@phdthesis{Sperfeld2011, author = {Sperfeld, Erik}, title = {Effects of temperature and co-limiting nutritional components on life history traits of Daphnia magna and its biochemical composition}, address = {Potsdam}, pages = {157 S.}, year = {2011}, language = {en} } @article{SammlerBleidornTiedemann2011, author = {Sammler, Svenja and Bleidorn, Christoph and Tiedemann, Ralph}, title = {Full mitochondrial genome sequences of two endemic Philippine hornbill species (Aves: Bucerotidae) provide evidence for pervasive mitochondrial DNA recombination}, series = {BMC genomics}, volume = {12}, journal = {BMC genomics}, number = {2}, publisher = {BioMed Central}, address = {London}, issn = {1471-2164}, doi = {10.1186/1471-2164-12-35}, pages = {10}, year = {2011}, abstract = {Background: Although nowaday it is broadly accepted that mitochondrial DNA (mtDNA) may undergo recombination, the frequency of such recombination remains controversial. Its estimation is not straightforward, as recombination under homoplasmy (i.e., among identical mt genomes) is likely to be overlooked. In species with tandem duplications of large mtDNA fragments the detection of recombination can be facilitated, as it can lead to gene conversion among duplicates. Although the mechanisms for concerted evolution in mtDNA are not fully understood yet, recombination rates have been estimated from "one per speciation event" down to 850 years or even "during every replication cycle". Results: Here we present the first complete mt genome of the avian family Bucerotidae, i.e., that of two Philippine hornbills, Aceros waldeni and Penelopides panini. The mt genomes are characterized by a tandemly duplicated region encompassing part of cytochrome b, 3 tRNAs, NADH6, and the control region. The duplicated fragments are identical to each other except for a short section in domain I and for the length of repeat motifs in domain III of the control region. Due to the heteroplasmy with regard to the number of these repeat motifs, there is some size variation in both genomes; with around 21,657 bp (A. waldeni) and 22,737 bp (P. panini), they significantly exceed the hitherto longest known avian mt genomes, that of the albatrosses. We discovered concerted evolution between the duplicated fragments within individuals. The existence of differences between individuals in coding genes as well as in the control region, which are maintained between duplicates, indicates that recombination apparently occurs frequently, i. e., in every generation. Conclusions: The homogenised duplicates are interspersed by a short fragment which shows no sign of recombination. We hypothesize that this region corresponds to the so-called Replication Fork Barrier (RFB), which has been described from the chicken mitochondrial genome. As this RFB is supposed to halt replication, it offers a potential mechanistic explanation for frequent recombination in mitochondrial genomes.}, language = {en} } @misc{PokornySharmaGoyaletal.2011, author = {Pokorny, Ina and Sharma, Reeta and Goyal, Surendra Prakash and Mishra, Sudanshu and Tiedemann, Ralph}, title = {MHC class I and MHC class II DRB gene variability in wild and captive Bengal tigers (Panthera tigris tigris) (vol 10, pg 667, 2010)}, series = {Immunogenetics}, volume = {63}, journal = {Immunogenetics}, number = {2}, publisher = {Springer}, address = {New York}, issn = {0093-7711}, doi = {10.1007/s00251-010-0496-2}, pages = {121 -- 121}, year = {2011}, language = {en} } @article{WiesnerLoxdaleKoehleretal.2011, author = {Wiesner, Kerstin R. and Loxdale, Hugh D. and K{\"o}hler, G{\"u}nter and Schneider, Anja R. R. and Tiedemann, Ralph and Weisser, Wolfgang W.}, title = {Patterns of local and regional genetic structuring in the meadow grasshopper, Chorthippus parallelus (Orthoptera: Acrididae), in Central Germany revealed using microsatellite markers}, series = {Biological journal of the Linnean Society : a journal of evolution}, volume = {103}, journal = {Biological journal of the Linnean Society : a journal of evolution}, number = {4}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0024-4066}, doi = {10.1111/j.1095-8312.2011.01698.x}, pages = {875 -- 890}, year = {2011}, abstract = {The meadow grasshopper, Chorthippus parallelus (Zetterstedt), is common and widespread in Central Europe, with a low dispersal range per generation. A population study in Central Germany (Frankenwald and Thuringer Schiefergebirge) showed strong interpopulation differences in abundance and individual fitness. We examined genetic variability using microsatellite markers within and between 22 populations in a short-to long-distance sampling (19 populations, Frankenwald, Schiefergebirge, as well as a southern transect), and in the Erzgebirge region (three populations), with the latter aiming to check for effects as a result of historical forest cover. Of the 671 C. parallelus captured, none was macropterous (functionally winged). All populations showed a high level of expected and observed heterozygosity (mean 0.80-0.90 and 0.60-0.75, respectively), whereas there was evidence of inbreeding (F(IS) values all positive). Allelic richness for all locus-population combinations was high (mean 9.3-11.2), whereas alleles per locus ranged from 15-62. At a local level, genic and genotypic differences were significant. Pairwise F(ST) values were in the range 0.00-0.04, indicating little interpopulation genetic differentiation. Similarly, the calculated gene flow was very high, based on the respective F(ST) (19.5) and using private alleles (7.7). A Neighbour-joining tree using Nei's D(A) and principal coordinate analysis separated two populations that were collected in the Erzgebirge region. Populations from this region may have escaped the effects of the historical forest cover. The visualization of the spatial arrangement of genotypes revealed one geographical barrier to gene flow in the short-distance sampling.}, language = {en} } @article{StoofLeichsenringJungingerOlakaetal.2011, author = {Stoof-Leichsenring, Kathleen Rosemarie and Junginger, Annett and Olaka, Lydia A. and Tiedemann, Ralph and Trauth, Martin H.}, title = {Environmental variability in Lake Naivasha, Kenya, over the last two centuries}, series = {Journal of paleolimnolog}, volume = {45}, journal = {Journal of paleolimnolog}, number = {3}, publisher = {Springer}, address = {Dordrecht}, issn = {0921-2728}, doi = {10.1007/s10933-011-9502-4}, pages = {353 -- 367}, year = {2011}, abstract = {Lake Naivasha, Kenya, is one of a number of freshwater lakes in the East African Rift System. Since the beginning of the twentieth century, it has experienced greater anthropogenic influence as a result of increasingly intensive farming of coffee, tea, flowers, and other horticultural crops within its catchment. The water-level history of Lake Naivasha over the past 200 years was derived from a combination of instrumental records and sediment data. In this study, we analysed diatoms in a lake sediment core to infer past lacustrine conductivity and total phosphorus concentrations. We also measured total nitrogen and carbon concentrations in the sediments. Core chronology was established by (210)Pb dating and covered a similar to 186-year history of natural (climatic) and human-induced environmental changes. Three stratigraphic zones in the core were identified using diatom assemblages. There was a change from littoral/epiphytic diatoms such as Gomphonema gracile and Cymbella muelleri, which occurred during a prolonged dry period from ca. 1820 to 1896 AD, through a transition period, to the present planktonic Aulacoseira sp. that favors nutrient-rich waters. This marked change in the diatom assemblage was caused by climate change, and later a strong anthropogenic overprint on the lake system. Increases in sediment accumulation rates since 1928, from 0.01 to 0.08 g cm(-2) year(-1) correlate with an increase in diatom-inferred total phosphorus concentrations since the beginning of the twentieth century. The increase in phosphorus accumulation suggests increasing eutrophication of freshwater Lake Naivasha. This study identified two major periods in the lake's history: (1) the period from 1820 to 1950 AD, during which the lake was affected mainly by natural climate variations, and (2) the period since 1950, during which the effects of anthropogenic activity overprinted those of natural climate variation.}, language = {en} } @article{SchwarteTiedemann2011, author = {Schwarte, Sandra and Tiedemann, Ralph}, title = {A Gene Duplication/Loss Event in the Ribulose-1,5-Bisphosphate-Carboxylase/Oxygenase (Rubisco) Small Subunit Gene Family among Accessions of Arabidopsis thaliana}, series = {Molecular biology and evolution}, volume = {28}, journal = {Molecular biology and evolution}, number = {6}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0737-4038}, doi = {10.1093/molbev/msr008}, pages = {1861 -- 1876}, year = {2011}, abstract = {Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39), the most abundant protein in nature, catalyzes the assimilation of CO(2) (worldwide about 10(11) t each year) by carboxylation of ribulose-1,5-bisphosphate. It is a hexadecamer consisting of eight large and eight small subunits. Although the Rubisco large subunit (rbcL) is encoded by a single gene on the multicopy chloroplast genome, the Rubisco small subunits (rbcS) are encoded by a family of nuclear genes. In Arabidopsis thaliana, the rbcS gene family comprises four members, that is, rbcS-1a, rbcS-1b, rbcS-2b, and rbcS-3b. We sequenced all Rubisco genes in 26 worldwide distributed A. thaliana accessions. In three of these accessions, we detected a gene duplication/loss event, where rbcS-1b was lost and substituted by a duplicate of rbcS-2b (called rbcS-2b*). By screening 74 additional accessions using a specific polymerase chain reaction assay, we detected five additional accessions with this duplication/loss event. In summary, we found the gene duplication/loss in 8 of 100 A. thaliana accessions, namely, Bch, Bu, Bur, Cvi, Fei, Lm, Sha, and Sorbo. We sequenced an about 1-kb promoter region for all Rubisco genes as well. This analysis revealed that the gene duplication/loss event was associated with promoter alterations (two insertions of 450 and 850 bp, one deletion of 730 bp) in rbcS-2b and a promoter deletion (2.3 kb) in rbcS-2b* in all eight affected accessions. The substitution of rbcS-1b by a duplicate of rbcS-2b (i.e., rbcS-2b*) might be caused by gene conversion. All four Rubisco genes evolve under purifying selection, as expected for central genes of the highly conserved photosystem of green plants. We inferred a single positive selected site, a tyrosine to aspartic acid substitution at position 72 in rbcS-1b. Exactly the same substitution compromises carboxylase activity in the cyanobacterium Anacystis nidulans. In A. thaliana, this substitution is associated with an inferred recombination. Functional implications of the substitution remain to be evaluated.}, language = {en} } @article{TiedemannPaulusHavensteinetal.2011, author = {Tiedemann, Ralph and Paulus, Kirsten B. and Havenstein, Katja and Thorstensen, Sverrir and Petersen, Aevar and Lyngs, Peter and Milinkovitch, Michel C.}, title = {Alien eggs in duck nests brood parasitism or a help from Grandma?}, series = {Molecular ecology}, volume = {20}, journal = {Molecular ecology}, number = {15}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0962-1083}, doi = {10.1111/j.1365-294X.2011.05158.x}, pages = {3237 -- 3250}, year = {2011}, abstract = {Intraspecific brood parasitism (IBP) is a remarkable phenomenon by which parasitic females can increase their reproductive output by laying eggs in conspecific females' nests in addition to incubating eggs in their own nest. Kin selection could explain the tolerance, or even the selective advantage, of IBP, but different models of IBP based on game theory yield contradicting predictions. Our analyses of seven polymorphic autosomal microsatellites in two eider duck colonies indicate that relatedness between host and parasitizing females is significantly higher than the background relatedness within the colony. This result is unlikely to be a by-product of relatives nesting in close vicinity, as nest distance and genetic identity are not correlated. For eider females that had been ring-marked during the decades prior to our study, our analyses indicate that (i) the average age of parasitized females is higher than the age of nonparasitized females, (ii) the percentage of nests with alien eggs increases with the age of nesting females, (iii) the level of IBP increases with the host females' age, and (iv) the number of own eggs in the nest of parasitized females significantly decreases with age. IBP may allow those older females unable to produce as many eggs as they can incubate to gain indirect fitness without impairing their direct fitness: genetically related females specialize in their energy allocation, with young females producing more eggs than they can incubate and entrusting these to their older relatives. Intraspecific brood parasitism in ducks may constitute cooperation among generations of closely related females.}, language = {en} } @article{PavesiDeMatthaeisTiedemannetal.2011, author = {Pavesi, Laura and De Matthaeis, Elvira and Tiedemann, Ralph and Ketmaier, Valerio}, title = {Temporal population genetics and COI phylogeography of the sandhopper macarorchestia remyi (Amphipoda: Talitridae)}, series = {Zoological studies}, volume = {50}, journal = {Zoological studies}, number = {2}, publisher = {Institute of Zoology, Academia Sinica}, address = {Taipei}, issn = {1021-5506}, pages = {220 -- 229}, year = {2011}, abstract = {Laura Pavesi, Elvira De Matthaeis, Ralph Tiedemann, and Valerio Ketmaier (2011) Temporal population genetics and COI phylogeography of the sandhopper Macarorchestia remyi (Amphipoda: Talitridae). Zoological Studies 50(2): 220-229. In this study we assessed levels of genetic divergence and variability in 208 individuals of the supralittoral sandhopper Macarorchestia remyi, a species strictly associated with rotted wood stranded on sand beaches, by analyzing sequence polymorphisms in a fragment of the mitochondrial DNA (mtDNA) gene coding cytochrome oxidase subunit I (COI). The geographical distribution and ecology of the species are poorly known. The study includes 1 Tyrrhenian and 2 Adriatic populations sampled along the Italian peninsula plus a single individual found on Corfu Is. (Greece). The Tyrrhenian population was sampled monthly for 1 yr. Genetic data revealed a deep phylogeographic break between the Tyrrhenian and Adriatic populations with no shared haplotypes. The single individual collected on Corfu Is. carried the most common haplotype found in the Tyrrhenian population. A mismatch analysis could not reject the hypothesis of a sudden demographic expansion in almost all but 2 monthly samples. When compared to previous genetic data centered on a variety of Mediterranean talitrids, our results place M. remyi among those species with profound intraspecific divergence (sandhoppers) and dissimilar from beachfleas, which generally display little population genetic structuring.}, language = {en} } @unpublished{WalzAdrianGilbertetal.2011, author = {Walz, Norbert and Adrian, Rita and Gilbert, John J. and Monaghan, Michael T. and Weithoff, Guntram and Zimmermann-Timm, Heike}, title = {Preface}, series = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica}, volume = {662}, journal = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica}, number = {1}, publisher = {Springer}, address = {Dordrecht}, issn = {0018-8158}, doi = {10.1007/s10750-010-0514-2}, pages = {1 -- 4}, year = {2011}, language = {en} } @article{SharmaStuckasBhaskaretal.2011, author = {Sharma, Reeta and Stuckas, Heiko and Bhaskar, Ranjana and Khan, Imran and Goyal, Surendra Prakash and Tiedemann, Ralph}, title = {Genetically distinct population of Bengal tiger (Panthera tigris tigris) in Terai Arc Landscape (TAL) of India}, series = {Mammalian biology = Zeitschrift f{\"u}r S{\"a}ugetierkunde}, volume = {76}, journal = {Mammalian biology = Zeitschrift f{\"u}r S{\"a}ugetierkunde}, number = {4}, publisher = {Elsevier}, address = {Jena}, issn = {1616-5047}, doi = {10.1016/j.mambio.2010.10.005}, pages = {484 -- 490}, year = {2011}, abstract = {We analyzed mtDNA polymorphisms (a total of 741 bp from a part of conserved control region, ND5, ND2, Cyt b and 12S) in 91 scats and 12 tissue samples of Bengal tiger (Panthera tigris tigris) populations across Terai Arc Landscape (TAL) located at the foothills of Himalayas in North Western India, Buxa Tiger Reserve (BTR), and North East India. In TAL and BTR, we found a specific haplotype at high frequency, which was absent elsewhere, indicating a genetically distinct population in these regions. Within the TAL region, there is some evidence for genetic isolation of the tiger populations west of river Ganges, i.e., in the western part of Rajaji National Park (RNP). Although the river itself might not constitute a significant barrier for tigers, recent human-induced changes in habitat and degradation of the Motichur-Chilla Corridor connecting the two sides of the tiger habitat of RNP might effectively prevent genetic exchange. A cohesive population is observed for the rest of the TAL. Even the more eastern BTR belongs genetically to this unit, despite the present lack of a migration corridor between BTR and TAL. In spite of a close geographic proximity, Chitwan (Nepal) constitutes a tiger population genetically different from TAL. Moreover, it is observed that the North East India tiger populations are genetically different from TAL and BTR, as well as from the other Bengal tiger populations in India.}, language = {en} } @article{NahavandiPlathTiedemannetal.2011, author = {Nahavandi, Nahid and Plath, Martin and Tiedemann, Ralph and Mirzajani, Ali R.}, title = {Sexual and natural selection on morphological traits in a marine amphipod, Pontogammarus maeoticus (Sowinsky, 1894)}, series = {Marine biology research}, volume = {7}, journal = {Marine biology research}, number = {2}, publisher = {Taylor \& Francis Group}, address = {Oslo}, issn = {1745-1000}, doi = {10.1080/17451001003713589}, pages = {135 -- 146}, year = {2011}, abstract = {Sexual selection often leads to sexual dimorphism, where secondary sexual traits are more expressed in the male sex. This may be due, for example, to increased fighting or mate-guarding abilities of males expressing those traits. We investigated sexually dimorphic traits in four populations of a marine amphipod, Pontogammarus maeoticus (Gammaridea: Pontogammaridae), the most abundant amphipod species in the sublittoral zone along the southern shoreline of the Caspian Sea. Male amphipods are typically larger in body size than females, and have relatively larger posterior gnathopods and antennae. However, it remains to be studied for most other body appendages whether or not, and to what extent, they are sexually dimorphic. Using Analysis of Covariance (ANCOVA), we compared the relationships between body size and trait expression for 35 metric characters between males and females, and among the four populations examined by performing three different Discriminant Function Analyses (DFA). We detected several thus far undescribed sexual dimorphic traits such as the seventh peraeopods or the epimeral plates. We also found that the size of the propodus of the first and second gnathopods increases with increasing body size, and this allometric increase was stronger in males than in females. Finally, we found that the degree of sexual dimorphism in the expression of the width of the third epimeral plate varies across sites, suggesting that differences in ecology might affect the strength of sexual selection in different populations.}, language = {en} } @article{VaterKoessl2011, author = {Vater, Marianne and Koessl, Manfred}, title = {Comparative aspects of cochlear functional organization in mammals}, series = {Hearing research}, volume = {273}, journal = {Hearing research}, number = {1-2}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0378-5955}, doi = {10.1016/j.heares.2010.05.018}, pages = {89 -- 99}, year = {2011}, abstract = {This review addresses the functional organization of the mammalian cochlea under a comparative and evolutionary perspective. A comparison of the monotreme cochlea with that of marsupial and placental mammals highlights important evolutionary steps towards a hearing organ dedicated to process higher frequencies and a larger frequency range than found in non-mammalian vertebrates. Among placental mammals, there are numerous cochlear specializations which relate to hearing range in adaptation to specific habitats that are superimposed on a common basic design. These are illustrated by examples of specialist ears which evolved excellent high frequency hearing and echolocation (bats and dolphins) and by the example of subterranean rodents with ears devoted to processing low frequencies. Furthermore, structural functional correlations important for tonotopic cochlear organization and predictions of hearing capabilities are discussed.}, language = {en} } @article{HagemannVaterKoessl2011, author = {Hagemann, Cornelia and Vater, Marianne and Koessl, Manfred}, title = {Comparison of properties of cortical echo delay-tuning in the short-tailed fruit bat and the mustached bat}, series = {Journal of comparative physiology : A, Neuroethology, sensory, neural, and behavioral physiology}, volume = {197}, journal = {Journal of comparative physiology : A, Neuroethology, sensory, neural, and behavioral physiology}, number = {5}, publisher = {Springer}, address = {New York}, issn = {0340-7594}, doi = {10.1007/s00359-010-0530-8}, pages = {605 -- 613}, year = {2011}, abstract = {Target-distance computation by cortical neurons sensitive to echo delay is an essential characteristic of the auditory system of insectivorous bats. To assess if functional requirements such as detection of small insects versus larger stationary surfaces of plants are reflected in cortical properties, we compare delay-tuned neurons in a frugivorous (C. perspicillata, CP) and an insectivorous (P. parnellii, PP) bat species that belong to related families within the superfamily of Noctilionoidea. The bandwidth and shape of delay-tuning curves and the range of characteristic delays are similar in both species and hence are not related to different echolocation strategies. Most units respond at 2-6 ms echo delay with most sensitive thresholds of 20-30 dB SPL. In CP, units tuned to delays > 12 ms are slightly more abundant and are more sensitive than in PP. All delay-tuned neurons in CP reliably respond to single pure-tone stimuli, whereas such responses are only observed in 49\% of delay-tuned units in PP. The cortical representation of echo delay (chronotopy) covers a larger area in CP but is less precise than described in PP. Since chronotopy is absent in certain other insectivorous bat species, it is open if these differences in topography are related to echolocation behaviour.}, language = {en} } @misc{MeyerKuhnertGraef2011, author = {Meyer, Irene and Kuhnert, Oliver and Gr{\"a}f, Ralph}, title = {Functional analyses of lissencephaly-related proteins in Dictyostelium}, series = {Seminars in cell \& developmental biology}, volume = {22}, journal = {Seminars in cell \& developmental biology}, number = {1}, publisher = {Elsevier}, address = {London}, issn = {1084-9521}, doi = {10.1016/j.semcdb.2010.10.007}, pages = {89 -- 96}, year = {2011}, abstract = {Lissencephaly is a severe brain developmental disease in human infants, which is usually caused by mutations in either of two genes, LIS1 and DCX. These genes encode proteins interacting with both the microtubule and the actin systems. Here, we review the implications of data on Dictyostelium LIS1 for the elucidation of LIS1 function in higher cells and emphasize the role of LIS1 and nuclear envelope proteins in nuclear positioning, which is also important for coordinated cell migration during neocortical development. Furthermore, for the first time we characterize Dictyostelium DCX, the only bona fide orthologue of human DCX outside the animal kingdom. We show that DCX functionally interacts with LIS1 and that both proteins have a cytoskeleton-independent function in chemotactic signaling during development. Dictyostelium LIS1 is also required for proper attachment of the centrosome to the nucleus and, thus, nuclear positioning, where the association of these two organelles has turned out to be crucial. It involves not only dynein and dynein-associated proteins such as LIS1 but also SUN proteins of the nuclear envelope. Analyses of Dictyostelium SUN1 mutants have underscored the importance of these proteins for the linkage of centrosomes and nuclei and for the maintenance of chromatin integrity. Taken together, we show that Dictyostelium amoebae, which provide a well-established model to study the basic aspects of chemotaxis, cell migration and development, are well suited for the investigation of the molecular and cell biological basis of developmental diseases such as lissencephaly.}, language = {en} } @article{SamereierBaumannMeyeretal.2011, author = {Samereier, Matthias and Baumann, Otto and Meyer, Irene and Gr{\"a}f, Ralph}, title = {Analysis of dictyostelium TACC reveals differential interactions with CP224 and unusual dynamics of dictyostelium microtubules}, series = {Cellular and molecular life sciences}, volume = {68}, journal = {Cellular and molecular life sciences}, number = {2}, publisher = {Springer}, address = {Basel}, issn = {1420-682X}, doi = {10.1007/s00018-010-0453-0}, pages = {275 -- 287}, year = {2011}, abstract = {We have localized TACC to the microtubule-nucleating centrosomal corona and to microtubule plus ends. Using RNAi we proved that Dictyostelium TACC promotes microtubule growth during interphase and mitosis. For the first time we show in vivo that both TACC and XMAP215 family proteins can be differentially localized to microtubule plus ends during interphase and mitosis and that TACC is mainly required for recruitment of an XMAP215-family protein to interphase microtubule plus ends but not for recruitment to centrosomes and kinetochores. Moreover, we have now a marker to study dynamics and behavior of microtubule plus ends in living Dictyostelium cells. In a combination of live cell imaging of microtubule plus ends and fluorescence recovery after photobleaching (FRAP) experiments of GFP-alpha-tubulin cells we show that Dictyostelium microtubules are dynamic only in the cell periphery, while they remain stable at the centrosome, which also appears to harbor a dynamic pool of tubulin dimers.}, language = {en} } @inproceedings{TikhonenkoMagidsonGraefetal.2011, author = {Tikhonenko, I. and Magidson, V. and Gr{\"a}f, Ralph and Khodjakov, A. and Koonce, M.}, title = {A kinesin-mediated linkage between centrosomes and the nuclear envelope}, series = {Molecular biology of the cell : the official publication of the American Society for Cell Biology}, volume = {22}, booktitle = {Molecular biology of the cell : the official publication of the American Society for Cell Biology}, number = {1}, publisher = {American Society for Cell Biology}, address = {Bethesda}, issn = {1059-1524}, pages = {1}, year = {2011}, language = {en} } @inproceedings{KuhnertBaumannMeyeretal.2011, author = {Kuhnert, Oliver and Baumann, Otto and Meyer, Irene and Gr{\"a}f, Ralph}, title = {Functional characterization of CP148, a novel key component for centrosome integrity in Dictyostelium}, series = {Molecular biology of the cell : the official publication of the American Society for Cell Biology}, volume = {22}, booktitle = {Molecular biology of the cell : the official publication of the American Society for Cell Biology}, publisher = {American Society for Cell Biology}, address = {Bethesda}, issn = {1059-1524}, pages = {2}, year = {2011}, language = {en} } @article{KleinpeterLaemmermannKuehn2011, author = {Kleinpeter, Erich and L{\"a}mmermann, Anica and K{\"u}hn, Heiner}, title = {The anisotropic effect of functional groups in H-1 NMR spectra is the molecular response property of spatial nucleus independent chemical shifts (NICS)-Conformational equilibria of exo/endo tetrahydrodicyclopentadiene derivatives}, year = {2011}, abstract = {The inversion of the flexible five-membered ring in tetrahydrodicyclopentadiene (TH-DCPD) derivatives remains fast on the NMR timescale even at 103 K. Since the intramolecular exchange process could not be sufficiently slowed for spectroscopic evaluation, the conformational equilibrium is thus inaccessible by dynamic NMR. Fortunately, the spatial magnetic properties of the aryl and carbonyl groups attached to the DCPD skeleton can be employed in order to evaluate the conformational state of the system. In this context, the anisotropic effects of the functional groups in the H-1 NMR spectra prove to be the molecular response property of spatial nucleus independent chemical shifts (NICS).}, language = {en} } @phdthesis{CamaraMattosMartins2011, author = {Camara Mattos Martins, Marina}, title = {What are the downstream targets of trehalose-6-phosphate signalling in plants?}, address = {Potsdam}, pages = {164 S.}, year = {2011}, language = {en} } @phdthesis{Klie2011, author = {Klie, Sebastian}, title = {Integrative analysis of hight-throughput "omics"-data and structured biological knowledge}, address = {Potsdam}, pages = {102 S.}, year = {2011}, language = {en} } @phdthesis{Sun2011, author = {Sun, Xiaoliang}, title = {Towards understanding the dynamics of biological systems from -Omics data}, address = {Potsdam}, pages = {114 S.}, year = {2011}, language = {en} } @phdthesis{Szecowka2011, author = {Szec{\´o}wka, Marek}, title = {Metabolic fluxes in photosynthetic and heterotrophic plant tissues}, address = {Potsdam}, pages = {XII, 145 S.}, year = {2011}, language = {en} } @phdthesis{Griessner2011, author = {Grießner, Matthias}, title = {Grenzfl{\"a}chenmodifizierung von Mikrosystemen f{\"u}r biochemische Assays}, address = {Potsdam}, pages = {95 S.}, year = {2011}, language = {de} } @phdthesis{Li2011, author = {Li, Xiaoqing}, title = {Structural and dynamic analysis of circadian oscillators and modelling seasonal response in Soay sheep}, address = {Potsdam}, pages = {163 S.}, year = {2011}, language = {en} } @phdthesis{Tiller2011, author = {Tiller, Nadine}, title = {Plastid translation : functions of plastid-specific ribosomal proteins and identification of a factor mediating plastid-to-nucleus retrograde sifnalling}, address = {Potsdam}, pages = {122 S.}, year = {2011}, language = {en} } @phdthesis{Mittag2011, author = {Mittag, Sonnhild}, title = {Vom Rosetta-Stone-Protein NitFhit zur Tumorsuppressorwirkung der humanen Nitrilase1}, address = {Potsdam}, pages = {113 S.}, year = {2011}, language = {de} } @phdthesis{Rott2011, author = {Rott, Markus}, title = {Die Rolle der plastid{\"a}ren APT Synthase in der Regulation des photosynthetischen Elektronenflusses}, address = {Potsdam}, pages = {131 S.}, year = {2011}, language = {de} } @phdthesis{Schroeder2011, author = {Schr{\"o}der, Florian}, title = {Funktionelle Charakterisierung der EXO/EXL-Proteinfamilie und NFXL2-Isoformen in Arabidopsis thaliana}, address = {Potsdam}, pages = {86 S.}, year = {2011}, language = {de} } @phdthesis{Nahavandi2011, author = {Nahavandi, Nahid}, title = {Genetic and morphological analysis on the evolution of the Ponto-Caspian amphipod Pontogammarus maeoticus}, address = {Potsdam}, pages = {54 S.}, year = {2011}, language = {en} } @phdthesis{Lehmann2011, author = {Lehmann, Martin}, title = {Back to the roots : regulation of arabidopsis root metabolism during oxidative stress}, address = {Potsdam}, pages = {154 S.}, year = {2011}, language = {en} } @phdthesis{Siewert2011, author = {Siewert, Katharina}, title = {Autoaggressive human t cell receptorrs and their antigen specificities}, address = {Potsdam}, pages = {145 S.}, year = {2011}, language = {en} } @phdthesis{Sharma2011, author = {Sharma, Tripti}, title = {Regulation of potassium channels in plants : biophysical mechanisms and physiological implacations}, address = {Potsdam}, pages = {104 S.}, year = {2011}, language = {en} } @phdthesis{Schudoma2011, author = {Schudoma, Christian}, title = {Bioinformatic approaches to sequence-structure relationships in RNA loops}, address = {Potsdam}, pages = {114}, year = {2011}, language = {en} } @phdthesis{Fettke2011, author = {Fettke, J{\"o}rg}, title = {Analysen St{\"a}rke-bezogener Kohlenstofffl{\"u}sse}, address = {Potsdam}, year = {2011}, language = {de} } @phdthesis{StoofLeichsenring2011, author = {Stoof-Leichsenring, Kathleen Rosemarie}, title = {Genetic analysis of diatoms and rotifers in tropical Kenyan lake sediments}, address = {Potsdam}, year = {2011}, language = {en} } @phdthesis{Borwankar2011, author = {Borwankar, Tejas}, title = {Natural osmolytes remodel the aggregation pathway of mutant huntingtin exon 1}, address = {Potsdam}, pages = {120 S.}, year = {2011}, language = {en} } @phdthesis{Piepho2011, author = {Piepho, Maike}, title = {Phytoplankton lipids in a changing world : more than just water flea feed}, address = {Potsdam}, pages = {111 S.}, year = {2011}, language = {en} } @article{LindeckeScheffler2011, author = {Lindecke, Oliver and Scheffler, Ingo}, title = {Zur Ektoparasitenfauna der Flederm{\"a}use in Sachsen Anhalt : Ectoparasites of bats in Saxony-Anhalt}, issn = {0018-0637}, year = {2011}, abstract = {During the summer 2010 several mist nettings for the monitoring of bat species were performed in Saxony-Anhalt. Captured individuals were tested for ectoparasitic infestation. The aim was to update the fauna of ectoparasites of this state and to collect data on the distribution of individual species. Regarding this, results of previous surveys are summarised. In the present study nine out of thirteen bat species were found to be infested with a total of one flea species, one species of bat flies and eight species of mites. The infestation with fleas was below the expectations. Six spinturnicid mite species out of those occurring in Germany could be ascertained for Saxony-Anhalt. These are Spinturnix acuminatus (Koch, 1836), S. andegavinus (Kolenati, 1857), S. helvetiae Deunff, Keller \& Aellen, 1986, S. mystacinus (Kolenati, 1857), S. plecotinus (Koch, 1839) and S. puncata (Sundevall, 1833). Details about the infestation with parasites (abundances) of the respective bat species are presented. Further information on the biology of spinturnicid mites are given and infestation characteristics are compared with those of other surveys. Keywords: ectoparasites, bats, Chiroptera, gamasine mite, Acari, Spinturnix, Ischnopsyllidae, Nycteribiidae, Saxony-Anhalt, Germany}, language = {de} } @article{HundertmarkDimovaLengefeldetal.2011, author = {Hundertmark, Michaela and Dimova, Rumiana and Lengefeld, Jan and Seckler, Robert and Hincha, Dirk K.}, title = {The intrinsically disordered late embryogenesis abundant protein LEA18 from Arabidopsis thaliana modulates membrane stability through binding and folding.}, issn = {0006-3002}, year = {2011}, abstract = {Intrinsically disordered proteins (IDPs) constitute a substantial part of cellular proteomes. Late embryogenesis abundant (LEA) proteins are mostly predicted to be IDPs associated with dehydration tolerance in many plant, animal and bacterial species. Their functions, however, are largely unexplored and also their structure and interactions with potential target molecules have only recently been experimentally investigated in a small number of proteins. Here, we report on the structure and interactions with membranes of the Pfam LEA_1 protein LEA18 from the higher plant Arabidopsis thaliana. This functionally uncharacterized positively charged protein specifically aggregated and destabilized negatively charged liposomes. Isothermal titration calorimetry showed binding of the protein to both charged and uncharged membranes. LEA18 alone was largely unstructured in solution. While uncharged membranes had no influence on the secondary structure of LEA18, the protein partially folded into ;-sheet structure in the presence of negatively charged liposomes. These data suggest that LEA18 does not function as a membrane stabilizing protein, as suggested for other LEA proteins. Instead, a possible function of LEA18 could be the composition-dependent modulation of membrane stability, e.g., during signaling or vesicle-mediated transport. Research Highlights}, language = {en} } @article{LilieBaerKettneretal.2011, author = {Lilie, Hauke and B{\"a}r, Dorit and Kettner, Karina and Weininger, Ulrich and Balbach, Jochen and Naumann, Manfred and M{\"u}ller, Eva-Christina and Otto, Albrecht and Gast, Klaus and Golbik, Ralph}, title = {Yeast hexokinase isoenzyme ScHxk2 : stability of a two-domain protein with discontinuous domains}, issn = {0269-2139}, year = {2011}, abstract = {The hexokinase isoenzyme 2 of Saccharomyces cerevisiae (ScHxk2) represents an archetype of a two-domain protein with the active site located in a cleft between the two domains. Binding of the substrate glucose results in a rigid body movement of the two domains leading to a cleft closure of the active site. Both domains of this enzyme are composed of discontinuous peptide sequences. This structural feature is reflected in the stability and folding of the ScHxk2 protein. Structural transitions induced by urea treatment resulted in the population of a thermodynamically stable folding intermediate, which, however, does not correspond to a molecule with one domain folded and the other unfolded. As demonstrated by different spectroscopic techniques, both domains are structurally affected by the partial denaturation. The intermediate possesses only 40\% of the native secondary structural content and a substantial increase in the Stokes radius as judged by circular dichroism and dynamic light scattering analyses. One-dimensional 1H NMR data prove that all tryptophan residues are in a non-native environment in the intermediate, indicating substantial changes in the tertiary structure. Still, the intermediate possesses quite a high stability for a transition intermediate of about ;G = ;22 kJ mol;1.}, language = {en} } @article{Scheffler2011, author = {Scheffler, Christiane}, title = {The change of skeletal robustness of 6 - 12 years old children in Brandenburg (Germany) - Comparison of body composition 1999 - 2009}, issn = {0003-5548}, year = {2011}, language = {en} } @article{VoigtScheffler2011, author = {Voigt, Andrea and Scheffler, Christiane}, title = {Manual abilities of the elderly - handgrip strength, finger and thumb push strength and opening strength in age comparison}, issn = {0003-5548}, year = {2011}, language = {en} } @phdthesis{Weiss2011, author = {Weiß, Julia}, title = {Computer assisted proteomics in a systems biology context}, address = {Potsdam}, pages = {VIII, 138, XVII S.}, year = {2011}, language = {en} } @phdthesis{Pyl2011, author = {Pyl, Eva-Theresa}, title = {Networks and growth in Arabidopsis: two strategies to pertub a complex system}, address = {Potsdam}, pages = {XIV, 145 S.}, year = {2011}, language = {en} } @phdthesis{Baumgartner2011, author = {Baumgartner, Jens}, title = {Nucleation and Growth of Magnetite Nanoparticles under Biomimetric Conditions}, address = {Potsdam}, pages = {102 S.}, year = {2011}, language = {en} } @phdthesis{Hojka2011, author = {Hojka, Marta}, title = {Lifetimes and biogenesis of photosynthetic complexes in higher plants (Nicotiana tabacum)}, address = {Potsdam}, pages = {138 S.}, year = {2011}, language = {en} } @phdthesis{Bandholtz2011, author = {Bandholtz, Sebastian}, title = {Entwicklung von Peptid-Analoga f{\"u}r die Rezeptor-vermittelte Tumordiagnostik}, address = {Potsdam}, pages = {133 S.}, year = {2011}, language = {de} } @article{Scheffler2011, author = {Scheffler, Ingo}, title = {Artenspektren und Wirtsbindung von Ektoparasiten der Flederm{\"a}use aus Nordbulgarien : Bewertung des Zusammenhangs von K{\"o}rperkondition und Ektoparasitenlast}, year = {2011}, abstract = {Waehrend der herbstlichen Schwaermpase wurden im Norden Bulgariens die Ektoparasiten von neun Fledermausarten untersucht. Die hoechsten Abundanzen erreichten Fledermausfliegen, von denen 6 verschiedene Arten determiniert wurden. In geringeren Dichten besiedelten auch Flughautmilben (6 Arten) sowie Macronyssidae und Ixodidae (jeweils eine Art) die Fledermaeuse. Die Bindung an den Wirt und die Verbreitung aller Ektoparasiten sind kurz zusammengefasst. Fuer die Berechnung der Parasitenlast wird ein neues Modell vorgeschlagen, dass unter Beruecksichtigung von Groessenrealtionen und Abundanzen vergleichbare Daten bei unterschiedlichen Befallsszenarien ermoeglicht. Parasitenkombinationen traten im Norden Bulgariens seltener auf, als erwartet. Mit den Werten der haeufigsten Fledermausarten wurde ueberprueft, ob es einen Zusammenhang zwischen Masse, Unterarmlaenge und Parasitierung gibt. In keinem Fall konnte eine sichere Korrelation zwischen diesen Faktoren ermittelt werden. Unter Verwendung eines adaptierten Body-Mass-Index (BMI) oder eines Body- Condition-Index (BCI) ergab sich ebenfalls kein Zusammenhang zwischen der Koerperkondition und der Parasitenlast. Im Verlaufe der Untersuchung kam es in einer Hoehle zu einer unerwarteten Zunahme der Abundanzen von Flughautmilben. Dieses Phaenomen koennte ein interessanter Ansatz weiterer Studien sein. Im Vergleich zu herbstlichen Untersuchungen in Deutschland waren die Fledermaeuse im Norden Bulgariens deutlich staerker parasitiert.}, language = {de} } @phdthesis{Rocha2011, author = {Rocha, Marcia Rosa}, title = {Time series analysis reveals links between functional traits, population dynamics and ecosystem functions in a diverse phytoplankton community}, address = {Potsdam}, pages = {126 S.}, year = {2011}, language = {en} } @phdthesis{Dimova2011, author = {Dimova, Rumiana}, title = {Probing the membrane nanoregime with optical microscopy}, address = {Potsdam}, pages = {50 S.}, year = {2011}, language = {en} } @article{Scheffler2011, author = {Scheffler, Ingo}, title = {Die Ektoparasiten der Flederm{\"a}use Europas : Teil 1}, year = {2011}, abstract = {Die vorliegende Arbeit liefert eine Zusammenstellung der bisher bekannten Ektoparasitenarten europaeischer Fledermausarten. Auf der Basis eigener Untersuchungen in Deutschland erfolgt eine Analyse der Abundanz der Parasiten. Fuer jede Wirtsart wird das Artenspektrum der haeufig vorkommenden Ektoparasiten angegeben und die Spezifitaet der Wirt- Parasit-Beziehung diskutiert. Teil 1 behandelt die Ektoparasiten der Mopsfledermaus (Barbastella barbastellus), der Nordfledermaus (Eptesicus nilssonii), der Breitfluegelfledermaus (Eptesicus serotinus), der Bechsteinfledermaus (Myotis bechsteinii),der Grossen Bartfledermaus (Myotis brandtii), der Teichfledermaus (Myotis dasycneme) und der Wasserfledermaus (Myotis daubentonii).}, language = {de} } @phdthesis{Ruprecht2011, author = {Ruprecht, Colin}, title = {Characterization of genetic modules involved in cellulose synthesis in Arabidopsis thaliana}, address = {Potsdam}, pages = {109 S.}, year = {2011}, language = {en} } @phdthesis{Guenl2011, author = {G{\"u}nl, Markus}, title = {Impact of apoplastic glycoside hydrolases on xyloglucan structure and function in arabidopsis}, address = {Potsdam}, pages = {145 S.}, year = {2011}, language = {en} } @phdthesis{Bauer2011, author = {Bauer, Barbara}, title = {The relevance of species traits for predicting the dynamics of diverse plankton communities}, address = {Potsdam}, pages = {190 S.}, year = {2011}, language = {en} } @phdthesis{Lachmuth2011, author = {Lachmuth, Susanne}, title = {Towards a mechanistic understanding of how demography, genetic differentiation and environmental factors interact to generate the invasion dynamics of senecio inaequidens}, address = {Potsdam}, pages = {172 S.}, year = {2011}, language = {en} } @phdthesis{Nguyen2011, author = {Nguyen, Hung Minh}, title = {Regulation of leaf growth and development by transcription factors in Arabidopsis thaliana}, address = {Potsdam}, pages = {152 S.}, year = {2011}, language = {en} } @phdthesis{Athikomrattanakul2011, author = {Athikomrattanakul, Umporn}, title = {Development and characterization of molecularly imprinted polymers as binding elements against nitrofurantoin}, address = {Potsdam}, pages = {97 S.}, year = {2011}, language = {en} } @phdthesis{CuadrosInostroza2011, author = {Cuadros-Inostroza, Alvaro}, title = {Integrated analysis of transcriptome and metabolome to understand grapevine development}, address = {Potsdam}, pages = {136 S.}, year = {2011}, language = {en} } @article{FerirVermeireHuskensetal.2011, author = {Ferir, Geoffrey and Vermeire, Kurt and Huskens, Dana and Balzarini, Jan and Van Damme, Els J. M. and Kehr, Jan-Christoph and Dittmann-Th{\"u}nemann, Elke and Swanson, Michael D. and Markovitz, David M. and Schols, Dominique}, title = {Synergistic in vitro anti-HIV type 1 activity of tenofovir with carbohydrate-binding agents (CBAs)}, series = {Antiviral research}, volume = {90}, journal = {Antiviral research}, number = {3}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0166-3542}, doi = {10.1016/j.antiviral.2011.03.188}, pages = {200 -- 204}, year = {2011}, abstract = {Tenofovir, a well-known and highly prescribed anti-HIV-1 drug for the treatment of HIV/AIDS infections, has recently also shown its effectiveness as a potential microbicide drug in the prevention of HIV transmission. Here, we evaluated the combination of tenofovir with various members of the class of carbohydrate-binding agents (CBAs) targeting the glycans on the viral envelope gp120 for their anti-HIV efficacy. The tenofovir/CBA combinations predominantly showed synergistic antiviral activity using the median effect principle. These findings illustrate that combination of tenofovir with CBAs may increase the antiviral potency of the individual drugs and reducing the risk on potential side-effects.}, language = {en} } @article{FranckvonBlohMuelleretal.2011, author = {Franck, Siegfried and von Bloh, Werner and M{\"u}ller, Christoph and Bondeau, Alberte and Sakschewski, B.}, title = {Harvesting the sun new estimations of the maximum population of planet Earth}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {222}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, number = {12}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2011.03.030}, pages = {2019 -- 2026}, year = {2011}, abstract = {The maximum population, also called Earth's carrying capacity, is the maximum number of people that can live on the food and other resources available on planet Earth. Previous investigations estimated the maximum carrying capacity as large as about 1 trillion people under the assumption that photosynthesis is the limiting process. Here we use a present state-of-the-art dynamic global vegetation model with managed planetary land surface, Lund-Potsdam-Jena managed Land (LPJmL), to calculate the yields of the most productive crops on a global 0.5 degrees x 0.5 degrees grid. Using the 2005 crop distribution the model predicts total harvested calories that are sufficient for the nutrition of 11.4 billion people. We define scenarios where humankind uses the whole land area for agriculture, saves the rain forests and the boreal evergreen forests or cultivates only pasture to feed animals. Every scenario is run in an extreme version with no allowance for urban and recreational needs and in two soft versions with a certain area per person for non-agricultural use. We find that there are natural limits of the maximum carrying capacity which are independent of any increase in agricultural productivity, if non-agricultural land use is accounted for. Using all land planet Earth can sustain 282 billion people. The save-forests-scenario yields 150 billion people. The scenario that cultivates only pasture to feed animals yields 96 billion people. Nevertheless, we should always have in mind that all our calculated numbers for the carrying capacity refer to extreme scenarios where humankind may only vegetate on this planet. Our numbers are considerably higher than the general median estimate of upper bounds of human population found in the literature in the order of 10 billion.}, language = {en} } @article{DavidMarashiLarhlimietal.2011, author = {David, Laszlo and Marashi, Sayed-Amir and Larhlimi, Abdelhalim and Mieth, Bettina and Bockmayr, Alexander}, title = {FFCA a feasibility-based method for flux coupling analysis of metabolic networks}, series = {BMC bioinformatics}, volume = {12}, journal = {BMC bioinformatics}, number = {12}, publisher = {BioMed Central}, address = {London}, issn = {1471-2105}, doi = {10.1186/1471-2105-12-236}, pages = {7}, year = {2011}, abstract = {Background: Flux coupling analysis (FCA) is a useful method for finding dependencies between fluxes of a metabolic network at steady-state. FCA classifies reactions into subsets (called coupled reaction sets) in which activity of one reaction implies activity of another reaction. Several approaches for FCA have been proposed in the literature. Results: We introduce a new FCA algorithm, FFCA (Feasibility-based Flux Coupling Analysis), which is based on checking the feasibility of a system of linear inequalities. We show on a set of benchmarks that for genome-scale networks FFCA is faster than other existing FCA methods. Conclusions: We present FFCA as a new method for flux coupling analysis and prove it to be faster than existing approaches. A corresponding software tool is freely available for non-commercial use at http://www.bioinformatics.org/ffca/.}, language = {en} } @article{SpeckArndtMueller2011, author = {Speck, Janina and Arndt, Katja Maren and M{\"u}ller, Kristian M.}, title = {Efficient phage display of intracellularly folded proteins mediated by the TAT pathway}, series = {Protein engineering design \& selection}, volume = {24}, journal = {Protein engineering design \& selection}, number = {6}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1741-0126}, doi = {10.1093/protein/gzr001}, pages = {473 -- 484}, year = {2011}, abstract = {Phage display with filamentous phages is widely applied and well developed, yet proteins requiring a cytoplasmic environment for correct folding still defy attempts at functional display. To extend applicability of phage display, we employed the twin-arginine translocation (TAT) pathway to incorporate proteins fused to the C-terminal domain of the geneIII protein into phage particles. We investigated functionality and display level of fluorescent proteins depending on the translocation pathway, which was the TAT, general secretory (SEC) or signal recognition particle (SRP) pathway mediated by the TorA, PelB or DsbA signal sequences, respectively. Importantly, for green fluorescent protein, yellow fluorescent protein and cyan fluorescent protein, only TAT, but not SEC or SRP, translocation led to fluorescence of purified phage particles, although all three proteins could be displayed regardless of the translocation pathway. In contrast, the monomeric red fluorescent protein mCherry was functionally displayed regardless of the translocation pathway. Hence, correct folding and fluorophor formation of mCherry is not limited to the cytosol. Furthermore, we successfully displayed firefly luciferase as well as an 83 kDa argonaute protein, both containing free cysteines. This demonstrates broad applicability of the TAT-mediated phagemid system for the display of proteins requiring cytoplasmic factors for correct folding and should prove useful for the display of proteins requiring incorporation of co-factors or oligomerization to gain function.}, language = {en} } @misc{VanDonkIanoraVos2011, author = {Van Donk, Ellen and Ianora, Adrianna and Vos, Matthijs}, title = {Induced defences in marine and freshwater phytoplankton a review}, series = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica}, volume = {668}, journal = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica}, number = {1}, publisher = {Springer}, address = {Dordrecht}, issn = {0018-8158}, doi = {10.1007/s10750-010-0395-4}, pages = {3 -- 19}, year = {2011}, abstract = {Many organisms have developed defences to avoid predation by species at higher trophic levels. The capability of primary producers to defend themselves against herbivores affects their own survival, can modulate the strength of trophic cascades and changes rates of competitive exclusion in aquatic communities. Algal species are highly flexible in their morphology, growth form, biochemical composition and production of toxic and deterrent compounds. Several of these variable traits in phytoplankton have been interpreted as defence mechanisms against grazing. Zooplankton feed with differing success on various phytoplankton species, depending primarily on size, shape, cell wall structure and the production of toxins and deterrents. Chemical cues associated with (i) mechanical damage, (ii) herbivore presence and (iii) grazing are the main factors triggering induced defences in both marine and freshwater phytoplankton, but most studies have failed to disentangle the exact mechanism(s) governing defence induction in any particular species. Induced defences in phytoplankton include changes in morphology (e.g. the formation of spines, colonies and thicker cell walls), biochemistry (such as production of toxins, repellents) and in life history characteristics (formation of cysts, reduced recruitment rate). Our categorization of inducible defences in terms of the responsible induction mechanism provides guidance for future work, as hardly any of the available studies on marine or freshwater plankton have performed all the treatments that are required to pinpoint the actual cue(s) for induction. We discuss the ecology of inducible defences in marine and freshwater phytoplankton with a special focus on the mechanisms of induction, the types of defences, their costs and benefits, and their consequences at the community level.}, language = {en} } @article{GriessnerHartigChristmannetal.2011, author = {Griessner, Matthias and Hartig, Dave and Christmann, Alexander and Pohl, Carsten and Schellhase, Michaela and Ehrentreich-F{\"o}rster, Eva}, title = {Development and characterization of a disposable plastic microarray printhead}, series = {Biomedical microdevices : bioMEMS and biomedical nanotechnology}, volume = {13}, journal = {Biomedical microdevices : bioMEMS and biomedical nanotechnology}, number = {3}, publisher = {Springer}, address = {Dordrecht}, issn = {1387-2176}, doi = {10.1007/s10544-011-9522-x}, pages = {533 -- 538}, year = {2011}, abstract = {During the last decade microarrays have become a powerful analytical tool. Commonly microarrays are produced in a non-contact manner using silicone printheads. However, silicone printheads are expensive and not able to be used as a disposable. Here, we show the development and functional characterization of 8-channel plastic microarray printheads that overcome both disadvantages of their conventional silicone counterparts. A combination of injection-molding and laser processing allows us to produce a high quantity of cheap, customizable and disposable microarray printheads. The use of plastics (e.g., polystyrene) minimizes the need for surface modifications required previously for proper printing results. Time-consuming regeneration processes, cleaning procedures and contaminations caused by residual samples are avoided. The utilization of plastic printheads for viscous liquids, such as cell suspensions or whole blood, is possible. Furthermore, functional parts within the plastic printhead (e.g., particle filters) can be included. Our printhead is compatible with commercially available TopSpot devices but provides additional economic and technical benefits as compared to conventional TopSpot printheads, while fulfilling all requirements demanded on the latter. All in all, this work describes how the field of traditional microarray spotting can be extended significantly by low cost plastic printheads.}, language = {en} } @article{NaafWulf2011, author = {Naaf, Tobias and Wulf, Monika}, title = {Traits of winner and loser species indicate drivers of herb layer changes over two decades in forests of NW Germany}, series = {Journal of vegetation science}, volume = {22}, journal = {Journal of vegetation science}, number = {3}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {1100-9233}, doi = {10.1111/j.1654-1103.2011.01267.x}, pages = {516 -- 527}, year = {2011}, abstract = {Questions What are the most likely environmental drivers for compositional herb layer changes as indicated by trait differences between winner and loser species? Location Weser-Elbe region (NW Germany). Methods We resurveyed the herb layer communities of ancient forest patches on base-rich sites of 175 semi-permanent plots. Species traits were tested for their ability to discriminate between winner and loser species using logistic regression analyses and deviance partitioning. Results Of 115 species tested, 31 were identified as winner species and 30 as loser species. Winner species had higher seed longevity, flowered later in the season and more often had an oceanic distribution compared to loser species. Loser species tended to have a higher specific leaf area, were more susceptible to deer browsing and had a performance optimum at higher soil pH compared to winner species. The loser species also represented several ancient forest and threatened species. Deviance partitioning indicated that local drivers (i.e. disturbance due to forest management) were primarily responsible for the species shifts, while regional drivers (i.e. browsing pressure and acidification from atmospheric deposition) and global drivers (i.e. climate warming) had moderate effects. There was no evidence that canopy closure, drainage or eutrophication contributed to herb layer changes. Conclusions The relative importance of the different drivers as indicated by the winner and loser species differs from that found in previous long-term studies. Relating species traits to species performance is a valuable tool that provides insight into the environmental drivers that are most likely responsible for herb layer changes.}, language = {en} } @article{SchmidtHoelterKellingetal.2011, author = {Schmidt, Bernd and H{\"o}lter, Frank and Kelling, Alexandra and Schilde, Uwe}, title = {Pd-Catalyzed arylation reactions with phenol diazonium salts application in the synthesis of diarylheptanoids}, series = {The journal of organic chemistry}, volume = {76}, journal = {The journal of organic chemistry}, number = {9}, publisher = {American Chemical Society}, address = {Washington}, issn = {0022-3263}, doi = {10.1021/jo2002787}, pages = {3357 -- 3365}, year = {2011}, abstract = {The first total synthesis of the natural product (3S,7R)-5,6-dehydro-de-O-methyl centrolobine and various analogues is reported, using a highly regio- and diastereoselective Mizoroki-Heck reaction of phenol diazonium salts and enantiopure dihydropyrans. The assigned relative configuration was confirmed by single-crystal X-ray structure analysis, but a revision of the absolute configuration is proposed based on polarimetric measurement.}, language = {en} } @inproceedings{KuekenshoenerJeanChristophSpecketal.2011, author = {K{\"u}kensh{\"o}ner, Tim and Jean-Christoph, N. and Speck, J. and M{\"u}ller, Kristian M. and Arndt, Katja Maren}, title = {Targeting the microphthalmia associated transcription factor coiled coil domain with interfering peptides}, series = {The FEBS journal}, volume = {278}, booktitle = {The FEBS journal}, number = {6}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {1742-464X}, pages = {159 -- 159}, year = {2011}, language = {en} } @article{KepplingerLisdatWollenberger2011, author = {Kepplinger, Christian and Lisdat, Fred and Wollenberger, Ursula}, title = {Cytochrome c/polyelectrolyte multilayers investigated by E-QCM-D - effect of temperature on the assembly structure}, series = {Langmuir}, volume = {27}, journal = {Langmuir}, number = {13}, publisher = {American Chemical Society}, address = {Washington}, issn = {0743-7463}, doi = {10.1021/la200860p}, pages = {8309 -- 8315}, year = {2011}, abstract = {Protein multilayers, consisting of cytochrome c (cyt c) and poly(aniline sulfonic acid) (PASA), are investigated by electrochemical quartz crystal microbalance with dissipation monitoring (E-QCM-D). This technique reveals that a four-bilayer assembly has rather rigid properties. A thickness of 16.3 +/- 0.8 nm is calculated with the Sauerbrey equation and is found to be in good agreement with a viscoelastic model. The electroactive amount of cyt c is estimated by the deposited mass under the assumption of 50\% coupled water. Temperature-induced stabilization of the multilayer assembly has been investigated in the temperature range between 30 and 45 degrees C. The treatment results in a loss of material and a contraction of the film. The electroactive amount of cyt c also decreases during heating and remains constant after the cooling period. The contraction of the film is accompanied by the enhanced stability of the assembly. In addition, it is found that cyt c and PASA can be assembled at higher temperatures, resulting in the formation of multilayer systems with less dissipation.}, language = {en} } @article{JersabekWeithoffWeisse2011, author = {Jersabek, Christian D. and Weithoff, Guntram and Weisse, Thomas}, title = {Cephalodella acidophila n. sp (Monogononta: Notommatidae), a new rotifer species from highly acidic mining lakes}, series = {Zootaxa : an international journal of zootaxonomy ; a rapid international journal for animal taxonomists}, journal = {Zootaxa : an international journal of zootaxonomy ; a rapid international journal for animal taxonomists}, number = {2939}, publisher = {Magnolia Press}, address = {Auckland}, issn = {1175-5326}, pages = {50 -- 58}, year = {2011}, abstract = {We describe a new species of Cephalodella, C. acidophila n. sp., from the plankton of two extremely acidic mining lakes (pH <3) in Austria and Germany. The species is morphologically closely related to Cephalodella delicata Wulfert. It shares with the latter an almost identical trophi morphology and anatomical organization, but differs clearly by form and length of its toes, larger body size, and ecology. Laboratory experiments revealed that the species is acidophilic, i.e. it thrives at low pH (<4) and does not survive at circumneutral conditions. The species occurs in man-made habitats at low to moderate abundance (usually 5-22 individuals l(-1)) and in stock cultures thrives on the green alga Chlamydomonas acidophila. The easily cultured species has previously been used in various experimental studies, but has only now been recognized as an undescribed species.}, language = {en} } @article{BierbachSchulteHerrmannetal.2011, author = {Bierbach, David and Schulte, Matthias and Herrmann, Nina and Tobler, Michael and Stadler, Stefan and Jung, Christian T. and Kunkel, Benjamin and Riesch, R{\"u}diger and Klaus, Sebastian and Ziege, Madlen and Rimber Indy, Jeane and Arias-Rodriguez, Lenin and Plath, Martin}, title = {Predator-induced changes of female mating preferences innate and experiential effects}, series = {BMC evolutionary biology}, volume = {11}, journal = {BMC evolutionary biology}, number = {3-4}, publisher = {BioMed Central}, address = {London}, issn = {1471-2148}, doi = {10.1186/1471-2148-11-190}, pages = {10}, year = {2011}, abstract = {Background: In many species males face a higher predation risk than females because males display elaborate traits that evolved under sexual selection, which may attract not only females but also predators. Females are, therefore, predicted to avoid such conspicuous males under predation risk. The present study was designed to investigate predator-induced changes of female mating preferences in Atlantic mollies (Poecilia mexicana). Males of this species show a pronounced polymorphism in body size and coloration, and females prefer large, colorful males in the absence of predators. Results: In dichotomous choice tests predator-naive (lab-reared) females altered their initial preference for larger males in the presence of the cichlid Cichlasoma salvini, a natural predator of P. mexicana, and preferred small males instead. This effect was considerably weaker when females were confronted visually with the non-piscivorous cichlid Vieja bifasciata or the introduced non-piscivorous Nile tilapia (Oreochromis niloticus). In contrast, predator experienced (wild-caught) females did not respond to the same extent to the presence of a predator, most likely due to a learned ability to evaluate their predators' motivation to prey. Conclusions: Our study highlights that (a) predatory fish can have a profound influence on the expression of mating preferences of their prey (thus potentially affecting the strength of sexual selection), and females may alter their mate choice behavior strategically to reduce their own exposure to predators. (b) Prey species can evolve visual predator recognition mechanisms and alter their mate choice only when a natural predator is present. (c) Finally, experiential effects can play an important role, and prey species may learn to evaluate the motivational state of their predators.}, language = {en} } @article{SchroederLissoMuessig2011, author = {Schr{\"o}der, Florian and Lisso, Janina and Muessig, Carsten}, title = {Exordium-Like1 promotes growth during low carbon availability in arabidopsis}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {156}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {3}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.111.177204}, pages = {1620 -- 1630}, year = {2011}, abstract = {Little is known about genes that control growth and development under low carbon (C) availability. The Arabidopsis (Arabidopsis thaliana) EXORDIUM-LIKE1 (EXL1) gene (At1g35140) was identified as a brassinosteroid-regulated gene in a previous study. We show here that the EXL1 protein is required for adaptation to C-and energy-limiting growth conditions. In-depth analysis of EXL1 transcript levels under various environmental conditions indicated that EXL1 expression is controlled by the C and energy status. Sugar starvation, extended night, and anoxia stress induced EXL1 gene expression. The C status also determined EXL1 protein levels. These results suggested that EXL1 is involved in the C-starvation response. Phenotypic changes of an exl1 loss-of-function mutant became evident only under corresponding experimental conditions. The mutant showed diminished biomass production in a short-day/low-light growth regime, impaired survival during extended night, and impaired survival of anoxia stress. Basic metabolic processes and signaling pathways are presumed to be barely impaired in exl1, because the mutant showed wild-type levels of major sugars, and transcript levels of only a few genes such as QUA-QUINE STARCH were altered. Our data suggest that EXL1 is part of a regulatory pathway that controls growth and development when C and energy supply is poor.}, language = {en} } @article{KocyanSnijmanForestetal.2011, author = {Kocyan, Alexander and Snijman, Deirdre A. and Forest, Felix and Devey, Dion S. and Freudenstein, John V. and Wiland-Szymanska, Justyna and Chase, Mark W. and Rudall, Paula J.}, title = {Molecular phylogenetics of Hypoxidaceae - Evidence from plastid DNA data and inferences on morphology and biogeography}, series = {Molecular phylogenetics and evolution}, volume = {60}, journal = {Molecular phylogenetics and evolution}, number = {1}, publisher = {Elsevier}, address = {San Diego}, issn = {1055-7903}, doi = {10.1016/j.ympev.2011.02.021}, pages = {122 -- 136}, year = {2011}, abstract = {Phylogenetic relationships of the monocot family Hypoxidaceae (Asparagales), which occurs mainly in the Southern Hemisphere, were reconstructed using four plastid DNA regions (rbcL, trnL intron, trnL-F intergenic spacer, and trnS-G intergenic spacer) for 56 ingroup taxa including all currently accepted genera and seven species of the closely related families Asteliaceae, Blandfordiaceae, and Lanariaceae. Data were analyzed by applying parsimony, maximum likelihood and Bayesian methods. The intergenic spacer trnS-G - only rarely used in monocot research - contributed a substantial number of potentially parsimony informative characters. Hypoxidaceae consist of three well-supported major clades, but their interrelationships remain unresolved. Our data indicate that in the Pauridia clade one long-distance dispersal event occurred from southern Africa to Australia. Long-distance dispersal scenarios may also be likely for the current distribution of Hypoxis, which occurs on four continents. In the Curculigo clade, the present distribution of Curculigo s.s. on four continents could support a Gondwanan origin, but the level of divergence is too low for this hypothesis to be likely. The main clades correspond well with some floral characters, habit and palynological data, whereas chromosomal data exhibit plasticity and probably result from polyploidization and subsequent dysploidy and/or aneuploidy. Evolutionary flexibility is also suggested by the number of reported pollination syndromes: melittophily, myophily, sapromyophily, and cantharophily. Based on our phylogenetic results, we suggest cautious nomenclatural reorganization to generate monophyly at the generic level.}, language = {en} } @article{PopovaHundertmarkSeckleretal.2011, author = {Popova, Antoaneta V. and Hundertmark, Michaela and Seckler, Robert and Hincha, Dirk K.}, title = {Structural transitions in the intrinsically disordered plant dehydration stress protein LEA7 upon drying are modulated by the presence of membranes}, series = {Biochimica et biophysica acta : Biomembranes}, volume = {1808}, journal = {Biochimica et biophysica acta : Biomembranes}, number = {7}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0005-2736}, doi = {10.1016/j.bbamem.2011.03.009}, pages = {1879 -- 1887}, year = {2011}, abstract = {Dehydration stress-related late embryogenesis abundant (LEA) proteins have been found in plants, invertebrates and bacteria. Most LEA proteins are unstructured in solution, but some fold into amphipathic a-helices during drying. The Pfam LEA_4 (Group 3) protein LEA7 from the higher plant Arabidopsis thaliana was predicted to be 87\% alpha-helical, while CD spectroscopy showed it to be largely unstructured in solution and only 35\% alpha-helical in the dry state. However, the dry protein contained 15\% beta-sheets. FTIR spectroscopy revealed the (beta-sheets to be largely due to aggregation. beta-Sheet content was reduced and alpha-helix content increased when LEA7 was dried in the presence of liposomes with secondary structure apparently influenced by lipid composition. Secondary structure was also affected by the presence of membranes in the fully hydrated state. A temperature-induced increase in the flexibility of the dry protein was also only observed in the presence of membranes. Functional interactions of LEA7 with membranes in the dry state were indicated by its influence on the thermotropic phase transitions of the lipids and interactions with the lipid headgroup phosphates.}, language = {en} } @article{GeyerKieferKreftetal.2011, author = {Geyer, Juliane and Kiefer, Iris and Kreft, Stefan and Chavez, Veronica and Salafsky, Nick and Jeltsch, Florian and Ibisch, Pierre L.}, title = {Classification of climate-change-induced stresses on biological diversity}, series = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {25}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, number = {4}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0888-8892}, doi = {10.1111/j.1523-1739.2011.01676.x}, pages = {708 -- 715}, year = {2011}, abstract = {Conservation actions need to account for and be adapted to address changes that will occur under global climate change. The identification of stresses on biological diversity (as defined in the Convention on Biological Diversity) is key in the process of adaptive conservation management. We considered any impact of climate change on biological diversity a stress because such an effect represents a change (negative or positive) in key ecological attributes of an ecosystem or parts of it. We applied a systemic approach and a hierarchical framework in a comprehensive classification of stresses to biological diversity that are caused directly by global climate change. Through analyses of 20 conservation sites in 7 countries and a review of the literature, we identified climate-change-induced stresses. We grouped the identified stresses according to 3 levels of biological diversity: stresses that affect individuals and populations, stresses that affect biological communities, and stresses that affect ecosystem structure and function. For each stress category, we differentiated 3 hierarchical levels of stress: stress class (thematic grouping with the coarsest resolution, 8); general stresses (thematic groups of specific stresses, 21); and specific stresses (most detailed definition of stresses, 90). We also compiled an overview of effects of climate change on ecosystem services using the categories of the Millennium Ecosystem Assessment and 2 additional categories. Our classification may be used to identify key climate-change-related stresses to biological diversity and may assist in the development of appropriate conservation strategies. The classification is in list format, but it accounts for relations among climate-change-induced stresses.}, language = {en} } @article{HoehenwarterLarhlimiHummeletal.2011, author = {H{\"o}henwarter, Wolfgang and Larhlimi, Abdelhalim and Hummel, Jan and Egelhofer, Volker and Selbig, Joachim and van Dongen, Joost T. and Wienkoop, Stefanie and Weckwerth, Wolfram}, title = {MAPA Distinguishes genotype-specific variability of highly similar regulatory protein isoforms in potato tuber}, series = {Journal of proteome research}, volume = {10}, journal = {Journal of proteome research}, number = {7}, publisher = {American Chemical Society}, address = {Washington}, issn = {1535-3893}, doi = {10.1021/pr101109a}, pages = {2979 -- 2991}, year = {2011}, abstract = {Mass Accuracy Precursor Alignment is a fast and flexible method for comparative proteome analysis that allows the comparison of unprecedented numbers of shotgun proteomics analyses on a personal computer in a matter of hours. We compared 183 LC-MS analyses and more than 2 million MS/MS spectra and could define and separate the proteomic phenotypes of field grown tubers of 12 tetraploid cultivars of the crop plant Solanum tuberosum. Protein isoforms of patatin as well as other major gene families such as lipoxygenase and cysteine protease inhibitor that regulate tuber development were found to be the primary source of variability between the cultivars. This suggests that differentially expressed protein isoforms modulate genotype specific tuber development and the plant phenotype. We properly assigned the measured abundance of tryptic peptides to different protein isoforms that share extensive stretches of primary structure and thus inferred their abundance. Peptides unique to different protein isoforms were used to classify the remaining peptides assigned to the entire subset of isoforms based on a common abundance profile using multivariate statistical procedures. We identified nearly 4000,proteins which we used for quantitative functional annotation making this the most extensive study of the tuber proteome to date.}, language = {en} } @article{McCoySyskaPlathetal.2011, author = {McCoy, Ellen and Syska, Norbert and Plath, Martin and Schlupp, Ingo and Riesch, R{\"u}diger}, title = {Mustached males in a tropical poeciliid fish - emerging female preference selects for a novel male trait}, series = {Behavioral ecology and sociobiology}, volume = {65}, journal = {Behavioral ecology and sociobiology}, number = {7}, publisher = {Springer}, address = {New York}, issn = {0340-5443}, doi = {10.1007/s00265-011-1154-x}, pages = {1437 -- 1445}, year = {2011}, abstract = {One possible mechanism for the (co-)evolution of seemingly novel male traits and female preferences for them is that males exploit pre-existing female biases, and livebearing fishes (Poeciliidae) have been at the forefront of this research for almost two decades. Here, using 13 poeciliid species from four different genera, we tested whether mustache-like rostral filaments found in males of some Mexican molly (Poecilia sphenops) populations could have evolved due to exploitation of a pre-existing female bias. While Mexican mollies were the only species with a significant female association preference for mustached males, we also did not find any species exhibiting significant aversion for mustached males; rather, variance in female preference scores was large throughout. For example, more than 25\% of females spent twice as much time with the mustached male compared to the non-mustached male in most species, but even 31\% of Mexican molly females spent more time near the non-mustached male. Hence, a comparison of the strength of preference was inconclusive. We discuss the possibility that the female preference of P. sphenops for mustached males could be due to a female pre-existing bias (sensu lato), even if population means were not significant for species other than P. sphenops. This highlights the importance of distinguishing between population means and individual preferences when interpreting mate choice, and thus, adds depth to the concept of mating preferences as a motor for evolutionary change.}, language = {en} } @article{SchudomaLarhlimiWalther2011, author = {Schudoma, Christian and Larhlimi, Abdelhalim and Walther, Dirk}, title = {The influence of the local sequence environment on RNA loop structures}, series = {RNA : a publication of the RNA Society}, volume = {17}, journal = {RNA : a publication of the RNA Society}, number = {7}, publisher = {Cold Spring Harbor Laboratory Press}, address = {Cold Spring Harbor, NY}, issn = {1355-8382}, doi = {10.1261/rna.2550211}, pages = {1247 -- 1257}, year = {2011}, abstract = {RNA folding is assumed to be a hierarchical process. The secondary structure of an RNA molecule, signified by base-pairing and stacking interactions between the paired bases, is formed first. Subsequently, the RNA molecule adopts an energetically favorable three-dimensional conformation in the structural space determined mainly by the rotational degrees of freedom associated with the backbone of regions of unpaired nucleotides (loops). To what extent the backbone conformation of RNA loops also results from interactions within the local sequence context or rather follows global optimization constraints alone has not been addressed yet. Because the majority of base stacking interactions are exerted locally, a critical influence of local sequence on local structure appears plausible. Thus, local loop structure ought to be predictable, at least in part, from the local sequence context alone. To test this hypothesis, we used Random Forests on a nonredundant data set of unpaired nucleotides extracted from 97 X-ray structures from the Protein Data Bank (PDB) to predict discrete backbone angle conformations given by the discretized eta/theta-pseudo-torsional space. Predictions on balanced sets with four to six conformational classes using local sequence information yielded average accuracies of up to 55\%, thus significantly better than expected by chance (17\%-25\%). Bases close to the central nucleotide appear to be most tightly linked to its conformation. Our results suggest that RNA loop structure does not only depend on long-range base-pairing interactions; instead, it appears that local sequence context exerts a significant influence on the formation of the local loop structure.}, language = {en} } @article{HeldPascaudEckertetal.2011, author = {Held, Katrin and Pascaud, Francois and Eckert, Christian and Gajdanowicz, Pawel and Hashimoto, Kenji and Corratge-Faillie, Claire and Offenborn, Jan Niklas and Lacombe, Benoit and Dreyer, Ingo and Thibaud, Jean-Baptiste and Kudla, J{\"o}rg}, title = {Calcium-dependent modulation and plasma membrane targeting of the AKT2 potassium channel by the CBL4/CIPK6 calcium sensor/protein kinase complex}, series = {Cell research}, volume = {21}, journal = {Cell research}, number = {7}, publisher = {Nature Publ. Group}, address = {Shanghai}, issn = {1001-0602}, doi = {10.1038/cr.2011.50}, pages = {1116 -- 1130}, year = {2011}, abstract = {Potassium (K(+)) channel function is fundamental to many physiological processes. However, components and mechanisms regulating the activity of plant K(+) channels remain poorly understood. Here, we show that the calcium (Ca(2+)) sensor CBL4 together with the interacting protein kinase CIPK6 modulates the activity and plasma membrane (PM) targeting of the K(+) channel AKT2 from Arabidopsis thaliana by mediating translocation of AKT2 to the PM in plant cells and enhancing AKT2 activity in oocytes. Accordingly, akt2, cbl4 and cipk6 mutants share similar developmental and delayed flowering phenotypes. Moreover, the isolated regulatory C-terminal domain of CIPK6 is sufficient for mediating CBL4- and Ca(2+)-dependent channel translocation from the endoplasmic reticulum membrane to the PM by a novel targeting pathway that is dependent on dual lipid modifications of CBL4 by myristoylation and palmitoylation. Thus, we describe a critical mechanism of ion-channel regulation where a Ca(2+) sensor modulates K(+) channel activity by promoting a kinase interaction-dependent but phosphorylation-independent translocation of the channel to the PM.}, language = {en} } @article{JuerchottGuoCatchpoleetal.2011, author = {Juerchott, Kathrin and Guo, Ke-Tai and Catchpole, Gareth and Feher, Kristen and Willmitzer, Lothar and Schichor, Christian and Selbig, Joachim}, title = {Comparison of metabolite profiles in U87 glioma cells and mesenchymal stem cells}, series = {Biosystems : journal of biological and information processing sciences}, volume = {105}, journal = {Biosystems : journal of biological and information processing sciences}, number = {2}, publisher = {Elsevier}, address = {Oxford}, issn = {0303-2647}, doi = {10.1016/j.biosystems.2011.05.005}, pages = {130 -- 139}, year = {2011}, abstract = {Gas chromatography-mass spectrometry (GC-MS) profiles were generated from U87 glioma cells and human mesenchymal stem cells (hMSC). 37 metabolites representing glycolysis intermediates, TCA cycle metabolites, amino acids and lipids were selected for a detailed analysis. The concentrations of these. metabolites were compared and Pearson correlation coefficients were used to calculate the relationship between pairs of metabolites. Metabolite profiles and correlation patterns differ significantly between the two cell lines. These profiles can be considered as a signature of the underlying biochemical system and provide snap-shots of the metabolism in mesenchymal stem cells and tumor cells.}, language = {en} } @article{ItonagaKoeppenPlathetal.2011, author = {Itonaga, Naomi and K{\"o}ppen, Ulrich and Plath, Martin and Wallschl{\"a}ger, Hans-Dieter}, title = {Declines in breeding site fidelity in an increasing population of White Storks Ciconia ciconia}, series = {IBIS}, volume = {153}, journal = {IBIS}, number = {3}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0019-1019}, pages = {636 -- 639}, year = {2011}, abstract = {Following a steep decline, White Stork Ciconia ciconia populations in Germany are currently increasing, allowing us to examine potential density-dependent effects on breeding dispersal. Our data suggest that the proportion of breeding dispersers has increased over time, indicating a density-dependent component in nest-site fidelity that may be linked to increased competition.}, language = {en} } @article{NiHerzschuh2011, author = {Ni, Jian and Herzschuh, Ulrike}, title = {Simulating biome distribution on the Tibetan Plateau using a modified global vegetation model}, series = {Arctic, antarctic, and alpine research : an interdisciplinary journal}, volume = {43}, journal = {Arctic, antarctic, and alpine research : an interdisciplinary journal}, number = {3}, publisher = {Institute of Arctic and Alpine Research, University of Colorado}, address = {Boulder}, issn = {1523-0430}, doi = {10.1657/1938-4246-43.3.429}, pages = {429 -- 441}, year = {2011}, abstract = {We used a regionally modified global vegetation model (BIOME4-Tibet) to simulate biome distribution on the Tibetan Plateau under current climate conditions derived from regional meteorological observations. The bioclimatic limits (mean temperatures of the coldest and warmest months, minimum temperature, growing degree-days on 5 degrees C and 0 degrees C bases) for some key alpine plant functional types (temperate deciduous and conifer trees, boreal deciduous and conifer trees, desert woody plants, tundra shrubs, cold herbaceous plants, and lichens/forbs) were redefined based on regional vegetation-climate relationships. Modern vegetation maps confirmed that the BIOME4-Tibet model does a better job of simulating biome patterns on the plateau (gridcell agreement 52\%) than the original BIOME4 model (35\%). This improved model enhanced our ability to simulate temperate conifer forest, cool conifer and mixed forest, evergreen taiga, temperate xerophytic shrubland, temperate grassland and desert, and steppe and shrub tundra biomes, but made a negligible or reduced difference to the prediction of temperate deciduous forest, warm-temperate mixed forest, and three tundra biomes (erect dwarf-shrub tundra, prostrate dwarf-shrub tundra, and cushion forb, lichen, and moss tundra). Future modification of the vegetation model, by increasing the number of shrub and herb plant functional types, re-parameterization of more precise bioclimatic constraints, and improved representation of soil, permafrost, and snow processes, will be needed to better characterize the distribution of alpine vegetation on the Tibetan Plateau.}, language = {en} } @misc{KehrPicchiDittmannThuenemann2011, author = {Kehr, Jan-Christoph and Picchi, Douglas Gatte and Dittmann-Th{\"u}nemann, Elke}, title = {Natural product biosyntheses in cyanobacteria a treasure trove of unique enzymes}, series = {Beilstein journal of organic chemistry}, volume = {7}, journal = {Beilstein journal of organic chemistry}, number = {2}, publisher = {Beilstein-Institut zur F{\"o}rderung der Chemischen Wissenschaften}, address = {Frankfurt, Main}, issn = {1860-5397}, doi = {10.3762/bjoc.7.191}, pages = {1622 -- 1635}, year = {2011}, abstract = {Cyanobacteria are prolific producers of natural products. Investigations into the biochemistry responsible for the formation of these compounds have revealed fascinating mechanisms that are not, or only rarely, found in other microorganisms. In this article, we survey the biosynthetic pathways of cyanobacteria isolated from freshwater, marine and terrestrial habitats. We especially emphasize modular nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) pathways and highlight the unique enzyme mechanisms that were elucidated or can be anticipated for the individual products. We further include ribosomal natural products and UV-absorbing pigments from cyanobacteria. Mechanistic insights obtained from the biochemical studies of cyanobacterial pathways can inspire the development of concepts for the design of bioactive compounds by synthetic-biology approaches in the future.}, language = {en} } @article{Martens2011, author = {Martens, D{\"o}rte}, title = {Well-being and acceptance - contradictory aims in forest management?}, series = {Eco.mont : journal on protected mountain areas research}, volume = {3}, journal = {Eco.mont : journal on protected mountain areas research}, number = {2}, publisher = {Austrian Academy of Sciences Press}, address = {Wien}, issn = {2073-106X}, pages = {63 -- 65}, year = {2011}, abstract = {Urban forests fulfil various functions, among them the restoration process and aesthetical needs of urban residents. This article reflects the attitudes towards different managed forests on the one hand and their influence on psychological well-being on the other. Results of empirical approaches from both fields show some inconsistency, suggesting that people have a more positive attitude towards wild forest areas, while the effect on well-being is more positive after a walk in tended forest areas. A discussion follows on the link between perception and the effect of urban forests. An outlook on necessary research reveals the need for longitudinal research. The article concludes by showing management implications.}, language = {en} } @article{ArbeiterTegetmeyer2011, author = {Arbeiter, Susanne and Tegetmeyer, Cosima}, title = {Home range and habitat use by aquatic warblers acrocephalus paludicola on their wintering grounds in Northwestern Senegal}, series = {Acta ornithologica}, volume = {46}, journal = {Acta ornithologica}, number = {2}, publisher = {Museum and Institute of Zoology, Polish Academy of Sciences}, address = {Warsaw}, issn = {0001-6454}, doi = {10.3161/000164511X625883}, pages = {117 -- 126}, year = {2011}, abstract = {The Aquatic Warbler Acrocephalus paludicola was once a common breeding bird in mesotrophic fen mires all over Central and Western Europe. In the last century large parts of its habitat have been destroyed by wetland drainage and agricultural intensification. Besides protecting the remaining breeding habitats, it is of great importance to preserve suitable migration stopover habitats and wintering grounds to avert the extinction of the species. We determined home-range size and the use of vegetation associations of Aquatic Warblers on the wintering grounds in a flooded plain north of the Djoudj National Park in Senegal. Individual birds (11) were caught in mist nets and equipped with radio transmitters. Locations were assessed by radiotelemetry and a compositional analysis was conducted to determine which vegetation types were preferred within home ranges. Similar to their behaviour on the breeding grounds, the Aquatic Warblers showed no territorial behaviour in their winter quarters. They used home ranges that averaged 4 ha in size, which they shared with conspecifics and other warblers. The home ranges overlapped 54\% on average, with a maximum of 90\% in an area used by four individuals. The vegetation structure of the wintering habitat is similar to breeding grounds and stopover sites of the species. Preferential vegetation had 80\% to 100\% cover and consisted of 60 to 90 cm high stands of Oryza longistaminata, Scirpus maritimus or Eleocharis mutata. Most birds stayed more often near the edge of open water, probably for foraging. A constant inundation seems essential, because Aquatic Warblers never occurred in desiccated parts of the study site.}, language = {en} } @article{VossNimtzLeimkuehler2011, author = {Voss, Martin and Nimtz, Manfred and Leimk{\"u}hler, Silke}, title = {Elucidation of the dual role of Mycobacterial MoeZR in Molybdenum Cofactor Biosynthesis and Cysteine Biosynthesis}, series = {PLoS one}, volume = {6}, journal = {PLoS one}, number = {11}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0028170}, pages = {9}, year = {2011}, abstract = {The pathway of molybdenum cofactor biosynthesis has been studied in detail by using proteins from Mycobacterium species, which contain several homologs associated with the first steps of Moco biosynthesis. While all Mycobacteria species contain a MoeZR, only some strains have acquired an additional homolog, MoeBR, by horizontal gene transfer. The role of MoeBR and MoeZR was studied in detail for the interaction with the two MoaD-homologs involved in Moco biosynthesis, MoaD1 and MoaD2, in addition to the CysO protein involved in cysteine biosynthesis. We show that both proteins have a role in Moco biosynthesis, while only MoeZR, but not MoeBR, has an additional role in cysteine biosynthesis. MoeZR and MoeBR were able to complement an E. coli moeB mutant strain, but only in conjunction with the Mycobacterial MoaD1 or MoaD2 proteins. Both proteins were able to sulfurate MoaD1 and MoaD2 in vivo, while only MoeZR additionally transferred the sulfur to CysO. Our in vivo studies show that Mycobacteria have acquired several homologs to maintain Moco biosynthesis. MoeZR has a dual role in Moco- and cysteine biosynthesis and is involved in the sulfuration of MoaD and CysO, whereas MoeBR only has a role in Moco biosynthesis, which is not an essential function for Mycobacteria.}, language = {en} } @article{WeizIshidaMakoweretal.2011, author = {Weiz, Annika R. and Ishida, Keishi and Makower, Katharina and Ziemert, Nadine and Hertweck, Christian and Dittmann-Th{\"u}nemann, Elke}, title = {Leader Peptide and a Membrane Protein Scaffold Guide the Biosynthesis of the Tricyclic Peptide Microviridin}, series = {Chemistry \& biology}, volume = {18}, journal = {Chemistry \& biology}, number = {11}, publisher = {Cell Press}, address = {Cambridge}, issn = {1074-5521}, doi = {10.1016/j.chembiol.2011.09.011}, pages = {1413 -- 1421}, year = {2011}, abstract = {Microviridins are unique protease inhibitors from bloom-forming cyanobacteria that have both ecological and pharmacological relevance. Their peptide backbones are produced ribosomally, and ATP grasp ligases introduce omega-ester and omega-amide bonds to yield rare cage-like structures. Bioinformatic analysis of the microviridin biosynthesis gene cluster suggests a novel type of processing machinery, which could rationalize the challenging in vivo/in vitro reconstitution of the pathway. In this work, we report the establishment of a minimal expression system for microviridins. Through bioinformatics and mutational analysis of the MdnA leader peptide we identified and characterized a strictly conserved binding motif that is specific for microviridin ligases. Furthermore, we showed that the ABC transporter MdnE is crucial for cyclization and processing of microviridins and demonstrated that MdnE is essential for stability of the microviridin biosynthesis complex.}, language = {en} } @article{PaascheEberle2011, author = {Paasche, Hendrik and Eberle, Detlef}, title = {Automated compilation of pseudo-lithology maps from geophysical data sets a comparison of Gustafson-Kessel and fuzzy c-means cluster algorithms}, series = {Exploration geophysics : the bulletin of the Australian Society of Exploration Geophysicists}, volume = {42}, journal = {Exploration geophysics : the bulletin of the Australian Society of Exploration Geophysicists}, number = {4}, publisher = {CSIRO}, address = {Collingwood}, issn = {0812-3985}, doi = {10.1071/EG11014}, pages = {275 -- 285}, year = {2011}, abstract = {The fuzzy partitioning Gustafson-Kessel cluster algorithm is employed for rapid and objective integration of multi-parameter Earth-science related databases. We begin by evaluating the Gustafson-Kessel algorithm using the example of a synthetic study and compare the results to those obtained from the more widely employed fuzzy c-means algorithm. Since the Gustafson-Kessel algorithm goes beyond the potential of the fuzzy c-means algorithm by adapting the shape of the clusters to be detected and enabling a manual control of the cluster volume, we believe the results obtained from Gustafson-Kessel algorithm to be superior. Accordingly, a field database comprising airborne and ground-based geophysical data sets is analysed, which has previously been classified by means of the fuzzy c-means algorithm. This database is integrated using the Gustafson-Kessel algorithm thus minimising the amount of empirical data processing required before and after fuzzy c-means clustering. The resultant zonal geophysical map is more evenly clustered matching regional geology information available from the survey area. Even additional information about linear structures, e. g. as typically caused by the presence of dolerite dykes or faults, is visible in the zonal map obtained from Gustafson-Kessel cluster analysis.}, language = {en} } @article{WuWollenbergerHofrichteretal.2011, author = {Wu, Yunhua and Wollenberger, Ursula and Hofrichter, Martin and Ullrich, Rene and Scheibner, Katrin and Scheller, Frieder W.}, title = {Direct electron transfer of Agrocybe aegerita peroxygenase at electrodes modified with chitosan-capped Au nanoparticles and its bioelectrocatalysis to aniline}, series = {Sensors and actuators : B, Chemical}, volume = {160}, journal = {Sensors and actuators : B, Chemical}, number = {1}, publisher = {Elsevier}, address = {Lausanne}, issn = {0925-4005}, doi = {10.1016/j.snb.2011.09.090}, pages = {1419 -- 1426}, year = {2011}, abstract = {Three different sizes of chitosan-capped Au nanoparticles were synthesized and were used to incorporate Agrocybe aegerita peroxygenase (AaeAPO) onto the surface of glassy carbon electrode. The direct electron transfer of AaeAPO was achieved in all films. The highest amount of electroactive enzyme and highest electron transfer rate constant k(s) of AaeAPO were obtained in the film with the smallest size of chitosan-capped Au nanoparticles. In anaerobic solutions, quasi-reversible oxidation and reduction are obtained with a formal potential of -0.280V vs. Ag/AgCl 1 M KCl in 100 mM (pH 7.0) PBS at scan rate of 1 V s(-1). Bioelectrocatalytic reduction currents can be obtained with the AaeAPO-modified electrode on addition of hydrogen peroxide. This reaction was suppressed when sodium azide, an inhibitor of AaeAPO, was present. Furthermore, the peroxide-dependent conversion of aniline was characterized and it was found that a polymer product via p-aminophenol is formed. And the AaeAPO biosensor was applied to determine aniline and p-aminophenol.}, language = {en} } @article{YarmanBadalyanGajovicEichelmannetal.2011, author = {Yarman, Aysu and Badalyan, Artavazd and Gajovic-Eichelmann, Nenad and Wollenberger, Ursula and Scheller, Frieder W.}, title = {Enzyme electrode for aromatic compounds exploiting the catalytic activities of microperoxidase-11}, series = {Biosensors and bioelectronics : the principal international journal devoted to research, design development and application of biosensors and bioelectronics}, volume = {30}, journal = {Biosensors and bioelectronics : the principal international journal devoted to research, design development and application of biosensors and bioelectronics}, number = {1}, publisher = {Elsevier}, address = {Oxford}, issn = {0956-5663}, doi = {10.1016/j.bios.2011.09.004}, pages = {320 -- 323}, year = {2011}, abstract = {Microperoxidase-11 (MR-11) which has been immobilised in a matrix of chitosan-embedded gold nanoparticles on the surface of a glassy carbon electrode catalyzes the conversion of aromatic substances. This peroxide-dependent catalysis of microperoxidase has been applied in an enzyme electrode for the first time to indicate aromatic compounds such as aniline. 4-fluoroaniline, catechol and p-aminophenol. The electrode signal is generated by the cathodic reduction of the quinone or quinoneimine which is formed in the presence of both MP-II and peroxide from the substrate. The same sensor principle will be extended to aromatic drugs.}, language = {en} } @article{WandHolzloehnerNeupertetal.2011, author = {Wand, Inga and Holzl{\"o}hner, Pamela and Neupert, Steffi and Micheel, Burkhard and Heilmann, Katja}, title = {Cooperation of dendritic cells with naive lymphocyte populations to induce the generation of antigen-specific antibodies in vitro}, series = {Journal of biotechnology}, volume = {156}, journal = {Journal of biotechnology}, number = {3}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0168-1656}, doi = {10.1016/j.jbiotec.2011.09.002}, pages = {173 -- 181}, year = {2011}, abstract = {The production of monoclonal antibodies by hybridoma technology is dependent on lymphocytes taken from vertebrates which have to be immunized against the corresponding antigen. We present here our first experiments which should allow the replacement of this in vivo immunization step by an in vitro immunization procedure. This work provides new possibilities for the specific activation of immune cells in order to use them for the generation of antibodies which are not of murine origin. Bone marrow-derived dendritic cells were loaded with antigen and co-cultured with naive T and B lymphocytes of non-immunized mice. The interaction and activation of the different cell types were investigated by measuring the expression of specific cell surface markers, the release of activation-dependent interleukins and the secretion of antigen-specific antibodies. We could demonstrate that dendritic cells process and present antigen fragments and activate T cells, that T cells proliferate and release activation-induced interleukins, and that B cells maturate under the influence of activated T cells and secrete antigen-specific antibodies.}, language = {en} } @article{TirokBauerWirtzetal.2011, author = {Tirok, Katrin and Bauer, Barbara and Wirtz, Kai and Gaedke, Ursula}, title = {Predator-Prey Dynamics Driven by Feedback between Functionally Diverse Trophic Levels}, series = {PLoS one}, volume = {6}, journal = {PLoS one}, number = {11}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0027357}, pages = {13}, year = {2011}, abstract = {Neglecting the naturally existing functional diversity of communities and the resulting potential to respond to altered conditions may strongly reduce the realism and predictive power of ecological models. We therefore propose and study a predator-prey model that describes mutual feedback via species shifts in both predator and prey, using a dynamic trait approach. Species compositions of the two trophic levels were described by mean functional traits-prey edibility and predator food-selectivity- and functional diversities by the variances. Altered edibility triggered shifts in food-selectivity so that consumers continuously respond to the present prey composition, and vice versa. This trait-mediated feedback mechanism resulted in a complex dynamic behavior with ongoing oscillations in the mean trait values, reflecting continuous reorganization of the trophic levels. The feedback was only possible if sufficient functional diversity was present in both trophic levels. Functional diversity was internally maintained on the prey level as no niche existed in our system, which was ideal under any composition of the predator level due to the trade-offs between edibility, growth and carrying capacity. The predators were only subject to one trade-off between food-selectivity and grazing ability and in the absence of immigration, one predator type became abundant, i.e., functional diversity declined to zero. In the lack of functional diversity the system showed the same dynamics as conventional models of predator-prey interactions ignoring the potential for shifts in species composition. This way, our study identified the crucial role of trade-offs and their shape in physiological and ecological traits for preserving diversity.}, language = {en} } @article{EstherGroeneveldEnrightetal.2011, author = {Esther, Alexandra and Groeneveld, J{\"u}rgen and Enright, Neal J. and Miller, Ben P. and Lamont, Byron B. and Perry, George L. W. and Tietjen, Britta and Jeltsch, Florian}, title = {Low-dimensional trade-offs fail to explain richness and structure in species-rich plant communities}, series = {Theoretical ecology}, volume = {4}, journal = {Theoretical ecology}, number = {4}, publisher = {Springer}, address = {Heidelberg}, issn = {1874-1738}, doi = {10.1007/s12080-010-0092-y}, pages = {495 -- 511}, year = {2011}, abstract = {Mathematical models and ecological theory suggest that low-dimensional life history trade-offs (i.e. negative correlation between two life history traits such as competition vs. colonisation) may potentially explain the maintenance of species diversity and community structure. In the absence of trade-offs, we would expect communities to be dominated by 'super-types' characterised by mainly positive trait expressions. However, it has proven difficult to find strong empirical evidence for such trade-offs in species-rich communities. We developed a spatially explicit, rule-based and individual-based stochastic model to explore the importance of low-dimensional trade-offs. This model simulates the community dynamics of 288 virtual plant functional types (PFTs), each of which is described by seven life history traits. We consider trait combinations that fit into the trade-off concept, as well as super-types with little or no energy constraints or resource limitations, and weak PFTs, which do not exploit resources efficiently. The model is parameterised using data from a fire-prone, species-rich Mediterranean-type shrubland in southwestern Australia. We performed an exclusion experiment, where we sequentially removed the strongest PFT in the simulation and studied the remaining communities. We analysed the impact of traits on performance of PFTs in the exclusion experiment with standard and boosted regression trees. Regression tree analysis of the simulation results showed that the trade-off concept is necessary for PFT viability in the case of weak trait expression combinations such as low seed production or small seeds. However, species richness and diversity can be high despite the presence of super-types. Furthermore, the exclusion of super-types does not necessarily lead to a large increase in PFT richness and diversity. We conclude that low-dimensional trade-offs do not provide explanations for multi-species co-existence contrary to the prediction of many conceptual models.}, language = {en} } @article{WeisseBerendonkKamjunkeetal.2011, author = {Weisse, Thomas and Berendonk, Thomas U. and Kamjunke, Norbert and Moser, Michael and Scheffel, U. and Stadler, P. and Weithoff, Guntram}, title = {Significant habitat effects influence protist fitness evidence for local adaptation from acidic mining lakes}, series = {Ecosphere : the magazine of the International Ecology University}, volume = {2}, journal = {Ecosphere : the magazine of the International Ecology University}, number = {12}, publisher = {Wiley}, address = {Washington}, issn = {2150-8925}, doi = {10.1890/ES11-00157.1}, pages = {14}, year = {2011}, abstract = {It is currently controversially discussed if the same freshwater microorganisms occur worldwide wherever their required habitats are realized, i.e., without any adaptation to local conditions below the species level. We performed laboratory experiments with flagellates and ciliates from three acidic mining lakes (AML, pH similar to 2.7) to investigate if similar habitats may affect similar organisms differently. Such man-made lakes provide suitable ecosystem models to test for the significance of strong habitat selection. To this end, we analyzed the growth response of three protist taxa (three strains of the phytoflagellate Chlamydomonas acidophila, two isolates of the phytoflagellate Ochromonas and two species of the ciliate genus Oxytricha) by exposing them to lake water of their origin and from the two other AML in a cross-factorial design. Population growth rates were measured as a proxy for their fitness. Results revealed significant effects of strain, lake (= habitat), and strain X habitat interaction. In the environmentally most adverse AML, all three protist taxa were locally adapted. In conclusion, our study demonstrates that (1) the same habitat may affect strains of the same species differently and that (2) similar habitats may harbor ecophysiologically different strains or species. These results contradict the 'everything is everywhere' paradigm.}, language = {en} } @article{RedelbergerSedukGenestetal.2011, author = {Redelberger, David and Seduk, Farida and Genest, Olivier and Mejean, Vincent and Leimk{\"u}hler, Silke and Iobbi-Nivol, Chantal}, title = {YcdY Protein of Escherichia coli, an Atypical Member of the TorD Chaperone Family}, series = {Journal of bacteriology}, volume = {193}, journal = {Journal of bacteriology}, number = {23}, publisher = {American Society for Microbiology}, address = {Washington}, issn = {0021-9193}, doi = {10.1128/JB.05927-11}, pages = {6512 -- 6516}, year = {2011}, abstract = {The TorD family of specific chaperones is divided into four subfamilies dedicated to molybdoenzyme biogenesis and a fifth one, exemplified by YcdY of Escherichia coli, for which no defined partner has been identified so far. We propose that YcdY is the chaperone of YcdX, a zinc protein involved in the swarming motility process of E. coli, since YcdY interacts with YcdX and increases its activity in vitro.}, language = {en} } @article{GiladiZivMayetal.2011, author = {Giladi, Itamar and Ziv, Yaron and May, Felix and Jeltsch, Florian}, title = {Scale-dependent determinants of plant species richness in a semi-arid fragmented agro-ecosystem}, series = {Journal of vegetation science}, volume = {22}, journal = {Journal of vegetation science}, number = {6}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {1100-9233}, doi = {10.1111/j.1654-1103.2011.01309.x}, pages = {983 -- 996}, year = {2011}, abstract = {Aims: (1) Understanding how the relationship between species richness and its determinants depends on the interaction between scales at which the response and explanatory variables are measured. (2) Quantifying the relative contributions of local, intermediate and large-scale determinants of species richness in a fragmented agro-ecosystem. (3) Testing the hypothesis that the relative contribution of these determinants varies with the grain size at which species richness is measured. Location: A fragmented agro-ecosystem in the Southern Judea Lowland, Israel, within a desert-Mediterranean transition zone. Methods: Plant species richness was estimated using hierarchical nested sampling in 81 plots, positioned in 38 natural vegetation patches within an agricultural matrix (mainly wheat fields) among three land units along a sharp precipitation gradient. Explanatory variables included position along that gradient, patch area, patch isolation, habitat heterogeneity and overall plant density. We used general linear models and hierarchical partitioning of variance to test and quantify the effect of each explanatory variable on species richness at four grain sizes (0.0625, 1, 25 and 225m(2)). Results: Species richness was mainly affected by position along a precipitation gradient and overall plant density, and to a lesser extent by habitat heterogeneity. It was also significantly affected by patch area and patch isolation, but only for small grain sizes. The contribution of each explanatory variable to explained variance in species richness varied with grain size, i.e. scale-dependent. The influence of geographic position and habitat heterogeneity on species richness increased with grain size, while the influence of plant density decreased with grain size. Main conclusions: Species richness is determined by the combined effect of several scale-dependent determinants. Ability to detect an effect and effect size of each determinant varies with the scale (grain size) at which it is measured. The combination of a multi-factorial approach and multi-scale sampling reveals that conclusions drawn from studies that ignore these dimensions are restricted and potentially misleading.}, language = {en} } @article{SchleicherMeyerWiegandetal.2011, author = {Schleicher, Jana and Meyer, Katrin M. and Wiegand, Kerstin and Schurr, Frank Martin and Ward, David}, title = {Disentangling facilitation and seed dispersal from environmental heterogeneity as mechanisms generating associations between savanna plants}, series = {Journal of vegetation science}, volume = {22}, journal = {Journal of vegetation science}, number = {6}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {1100-9233}, doi = {10.1111/j.1654-1103.2011.01310.x}, pages = {1038 -- 1048}, year = {2011}, abstract = {Question: How can we disentangle facilitation and seed dispersal from environmental heterogeneity as mechanisms causing spatial associations of plant species? Location: Semi-arid savanna in the Kimberley Thorn Bushveld, South Africa. Methods: We developed a two-step protocol for the statistical differentiation of association-promoting mechanisms in plants based on the Acacia erioloba-Grewia flava association. Individuals of the savanna shrub G. flava and the tree A. erioloba were mapped on four study plots. Disentangling the mechanism causing the association of G. flava and A. erioloba involved tests of three spatial and one non-spatial null model. The spatial null models include homogeneous and heterogeneous Poisson processes for spatial randomness based on the bivariate spatial point patterns of the four plots. With the non-spatial analysis, we determined the relationship between the canopy diameter of A. erioloba trees and presence or absence of G. flava shrubs in the tree understorey to find whether shrub presence requires a minimum tree canopy diameter. Results: We first showed a significant positive spatial association of the two species. Thereafter, the non-spatial analysis supported an exclusion of environmental heterogeneity as the sole cause of this positive association. We found a minimum tree size under which no G. flava shrubs occurred. Conclusions: Our two-step analysis showed that it is unlikely that heterogeneous environmental conditions caused the spatial association of A. erioloba and G. flava. Instead, this association may have been caused by seed dispersal and/or facilitation (e.g. caused by hydraulic lift and/or nitrogen fixation by the host tree).}, language = {en} } @article{KupstatRitschelKumke2011, author = {Kupstat, Annette and Ritschel, Thomas and Kumke, Michael Uwe}, title = {Oxazine Dye-Conjugated DNA Oligonucleotides Forster Resonance Energy Transfer in View of Molecular Dye-DNA Interactions}, series = {Bioconjugate chemistry}, volume = {22}, journal = {Bioconjugate chemistry}, number = {12}, publisher = {American Chemical Society}, address = {Washington}, issn = {1043-1802}, doi = {10.1021/bc200379y}, pages = {2546 -- 2557}, year = {2011}, abstract = {In this work, the photophysical properties of two oxazine dyes (ATTO 610 and ATTO 680) covalently attached via a C6-amino linker to the 5'-end of short single-stranded as well as double-stranded DNA (ssDNA and dsDNA, respectively) of different lengths were investigated. The two oxazine dyes were chosen because of the excellent spectral overlap, the high extinction coefficients, and the high fluorescence quantum yield of ATTO 610, making them an attractive Forster resonance energy transfer (FRET) pair for bioanalytical applications in the far-red spectral range. To identify possible molecular dye-DNA interactions that cause photophysical alterations, we performed a detailed spectroscopic study, including time-resolved fluorescence anisotropy and fluorescence correlation spectroscopy measurements. As an effect of the DNA conjugation, the absorption and fluorescence maxima of both dyes were bathochromically shifted and the fluorescence decay times were increased. Moreover, the absorption of conjugated ATTO 610 was spectrally broadened, and a dual fluorescence emission was observed. Steric interactions with ssDNA as well as dsDNA were found for both dyes. The dye-DNA interactions were strengthened from ssDNA to dsDNA conjugates, pointing toward interactions with specific dsDNA domains (such as the top of the double helix). Although these interactions partially blocked the dye-linker rotation, a free (unhindered) rotational mobility of at least one dye facilitated the appropriate alignment of the transition dipole moments in doubly labeled ATTO 610/ATTO 680-dsDNA conjugates for the performance of successful FRET. Considering the high linker flexibility for the determination of the donor-acceptor distances, good accordance between theoretical and experimental FRET parameters was obtained. The considerably large Forster distance of similar to 7 nm recommends the application of this FRET pair not only for the detection of binding reactions between nucleic acids in living cells but also for monitoring interactions of larger biomolecules such as proteins.}, language = {en} } @article{Weber2011, author = {Weber, Ewald}, title = {Strong regeneration ability from rhizome fragments in two invasive clonal plants (Solidago canadensis and S. gigantea)}, series = {Biological invasions : unique international journal uniting scientists in the broad field of biological invasions}, volume = {13}, journal = {Biological invasions : unique international journal uniting scientists in the broad field of biological invasions}, number = {12}, publisher = {Springer}, address = {Dordrecht}, issn = {1387-3547}, doi = {10.1007/s10530-011-9977-y}, pages = {2947 -- 2955}, year = {2011}, abstract = {The two rhizomatous perennials Solidago canadensis and S. gigantea belong to the most widespread alien plants in Europe. Anecdotal observations suggest that they disperse also by rhizome fragments. For testing their resprouting ability, rhizome fragments of different sizes from both species were buried at four different soil depths (0, 5, 10 and 20 cm, respectively) in a common garden. Rhizome fragments of S. canadensis ranged 3-6 cm in length, those of S. gigantea 5-20 cm in length. Resprouting plants were harvested after 3 months and growth related traits measured to assess their vitality. Resprouting rate in S. gigantea was far higher than in S. canadensis (85 and 19\%, respectively). In S. gigantea, fragments of all sizes resprouted from all soil depths whereas none rhizome of S. canadensis emerged from 20 cm burial depth. In S. gigantea, size related traits showed significant interactions between fragment size and burial depth, but not relative shoot growth rate. At all burial depths, vitality of plants emerging from small rhizomes was lower than plants emerging from large rhizomes. Effects of rhizome size became stronger with increasing burial depth. The results show that both species are able to resprout from buried rhizome fragments, and that succesful regeneration is more likely to occur in S. gigantea. Managing these species should avoid any activities promoting rhizome fragmentation and dispersal of fragments.}, language = {en} } @article{FrascaRichtervonGrabergetal.2011, author = {Frasca, Stefano and Richter, Claudia and von Graberg, Till and Smarsly, Bernd M. and Wollenberger, Ursula}, title = {Electrochemical switchable protein-based optical device}, series = {Engineering in life sciences : Industry, Environment, Plant, Food}, volume = {11}, journal = {Engineering in life sciences : Industry, Environment, Plant, Food}, number = {6}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {1618-0240}, doi = {10.1002/elsc.201100079}, pages = {554 -- 558}, year = {2011}, abstract = {The present work contributes to the development of reusable sensing systems with a visual evaluation of the detection process related to an analyte. An electrochemical switchable protein-based optical device was designed with the core part composed of cytochrome c immobilized in a mesoporous indium tin oxide film. A color-developing redox-sensitive dye was used as switchable component of the system. The cytochrome c-catalyzed oxidation of the dye by hydrogen peroxide is spectroscopically investigated. When the dye is co-immobilized with the protein, its redox state is easily controlled by application of an electrical potential at the supporting material. This enables to electrochemically reset the system to the initial state and repetitive signal generation. The implemented reset function of the color forming reaction will make calibration of small test devices possible. The principle can be extended to other color forming redox reactions and to coupled enzyme systems, such as rapid food testing and indication of critical concentrations of metabolites for health care.}, language = {en} } @article{SchmidtStaude2011, author = {Schmidt, Bernd and Staude, Lucia}, title = {Desymmetrization of (R,R)-Hexa-1,5-diene-3,4-diol via Monofunctionallization and Rhodium-Catalyzed Allylic Substitution}, series = {The journal of organic chemistry}, volume = {76}, journal = {The journal of organic chemistry}, number = {7}, publisher = {American Chemical Society}, address = {Washington}, issn = {0022-3263}, doi = {10.1021/jo2001337}, pages = {2220 -- 2226}, year = {2011}, abstract = {A sequence of selective monoprotection and Rh-catalyzed enantioconservative allylic subEtitution is established as a desymmetrization strategy for C-2-symmetric hexa-1,5-diene-3,4-diol. A benzyl protecting group and ethyl carbonate as a leaving group emerged as the most useful combination with respect to reproducibility, stereoselectivity, and yield: A remarkable deviation from the normally observed regiospecificity of Rh-catalyzed allylic alkylations was observed for unprotected carbonates. In this case, a linear, rather than a branched alkylation product was obtained exclusively.}, language = {en} }