = {1477-0520}, year = {2005}, abstract = {Four derivatives of 2,6-diaminopurine (1) were synthesised and characterised. When 1 was reacted with chloroacetaldehyde, 5-aminoimidazo[2,1- i] purine (2), 9-aminoimidazo[2,1-b]purine (3), 9-aminoimidazo[1,2- a]purine (4) and diimidazo[2,1-b: 2', 1'-i]purine (5) were formed. The purified products (3 - 5) were fully characterised by MS, complete NMR assignments as well as fluorescence and UV spectroscopy. The purified, isolated yields of these products ( 3 - 5) varied from 2.5 to 30\%. The relative stability of different tautomers was investigated by theoretical calculations. Fluorescence characteristics are also discussed and compared to the starting material 1 and a reference molecule 2-aminopurine}, language = {en} } @article{XieTechritzHaebeletal.2005, author = {Xie, J. and Techritz, S. and Haebel, Sophie and Horn, A. and Neitzel, H. and Klose, J. and Schuelke, M.}, title = {A two-dimensional electrophoretic map of human mitochondrial proteins from immortalized lymphoblastoid cell lines: a prerequisite to study mitochondrial disorders in patients}, issn = {1615-9853}, year = {2005}, abstract = {Mitochondrial diseases may be caused by numerous mutations that alter proteins of the respiratory chain and of other metabolic pathways in the mitochondrium. For clinicians this disease group poses a considerable diagnostic challenge due to ambiguous genotype-phenotype relationships. Until now, only 30 \% of the mitochondriopathies can be diagnosed at the molecular level. We therefore need a new diagnostic tool that offers a wide view on the mitochondrial proteins. Here, we present a method to generate a high-resolution, large-gel two-dimensional gel electrophoretic (2-DE) map of a purified fraction of mitochondrial proteins from Epstein-Barr virus-immortalized lymphoblastoid cell line (LCL). LCLs can be easily obtained from patients and control subjects in a routine clinical setting. They often express the biochemical phenotype and can be cultured to high cell numbers, sufficient to gain enough purified material for 2- DE. In total we identified 166 mitochondrial proteins. Thirteen proteins were earlier not known to be of mitochondrial origin. Thirty-nine proteins were associated with human diseases ranging from respiratory chain enzyme deficiencies to disorders of P-oxidation and amino acid metabolism. This 2-DE map is intended to be the first step to diagnose mitochondrial diseases at the proteomic level}, language = {en} } @article{WichmannGroeneveldJeltschetal.2005, author = {Wichmann, Matthias and Groeneveld, J{\"u}rgen and Jeltsch, Florian and Grimm, Volker}, title = {Mitigation of climate change impacts on raptors by behavioural adaptation : ecological buffering mechanisms}, issn = {0921-8181}, year = {2005}, abstract = {The predicted climate change causes deep concerns on the effects of increasing temperatures and changing precipitation patterns on species viability and, in turn, on biodiversity. Models of Population Viability Analysis (PVA) provide a powerful tool to assess the risk of species extinction. However, most PVA models do not take into account the potential effects of behavioural adaptations. Organisms might adapt to new environmental situations and thereby mitigate negative effects of climate change. To demonstrate such mitigation effects, we use an existing PVA model describing a population of the tawny eagle (Aquila rapax) in the southern Kalahari. This model does not include behavioural adaptations. We develop a new model by assuming that the birds enlarge their average territory size to compensate for lower amounts of precipitation. Here, we found the predicted increase in risk of extinction due to climate change to be much lower than in the original model. However, this "buffering" of climate change by behavioural adaptation is not very effective in coping with increasing interannual variances. We refer to further examples of ecological "buffering mechanisms" from the literature and argue that possible buffering mechanisms should be given due consideration when the effects of climate change on biodiversity are to be predicted. (c) 2004 Elsevier B.V. All rights reserved}, language = {en} } @article{Weithoff2005, author = {Weithoff, Guntram}, title = {On the ecology of the rotifer Cephalodella hoodi from an extremely acidic lake}, issn = {0046-5070}, year = {2005}, abstract = {1. The biovolume-specific carbon content, relative egg volume (a measure of per-offspring reproductive investment), growth and grazing rates, and the gross growth efficiency (GGE) of the rotifer Cephalodella hoodi, isolated from an extremely acidic habitat (pH 2.65), were determined and compared with literature values for rotifers living in circum-neutral habitats in order to reveal potential special features or adaptations related to the extreme habitat of C. hoodi. 2. Of the two dominant phytoflagellates (Ochromonas sp. and Chlamydomonas acidophila) that occur in the natural habitat of C. hoodi, only C. acidophila promoted positive growth and reproduction and, thus, the following results were obtained with C. acidophila as a food alga. 3. The body volume-specific carbon content of C. hoodi is in the range of that found in rotifers from circum-neutral lakes, suggesting that no costly carbon investment, brought about by the thickening of the lorica, for example, was required to withstand low pH. 4. The egg volume of C. hoodi exhibited no phenotypic plasticity dependent on the food concentration and, thus, C. hoodi allocated a constant, absolute amount of energy to each individual offspring. No adaptation to low food densities was found. 5. A dome-shaped type II functional response curve was found to describe the ingestion of Chlamydomonas as a source of food. 6. Compared with other rotifers, C. hoodi had a high threshold and half-saturating food concentration (=low affinity) but also a high maximum growth rate and a relatively high GGE, suggesting no severe adverse effect of low pH}, language = {en} } @article{VorgerdvanderVenBruchertseiferetal.2005, author = {Vorgerd, M. and vanderVen, Peter F. M. and Bruchertseifer, V. and Lowe, T. and Kley, R. A. and Schr{\"o}der, Rolf and Lochmuller, H. and Himmel, Mirko and Koehler, K. and F{\"u}rst, Dieter Oswald and Huebner, A.}, title = {A mutation in the dimerization domain of filamin C causes a novel type of autosomal dominant myofibrillar myopathy}, issn = {0002-9297}, year = {2005}, abstract = {Myofibrillar myopathy (MFM) is a human disease that is characterized by focal myofibrillar destruction and pathological cytoplasmic protein aggregations. In an extended German pedigree with a novel form of MFM characterized by clinical features of a limb-girdle myopathy and morphological features of MFM, we identified a cosegregating, heterozygous nonsense mutation (8130G -> A; W2710X) in the filamin c gene ( FLNC) on chromosome 7q32.1. The mutation is the first found in FLNC and is localized in the dimerization domain of filamin c. Functional studies showed that, in the truncated mutant protein, this domain has a disturbed secondary structure that leads to the inability to dimerize properly. As a consequence of this malfunction, the muscle fibers of our patients display massive cytoplasmic aggregates containing filamin c and several Z-disk-associated and sarcolemmal proteins}, language = {en} } @article{VenevskyVenevskaia2005, author = {Venevsky, Sergey and Venevskaia, Irina}, title = {Hierarchical systematic conservation planning at the national level : Identifying national biodiversity hotspots using abiotic factors in Russia}, year = {2005}, abstract = {National conservation planning should operate with measures of biodiversity similar to those applied globally in order to harmonize national and international conservation strategies. Here we suggest quantitative measures which enable two criteria of the global biodiversity hotspots to be applied on a national level for 74 large countries, and show how these measures can be applied to map national biodiversity hotspots. The plant endemism criteria of global hotspots are captured by quantitative measures of endemism, which are approximately scale-independent and can be corrected to account for a country's environmental conditions and conservation priorities. The flexible land use criteria for national biodiversity hotspots are defined from percentage of natural vegetation remaining in the global hotspots. The minimum-area-required approach is applied to define the borders of national biodiversity hotspots using data on vascular plants species richness. We show how national biodiversity hotspots can be mapped from the species- energy relationship for vascular plants using climate, topographical and land use data when spatial pattern of species richness is not known. This methodology to map national biodiversity hotspots from abiotic factors is applied to Russia as a case study. Three Russian biodiversity hotspots, North Caucasus, South Siberia and Far East were identified. The resulting hotspot maps cover national-scale environmental gradients across Russia and although they are also identified by Russian experts their actual geographical locations were hitherto unspecified. The large-scale national hotspots, identified for Russia, can be used for further fine scale and more detailed conservation planning. (c) 2005 Elsevier Ltd. All rights reserved}, language = {en} } @article{SankaranHananScholesetal.2005, author = {Sankaran, Mahesh and Hanan, Niall P. and Scholes, Robert J. and Ratnam, Jayashree and Cade, Brian S. and Ardo, Jonas and Augustine, David J. and Banyikwa, Feetham and Bronn, Andries and Bucini, Gabriela and Caylor, Kelly K. and Coughenour, Michael B. and Diouf, Alioune and Feral, Christie J. and February, Edmund C. and Frost, Peter G. H.}, title = {Determinants of woody cover in African savannas}, year = {2005}, abstract = {Savannas are globally important ecosystems of great significance to human economies. In these biomes, which are characterized by the co-dominance of trees and grasses, woody cover is a chief determinant of ecosystem properties(1-3). The availability of resources ( water, nutrients) and disturbance regimes ( fire, herbivory) are thought to be important in regulating woody cover(1,2,4,5), but perceptions differ on which of these are the primary drivers of savanna structure. Here we show, using data from 854 sites across Africa, that maximum woody cover in savannas receiving a mean annual precipitation (MAP) of less than similar to 650 mm is constrained by, and increases linearly with, MAP. These arid and semi-arid savannas may be considered 'stable' systems in which water constrains woody cover and permits grasses to coexist, while fire, herbivory and soil properties interact to reduce woody cover below the MAP- controlled upper bound. Above a MAP of similar to 650 mm, savannas are 'unstable' systems in which MAP is sufficient for woody canopy closure, and disturbances ( fire, herbivory) are required for the coexistence of trees and grass. These results provide insights into the nature of African savannas and suggest that future changes in precipitation(6) may considerably affect their distribution and dynamics}, language = {en} } @article{vanKleunenJohnson2005, author = {van Kleunen, Mark and Johnson, S. D.}, title = {Testing for ecological and genetic Allee effects in the invasive shrub Senna didymobotrya (Fabaceae)}, year = {2005}, abstract = {For an introduced plant species to become invasive, it must be able to reproduce even in initially small populations We tested for Aliee effects (reduced reproductive performance of individuals in small populations) in the nonclonal, NW-pollinated shrub Senna didymobotrya in its invasive range in South Africa. The species is self-compatible. but we found that in its invasive range in South Africa it requires pollinators to set seed. Nearly all stigmas (90\%) received pollen. but natural fruit set has very low (3-20\%), Pollen receipt and fruit set were not significantly correlated with population size. We thus found no evidence for an ecological Alice effect arising from pollen limitation in small populations. Offspring seedling performance, measured in terms of stern volume and leaf area, was also not significantly correlated with the number of plants in the source population. indicating that genetic Alice effects, such as inbreeding depression, are either absent or of such a small magnitude that they would be unlikely to limit further spread of S. didymobotrya in South Africa}, language = {en} } @article{vanKleunenFischerSchmid2005, author = {van Kleunen, Mark and Fischer, Markus and Schmid, Bernhard}, title = {Three generations under low versus high neighborhood density affect the life history of a clonal plant through differential selection and genetic drift}, year = {2005}, abstract = {We tested whether neighborhood density affects the clonal life history of the stoloniferous plant Ranunculus reptans through selection and genetic drift. After three generations of sexual reproduction of 16 low- and 16 high- density lines, we studied traits related to growth form and reproduction in a common competition free environment. A 7.7\% lower branching frequency and slightly longer internodes indicated an evolutionary shift towards a less compact growth form under high neighborhood density, but because stolons grew also more vertically, horizontal spread per ramet was slightly decreased. Neighborhood density had no directional effects on the evolution of allocation to sexual and vegetative reproduction in R. reptans. Variation among replicated high-density lines was significantly lower than among replicated low-density lines in both growth form and reproductive characteristics, indicating less pronounced genetic drift under high neighborhood density. This study demonstrates that a clonal plant can respond to selection imposed by neighborhood density. Moreover, it shows that the effect of random genetic drift increases with decreasing neighborhood density. In a declining species, such as R. reptans in central Europe, this may lower the potential for adaptive evolutionary change and increase extinction risk}, language = {en} } @article{vanKleunenFischer2005, author = {van Kleunen, Mark and Fischer, Markus}, title = {Constraints on the evolution of adaptive phenotypic plasticity in plants}, year = {2005}, abstract = {The high potential fitness benefit of phenotypic plasticity tempts us to expect phenotypic plasticity as a frequent adaptation to environmental heterogeneity. Examples of proven adaptive plasticity in plants, however, are scarce and most plastic responses actually may be 'passive' rather than adaptive. This suggests that frequently requirements for the evolution of adaptive plasticity are not met or that such evolution is impeded by constraints. Here we outline requirements and potential constraints for the evolution of adaptive phenotypic plasticity, identify open questions, and propose new research approaches. Important open questions concern the genetic background of plasticity, genetic variation in plasticity, selection for plasticity in natural habitats, and the nature and occurrence of costs and limits of plasticity. Especially promising tools to address these questions are selection gradient analysis, meta-analysis of studies on genotype-by-environment interactions, QTL analysis, cDNA-microarray scanning and quantitative PCR to quantify gene expression, and two-dimensional gel electrophoresis to quantify protein expression. Studying plasticity along the pathway from gene expression to the phenotype and its relationship with fitness will help us to better understand why adaptive plasticity is not more universal, and to more realistically predict the evolution of plastic responses to environmental change}, language = {en} } @article{TittelBissingerGaedkeetal.2005, author = {Tittel, J{\"o}rg and Bissinger, Vera and Gaedke, Ursula and Kamjunke, Norbert}, title = {Inorganic carbon limitation and mixotrophic growth in Chlamydomonas from an acidic mining lake}, issn = {1434-4610}, year = {2005}, abstract = {Plankton communities in acidic mining lakes (pH 2.5-3.3) are species-poor because they face extreme environmental conditions, e.g. 150 mg l(-1) Fe2++Fe3+. We investigated the growth characteristics of the dominant pigmented species, the flagellate Chlamydomonas acidophila, in semi-continuous culture experiments under in situ conditions. The following hypotheses were tested: (1) Low inorganic carbon (IC) concentrations in the epilimnion (e.g. 0.3 mg l(-1)) arising from the low pH limit phototrophic growth (H-1); (2) the additional use of dissolved organic carbon (mixotrophy) leads to higher growth rates under IC-limitation (H-2), and (3) phagotrophy is not relevant (H-3). H- 1 was supported as the culture experiments, in situ PAR and IC concentrations indicated that IC potentially limited phototrophic growth in the mixed surface layers. H-2 was also supported: mixotrophic growth always exceeded pure phototrophic growth even when photosynthesis was saturated. Dark growth in filtered lake water illuminated prior to inoculation provided evidence that Chlamydomonas was able to use the natural DOC. The alga did not grow on bacteria, thus confirming H-3. Chlamydomonas exhibited a remarkable resistance to starvation in the dark. The compensation light intensity (ca. 20 mu mol photons m(-2) s(-1)) and the maximum phototrophic growth (1.50 d(-1)) fell within the range of algae from non-acidic waters. Overall, Chlamydomonas, a typical r-strategist in circum-neutral systems, showed characteristics of a K-strategist in the stable, acidic lake environment in achieving moderate growth rates and minimizing metabolic losses. (c) 2005 Elsevier GmbH. All rights reserved}, language = {en} } @article{TirrellKatz2005, author = {Tirrell, M. V. and Katz, A.}, title = {Self-assembly in materials synthesis}, issn = {0883-7694}, year = {2005}, abstract = {The synthesis of materials via self-assembly typically involves the spontaneous and reversible organization,of small building blocks for the purpose of creating conglomerate assembly structures over larger length scales. This introductory article, describes self processes on several length scales, from subnanometer, up to millimeter scales, and briefly summarizes some of the incredible diversity of materials that exhibit self-assembly. Articles in this issue cover self-assembly using zeolitic structures, organic molecular crystals; block copolymers, surfactants, mesoscale templates, and soluble. crystallization additives}, language = {en} } @article{TiedemannMollPaulusetal.2005, author = {Tiedemann, Ralph and Moll, K. and Paulus, Kirsten B. and Schlupp, Ingo}, title = {New microsatellite loci confirm hybrid origin, parthenogenetic inheritance, and mitotic gene conversion in the gynogenetic Amazon molly (Poecilia formosa)}, issn = {1471-8278}, year = {2005}, abstract = {We describe the first microsatellite loci for the gynogenetic Amazon molly, Poecilia formosa, an all-female species arisen through hybridization of the bisexual species Poecilia mexicana and Poecilia latipinna. The loci showed one to six alleles and an expected heterozygosity between zero and 0.75. As expected with parthenogenetic inheritance, most loci were either constantly homozygous (five loci) or constantly heterozygous (eight loci). For six loci, both heterozygotes and homozygotes occurred. This and the fact that some loci only showed alleles of one of the ancestral species could indicate genome homogenization through mitotic gene conversion. Our new loci conformed to the hybrid origin of Amazon molly and are also applicable to both ancestral bisexual species}, language = {en} } @article{SteffenvonNickischRosenegkBier2005, author = {Steffen, Jenny and von Nickisch-Rosenegk, Markus and Bier, Frank Fabian}, title = {In vitro transcription of a whole gene on a surface-coupled template}, issn = {1473-0189}, year = {2005}, abstract = {An artificial gene was constructed combining the T7 promoter and terminator with the EGFP-gene from the plasmid pEGFP. The functionality of the construct was shown by in vitro translation. The gene-construct was immobilised on a planar glass surface. The transcription was performed on the immobilised gene and mRNA was determined by RT-PCR. Multiple use of the immobilised gene was demonstrated}, language = {en} } @article{SchurrBondMidgleyetal.2005, author = {Schurr, Frank Martin and Bond, William J. and Midgley, Guy F. and Higgins, Steven I.}, title = {A mechanistic model for secondary seed dispersal by wind and its experimental validation}, issn = {0022-0477}, year = {2005}, abstract = {1 Secondary seed dispersal by wind, the wind-driven movement of seeds along the ground surface, is an important dispersal mechanism for plant species in a range of environments. 2 We formulate a mechanistic model that describes how secondary dispersal by wind is affected by seed traits, wind conditions and obstacles to seed movement. The model simulates the movement paths of individual seeds and can be fully specified using independently measured parameters. 3 We develop an explicit version of the model that uses a spatially explicit representation of obstacle patterns, and also an aggregated version that uses probability distributions to model seed retention at obstacles and seed movement between obstacles. The aggregated version is computationally efficient and therefore suited to large-scale simulations. It provides a very good approximation of the explicit version (R-2 > 0.99) if initial seed positions vary randomly relative to the obstacle pattern. 4 To validate the model, we conducted a field experiment in which we released seeds of seven South African Proteaceae species that differ in seed size and morphology into an arena in which we systematically varied obstacle patterns. When parameterized with maximum likelihood estimates obtained from independent measurements, the explicit model version explained 70-77\% of the observed variation in the proportion of seeds dispersed over 25 m and 67- 69\% of the observed variation in the direction of seed dispersal. 5 The model tended to underestimate dispersal rates, possibly due to the omission of turbulence from the model, although this could also be explained by imprecise estimation of one model parameter (the aerodynamic roughness length). 6 Our analysis of the aggregated model predicts a unimodal relationship between the distance of secondary dispersal by wind and seed size. The model can also be used to identify species with the potential for long-distance seed transport by secondary wind dispersal. 7 The validated model expands the domain of mechanistic dispersal models, contributes to a functional understanding of seed dispersal, and provides a tool for predicting the distances that seeds move}, language = {en} } @article{XuBrearleyLinetal.2005, author = {Xu, J. and Brearley, C. A. and Lin, W. H. and Wang, Y. and Ye, R. and M{\"u}ller-R{\"o}ber, Bernd and Xu, Z. H. and Xue, H. W.}, title = {A role of Arabidopsis inositol polyphosphate kinase, AtIPK2 alpha, in pollen germination and root growth}, issn = {0032-0889}, year = {2005}, abstract = {Inositol polyphosphates, such as inositol trisphosphate, are pivotal intracellular signaling molecules in eukaryotic cells. In higher plants the mechanism for the regulation of the type and the level of these signaling molecules is poorly understood. In this study we investigate the physiological function of an Arabidopsis (Arabidopsis thaliana) gene encoding inositol polyphosphate kinase (AtIPK2alpha), which phosphorylates inositol 1,4,5-trisphosphate successively at the D-6 and D-3 positions, and inositol 1,3,4,5-tetrakisphosphate at D-6, resulting in the generation of inositol 1,3,4,5,6-pentakisphosphate. Semiquantitative reverse transcription-PCR and promoter-beta-glucuronidase reporter gene analyses showed that AtIPK2alpha is expressed in various tissues, including roots and root hairs, stem, leaf, pollen grains, pollen tubes, the flower stigma, and siliques. Transgenic Arabidopsis plants expressing the AtIPK2alpha antisense gene under its own promoter were generated. Analysis of several independent transformants exhibiting strong reduction in AtIPK2alpha transcript levels showed that both pollen germination and pollen tube growth were enhanced in the antisense lines compared to wild-type plants, especially in the presence of nonoptimal low Ca2+ concentrations in the culture medium. Furthermore, root growth and root hair development were also stimulated in the antisense lines, in the presence of elevated external Ca2+ concentration or upon the addition of EGTA. In addition, seed germination and early seedling growth was stimulated in the antisense lines. These observations suggest a general and important role of AtIPK2alpha, and hence inositol polyphosphate metabolism, in the regulation of plant growth most likely through the regulation of calcium signaling, consistent with the well-known function of inositol trisphosphate in the mobilization of intracellular calcium stores}, language = {en} } @article{SchmalzlinvanDongenKlimantetal.2005, author = {Schmalzlin, E. and van Dongen, J. T. and Klimant, I. and Marmodee, Bettina and Steup, Martin and Fisahn, Joachim and Geigenberger, Peter Ludwig and L{\"o}hmannsr{\"o}ben, Hans-Gerd}, title = {An optical multifrequency phase-modulation method using microbeads for measuring intracellular oxygen concentrations in plants}, issn = {0006-3495}, year = {2005}, abstract = {A technique has been developed to measure absolute intracellular oxygen concentrations in green plants. Oxygen- sensitive phosphorescent microbeads were injected into the cells and an optical multifrequency phase-modulation technique was used to discriminate the sensor signal from the strong auto fluorescence of the plant tissue. The method was established using photosynthesis- competent cells of the giant algae Chara corallina L., and was validated by application to various cell types of other plant species}, language = {en} } @article{Spijkerman2005, author = {Spijkerman, Elly}, title = {Inorganic carbon acquisition by Chlamydomonas acidophila across a pH range}, issn = {0008-4026}, year = {2005}, abstract = {Chlamydomonas acidophila Negoro had a higher maximum growth rate upon aeration with 5\% CO2 (v/v) than in nonaerated conditions at an external pH above 2. In medium with a pH of 1.0 or 2.0, a decrease in the maximum growth rate was observed upon CO2 aeration in comparison with nonaerated conditions. At both very low and very high external pH conditions, an induction of external carbonic anhydrase was detected; this being more pronounced in CO2-aerated cells than in nonaerated cells. It is therefore suggested that the induction of carbonic anhydrase is part of a stress response in Chlamydomonas acidophila. Comparison of some physiological characteristics of Chlamydomonas acidophila acclimated at pH 2.65 and at pH 6.0, revealed that CO2 aeration increased gross maximum photosynthesis at both pHs, whereas respiration, light acclimation, and photoinhibition were not effected. At pH 2.65, Chlamydomonas acidophila was found to have a carbon-concentrating mechanism under nonaerated conditions, whereas it did not under CO2-aerated conditions at pH 6. The affinity for CO2 use in O-2 production was not dependent on CO2 aeration, but it was much lower at pH 6 than it was at pH 2.65. CO2 kinetic characteristics indicate that the photosynthesis of Chlamydomonas acidophila in its natural environment is not limited by inorganic carbon}, language = {en} } @article{RoggeItagakiFishkinetal.2005, author = {Rogge, B. and Itagaki, Y. and Fishkin, N. and Levi, E. and Ruhl, R. and Yi, S. S. and Nakanishi, K. and Hammerling, U.}, title = {Retinoylserine and retinoylalanine, natural products of the moth Trichoplusia ni}, issn = {0163-3864}, year = {2005}, abstract = {Insect cells convert vitamin A into a number of retinoids that are evolutionarily conserved with those of mammalian cells. However, insect cells also produce additional natural retinoids. Namely, two retinoic acid peptides, N- trans-retinoylserine (1) and N-trans-retinoylalanine (2), have been isolated from a cell line of the common cabbage looper, Trichoplusia ni. These are the first examples of naturally occurring retinoic acid linked to amino acids through an amide bond; the amino acid moieties are depicted in the more common L-configuration, although the absolute configuration was not determined due to the minuscule sample amount}, language = {en} } @article{RietdorfBlenauWalz2005, author = {Rietdorf, Katja and Blenau, Wolfgang and Walz, Bernd}, title = {Protein secretion in cockroach salivary glands requires an increase in intracellular cAMP and Ca2+ concentrations}, issn = {0022-1910}, year = {2005}, abstract = {The salivary glands in the cockroach Periplaneta americana secrete protein-containing saliva when stimulated by serotonin (5-HT) and protein-free saliva upon dopamine stimulation. In order to obtain information concerning the signalling pathways involved in 5-HT-induced protein secretion, we have determined the protein content of saliva secreted after experimental manipulations that potentially elevate intracellular Ca2+ and cyclic nucleotide concentrations in isolated glands. We have found that 5-HT stimulates the rate of protein secretion in a dose-dependent manner (threshold: 3 x 10(-8) M; EC50 1.5 x 10(-6) M). The maximal rate of 5-HT-induced protein secretion was 2.2 +/- 0.2 mu g/min. Increasing intracellular Ca2+ or cAMP by bath application of ionomycin (5 mu M), db cAMP (10 mM), forskolin (100 mu M) or IBMX (100 mu M), respectively, stimulated protein secretion at significantly lower rates, whereas db cGMP (1 mM) did not activate protein secretion. The high rates and the kinetics of 5-HT-induced protein secretion could only be mimicked by either applying forskolin together with IBMX (with or without ionomycin) or by applying IBMX together with ionomycin. Our measurements suggest that 5-HT-induced protein secretion is mediated by an elevation of [cAMP](i) and that Ca2+ may function as a co-agonist and augment the rate of protein secretion. (c) 2005 Elsevier Ltd. All rights reserved}, language = {en} } @article{RianoPachonDreyerMuellerRoeber2005, author = {Riano-Pachon, Diego Mauricio and Dreyer, Ingo and M{\"u}ller-R{\"o}ber, Bernd}, title = {Orphan transcripts in Arabidopsis thaliana : identification of several hundred previously unrecognized genes}, issn = {0960-7412}, year = {2005}, abstract = {Expressed sequence tags (ESTs) represent a huge resource for the discovery of previously unknown genetic information and functional genome assignment. In this study we screened a collection of 178 292 ESTs from Arabidopsis thaliana by testing them against previously annotated genes of the Arabidopsis genome. We identified several hundreds of new transcripts that match the Arabidopsis genome at so far unassigned loci. The transcriptional activity of these loci was independently confirmed by comparison with the Salk Whole Genome Array Data. To a large extent, the newly identified transcriptionally active genomic regions do not encode 'classic' proteins, but instead generate non-coding RNAs and/or small peptide-coding RNAs of presently unknown biological function. More than 560 transcripts identified in this study are not represented by the Affymetrix GeneChip arrays currently widely used for expression profiling in A. thaliana. Our data strongly support the hypothesis that numerous previously unknown genes exist in the Arabidopsis genome}, language = {en} } @article{SpijkermanMaberlyCoesel2005, author = {Spijkerman, Elly and Maberly, Stephen C. and Coesel, P. F. M.}, title = {Carbon acquisition mechanisms by planktonic desmids and their link to ecological distribution}, issn = {0008-4026}, year = {2005}, abstract = {To test if different inorganic carbon (C-i) uptake mechanisms underlie the ecological distribution pattern of planktonic desmids, we performed pH-drift experiments with 12 strains, belonging to seven species, originating from lakes of different pH. Staurastrum brachiatum Ralfs and Staurodesmus cuspidatus (Ralfs) Teil. var. curvatus (W. West) Teil., species confined to acidic, soft water habitats, showed remarkably different behavior in the pH drift experiments: S. brachiatum appeared to use CO2 only, whereas Staurodesmus cuspidatus appeared to use HCO3- as well. Staurastrum chaetoceras (Schr.) Smith and Staurastrum planctonicum Teil, species well-known for their abundant occurrence in alkaline waters, were the most effective at using HCO3-. Other species, to be encountered in both slightly acidic and slightly alkaline waters, took an intermediate position. Experiments using specific inhibitors suggested that Cosmarium abbreviatum Rac. var. planctonicum W. \& G.S. West and S. brachiatum use CO2 by an active CO2 uptake mechanism, whereas S. chaetoceras and Staurodesmus cuspidatus showed an active HCO3- uptake pattern. Most likely, these active uptake mechanisms make use of H+-ATPase, as none of the desmids expressed significant carbonic anhydrase activity. A series of strains of Staurastrum planctonicum isolated from different habitats, all clustered in between the species using HCO3-, but no further differentiation was observed. Therefore, desmids cannot be simply characterized as exclusive CO2 users, and the ecological distribution pattern of a desmid species does not unequivocally link to a certain C-i uptake mechanism. Nevertheless, there does appear to be a general ecological link between a species' C-i uptake mechanism and its ecological distribution}, language = {en} } @article{PoreeWulfetangeNasoetal.2005, author = {Poree, Fabien and Wulfetange, K. and Naso, A. and Carpaneto, Armando and Roller, A. and Natura, G. and Bertl, Adam and Sentenac, H. and Thibaud, Jean-Baptiste and Dreyer, Ingo}, title = {Plant K-in and K-out channels : Approaching the trait of opposite rectification by analyzing more than 250 KAT1- SKOR chimeras}, issn = {0006-291X}, year = {2005}, abstract = {Members of the Shaker-like plant K+ channel family share a common structure, but are highly diverse in their function: they behave as either hyperpolarization-activated inward-rectifying (K-in) channels, or leak-like (K-weak) channels, or depolarization-activated outward-rectifying (K-out) channels. Here we created 256 chimeras between the K-in channel KAT1 and the K-out channel SKOR. The chimeras were screened in a potassium-uptake deficient yeast strain to identify those, which mediate potassium inward currents, i.e., which are functionally equivalent to KAT1. This strategy allowed Lis to identify three chimeras which differ from KAT1 in three parts of the polypeptide: the cytosolic N- terminus, the cytosolic C-terminus, and the putative voltage-sensor S4. Additionally, mutations in the K-out Channel SKOR were generated in order to localize molecular entities underlying its depolarization activation. The triple mutant SKOR-D312N-M313L-1314G, carrying amino-acid changes in the S6 segment, was identified as a channel which did not display any rectification in the tested voltage-range. (C) 2005 Elsevier Inc. All rights reserved}, language = {en} } @article{PieperFuerst2005, author = {Pieper-F{\"u}rst, U.}, title = {Gold nanoparticle-enhanced surface plasmon resonance measurement with a highly sensitive quantification for human tissue inhibitor of metalloproteinases-2}, year = {2005}, abstract = {Two different methods for the quantification of human tissue inhibitor of metalloproteinases-2 (TIMP-2) were developed using surface plasmon resonance (SPR) and gold nanoparticles for signal enhancement. The first method, a competitive assay, used TIMP-2 immobilized to the sensor surface and the inactive form of matrix metalloproteinase-2 (proMMP-2) (EC 3.4.24.24) adsorbed to gold nanoparticles. The sensor signals resulting from the interaction of MMP-2- gold nanoparticles with immobilized TIMP-2 were inversely proportional to the amounts of TIMP-2 of the sample. The measuring range for TIMP-2 was about 15-180pM. The second method, a one-step sandwich assay, used proMMP-2 immobilized to the sensor surface and an anti-TIMP-2 monoclonal antibody coupled to gold nanoparticles. The lower detection limit of this assay format was 0.5 pM of TIMP-2. The binding signals were highly reproducible up to 100 pM of the inhibitor. The improvements obtained in TIMP-2 quantification over already existing tests could contribute to a better understanding and diagnosis of diseases like cancer. (c) 2005 Elsevier B.V. All rights reserved}, language = {en} } @article{Mussig2005, author = {Mussig, C.}, title = {Brassinosteroid-promoted growth}, issn = {1435-8603}, year = {2005}, abstract = {Brassinosteroids (BRs) are highly potent growth-promoting sterol derivatives. BR-deficient or BR-insensitive mutants display dwarfism. Whole plants and excised tissues have been used to analyse the mechanisms involved in BR- promoted growth. BR stimulates cell elongation and cell division, and BR has specific effects on differentiation. Underlying physiological pathways include modification of cell wall properties, effects on carbohydrate assimilation and allocation, and control of aquaporin activities. BR apparently coordinates and integrates diverse processes required for growth, partly via interactions with other phytohormones setting the frame for BR responses. Ultimately, BR-promoted growth is mediated through genomic pathways. Positive regulators of the BR response (such as BZR1 and BES1) and putative downstream components (such as EXO) are involved in the regulation of BR-responsive genes and growth promotion. BR- responsive genes have been identified in several plant species. However, causal links between physiological effects and changes of transcript patterns, for the most part, are still unresolved. This review focuses on physiology and molecular mechanisms underlying BR-promoted growth in the different plant organs. Interactions with other phytohormones are discussed}, language = {en} } @article{MishraSecklerBhat2005, author = {Mishra, Rajesh and Seckler, Robert and Bhat, Rajiv}, title = {Efficient refolding of aggregation-prone citrate synthase by polyol osmolytes : how well are protein folding and stability aspects coupled?}, issn = {0021-9258}, year = {2005}, abstract = {Efficient refolding of proteins and prevention of their aggregation during folding are of vital importance in recombinant protein production and in finding cures for several diseases. We have used citrate synthase ( CS) as a model to understand the mechanism of aggregation during refolding and its prevention using several known structure-stabilizing cosolvent additives of the polyol series. Interestingly, no parallel correlation between the folding effect and the general stabilizing effect exerted by polyols was observed. Although increasing concentrations of polyols increased protein stability in general, the refolding yields for CS decreased at higher polyol concentrations, with erythritol reducing the folding yields at all concentrations tested. Among the various polyols used, glycerol was the most effective in enhancing the CS refolding yield, and a complete recovery of enzymatic activity was obtained at 7 M glycerol and 10 mu g/ml protein, a result superior to the action of the molecular chaperones GroEL and GroES in vitro. A good correlation between the refolding yields and the suppression of protein aggregation by glycerol was observed, with no aggregation detected at 7 M. The polyols prevented the aggregation of CS depending on the number of hydroxyl groups in them. Stopped-flow fluorescence kinetics experiments suggested that polyols, including glycerol, act very early in the refolding process, as no fast and slow phases were detectable. The results conclusively demonstrate that both the thermodynamic and kinetic aspects are critical in the folding process and that all structure-stabilizing molecules need not always help in productive folding to the native state. These findings are important for the rational design of small molecules for efficient refolding of various aggregation-prone proteins of commercial and medical relevance}, language = {en} } @article{MikhailyukLoksteinRazjivin2005, author = {Mikhailyuk, Igor K. and Lokstein, Heiko and Razjivin, Andrei P.}, title = {A method of spectral subband decomposition by simultaneous fitting the initial spectrum and a set of its derivatives}, year = {2005}, abstract = {An improved method for spectral subband decomposition based on simultaneous fitting of the initial spectrum and a set of its derivatives is introduced. Additionally, it procedure for finding an optimal smoothing filter to obtain undistorted derivatives IS Suggested. The proposed method is demonstrated with a model spectrum as well its with experimental absorption spectra of the photosynthetic antenna complexes, peridinin-chlorophyll a-protein (PCP) and the main light-harvesting complex of higher plants (LHC II). (c) 2005 Elsevier B.V. All rights reserved}, language = {en} } @article{MatthiesNimtzLeimkuehler2005, author = {Matthies, A. and Nimtz, M. and Leimk{\"u}hler, Silke}, title = {Molybdenum cofactor biosynthesis in humans : Identification of a persulfide group in the rhodanese-like domain of MOCS3 by mass spectrometry}, issn = {0006-2960}, year = {2005}, abstract = {The human MOCS3 protein contains an N-terminal domain similar to the Escherichia coli MoeB protein and a C- terminal segment displaying similarities to the sulfurtransferase rhodanese. MOCS3 is proposed to catalyze both the adenylation and the subsequent generation of a thiocarboxylate group at the C-terminus of the smaller subunit of molybdopterin (MPT) synthase during Moco biosynthesis in humans. Recent studies have shown that the MOCS3 rhodanese-like domain (MOCS3-RLD) catalyzes the transfer of sulfur from thiosulfate to cyanide and is also able to provide the sulfur for the thiocarboxylation of MOCS2A in a defined in vitro system for the generation of MPT from precursor Z. MOCS3-RLD contains four cysteine residues of which only C412 in the six amino acid active loop is conserved in homologous proteins from other organisms. ESI-MS/MS studies gave direct evidence for the formation of a persulfide group that is exclusively formed on C412. Simultaneous mutagenesis of the remaining three cysteine residues showed that none of them is involved in the sulfur transfer reaction in vitro. A disulfide bridge was identified to be formed between C316 and C324, and possible roles of the three noncatalytic cysteine residues are discussed. By ESI-MS/MS a partially gluconoylated N- terminus of the His(6)-tagged MOCS3-RLD was identified (mass increment of 178 Da) which resulted in a heterogeneity of the protein but did not influence sulfurtransferase activity}, language = {en} } @article{MakCheungTrauetal.2005, author = {Mak, Wing Cheung and Cheung, Kwan Yee and Trau, Dieter and Warsinke, Axel and Scheller, Frieder W. and Renneberg, Reinhard}, title = {Electrochemical bioassay utilizing encapsulated electrochemical active microcrystal biolabels}, issn = {0003-2700}, year = {2005}, abstract = {A new approach to perform electrochemical immunoassay based on the utilization of encapsulated microcrystal was developed. The microcrystal labels create a "supernova effect" upon exposure to a desired releasing agent. The microcrystal cores dissolve, and large amounts of signal-generating molecules diffuse across the capsule wall into the outer environment. Layer-by-Layer (LbL) technology was employed for the encapsulation of electrochemical signal- generating microcrystals (ferrocene microcrystals). The encapsulated microcrystals were conjugated with antibody molecules through the adsorption process. The biofunctionalized microcrystals were utilized as a probe for immunoassays. The microcrystal-based label system provided a high-signal molecule to antibody (SIP) ratio of 10(4)-10(5). Microcrystal biolabels with different antibody surface coverage (1.60-5.05 mg m(-2)) were subjected to a solid-phase immunoassay for the detection of mouse immunoglobulin G (M-IgG) molecules. The microcrystal-based immunoassay for the detection of M-IgG performed with microcrystals having antibody surface coverage of 5.05 mg m(-2) showed a sensitivity of 3.93 nA g(- 1) L-1 with a detection limit of 2.82 g L-1}, language = {en} } @article{LloydKossmannRitte2005, author = {Lloyd, James R. and Kossmann, Jens and Ritte, Gerhard}, title = {Leaf starch degradation comes out of the shadows}, year = {2005}, abstract = {During the day, plants accumulate starch in their leaves as an energy source for the coming night. Based on recent findings, the prevailing view of how the transitory starch is remobilized needs considerable revision. Analyses of transgenic and mutant plants demonstrate that plastidic glucan phosphorylase is not required for normal starch breakdown and cast doubt on the presumed essential role of alpha-amylase but do show that beta-amylase is important. Repression of the activity of a plastidic beta-amylase, the export of its product (maltose) or further metabolism of maltose by a newly identified transglucosidase impairs starch degradation. Breakdown of particulate starch also depends on the activity of glucan-water dikinase, which phosphorylates glucosyl residues within the polymer}, language = {en} } @article{LiuWollenbergerHalameketal.2005, author = {Liu, Songqin and Wollenberger, Ursula and Halamek, Jan and Leupold, Eik and St{\"o}cklein, Walter F. M. and Warsinke, Axel and Scheller, Frieder W.}, title = {Affinity interaction betwen phenylboronic acid-carrying self-assembled monolayers and FAD or HRP}, year = {2005}, abstract = {A method is provided for the recognition of glycated molecules based on their binding affinities to boronate- carrying monolayers. The affinity interaction of flavin adenine dinucleotide (FAD) and horseradish peroxidase (HRP) with phenylboronic acid monolayers on gold was investigated by using voltammetric and microgravimetric methods. Conjugates of 3-aminopherrylboronic acid and 3,3'-dithiodipropionic acid di(N-hydroxysuccinimide ester) or 11-mercaptoundecanoic acid were prepared and self-assembled on gold surfaces to generate monolayers. FAD is bound to this modified sur-face and recognized by a pair of redox peaks with a formal potential of -0.433 V in a 0.1 m phosphate buffer solution, pH 6.5. Upon addition of a sugar to the buffer, the bound FAD could be replaced, indicating that the binding is reversible. Voltammetric, mass measurements, and photometric activity assays show that the HRP can also be bound to the interface. This binding is reversible, and HRP can be replaced by sorbitol or removed in acidic solution. The effects of pH, incubation time, and concentration of H2O2 were studied by comparing the catalytic reduction of H2O2 in the presence of the electron-donor thionine. The catalytic current of the HRP-loaded electrode was proportional to HRP concentrations in the incubation solution in the range between 5 mu g mL(-1) and 0.4 mg mL(-1) with a linear slope of 3.34 mu A mL mg(-1) and a correlation coefficient of 0.9945}, language = {en} } @article{LissoSteinhaeuserAltmannetal.2005, author = {Lisso, Janina and Steinhaeuser, Dirk and Altmann, Thomas and Kopka, Joachim and M{\"u}ssig, Carsten}, title = {Identification of brassinosteroid-related genes by means of transcript co-response analyses}, issn = {0305-1048}, year = {2005}, abstract = {The comprehensive systems-biology database (CSB.DB) was used to reveal brassinosteroid (BR)-related genes from expression profiles based on co-response analyses. Genes exhibiting simultaneous changes in transcript levels are candidates of common transcriptional regulation. Combining numerous different experiments in data matrices allows ruling out outliers and conditional changes of transcript levels. CSB.DB was queried for transcriptional co-responses with the BR-signalling components BRI1 and BAK1: 301 out of 9694 genes represented in the nasc0271 database showed co-responses with both genes. As expected, these genes comprised pathway-involved genes (e.g. 72 BR-induced genes), because the BRI1 and BAK1 proteins are required for BR-responses. But transcript co-response takes the analysis a step further compared with direct approaches because BR-related non BR-responsive genes were identified. Insights into networks and the functional context of genes are provided, because factors determining expression patterns are reflected in correlations. Our findings demonstrate that transcript co-response analysis presents a valuable resource to uncover common regulatory patterns of genes. Different data matrices in CSB.DB allow examination of specific biological questions. All matrices are publicly available through CSB.DB. This work presents one possible roadmap to use the CSB.DB resources}, language = {en} } @article{LinWangMuellerRoeberetal.2005, author = {Lin, W. H. and Wang, Y. and M{\"u}ller-R{\"o}ber, Bernd and Brearley, C. A. and Xu, Z. H. and Xue, H. W.}, title = {At5PTase13 modulates cotyledon vein development through regulating auxin homeostasis}, issn = {0032-0889}, year = {2005}, abstract = {Phosphatidylinositol signaling pathway and the relevant metabolites are known to be critical to the modulation of different aspects of plant growth, development, and stress responses. Inositol polyphosphate 5-phosphatase is a key enzyme involved in phosphatidylinositol metabolism and is encoded by an At5PTase gene family in Arabidopsis thaliana. A previous study shows that At5PTase11 mediates cotyledon vascular development probably through the regulation of intracellular calcium levels. In this study, we provide evidence that At5PTase13 modulates the development of cotyledon veins through its regulation of auxin homeostasis. A T-DNA insertional knockout mutant, At5pt13-1, showed a defect in development of the cotyledon vein, which was rescued completely by exogenous auxin and in part by brassinolide, a steroid hormone. Furthermore, the mutant had reduced auxin content and altered auxin accumulation in seedlings revealed by the DR5:beta-glucuronidase fusion construct in seedlings. In addition, microarray analysis shows that the transcription of key genes responsible for auxin biosynthesis and transport was altered in At5pt13-1. The At5pt13-1 mutant was also less sensitive to auxin inhibition of root elongation. These results suggest that At5PTase13 regulates the homeostasis of auxin, a key hormone controlling vascular development in plants}, language = {en} } @article{LeimkuehlerCharcossetLatouretal.2005, author = {Leimk{\"u}hler, Silke and Charcosset, M. and Latour, P. and Dorche, C. and Kleppe, S. and Scaglia, F. and Szymczak, I. and Schupp, P. and Hahnewald, Rita and Reiss, J.}, title = {Ten novel mutations in the molybdenum cofactor genes MOCS1 and MOCS2 and in vitro characterization of a MOCS2 mutation that abolishes the binding ability of molybdopterin synthase}, issn = {0340-6717}, year = {2005}, abstract = {Molybdenum cofactor deficiency (MIM\#252150) is a severe autosomal- recessive disorder with a devastating outcome. The cofactor is the product of a complex biosynthetic pathway involving four different genes (MOCS1, MOCS2, MOCS3 and GEPH). This disorder is caused almost exclusively by mutations in the MOCS1 or MOCS2 genes. Mutations affecting this biosynthetic pathway result in a lethal phenotype manifested by progressive neurological damage via the inactivation of the molybdenum cofactor-dependent enzyme, sulphite oxidase. Here we describe a total of ten novel disease-causing mutations in the MOCS1 and MOCS2 genes. Nine out of these ten mutations were classified as pathogenic in nature, since they create a stop codon, affect constitutive splice site positions, or change strictly conserved motifs. The tenth mutation abolishes the stop codon of the MOCS2B gene, thus elongating the corresponding protein. The mutation was expressed in vitro and was found to abolish the binding affinities of the large subunit of molybdopterin synthase (MOCS2B) for both precursor Z and the small subunit of molybdopterin synthase (MOCS2A)}, language = {en} } @article{KoettingPuschTiessenetal.2005, author = {K{\"o}tting, Oliver and Pusch, Kerstin and Tiessen, Axel and Geigenberger, Peter Ludwig and Steup, Martin and Ritte, Gerhard}, title = {Identification of a novel enzyme required for starch metabolism in Arabidopsis leaves : the phosphoglucan, water dikinase}, year = {2005}, abstract = {The phosphorylation of amylopectin by the glucan, water dikinase (GWD; EC 2.7.9.4) is an essential step within starch metabolism. This is indicated by the starch excess phenotype of GWD-deficient plants, such as the sex1-3 mutant of Arabidopsis (Arabidopsis thaliana). To identify starch-related enzymes that rely on glucan-bound phosphate, we studied the binding of proteins extracted from Arabidopsis wild-type leaves to either phosphorylated or nonphosphorylated starch granules. Granules prepared from the sex1-3 mutant were prephosphorylated in vitro using recombinant potato (Solanum tuberosum) GWD. As a control, the unmodified, phosphate free granules were used. An as-yet uncharacterized protein was identified that preferentially binds to the phosphorylated starch. The C-terminal part of this protein exhibits similarity to that of GWD. The novel protein phosphorylates starch granules, but only following prephosphorylation with GWD. The enzyme transfers the beta-P of ATP to the phosphoglucan, whereas the gamma-P is released as orthophosphate. Therefore, the novel protein is designated as phosphoglucan, water dikinase (PWD). Unlike GWD that phosphorylates preferentially the C6 position of the glucose units, PWD phosphorylates predominantly (or exclusively) the C3 position. Western-blot analysis of protoplast and chloroplast fractions from Arabidopsis leaves reveals a plastidic location of PWD. Binding of PWD to starch granules strongly increases during net starch breakdown. Transgenic Arabidopsis plants in which the expression of PWD was reduced by either RNAi or a T-DNA insertion exhibit a starch excess phenotype. Thus, in Arabidopsis leaves starch turnover requires a close collaboration of PWD and GWD}, language = {en} } @article{MartinCreuzburgWackervonElert2005, author = {Martin-Creuzburg, Dominik and Wacker, Alexander and von Elert, Eric}, title = {Life history consequences of sterol availability in the aquatic keystone species Daphnia}, issn = {0029-8549}, year = {2005}, abstract = {The absence of essential biochemical nutrients, such as polyunsaturated fatty acids or sterols, has been considered as a mechanism determining trophic interactions between the herbivore Daphnia and its phytoplankton food source. Here, we experimentally quantify the sensitivity of two Daphnia species to decreasing amounts of dietary sterols by measuring variations in life history traits. The two species Daphnia magna and D. galeata were fed different mixtures of the sterol-containing green alga Scenedesmus obliquus and the sterol-free cyanobacterium Synechococcus elongatus; a higher proportion of Synechococcus in the food is equivalent to a decrease in dietary sterols. To address the significance of sterol limitation, the Daphnia species were also fed Synechococcus supplemented with cholesterol. In both species, somatic and population growth rates, maternal dry mass, the number of viable offspring, and the probability of survival were significantly reduced with the lower availability of sterols. A high correlation between the sterol content of the mixed diet and the somatic and population growth rates was found, and growth on cholesterol- supplemented Synechococcus fitted well into this correlation. Somatic growth of first-clutch neonates grown on 100\% Synechococcus exhibited a pattern similar to that of somatic growth of their mothers grown on the different food regimes, which demonstrated the significance of maternal effects for sterol-limited population growth. Daphnia galeata had a twofold higher incipient limiting sterol level than D. magna, which indicated interspecific differences in sterol requirements between the two Daphnia species. The results suggest a strong impact of dietary sterols on life history traits and therefore, population dynamics of the keystone species Daphnia}, language = {en} } @article{KetmaierBernardini2005, author = {Ketmaier, Valerio and Bernardini, C.}, title = {Structure of the mitochondrial control region of the Eurasian otter (Lutra lutra ; Carnivora, Mustelidae): patterns of genetic heterogeneity and implications for conservation of the species in Italy}, issn = {0022-1503}, year = {2005}, abstract = {In this study we determined the complete sequence of the mitochondrial DNA (mtDNA) control region of the Eurasian otter (Lutra lutra). We then compared these new sequences with orthologues of nine carnivores belonging to six families (Mustelidae, Mephitidae, Canidae, Hyaenidae, Ursidae, and Felidae). The comparative analyses identified all the conserved regions previously found in mammals. The Eurasian otter and seven other species have a single location with tandem repeats in the right domain, while the spotted hyena (Hyaenidae) and the tiger (Felidae) have repeated sequences in both the right and left domains. To assess the degree of genetic heterogeneity of the Eurasian otter in Italy we sequenced two fragments of the gene and analyzed length polymorphisms of repeated sequences and heteroplasmy in 32 specimens. The study includes 23 museum specimens collected in northern, central, and southern Italy; most of these specimens are from extinct populations, while the southern Italian samples belong to the sole extant Italian population of the Eurasian otter. The study also includes all the captive-reared animals living in the colony "Centro Lontra, Caramanico Terme" (Pescara, central Italy). The colony is maintained for reintroduction of the species. We found a low level of genetic polymorphism; a single haplotype is dominant, but our data indicate the presence in central and southern Italy of two slightly divergent haplotypes. One haplotype belongs to an extinct population, the other is present in the single extant Italian population. Analyses of length polymorphisms and heteroplasmy indicate that the autochthonous Italian samples are characterized by a distinct array of repeated sequences from captive-reared animals}, language = {en} } @article{KaufmannBaxaChipmanetal.2005, author = {Kaufmann, B. and Baxa, Ulrich and Chipman, P. R. and Rossmann, M. G. and Modrow, Susanne and Seckler, Robert}, title = {Parvovirus B19 does not bind to membrane-associated globoside in vitro}, issn = {0042-6822}, year = {2005}, abstract = {The glycosphingolipid globoside (globotetraosylceramide, Gb4Cer) has been proposed to be the cellular receptor of human parvovirus B19. Quantitative measurements of the binding of parvovirus B19 to Gb4Cer were performed to explore the molecular basis of the virus tropism. Solid-phase assays with fluorescence-labeled liposomes or (125)iodine-labeled empty capsids were used to characterize the specificity of binding. In addition, surface plasmon resonance on lipid layers, as well as isothermal titration microcalorimetry, was utilized for real-time analysis of the virus-receptor interaction. These studies did not confirm binding of Gb4Cer to recombinant B19 VP2 capsids, suggesting that Gb4Cer does not function on its own as the cellular receptor of human parvovirus B19, but might be involved in a more complex recognition event. The biochemical results were further confirmed by cryo-electron microscopy image reconstructions at 10 A resolution, in which the structures of empty capsids were compared with empty capsids incubated with Gb4Cer. (C) 2004 Elsevier Inc. All rights reserved}, language = {en} } @article{KamjunkeTittelKrumbecketal.2005, author = {Kamjunke, Norbert and Tittel, J{\"o}rg and Krumbeck, H. and Beulker, Camilla and Poerschmann, J.}, title = {High heterotrophic bacterial production in acidic, iron-rich mining lakes}, issn = {0095-3628}, year = {2005}, abstract = {The acidic mining lakes of Eastern Germany are characterized by their extremely low pH and high iron concentrations. Low concentrations of CO2 in the epilimnion due to the low pH and reduced light transmission due to dissolved ferric iron potentially limit phytoplankton primary production (PP), whereas dissolved organic carbon (DOC) may promote heterotrophic production of bacteria (HP). We, therefore, tested whether HP exceeds PP in three lakes differing in pH and iron concentration (mean pH 2.3-3.0, 23-500 mg Fe L-1). Bacterial biomass and HP achieved highest values in the most acidic, most iron-rich lake, whereas PP was highest in the least acidic lake. HP was often higher than PP (ratio HP/PP up to 11), indicating that planktonic PP was not the main carbon source for the bacteria. HP was not related to PP and DOC, but HP as well as bacterial biomass increased with decreasing pH. Light stimulated the formation of ferrous iron, changed the DOC composition, and increased the HP in laboratory experiments, suggesting that iron photoreduction caused DOC degradation. This may explain why we found the highest HP in the most acidic and most rich lake. Overall, the importance of bacteria in the cycling of matter and as a basis for the whole food web seemed to increase in more acidic lakes with higher iron concentrations}, language = {en} } @article{HummelKeshvariWeckwerthetal.2005, author = {Hummel, Jan and Keshvari, N. and Weckwerth, Wolfram and Selbig, Joachim}, title = {Species-specific analysis of protein sequence motifs using mutual information}, issn = {1471-2105}, year = {2005}, abstract = {Background: Protein sequence motifs are by definition short fragments of conserved amino acids, often associated with a specific function. Accordingly protein sequence profiles derived from multiple sequence alignments provide an alternative description of functional motifs characterizing families of related sequences. Such profiles conveniently reflect functional necessities by pointing out proximity at conserved sequence positions as well as depicting distances at variable positions. Discovering significant conservation characteristics within the variable positions of profiles mirrors group-specific and, in particular, evolutionary features of the underlying sequences. Results: We describe the tool PROfile analysis based on Mutual Information (PROMI) that enables comparative analysis of user-classified protein sequences. PROMI is implemented as a web service using Perl and R as well as other publicly available packages and tools on the server-side. On the client-side platform-independence is achieved by generally applied internet delivery standards. As one possible application analysis of the zinc finger C2H2-type protein domain is introduced to illustrate the functionality of the tool. Conclusion: The web service PROMI should assist researchers to detect evolutionary correlations in protein profiles of defined biological sequences. It is available at http:// promi.mpimpgolm. mpg.de where additional documentation can be found}, language = {en} } @article{KetmaierMandatoriDeMatthaeisetal.2005, author = {Ketmaier, Valerio and Mandatori, R. and De Matthaeis, E. and Mura, G.}, title = {Molecular systematics and phylogeography in the fairy shrimp Tanymastix stagnalis based on mitochondrial DNA}, issn = {0952-8369}, year = {2005}, abstract = {Patterns of sequence divergence in about 1 kb of mitochondrial DNA coding for two genes (16s rRNA and cytochrome oxidase I, COI) were analysed in 13 populations of the fairy shrimp Tanymastix stagnalis from Norway, Germany, France, Italy (northern and central Italy plus insular populations from Sardinia and the Tuscan Archipelago) and Spain, and in one presumed population of Tanymastix stellae from Corsica. The latter species was originally known only from a single locality in Sardinia, which has been destroyed by urbanization; the Corsican population was referred to T stellae by some French authors on the basis of the collection of several cysts from mud. mtDNA data revealed a very low level of genetic divergence between the presumed population of T stellae and the other T stagnalis populations included in the study. Our genetic findings do not support the presence of T stellae in Corsica and are in line with previous SEM studies revealing that all species belonging to the genus Tanymastix produce cysts with identical morphology. The results indicate complex phylogeographic relationships and pronounced genetic differentiation among T stagnalis populations. The islands of Corsica and Sardinia on the one hand and the island of Capraia (Tuscan Archipelago) on the other were probably colonized independently at different times. Genetic relationships among continental populations do not follow a clear geographical trend, indicating that geographical distance is not the main force shaping the pattern of genetic structuring of the species. Stochastic factors such as multiple and independent founder events probably contributed to the striking pattern of genetic differentiation along with subsequent local adaptation. These results agree with previously published molecular work on several groups of aquatic organisms and further support the high potential for dispersal-low gene flow paradox shown by a large array of animals living in lentic habitats}, language = {en} } @article{HauswaldtGlenn2005, author = {Hauswaldt, J. S. and Glenn, T. C.}, title = {Population genetics of the diamondback terrapin (Malaclemys terrapin)}, issn = {0962-1083}, year = {2005}, abstract = {We examined the population genetic structure of the diamondback terrapins (Malaclemys terrapin), within and among estuaries. Based on mark-recapture studies, these estuarine turtles have high site fidelity that is likely to make them vulnerable to local extinctions. We tested if observed site fidelity of adults would be reflected in intraestuarine population genetic structure of six highly polymorphic microsatellite loci (five tetranucleotide and one dinucleotide). No evidence was found for population structuring within the Charleston estuary nor among three different estuaries in South Carolina. We then examined four other terrapin populations from North Carolina to New York, as well as from the Florida Keys and from Texas. With increasing geographical distance, genetic differentiation increased from South Carolina through New York, but overall values were low. The dinucleotide locus contributed significantly more to the genetic differentiation of some population comparisons than any of the other loci. Interestingly, terrapins from South Carolina to New York were much more genetically similar to those from Texas (rho = 0.154) than to those from Florida (rho = 0.357). We attribute this pattern to extensive translocations of terrapins during the early 20th century to replenish diminished populations and to provide turtle farms with stocks. Terrapins collected in Texas were especially sought for shipment to the northeastern US because of their larger size. Our study indicates no population structure within or among adjacent estuaries. Thus, the mark-recapture information from adult and subadult feeding locations is a poor predictor of population genetic structure. Additionally, it appears that past human activities may have drastically altered the genetics of current populations. Finally, our data suggest that translocation of eggs or head starting of terrapins within estuaries or among adjacent estuaries is acceptable from a genetic standpoint}, language = {en} } @article{Halamek2005, author = {Halamek, Jan}, title = {Sensitive detection of organophosphates in river water by means of a piezoelectric biosensor}, year = {2005}, abstract = {A highly sensitive piezoelectric biosensor has been developed for detection of cholinesterase inhibitors. The inhibitor benzoylecgonine-1,8-diamino-3,4-dioxaoctane (BZE-DADOO) was immobilized on a monolayer of 11- mercaptomonoundecanoic acid (MUA) self-assembled on the gold surface of the sensor. The binding of high-molecular-weight cholinesterase to the immobilized cocaine derivative was monitored with a mass sensitive piezoelectric quartz crystal (quartz crystal nanobalance; QCN). In the presence of an inhibiting substance in the sample, the binding of cholinesterase to the immobilized inhibitor was reduced. The decrease of the rate of mass change was proportional to the concentration of free inhibitor in the sample. This way the affinity sensor followed anti-cholinesterase toxicity and the enzyme activity of ChE was not addressed. A assay for detection of organophosphates (OP) was optimized. Regeneration of the sensor surface was achieved with 1 mol L-1 formic acid, which enabled 40 measurements with one sensor. All assays were carried out in a flow-through arrangement. The total measurement time (binding + regeneration) was 25 min and the detection limit for different OP (paraoxon, diisopropylfluorophosphate, chlorpyriphos, and chlorfenvinphos) was down to 10(-10) mol L-1 (0.02 mu g L-1). This sensor was used for determination of organophosphate (diisopropylfluorophosphate) levels in river water samples}, language = {en} } @article{HalamekMakowerKnoescheetal.2005, author = {Halamek, Jan and Makower, Alexander and Kn{\"o}sche, Kristina and Skladal, Petr and Scheller, Frieder W.}, title = {Piezoelectric affinity sensors for cocaine and cholinesterase inhibitors}, year = {2005}, abstract = {We report here the development of piezoelectric affinity sensors for cocaine and cholinesterase inhibitors based on the formation of affinity complexes between an immobilized cocaine derivative and an anti-cocaine antibody or cholinesterase. For both binding reactions benzoylecgonine-1,8-diamino-3,4-dioxaoctane (BZE-DADOO) was immobilized on the surface of the sensor. For immobilization. pre-conjugated BZE-DADOO with 11-mercaptomonoundecanoic acid (MUA) via 2- (5-norbornen-2,3-dicarboximide)-1,1,3,3-tetramethyluronium-tetrafluoro borate (TNTU) allowed the formation of a chemisorbed monolayer on the piezosensor surface. The detection of cocaine was based oil a competitive assay. The change of frequency measured after 300 s of the binding reaction was used as the signal. The maximum binding of the antibody resulted in a frequency decrease of 35 Hz (with an imprecision 3\%, n = 3) while the presence of 100 pmol I-1 cocaine decreased the binding by 11\%. The limit of detection was consequently below 100 pmol I-1 for cocaine. The total time of one analysis was 15 min. This BZE-DADOO-modified sensor was adapted for the detection of organophosphates. BZE-DADOO - a competitive inhibitor - served as binding element for cholinesterase in a competitive assay. (C) 2004 Elsevier B.V. All rights reserved}, language = {en} } @article{GroblerHartlGrobleretal.2005, author = {Grobler, J. P. and Hartl, G. B. and Grobler, N. and Kotze, A. and Botha, K. and Tiedemann, Ralph}, title = {The genetic status of an isolated black wildebeest (Connochaetes gnou) population from the Abe Bailey Nature Reserve, South Africa : Microsatellite data on a putative past hybridization with blue wildebeest (C-taurinus)}, issn = {1616-5047}, year = {2005}, abstract = {The present study aimed at assessing genetic purity of black wildebeest (Connochoetes gnou) at Abe Bailey Nature Reserve, Gauteng Province, South Africa, using a multitocus microsatellite approach. Five loci were studied in black and blue (C. taurinus) wildebeest, the latter being a closely related species and known to produce hybrids with the morphologically very similar black wildebeest. In fact, the entire national black wildebeest population of South Africa potentially contains a significant proportion of introgressed blue wildebeest genes. In our case, eight out of 39 alleles were unique to black and 22 to blue wildebeest, with nine alleles shared between pure populations of the two species in Line with their taxonomic proximity. A possible Limited past introgression of blue wildebeest genes into the Abe Bailey population, corresponding to documents on population history, was only supported by the presence of a single allele otherwise exclusively found in samples of four pure blue but not in samples of two pure black wildebeest control populations. However, an assignment test and coefficients of population divergence did not support an extended introgression of C. taurinus alleles into the C. gnou population under study. Average heterozygosity at Abe Bailey proved to be intermediate between black and blue wildebeest, the tatter species generally harbouring more genetic variation than the former owing to larger population sizes and the absence of population bottlenecks in historical times. The implications of our data are discussed with reference to the persistence of introgressed genes and the conservation of pure black wildebeest gene pools}, language = {en} } @article{GrimmRevillaBergeretal.2005, author = {Grimm, Volker and Revilla, Eloy and Berger, Uta and Jeltsch, Florian and Mooij, Wolf M. and Railsback, Steven Floyd and Thulke, Hans-Hermann and Weiner, Jacob and Wiegand, Thorsten and DeAngelis, Donald L.}, title = {Pattern-oriented modeling of agend-based complex systems : lessons from ecology}, year = {2005}, abstract = {Agent-based complex systems are dynamic networks of many interacting agents; examples include ecosystems, financial markets, and cities. The search for general principles underlying the internal organization of such systems often uses bottom-up simulation models such as cellular automata and agent-based models. No general framework for designing, testing, and analyzing bottom-up models has yet been established, but recent advances in ecological modeling have come together in a general strategy we call pattern-oriented modeling. This strategy provides a unifying framework for decoding the internal organization of agent-based complex systems and may lead toward unifying algorithmic theories of the relation between adaptive behavior and system complexity}, language = {en} } @article{GomezMerinoAranaCeballosTrejoTellezetal.2005, author = {Gomez-Merino, Fernando Carlos and Arana-Ceballos, Fernando Alberto and Trejo-Tellez, L. I. and Skirycz, Aleksandra and Brearley, C. A. and Dormann, P. and M{\"u}ller-R{\"o}ber, Bernd}, title = {Arabidopsis AtDGK7, the smallest member of plant diacylglycerol kinases (DGKs), displays unique biochemical features and saturates at low substrate concentration : the DGK inhibitor R59022 differentially affects AtDGK2 and AtDGK7 activity in vitro and alters plant growth and development}, issn = {0021-9258}, year = {2005}, abstract = {Diacylglycerol kinase (DGK) regulates the level of the second messenger diacylglycerol and produces phosphatidic acid (PA), another signaling molecule. The Arabidopsis thaliana genome encodes seven putative diacylglycerol kinase isozymes (named AtDGK1 to -7), structurally falling into three major clusters. So far, enzymatic activity has not been reported for any plant Cluster II DGK. Here, we demonstrate that a representative of this cluster, AtDGK7, is biochemically active when expressed as a recombinant protein in Escherichia coli. AtDGK7, encoded by gene locus At4g30340, contains 374 amino acids with an apparent molecular mass of 41.2 kDa. AtDGK7 harbors an N-terminal catalytic domain, but in contrast to various characterized DGKs (including AtDGK2), it lacks a cysteine-rich domain at its N terminus, and, importantly, its C-terminal DGK accessory domain is incomplete. Recombinant AtDGK7 expressed in E. coli exhibits Michaelis-Menten type kinetics with 1,2-dioleoyl-sn-glycerol as substrate. AtDGK7 activity was affected by pH, detergents, and the DGK inhibitor R59022. We demonstrate that both AtDGK2 and AtDGK7 phosphorylate diacylglycerol molecular species that are typically found in plants, indicating that both enzymes convert physiologically relevant substrates. AtDGK7 is expressed throughout the Arabidopsis plant, but expression is strongest in flowers and young seedlings. Expression of AtDGK2 is transiently induced by wounding. R59022 at similar to 80 mu M inhibits root elongation and lateral root formation and reduces plant growth, indicating that DGKs play an important role in plant development}, language = {en} } @article{GruszeckiStielNiedzwiedzkietal.2005, author = {Gruszecki, Wieslaw I. and Stiel, H. and Niedzwiedzki, Dariusz and Beck, Michael and Milanowska, J. and Lokstein, Heiko and Leupold, Dieter}, title = {Towards elucidating the energy of the first excited singlet state of xanthophyll cycle pigments investigated by x-ray absorption spectroscopy}, year = {2005}, language = {en} } @article{GerloffEliasSpijkermanSchubert2005, author = {Gerloff-Elias, Antje and Spijkerman, Elly and Schubert, H.}, title = {Light acclimation of Chlamydomonas acidophila accumulating in the hypolimnion of an acidic lake (pH 2.6)}, issn = {0046-5070}, year = {2005}, abstract = {1. The unicellular green alga Chlamydomonas acidophila accumulates in a thin phytoplankton layer in the hypolimnion (deep chlorophyll maximum, DCM) of an extremely acidic lake (Lake 111, pH 2.6, Lusatia, Germany), in which the underwater light spectrum is distorted and red-shifted. 2. Chlamydomonas acidophila exhibited a significantly higher absorption efficiency and a higher cellular chlorophyll b content when incubated in the red shifted underwater light of Lake 111 than in a typical, blue-green dominated, light spectrum. 3. Chlamydomonas acidophila has excellent low light acclimation properties (increased chlorophyll b content, increased oxygen yield and a low light saturation point for photosynthesis) that support survival of the species in the low light climate of the DCM. 4. In situ acclimation to the DCM under low light and temperature decreased maximum photosynthetic rate in autotrophic C. acidophila cultures, whereas the presence of glucose under these conditions enhanced photosynthetic efficiency and capacity. 5. The adaptive abilities of C. acidophila to light and temperature shown in this study, in combination with the absence of potent competitors because of low lake pH, most probably enable the unusual dominance of the green alga in the DCM of Lake 111}, language = {en} } @article{GerloffEliasSpijkermanProschold2005, author = {Gerloff-Elias, Antje and Spijkerman, Elly and Proschold, T.}, title = {Effect of external pH on the growth, photosynthesis and photosynthetic electron transport of Chlamydomonas acidophila Negoro, isolated from an extremely acidic lake (pH 2.6)}, issn = {0140-7791}, year = {2005}, abstract = {In extremely acidic lakes, low primary production rates have been measured. We assumed that proton stress might explain these observations and therefore investigated the photosynthetic behaviour of a Chlamydomonas species, a main primary producer in acidic lakes, over a range of pH values. Identified as C. acidophila using small subunit rDNA analysis, this species is identical to other isolates from acidic environments in Europe and South America, suggesting a worldwide distribution. Laboratory experiments with C. acidophila, revealed a broad pH-tolerance for growth and photosynthesis, the lower pH limit lying at pH 1.5 and the upper limit at pH 7. Growth rates at optimum pH conditions (pH 3 and 5) were equal to those of the mesophilic Chlamydomonas reinhardtii. In contrast, photosynthetic rates were significantly higher, suggesting that higher photosynthetic rates compensated for higher dark respiration rates, as confirmed experimentally. Electron transport capacities of PSI and PSII, P700(+) re-reduction times and measurements of PSII fluorescence revealed the induction of alternative electron transport mechanisms, such as chlororespiration, state transitions and cyclic electron transport, only at suboptimal pH values (pH 1.5; 4 and 6-7). The results indicate, that C. acidophila is well adapted to low pH and that the relatively low primary production rates are not a result of pH stress}, language = {en} } @article{FischerGaleuchetPerret2005, author = {Fischer, Markus and Galeuchet, D. and Perret, C.}, title = {Microsatellite variation and structure of 28 populations of the common wetland plant Lychnis flos-cuculi L. in a fragemented landscape}, issn = {0962-1083}, year = {2005}, abstract = {Habitat fragmentation is known to cause genetic differentiation between small populations of rare species and decrease genetic variation within such populations. However, common species with recently fragmented populations have rarely been studied in this context. We investigated genetic variation and its relationship to population size and geographical isolation of populations of the common plant species, Lychnis flos-cuculi L., in fragmented fen grasslands. We analysed 467 plants from 28 L. flos-cuculi populations of different sizes (60 000-54 000 flowering individuals) in northeastern Switzerland using seven polymorphic microsatellite loci. Genetic differentiation between populations is small (F-ST = 0.022; AMOVA; P < 0.001), suggesting that gene flow among populations is still high or that habitat fragmentation is too recent to result in pronounced differentiation. Observed heterozygosity (H-O = 0.44) significantly deviates from Hardy-Weinberg equilibrium, and within-population inbreeding coefficient F-IS is high (0.30-0.59), indicating a mixed mating breeding system with substantial inbreeding in L. flos-cuculi. Gene diversity is the only measure of genetic variation which decreased with decreasing population size (R = 0.42; P < 0.05). While our results do not indicate pronounced effects of habitat fragmentation on genetic variation in the still common L. flos-cuculi, the lower gene diversity of smaller populations suggests that the species is not entirely unaffected}, language = {en} } @article{FussmannWeithoffYoshida2005, author = {Fussmann, Gregor F. and Weithoff, Guntram and Yoshida, Takehito}, title = {A direct, experimental test of resource vs. consumer dependence}, year = {2005}, abstract = {The uptake of resources from the environment is a vital process for all organisms. Many experimental studies have revealed that the rate at which this process occurs depends critically on the resource concentration, a relationship called "functional response." However, whether the concentration of the consumer normally affects the functional response has been the subject of a long-standing, predominantly theoretical, debate in ecology. Here we present an experimental test between the alternative hypotheses that food uptake depends either only on the resource concentration or on both the resource and the consumer concentrations. In short-term laboratory experiments, we measured the uptake of radioactively labeled, unicellular green algae (Monoraphidium minutum, resource) by the rotifer Brachionus calyciflorus (a consumer) for varying combinations of resource and consumer concentrations. We found that the food uptake by Brachionus depended on the algal concentration with the relationship best described by a Holling type 3 functional response. We detected significant consumer effects on the functional response only at an extraordinarily high Brachionus density (similar to 125 rotifers/mL), which by far exceeds concentrations normally encountered in the field. We conclude that con sumer-dependent food uptake by planktonic rotifers is a phenomenon that can occur under extreme conditions, but probably plays a minor role in natural environments}, language = {en} } @article{FeulnerKirschbaumTiedemann2005, author = {Feulner, Philine g. d. and Kirschbaum, Frank and Tiedemann, Ralph}, title = {Eighteen microsatellite loci for endemic African weakly electric fish (Campylomormyrus, Mormyridae) and their cross species applicability among related taxa}, year = {2005}, abstract = {We describe isolation and characterization of the first microsatellite loci specifically developed for African weakly electric fish (Mormyridae), for the genus Campylomormyrus. Seventeen of our 18 loci are polymorphic within the Campylomormyrus numenius species complex. The polymorphic loci showed four to 15 alleles per locus, an expected heterozygosity between 0.46 and 0.94, and an observed heterozygosity between 0.31 and 1.00. Most primers also yield reproducible results in several other mormyrid species. These loci comprise a set of molecular markers for various applications, from moderately polymorphic loci suitable for population studies to highly polymorphic loci for pedigree analysis in mormyrids}, language = {en} } @article{FettkeEckermannTiessenetal.2005, author = {Fettke, J{\"o}rg and Eckermann, Nora and Tiessen, Axel and Geigenberger, Peter Ludwig and Steup, Martin}, title = {Identification, subcellular localization and biochemical characterization of water-soluble heteroglycans (SHG) in leaves of Arabidopsis thaliana L. : distinct SHG reside in the cytosol and in the apoplast}, issn = {0960-7412}, year = {2005}, abstract = {Water-soluble heteroglycans (SHG) were isolated from leaves of wild-type Arabidopsis thaliana L. and from two starch-deficient mutants. Major constituents of the SHG are arabinose, galactose, rhamnose, and glucose. SHG was separated into low (< 10 kDa; SHG(S)) and high (> 10 kDa; SHG(L)) molecular weight compounds. SHG(S) was resolved into approximately 25 distinct oligoglycans by ion exchange chromatography. SHG(L) was further separated into two subfractions, designated as subfraction I and II, by field flow fractionation. For the intracellular localization of the various SHG compounds several approaches were chosen: first, leaf material was subjected to non-aqueous fractionation. The apolar gradient fractions were characterized by monitoring markers and were used as starting material for the SHG isolation. Subfraction I and SHG(S) exhibited a distribution similar to that of cytosolic markers whereas subfraction II cofractionated with crystalline cellulose. Secondly, intact organelles were isolated and used for SHG isolation. Preparations of intact organelles (mitochondria plus peroxisomes) contained no significant amount of any heteroglycan. In isolated intact microsomes a series of oligoglycans was recovered but neither subfraction I nor II. In in vitro assays using glucose 1-phosphate and recombinant cytosolic (Pho 2) phosphorylase both SHG(S) and subfraction I acted as glucosyl acceptor whereas subfraction II was essentially inactive. Rabbit muscle phosphorylase a did not utilize any of the plant glycans indicating a specific Pho 2-glycan interaction. As revealed by in vivo labeling experiments using (CO2)-C-14 carbon fluxes into subfraction I and II differed. Furthermore, in leaves the pool size of subfraction I varied during the light-dark regime}, language = {en} } @article{FabianGastFilimonovetal.2005, author = {Fabian, H. and Gast, Klaus and Filimonov, Vladimir V. and Zamyatkin, D. F. and Rogov, V. V.}, title = {Thermal unfolding of two designed monomeric lambda Cro repressor variants}, issn = {0924-2031}, year = {2005}, abstract = {The thermal unfolding of the wild-type lambda Cro repressor and of two designed variants, Cro K56-[DGEVK] and Cro K56-[DGEVK] Q16L, was studied by Fourier transform infrared spectroscopy and dynamic light scattering. The engineered Cro K56-[DGEVK] monomer has five additional amino acids inserted after position 56 of the wild-type sequence, while the K56-[DGEVK] Q16L variant differs only in one position (Gln-16 to Leu substitution) from the Cro K56-[DGEVK] sequence. The temperature dependence of selected protein backbone infrared `marker' bands revealed that Cro K56- [DGEVK] is slightly more stable than the wild-type protein, while the replacement of Gln-16 by Leu increases the thermal transition temperature by similar to 20 degrees C. Moreover, thermal unfolding of the two Cro variants was found to proceed through equilibrium unfolding intermediates and to involve the formation of oligomers. The first thermal transition of Cro K56-[DGEVK] involves the melting of major parts of its native secondary structure and is accompanied by the formation of dinners and non-native beta-sheet structures. These structures unfold during a second transition at higher temperatures, accompanied by the dissociation of the dimers. In contrast to the Cro K56-[DGEVK] protein, the intermediate state of the Cro K56-[DGEVK] Q16L variant is less well defined, and involves the formation of oligomers of different size. (c) 2005 Elsevier B.V. All rights reserved}, language = {en} } @article{BogenBenderSchlenstedtetal.2005, author = {Bogen, Oliver and Bender, Olaf and Schlenstedt, Jana and Goswami, C. and Schroder, W. and Blenau, Wolfgang and Gillen, C. and Dreger, M. and Hucho, F.}, title = {Neuronal expression of the IB4-binding versican}, issn = {0022-3042}, year = {2005}, language = {en} } @article{BlenauBaumann2005, author = {Blenau, Wolfgang and Baumann, Arnd}, title = {Molecular characterization of the ebony gene from the American cockroach, Periplaneta americana}, year = {2005}, abstract = {Biogenic amines are an important class of primary messengers in the central (CNS) and peripheral nervous systems and in peripheral organs. These substances regulate and modulate many physiological and behavioral processes. Various inactivation mechanisms for these substances exist to terminate biogenic amine-mediated signal transduction. In vertebrates, the enzymes monoamine oxidase and/or catechol-O-methyl-transferase are involved in these processes. In insects, however, in which both enzymes are low in abundance or absent, biogenic amines are inactivated mainly by N- acetylation or O-sulphation. In Droso-philo, beta-alanyl conjugation mediated by the Ebony protein has recently been shown to be a novel and alternative pathway for biogenic amine inactivation. Here, we report the cloning of ebony cDNA (Peaebony) from a brain-specific cDNA library of the cockroach Periplaneta americana. The open reading frame encodes a protein of 860 amino acid residues (PeaEbony). The PeaEbony polypeptide shares homology to Ebony sequences from Anopheles gambiae, Apis mellifera, and Drosophila melonogaster. In addition, PeaEbony exhibits sequence similarity to a family of microbial non-ribosomal peptide synthetases. The mRNA encoding PeaEbony is highly expressed in the cockroach brain and to a lesser extent in the salivary glands. PeaEbony is, therefore, probably involved in the inactivation of various biogenic amines through beta-alanyl conjugation in the cockroach CNS. Since the salivary glands in Periplaneta are innervated by dopaminergic and serotonergic neurons, PeaEbony probably also biochemically modifies dopamine and serotonin in these acinar glands. Arch. Insect Biochem. (c) 2005 Wiley-Liss, Inc}, language = {en} } @article{BinzenhoeferSchroderStraussetal.2005, author = {Binzenh{\"o}fer, Birgit and Schroder, B. and Strauss, B. and Biedermann, Robert and Settele, Josef}, title = {Habitat models and habitat connectivity analysis for butterflies and burnet moths : the example of Zygaena carniolica and Coenonympha arcania}, year = {2005}, abstract = {In this paper, habitat models were used to predict potential habitat for endangered species, which is an important question in landscape and conservation planning. Based on logistic regression, we developed habitat distribution models for the burnet moth Zygaena carniolica and the nymphalid butterfly Coenonympha arcania in Northern Bavaria, Germany. The relation between adult occurrence and habitat parameters, including the influence of landscape context, was analyzed on, 118 sites. Habitat connectivity analyses were carried out on the basis of (1) habitat suitability maps generated from these models and (2) dispersal data from mark recapture studies. Our results showed that (1) the presence of the burnet depended mainly on the presence of nectar plants and of nutrient-poor dry grasslands in direct vicinity, that of the nymphalid on larger areas of extensively used dry grasslands within 100 m vicinity in combination with small patches of higher shrubs and bushes. (2) Internal as well as external validation indicated the robustness and general applicability of the models. Transferability in time and space indicated their high potential relevance for applications in nature conservation, such as predicting possible effects of land use changes. (3) Habitat connectivity analyses revealed a high degree of habitat connectivity within the study area. Thus, we could show no effects of isolation or habitat size for both species. (c) 2005 Elsevier Ltd. All rights reserved}, language = {en} } @article{BihlerEingHebeisenetal.2005, author = {Bihler, Hermann and Eing, C. and Hebeisen, S. and Roller, A. and Czempinski, Katrin and Bertl, Adam}, title = {TPK1 is a vacuolar ion channel different from the slow-vacuolar cation channel}, year = {2005}, abstract = {TPK1 ( formerly KCO1) is the founding member of the family of two-pore domain K 1 channels in Arabidopsis ( Arabidopsis thaliana), which originally was described following expression in Sf9 insect cells as a Ca2(+)- and voltage- dependent outwardly rectifying plasma membrane K 1 channel. In plants, this channel has been shown by green fluorescent protein fusion to localize to the vacuolar membrane, which led to speculations that the TPK1 gene product would be a component of the nonselective, Ca2+ and voltage- dependent slow-vacuolar (SV) cation channel found in many plants species. Using yeast ( Saccharomyces cerevisiae) as an expression system for TPK1, we show functional expression of the channel in the vacuolar membrane. In isolated vacuoles of yeast yvc1 disruption mutants, the TPK1 gene product shows ion channel activity with some characteristics very similar to the SV-type channel. The open channel conductance of TPK1 in symmetrically 100mM KCl is slightly asymmetric with roughly 40 pS at positive membrane voltages and 75 pS at negative voltages. Similar to the SV-type channel, TPK1 is activated by cytosolic Ca2+, requiring micromolar concentration for activation. However, in contrast to the SV- type channel, TPK1 exhibits strong selectivity for K+ over Na+, and its activity turned out to be independent of the membrane voltage over the range of +/- 80mV. Our data clearly demonstrate that TPK1 is a voltage- independent, Ca2+- activated, K+- selective ion channel in the vacuolar membrane that does not mediate SV- type ionic currents}, language = {en} } @article{BarbierOesterheltLarsonetal.2005, author = {Barbier, Guillaume and Oesterhelt, Christine and Larson, Matthew D. and Halgren, Robert G. and Wilkerson, Curtis and Garavito, Michael R. and Benning, Christoph and Weber, Andreas P. M.}, title = {Comparative genomics of two closely related unicellular thermo-acidophilic red algae, Galdieria sulphuraria and Cyanidioschyzon merolae, reveals the molecular basis of the metabolic flexibility of Galdieria sulphuraria and sigant differences in carbohydrate metabolism of both algae}, year = {2005}, abstract = {Unicellular algae serve as models for the study and discovery of metabolic pathways, for the functional dissection of cell biological processes such as organellar division and cell motility, and for the identification of novel genes and gene functions. The recent completion of several algal genome sequences and expressed sequence tag collections and the establishment of nuclear and organellar transformation methods has opened the way for functional genomics approaches using algal model systems. The thermo-acidophilic unicellular red alga Galdieria sulphuraria represents a particularly interesting species for a genomics approach owing to its extraordinary metabolic versatility such as heterotrophic and mixotrophic growth on more than 50 different carbon sources and its adaptation to hot acidic environments. However, the ab initio prediction of genes required for unknown metabolic pathways from genome sequences is not trivial. A compelling strategy for gene identification is the comparison of similarly sized genomes of related organisms with different physiologies. Using this approach, candidate genes were identified that are critical to the metabolic versatility of Galdieria. Expressed sequence tags and high-throughput genomic sequence reads covering >70\% of the G. sulphuraria genome were compared to the genome of the unicellular, obligate photoautotrophic red alga Cyanidioschyzon merolae. More than 30\% of the Galdieria sequences did not relate to any of the Cyandioschyzon genes. A closer inspection of these sequences revealed a large number of membrane transporters and enzymes of carbohydrate metabolism that are unique to Galdieria. Based on these data, it is proposed that genes involved in the uptake of reduced carbon compounds and enzymes involved in their metabolism are crucial to the metabolic flexibility of G. sulphuraria}, language = {en} } @article{BistolasWollenbergerJungetal.2005, author = {Bistolas, Nikitas and Wollenberger, Ursula and Jung, Christiane and Scheller, Frieder W.}, title = {Cytochrome P450 biosensors : a review}, year = {2005}, abstract = {Cytochrome P450 (CYP) is a large family of enzymes containing heme as the active site. Since their discovery and the elucidation of their structure, they have attracted the interest of scientist for many years, particularly due to their catalytic abilities. Since the late 1970s attempts have concentrated on the construction and development of electrochemical sensors. Although sensors based on mediated electron transfer have also been constructed, the direct electron transfer approach has attracted most of the interest. This has enabled the investigation of the electrochemical properties of the various isoforms of CYP. Furthermore, CYP utilized to construct biosensors for the determination of substrates important in environmental monitoring, pharmaceutical industry and clinical practice. (c) 2004 Elsevier B. V. All rights reserved}, language = {en} } @article{GoetzSuopankiSchuleretal.2005, author = {Goetz, C. and Suopanki, J. and Schuler, Benjamin and Wanker, E. and Herrmann, Andreas}, title = {Perturbation of brain lipid membrane by soluble Huntingtin depends on its polyproline tract}, issn = {0006-3495}, year = {2005}, language = {en} } @article{LangeHimmelAuerbachetal.2005, author = {Lange, Stephan and Himmel, Mirko and Auerbach, Daniel and Agarkova, Irina and Hayess, Katrin and F{\"u}rst, Dieter Oswald and Perriard, Jean-Claude and Ehler, Elisabeth}, title = {Dimerisation of myomesin : implications for the structure of the sarcomeric M-band}, issn = {0022-2836}, year = {2005}, abstract = {The sarcomeric M-band is thought to provide a link between the thick and the elastic, filament systems. So far, relatively little is known about its structural components and their three-dimensional organisation. Myomesin seems to be an essential component of the M-band, since it is expressed in all types of vertebrate striated muscle fibres investigated and can be found in its mature localisation pattern as soon as the first myofibrils are assembled. Previous work has shown that the N-terminal and central part of myomesin harbour binding sites for myosin, titin and muscle creatine kinase. Intrigued by the highly conserved domain layout of the C-terminal half, we screened for new interaction partners by yeast two-hybrid analysis. This revealed a strong interaction of myomesin with itself. This finding was confirmed by several biochemical assays. Our data suggest that myomesin can form antiparallel dimers via a binding site residing in its C-terminal domain 13. We suggest that, similar to alpha-actinin in the Z-disc, the myomesin dimers cross- link the contractile filaments in the M-band. The new and the already previously identified myomesin interaction sites are integrated into the first three-dimensional model of the sarcomeric M-band on a molecular basis. (C) 2004 Elsevier Ltd. All rights reserved}, language = {en} } @article{BoelJurrmannBrigeliusFlohe2005, author = {B{\"o}l, Gaby Fleur and Jurrmann, Nadine and Brigelius-Floh{\´e}, Regina}, title = {Cellular trafficking of the IL-1RI-associated kinase-1 requires intact kinase activity}, issn = {0006-291X}, year = {2005}, abstract = {Upon stimulation of cells with interleukin-1 (IL-1) the IL-1 receptor type 1 (IL-1RI) associated kinase-1 (IRAK- 1) transiently associates to and dissociates front the IL-IRI and thereafter translocates into the nucleus. Here we show that nuclear translocation of IRAK-I depends on its kinase activity since translocation was not observed in EL-4 cells overexpressing a kinase negative IRAK-1 mutant (EL-4(IRAK-1-K239S)). IRAK-1 itself, an endogenous substrate with an apparent molecular weight of 24 kDa (p24). and exogenous substrates like histone and myelin basic protein are phosphorylated by nuclear located IRAK-1. Phosphorylation of p24 cannot be detected in EL-4(IRAK-1-K239S) cells. IL-1- dependent recruitment of IRAK-1 to the IL-1RI and subsequent phosphorylation of IRAK-l is a prerequisite for nuclear translocation of IRAK-1. It is therefore concluded that intracellular localization of IRAK-1 depends on its kinase activity and that IRAK-1 may also function as a kinase in the nucleus as shown by a new putative endogenous substrate. (c) 2005 Elsevier Inc. All rights reserved}, language = {en} } @article{FettkePoesteEckermannetal.2005, author = {Fettke, J{\"o}rg and Poeste, Simon and Eckermann, Nora and Tiessen, Axel and Pauly, Markus and Geigenberger, Peter Ludwig and Steup, Martin}, title = {Analysis of cytosolic heteroglycans from leaves of transgenic potato (Solanum tuberosum L.) plants that under- or overexpress the Pho 2 phosphorylase isozyme}, year = {2005}, abstract = {During starch degradation, chloroplasts export neutral sugars into the cytosol where they appear to enter a complex glycan metabolism. Interactions between glycans and glucosyl transferases residing in the cytosol were studied by analyzing transgenic potato (Solanum tuberosum L.) plants that possess either decreased or elevated levels of the cytosolic (Pho 2) phosphorylase isoform. Water-soluble heteroglycans (SHGs) were isolated from these plants and were characterized. SHG contains, as major constituents, arabinose, rhamnose, galactose and glucose. Non-aqueous fractionation combined with other separation techniques revealed a distinct pool of the SHG that is located in the cytosol. Under in vitro conditions, the cytosolic heteroglycans act as glucosyl acceptor selectively for Pho 2. Acceptor sites were characterized by a specific hydrolytic degradation following the Pho 2-catalyzed glucosyl transfer. The size distribution of the cytosolic SHG increased during the dark period, indicating a distinct metabolic activity related to net starch degradation. Antisense inhibition of Pho 2 resulted in increased glucosyl and rhamnosyl contents of the glycans. Overexpression of Pho 2 decreased the content of both residues. Compared with the wild type, in both types of transgenic plants the size of the cytosolic glycans was increased}, language = {en} } @article{Beissenhirtz2005, author = {Beissenhirtz, Moritz Karl}, title = {Electrochemical quartz crystal microbalance studies on cytochrome c/polyelectrode multilayer assemblies on gold electrodes}, year = {2005}, abstract = {Polyelectrolyte multilayer assemblies containing proteins are of interest for applications such as sensors, bioreactors, and bioelectronics. A multilayer electrode was built up by the layer-by-layer strategy consisting of alternating layers of cytochrome c and poly(aniline sulfonic acid). The electrode showed a linear increase of redox active protein with the number of deposited layers. The principle of electrode preparation was transferred from needle electrodes to planar surfaces in order to further the understanding of electron transfer through the layer assembly by means of electrochemical quartz crystal microbalance studies. The deposition process was followed on-line by detection of the frequency shift of the crystals and was found to be rather fast (minutes). The total mass deposited was found to correlate well with the electrochemical response of the immobilized cyt.c. Furthermore, the influence of the polyelectrolyte was investigated by addition of PSS to the PASA solution. The strong interaction of the former polyelectrolyte seemed to hinder the electron transfer although a multilayer formation was proved. Dilution of the protein solution with redox inactive apo-cyt.c led to a strong decrease of the voltammetric signal, well beyond the percentage of apo-cyt.c inside the assembly. Thus, arguments for an electron transfer via protein-protein interaction were found}, language = {en} } @article{MichardLacombePoreeetal.2005, author = {Michard, Erwan and Lacombe, Beno{\^i}t and Poree, Fabien and M{\"u}ller-R{\"o}ber, Bernd and Sentenac, Herv{\´e} and Thibaud, Jean-Baptiste and Dreyer, Ingo}, title = {A unique voltage sensor sensitizes the potassium channel AKT2 to phosphoregulation}, year = {2005}, abstract = {Among all voltage-gated K+ channels from the model plant Arabidopsis thaliana, the weakly rectifying K+ channel (K-weak channel) AKT2 displays unique gating properties. AKT2 is exceptionally regulated by phosphorylation: when nonphosphorylated AKT2 behaves as an inward-rectifying potassium channel; phosphorylation of AKT2 abolishes inward rectification by shifting its activation threshold far positive (>200 mV) so that it closes only at voltages positive of + 100 mV. In its phosphorylated form, AKT2 is thus locked in the open state in the entire physiological voltage range. To understand the molecular grounds of this unique gating behavior, we generated chimeras between AKT2 and the conventional inward-rectifying channel KAT1. The transfer of the pore from KAT1 to AKT2 altered the permeation properties of the channel. However, the gating properties were unaffected, suggesting that the pore region of AKT2 is not responsible for the unique K-weak gating. Instead, a lysine residue in S4, highly conserved among all K-weak channels but absent from other plant K+ channels, was pinpointed in a site-directed mutagenesis approach. Substitution of the lysine by serine or aspartate abolished the "open-lock" characteristic and converted AKT2 into an inward- rectifying channel. Interestingly, phosphoregulation of the mutant AKT2-K197S appeared to be similar to that of the K-in channel KAT1: as suggested by mimicking the phosphorylated and dephosphorylated states, phosphorylation induced a shift of the activation threshold of AKT2-K197S by about +50 mV. We conclude that the lysine residue K197 sensitizes AKT2 to phosphoregulation. The phosphorylation-induced reduction of the activation energy in AKT2 is similar to 6 kT larger than in the K197S mutant. It is discussed that this hypersensitive response of AKT2 to phosphorylation equips a cell with the versatility to establish a potassium gradient and to make efficient use of it}, language = {en} } @article{RautengartenSteinhaeuserBussisetal.2005, author = {Rautengarten, Carsten and Steinhaeuser, Dirk and Bussis, D and Stintzi, A and Schaller, A and Kopka, Joachim and Altmann, Thomas}, title = {Inferring hypotheses on functional relationships of genes : Analysis of the Arabidopsis thaliana subtilase gene family}, year = {2005}, abstract = {The gene family of subtilisin-like serine proteases (subtilases) in Arabidopsis thaliana comprises 56 members, divided into six distinct subfamilies. Whereas the members of five subfamilies are similar to pyrolysins, two genes share stronger similarity to animal kexins. Mutant screens confirmed 144 T-DNA insertion lines with knockouts for 55 out of the 56 subtilases. Apart from SDD1, none of the confirmed homozygous mutants revealed any obvious visible phenotypic alteration during growth under standard conditions. Apart from this specific case, forward genetics gave us no hints about the function of the individual 54 non-characterized subtilase genes. Therefore, the main objective of our work was to overcome the shortcomings of the forward genetic approach and to infer alternative experimental approaches by using an integrative biolinformatics and biological approach. Computational analyses based on transcriptional co-expression and co-response pattern revealed at least two expression networks, suggesting that functional redundancy may exist among subtilases with limited similarity. Furthermore, two hubs were identified, which may be involved in signalling or may represent higher-order regulatory factors involved in responses to environmental cues. A particular enrichment of co- regulated genes with metabolic functions was observed for four subtilases possibly representing late responsive elements of environmental stress. The kexin homologs show stronger associations with genes of transcriptional regulation context. Based on the analyses presented here and in accordance with previously characterized subtilases, we propose three main functions of subtilases: involvement in (i) control of development, (ii) protein turnover, and (iii) action as downstream components of signalling cascades}, language = {en} } @article{BolayBraunDelheyetal.2005, author = {Bolay, Adrien and Braun, Uwe and Delhey, Rolf and Kummer, Volker and Piatek, Marcin and Wolczanska, Agata}, title = {Erysiphe deutziae - a new epidemic spread in Europe}, year = {2005}, abstract = {Erysiphe deutziae (Bunkina) U. Braun \& S. Takam. is powdery mildew fungus that is currently spreading in Europe. The anamorph of this species has been found in France, Germany, Poland and Switzerland on Deutzia sp. (cult.), Deutzia x magnifica (Lemoine) Rehder and Deutzia scabra Thunb. The morphology, taxonomy and worldwide distribution of Erysiphe deutziae are described, illustrated and discussed}, language = {en} } @article{MaurerGautschiWeyandetal.2005, author = {Maurer, Katrin and Gautschi, B and Weyand, Anne and Stocklin, J and Fischer, Markus}, title = {Isolation and characterization of microsatellite DNA markers in the grass Poa alpina L.}, year = {2005}, abstract = {The important fodder grass Poa alpina L. occurs at several ploidy levels with common aneuploidy. We isolated and characterized five polymorphic microsatellite markers for the study of molecular genetic variation of this species. As first examples of the value of the developed markers for population genetic analyses, we show that plants with more chromosomes have more microsatellite bands and that isolation by distance plays a small role in shaping microsatellite diversity of P. alpina in the Swiss Alps}, language = {en} } @article{Wacker2005, author = {Wacker, Alexander}, title = {Lipids in the food of a terrestrial snail}, year = {2005}, abstract = {Animals depend on a large set of essential compounds in their food. A reduced supply of specific lipid compounds has been shown to be critical for growth, reproduction and survival of aquatic molluscs and might also be critical for terrestrial gastropods. The effects were investigated of different fatty acid and cholesterol supplies on the growth, reproduction, and survival of the land snail Arianta arbustorum. Surprisingly, differences in diet did not affect shell growth, time to reach adulthood, and reproductive traits such as the number of eggs, dry mass and volume of spermatophores. However, snails reared on low cholesterol diets and low polyunsaturated fatty acid (PUFA) diets decreased their consumption rates and had a higher mortality. Snails fed a PUFA-rich diet showed higher mating activity than snails fed a diet deficient in PUFAs. A depletion of internal PUFA reserves may affect the regulation of mating behaviour because PUFAs play an important role as precursors for signal-transduction involved in the regulation of mating and reproduction. In contrast, when the diets were deficient in cholesterol, mating activity was not affected}, language = {en} } @article{BroseTielboerger2005, author = {Brose, Ulrich and Tielb{\"o}rger, Katja}, title = {Subtle differences in environmental stress along a flooding gradient affect the importance of inter-specific competition in an annual plant community}, issn = {1385-0237}, year = {2005}, abstract = {Empirical evidence suggests that the direction and intensity of plant-plant interactions may depend on the favourability of the environment. Previous studies have mainly focused on steep gradients of environmental stress or disturbance, while the interplay of competition and environment has not been tested for subtle environmental differences. Here, we present results from a study on plant communities of temporary wetlands in East-German farmland. Due to yearly ploughing in autumn, the vegetation is composed of annual species. Flooding does not affect adult plants and the elevation on the gradient expresses differences in the length of the growing season rather than in disturbance intensity or severe environmental stress. We tested whether such subtle differences in environmental stress may affect the importance of interspecific competition by the dominant species. Two treatments were applied at two elevations: removal of the dominant species (Matricaria maritima ssp. inodora) and reciprocal transplants of the seed-bank of the two elevations. At both elevations, removal of Matricaria inodora led to an increase in total species richness and number of wetland species, but the effects were substantially stronger at high elevations. Removal and the elevation on the flooding gradient significantly influenced the plant community composition. In particular, the weed communities became more similar to the wetland communities after the removal. Transplanted weed species did not emerge at low elevations. While two of four target species had significantly higher densities after the removal at high elevations, none of them was influenced by removal at low elevations. This indicates that, consistent with previous studies from other habitat types, competition by the dominant species was more intense under conditions of low environmental stress. The overall results suggest that both flooding as well as interspecific competition are important in structuring the plant communities along the freshwater gradient studied}, language = {en} } @article{ForlaniCeredaFreueretal.2005, author = {Forlani, Fabio and Cereda, Angelo and Freuer, Andrea and Nimtz, Manfred and Leimk{\"u}hler, Silke and Pagani, Silvia}, title = {The cysteine-desulfurase IscS promotes the production of the rhodanese RhdA in the persulfurated form}, issn = {0014-5793}, year = {2005}, abstract = {After heterologous expression in Escherichia coli, the Azotobacter vinelandii rhodanese RhdA is purified in a persulfurated form (RhdA-SSH). We identified L-cysteine as the most effective sulfur source in producing RhdA-SSH. An E. coli soluble extract was required for in vitro persulfuration of RhdA, and the addition of pyridoxal-5'-phosphate increased RhdA-SSH production, indicating a likely involvement of a cysteine desulfurase. We were able to show the formation of a covalent complex between IscS and RhdA. By combining a time-course fluorescence assay and mass spectrometry analysis, we demonstrated the transfer of sulfur from E. coli IscS to RhdA. (c) 2005 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved}, language = {en} } @article{WoltersBittmannKummer2005, author = {Wolters, Steffen and Bittmann, Felix and Kummer, Volker}, title = {The first subfossil records of Urtica kioviensis Rogow. and their consequences for palaeoecological interpretations}, year = {2005}, abstract = {Among plant remains from Mesolithic layers dating from 9249 to 7779 B.C. at the excavation site of Friesack IV in north-eastern Germany, nutlets of Urtica kioviensis were identified. Morphological studies have shown that they clearly differed from all other European Urtica species investigated. In contrast, pollen morphological investigations revealed only slight differences between the central European Urtica species, which could hardly have been noticed during routine or normal pollen analyses. The records of U. kioviensis nutlets are the first subfossil finds reported and prove the indigenous status of this taxon in north-eastern Germany. The records are discussed in the context of the overall species spectrum of the Mesolithic layers and consequences for the interpretation of pollen analytical studies concerning human impact are pointed out}, language = {en} } @article{HeiseBier2005, author = {Heise, Christian and Bier, Frank Fabian}, title = {Immobilization of DNA on microarrays}, year = {2005}, abstract = {Microarrays are new analytical devices that allow the parallel and simultaneous detection of thousands of target compounds. Microarrays, also called DNA chips, are widely used in gene expression, the genotyping of individuals, point mutations, detection of single nucleotide polymorphisms, and short tandem repeats. Microarrays have highly specific base-pair interactions with labeled complementary strands, which makes this technology to a powerful analytical device for monitoring whole genomes. In this article, we provide a survey of the common microarray manufacturing methods, from the selection of support material to surface structuring, immobilization and hybridization, and finally the detection with labeled complementary strands. Special attention is given to the immobilization of single strands, since fast chemical reactions, the creation of homogeneous surface functionalities as well as an oriented coupling are crucial pre-conditions for a good spot morphology and microarrays of high quality}, language = {en} } @article{FischerWipfRixenetal.2005, author = {Fischer, Markus and Wipf, S. and Rixen, C. and St{\"o}ckli, V.}, title = {Effects of ski piste preparation on alpine vegetation}, issn = {0021-8901}, year = {2005}, abstract = {1. Ski resorts increasingly affect alpine ecosystems through enlargement of ski pistes, machine-grading of ski piste areas and increasing use of artificial snow. 2. In 12 Swiss alpine ski resorts, we investigated the effects of ski piste management on vegetation structure and composition using a pairwise design of 38 plots on ski pistes and 38 adjacent plots off-piste. 3. Plots on ski pistes had lower species richness and productivity, and lower abundance and cover of woody plants and early flowering species, than reference plots. Plots on machine-graded pistes had higher indicator values for nutrients and light, and lower vegetation cover, productivity, species diversity and abundance of early flowering and woody plants. Time since machine-grading did not mitigate the impacts of machine-grading, even for those plots where revegetation had been attempted by sowing. 4. The longer artificial snow had been used on ski pistes (2-15 years), the higher the moisture and nutrient indicator values. Longer use also affected species composition by increasing the abundance of woody plants, snowbed species and late-flowering species, and decreasing wind-edge species. 5. Synthesis and applications. All types of ski piste management cause deviations from the natural structure and composition of alpine vegetation, and lead to lower plant species diversity. Machine-grading causes particularly severe and lasting impacts on alpine vegetation, which are mitigated neither by time nor by revegetation measures. The impacts of artificial snow increase with the period of time since it was first applied to ski piste vegetation. Extensive machine-grading and snow production should be avoided, especially in areas where nutrient and water input are a concern. Ski pistes should not be established in areas where the alpine vegetation has a high conservation value}, language = {en} } @article{BolayBraunDelheyetal.2005, author = {Bolay, Adrien and Braun, Uwe and Delhey, Rolf and Kummer, Volker and Piatek, Marcin and Wolczanska, Agata}, title = {Erysiphe deutziae : a new epidemic spread in Europe}, year = {2005}, abstract = {Erysiphe deutziae (Bunkina) U. Braun \& S. Takam. is powdery mildew fungus that is currently spreading in Europe. The anamorph of this species has been found in France, Germany, Poland and Switzerland on Deutzia sp. (cult.), Deutzia x magnifica (Lemoine) Rehder and Deutzia scabra Thunb. The morphology, taxonomy and worldwide distribution of Erysiphe deutziae are described, illustrated and discussed}, language = {en} } @article{SchellerBistolasLiuetal.2005, author = {Scheller, Frieder W. and Bistolas, Nikitas and Liu, Songqin and J{\"a}nchen, Michael and Katterle, Martin and Wollenberger, Ursula}, title = {Thirty years of haemoglobin electrochemistry}, year = {2005}, abstract = {Electrochemical investigations of the blood oxygen carrier protein include both mediated and direct electron transfer. The reaction of haemoglobin (Hb) with typical mediators, e.g., ferricyanide, can be quantified by measuring the produced ferrocyanide which is equivalent to the Hb concentration. Immobilization of the mediator within the electrode body allows reagentless electrochemical measuring of Hb. On the other hand, entrapment of the protein within layers of polyclectrolytes, lipids, nanoparticles of clay or gold leads to a fast heterogeneous electron exchange of the partially denatured Hb. (c) 2005 Elsevier B.V. All rights reserved}, language = {en} }