TY - JOUR A1 - Scheffler, Christiane ED - Hermanussen, Michael T1 - Biological age JF - Auxology : Studying Human Growth and Development Y1 - 2013 SN - 978-3-510-65278-5 SP - 44 EP - 47 PB - Schweizerbart Science Publishers CY - Stuttgart ER - TY - JOUR A1 - Bröker, Nina Kristin A1 - Gohlke, Ulrich A1 - Müller, Jürgen J. A1 - Uetrecht, Charlotte A1 - Heinemann, Udo A1 - Seckler, Robert A1 - Barbirz, Stefanie T1 - Single amino acid exchange in bacteriophage HK620 tailspike protein results in thousand-fold increase of its oligosaccharide affinity JF - Glycobiology N2 - Bacteriophage HK620 recognizes and cleaves the O-antigen polysaccharide of Escherichia coli serogroup O18A1 with its tailspike protein (TSP). HK620TSP binds hexasaccharide fragments with low affinity, but single amino acid exchanges generated a set of high-affinity mutants with submicromolar dissociation constants. Isothermal titration calorimetry showed that only small amounts of heat were released upon complex formation via a large number of direct and solvent-mediated hydrogen bonds between carbohydrate and protein. At room temperature, association was both enthalpy- and entropy-driven emphasizing major solvent rearrangements upon complex formation. Crystal structure analysis showed identical protein and sugar conformers in the TSP complexes regardless of their hexasaccharide affinity. Only in one case, a TSP mutant bound a different hexasaccharide conformer. The extended sugar binding site could be dissected in two regions: first, a hydrophobic pocket at the reducing end with minor affinity contributions. Access to this site could be blocked by a single aspartate to asparagine exchange without major loss in hexasaccharide affinity. Second, a region where the specific exchange of glutamate for glutamine created a site for an additional water molecule. Side-chain rearrangements upon sugar binding led to desolvation and additional hydrogen bonding which define this region of the binding site as the high-affinity scaffold. KW - bacterial O-antigen KW - carbohydrate interaction KW - site-directed mutagenesis KW - structural thermodynamics KW - tailspike protein Y1 - 2013 U6 - https://doi.org/10.1093/glycob/cws126 SN - 0959-6658 VL - 23 IS - 1 SP - 59 EP - 68 PB - Oxford Univ. Press CY - Cary ER - TY - JOUR A1 - Taylan, Mehmet Sait A1 - Di Russo, Claudio A1 - Rampini, Mauro A1 - Ketmaier, Valerio T1 - Molecular systematics of the genus Troglophilus (Rhaphidophoridae, Orthoptera) in Turkey mitochondrial 16S rDNA evidences JF - ZooKeys N2 - This study focuses on the evolutionary relationships among Turkish species of the cave cricket genus Troglophilus. Fifteen populations were studied for sequence variation in a fragment (543 base pairs) of the mitochondrial DNA (mtDNA) 16S rDNA gene (16S) to reconstruct their phylogenetic relationships and biogeographic history. Genetic data retrieved three main clades and at least three divergent lineages that could not be attributed to any of the taxa known for the area. Molecular time estimates suggest that the diversification of the group took place between the Messinian and the Plio-Pleistocene. KW - Troglophilus KW - Rhaphidophoridae KW - Orthoptera KW - 16S rDNA KW - mitochondrial DNA KW - molecular systematics KW - cave crickets Y1 - 2013 U6 - https://doi.org/10.3897/zookeys.257.4133 SN - 1313-2989 IS - 257 SP - 33 EP - 46 PB - Pensoft Publ. CY - Sofia ER - TY - JOUR A1 - Pedersen, Henrik AE. A1 - Watthana, Santi A1 - Kocyan, Alexander A1 - Srimuang, Kanok-orn T1 - Pollination biology of Luisia curtisii (Orchidaceae) indications of a deceptive system operated by beetles JF - Plant systematics and evolution N2 - A population of Luisia curtisii (Orchidaceae: Aeridinae) in northern Thailand was studied with regard to pollination biology. Although a high level of self-compatibility was demonstrated experimentally, the very low natural fruit set (1.4-1.9 %) clearly indicated that the species depends on external agents for pollination. Our observations suggest that L. curtisii is pollinated by beetles, as Lema unicolor (Chrysomelidae) and Clinteria ducalis (Scarabaeidae) were the only flower visitors observed to carry pollinaria of this species. The hypothesis of specialised cantharophily is further supported by 2-methylbutyric acid and caproic acid being striking components of the floral scent. Judging from the lack of nectar and the behaviour of visiting beetles, the pollination system seems to rely on food or brood site deception. Retention of the anther on the pollinarium for some time after pollinarium removal probably reduces the frequency of insect-mediated autogamy and geitonogamy in Luisia curtisii-a possibility that was supported by comparative data on (1) the anther retention time and inflorescence visitation time of Lema unicolor and (2) stigma and anther length in the orchid. Existing reports of specialised beetle pollination in orchids are reviewed, and we conclude that there is accumulating evidence that specialised cantharophily is more common in the Orchidaceae than previously assumed. KW - Allogamy KW - Anther retention KW - Cantharophily KW - Floral scent KW - Fruit set KW - Outcrossing Y1 - 2013 U6 - https://doi.org/10.1007/s00606-012-0713-6 SN - 0378-2697 VL - 299 IS - 1 SP - 177 EP - 185 PB - Springer CY - Wien ER - TY - JOUR A1 - Fiorentino, V. A1 - Manganelli, Giuseppe A1 - Giusti, Folco A1 - Tiedemann, Ralph A1 - Ketmaier, Valerino T1 - A question of time the land snail Murella muralis (Gastropoda: Pulmonata) reveals constraints on past ecological speciation JF - Molecular ecology N2 - The lively debate about speciation currently focuses on the relative importance of factors driving population differentiation. While many studies are increasingly producing results on the importance of selection, little is known about the interaction between drift and selection. Moreover, there is still little knowledge on the spatial-temporal scales at which speciation occurs, that is, arrangement of habitat patches, abruptness of habitat transitions, climate and habitat changes interacting with selective forces. To investigate these questions, we quantified variation on a fine geographical scale analysing morphological (shell) and genetic data sets coupled with environmental data in the land snail Murella muralis, endemic to the Mediterranean island of Sicily. Analysis of a fragment of the mitochondrial DNA cytochrome oxidase I gene (COI) and eight nuclear microsatellite loci showed that genetic variation is highly structured at a very fine spatial scale by local palaeogeographical events and historical population dynamics. Molecular clock estimates, calibrated here specifically for Tyrrhenian land snails, provided a framework of palaeogeographical events responsible for the observed geographical variations and migration routes. Finally, we showed for the first time well-documented lines of evidence of selection in the past, which explains divergence of land snail shell shapes. We suggest that time and palaeogeographical history acted as constraints in the progress along the ecological speciation continuum. Our study shows that testing for correlation among palaeogeography, morphology and genetic data on a fine geographical scale provides information fundamental for a detailed understanding of ecological speciation processes. KW - allopatry KW - cytochrome oxidase I gene KW - ecological speciation KW - land snails KW - microsatellites KW - Murella Y1 - 2013 U6 - https://doi.org/10.1111/mec.12107 SN - 0962-1083 SN - 1365-294X VL - 22 IS - 1 SP - 170 EP - 186 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Hechavarria, Julio C. A1 - Macias, Silvio A1 - Vater, Marianne A1 - Mora, Emanuel C. A1 - Kössl, Manfred T1 - Evolution of neuronal mechanisms for echolocation specializations for target-range computation in bats of the genus Pteronotus JF - The journal of the Acoustical Society of America N2 - Delay tuning was studied in the auditory cortex of Pteronotus quadridens. All the 136 delay-tuned units that were studied responded strongly to heteroharmonic pulse-echo pairs presented at specific delays. In the heteroharmonic pairs, the first sonar call harmonic marks the timing of pulse emission while one of the higher harmonics (second or third) indicates the timing of the echo. Delay-tuned units are organized chronotopically along a rostrocaudal axis according to their characteristic delay. There is no obvious indication of multiple cortical axes specialized in the processing of different harmonic combinations of pulse and echo. Results of this study serve for a straight comparison of cortical delay-tuning between P. quadridens and the well-studied mustached bat, Pteronotus parnellii. These two species stem from the most recent and most basal nodes in the Pteronotus lineage, respectively. P. quadridens and P. parnellii use comparable heteroharmonic target-range computation strategies even though they do not use biosonar calls of a similar design. P. quadridens uses short constant-frequency (CF)/frequency-modulated (FM) echolocation calls, while P. parnellii uses long CF/FM calls. The ability to perform "heteroharmonic" target-range computations might be an ancestral neuronal specialization of the genus Pteronotus that was subjected to positive Darwinian selection in the evolution. Y1 - 2013 U6 - https://doi.org/10.1121/1.4768794 SN - 0001-4966 VL - 133 IS - 1 SP - 570 EP - 578 PB - American Institute of Physics CY - Melville ER - TY - JOUR A1 - Tsukaya, Hirokazu A1 - Byrne, Mary E. A1 - Horiguchi, Gorou A1 - Sugiyama, Munetaka A1 - Van Lijsebettens, Mieke A1 - Lenhard, Michael T1 - How do 'housekeeping' genes control organogenesis?-unexpected new findings on the role of housekeeping genes in cell and organ differentiation JF - Journal of plant research N2 - In recent years, an increasing number of mutations in what would appear to be 'housekeeping genes' have been identified as having unexpectedly specific defects in multicellular organogenesis. This is also the case for organogenesis in seed plants. Although it is not surprising that loss-of-function mutations in 'housekeeping' genes result in lethality or growth retardation, it is surprising when (1) the mutant phenotype results from the loss of function of a 'housekeeping' gene and (2) the mutant phenotype is specific. In this review, by defining housekeeping genes as those encoding proteins that work in basic metabolic and cellular functions, we discuss unexpected links between housekeeping genes and specific developmental processes. In a surprising number of cases housekeeping genes coding for enzymes or proteins with functions in basic cellular processes such as transcription, post-transcriptional modification, and translation affect plant development. KW - Development KW - Housekeeping genes KW - Post-transcriptional modification KW - RNAPII KW - Pre-mRNA splicing KW - Ribosome KW - 3 '-end processing KW - Transcription KW - Translation Y1 - 2013 U6 - https://doi.org/10.1007/s10265-012-0518-2 SN - 0918-9440 VL - 126 IS - 1 SP - 3 EP - 15 PB - Springer CY - Tokyo ER - TY - JOUR A1 - Hartwich, Melanie A1 - Martin-Creuzburg, Dominik A1 - Wacker, Alexander T1 - Seasonal changes in the accumulation of polyunsaturated fatty acids in zooplankton JF - Journal of plankton research N2 - In aquatic food webs, consumers, such as daphnids and copepods, differ regarding their accumulation of polyunsaturated fatty acids (PUFAs). We tested if the accumulation of PUFAs in a seston size fraction containing different consumers and in Daphnia as a separate consumer is subject to seasonal changes in a large deep lake due to changes in the dietary PUFA supply and specific demands of different consumers. We found that the accumulation of arachidonic acid (ARA) in Daphnia increased from early summer to late summer and autumn. However, ARA requirements of Daphnia appeared to be constant throughout the year, because the accumulation of ARA increased when the dietary ARA supply decreased. In the size fraction 140 m, we found an increased accumulation of docosahexaenoic acid (DHA) during late summer and autumn. These seasonal changes in DHA accumulation were linked to changes in the proportion of copepods in this size fraction, which may have increasingly accumulated DHA for active overwintering. We show that consumer-specific PUFA demands can result in seasonal changes in PUFA accumulation, which may influence the trophic transfer of PUFAs within the food web. KW - accumulation KW - Daphnia KW - copepods KW - ARA KW - DHA Y1 - 2013 U6 - https://doi.org/10.1093/plankt/fbs078 SN - 0142-7873 VL - 35 IS - 1 SP - 121 EP - 134 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Wissel, Jörg A1 - Manack, Aubrey A1 - Brainin, Michael T1 - Toward an epidemiology of poststroke spasticity JF - Neurology : official journal of the American Academy of Neurology N2 - Poststroke spasticity (PSS)-related disability is emerging as a significant health issue for stroke survivors. There is a need for predictors and early identification of PSS in order to minimize complications and maladaptation from spasticity. Reviewing the literature on stroke and upper motor neuron syndrome, spasticity, contracture, and increased muscle tone measured with the Modified Ashworth Scale and the Tone Assessment Scale provided data on the dynamic time course of PSS. Prevalence estimates of PSS were highly variable, ranging from 4% to 42.6%, with the prevalence of disabling spasticity ranging from 2% to 13%. Data on phases of the PSS continuum revealed evidence of PSS in 4% to 27% of those in the early time course (1-4 weeks poststroke), 19% to 26.7% of those in the postacute phase (1-3 months poststroke), and 17% to 42.6% of those in the chronic phase (>3 months poststroke). Data also identified key risk factors associated with the development of spasticity, including lower Barthel Index scores, severe degree of paresis, stroke-related pain, and sensory deficits. Although such indices could be regarded as predictors of PSS and thus enable early identification and treatment, the different measures of PSS used in those studies limit the strength of the findings. To optimize evaluation in the different phases of care, the best possible assessment of PSS would make use of a combination of indicators for clinical impairment, motor performance, activity level, quality of life, and patient-reported outcome measures. Applying these recommended measures, as well as increasing our knowledge of the physiologic predictors of PSS, will enable us to perform clinical and epidemiologic studies that will facilitate identification and early, multimodal treatment. Y1 - 2013 SN - 0028-3878 VL - 80 IS - 1 SP - S13 EP - S19 PB - Lippincott Williams & Wilkins CY - Philadelphia ER - TY - JOUR A1 - Sachse, Rita A1 - Wüstenhagen, Doreen Anja A1 - Samalikova, Maria A1 - Gerrits, Michael A1 - Bier, Frank Fabian A1 - Kubick, Stefan T1 - Synthesis of membrane proteins in eukaryotic cell-free systems JF - Engineering in life sciences : Industry, Environment, Plant, Food N2 - Cell-free protein synthesis (CFPS) is a valuable method for the fast expression of difficult-to-express proteins as well as posttranslationally modified proteins. Since cell-free systems circumvent possible cytotoxic effects caused by protein overexpression in living cells, they significantly enlarge the scale and variety of proteins that can be characterized. We demonstrate the high potential of eukaryotic CFPS to express various types of membrane proteins covering a broad range of structurally and functionally diverse proteins. Our eukaryotic cell-free translation systems are capable to provide high molecular weight membrane proteins, fluorescent-labeled membrane proteins, as well as posttranslationally modified proteins for further downstream analysis. KW - Cell-free protein expression KW - In vitro protein synthesis KW - Labeled membrane proteins KW - Synthetic glycoprotein Y1 - 2013 U6 - https://doi.org/10.1002/elsc.201100235 SN - 1618-0240 VL - 13 IS - 1 SP - 39 EP - 48 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Häring, Tim A1 - Reger, Birgit A1 - Ewald, Jörg A1 - Hothorn, Torsten A1 - Schröder-Esselbach, Boris T1 - Predicting Ellenberg's soil moisture indicator value in the Bavarian Alps using additive georegression JF - Applied vegetation science : official organ of the International Association for Vegetation Science N2 - Questions Can forest site characteristics be used to predict Ellenberg indicator values for soil moisture? Which is the best averaged mean value for modelling? Does the distribution of soil moisture depend on spatial information? Location Bavarian Alps, Germany. Methods We used topographic, climatic and edaphic variables to model the mean soil moisture value as found on 1505 forest plots from the database WINALPecobase. All predictor variables were taken from area-wide geodata layers so that the model can be applied to some 250 000 ha of forest in the target region. We adopted methods developed in species distribution modelling to regionalize Ellenberg indicator values. Therefore, we use the additive georegression framework for spatial prediction of Ellenberg values with the R-library mboost, which is a feasible way to consider environmental effects, spatial autocorrelation, predictor interactions and non-stationarity simultaneously in our data. The framework is much more flexible than established statistical and machine-learning models in species distribution modelling. We estimated five different mboost models reflecting different model structures on 50 bootstrap samples in each case. Results Median R2 values calculated on independent test samples ranged from 0.28 to 0.45. Our results show a significant influence of interactions and non-stationarity in addition to environmental covariates. Unweighted mean indicator values can be modelled better than abundance-weighted values, and the consideration of bryophytes did not improve model performance. Partial response curves indicate meaningful dependencies between moisture indicator values and environmental covariates. However, mean indicator values <4.5 and >6.0 could not be modelled correctly, since they were poorly represented in our calibration sample. The final map represents high-resolution information of site hydrological conditions. Conclusions Indicator values offer an effect-oriented alternative to physically-based hydrological models to predict water-related site conditions, even at landscape scale. The presented approach is applicable to all kinds of Ellenberg indicator values. Therefore, it is a significant step towards a new generation of models of forest site types and potential natural vegetation. KW - Boosting KW - Mboost KW - Non-stationarity KW - Predictive vegetation mapping KW - Site ecology KW - Species distribution modelling Y1 - 2013 U6 - https://doi.org/10.1111/j.1654-109X.2012.01210.x SN - 1402-2001 VL - 16 IS - 1 SP - 110 EP - 121 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Badalyan, Artavazd A1 - Neumann-Schaal, Meina A1 - Leimkühler, Silke A1 - Wollenberger, Ursula T1 - A Biosensor for aromatic aldehydes comprising the mediator dependent PaoABC-Aldehyde oxidoreductase JF - Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis N2 - A novel aldehyde oxidoreductase (PaoABC) from Escherichia coli was utilized for the development of an oxygen insensitive biosensor for benzaldehyde. The enzyme was immobilized in polyvinyl alcohol and currents were measured for aldehyde oxidation with different one and two electron mediators with the highest sensitivity for benzaldehyde in the presence of hexacyanoferrate(III). The benzaldehyde biosensor was optimized with respect to mediator concentration, enzyme loading and pH using potassium hexacyanoferrate(III). The linear measuring range is between 0.5200 mu M benzaldehyde. In correspondence with the substrate selectivity of the enzyme in solution the biosensor revealed a preference for aromatic aldehydes and less effective conversion of aliphatic aldehydes. The biosensor is oxygen independent, which is a particularly attractive feature for application. The biosensor can be applied to detect contaminations with benzaldehyde in solvents such as benzyl alcohol, where traces of benzaldehyde in benzyl alcohol down to 0.0042?% can be detected. KW - Aldehyde oxidoreductase KW - Benzaldehyde KW - Biosensor KW - Aromatic aldehydes KW - Molybdenum cofactor Y1 - 2013 U6 - https://doi.org/10.1002/elan.201200362 SN - 1040-0397 VL - 25 IS - 1 SP - 101 EP - 108 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Scheffler, Christiane T1 - Variable and invariable proportions in the ontogenesis of the human face JF - The journal of craniofacial surgery : an international journal dedicated to the practice of the art and science of craniofacial surgery ; official publication of the American Association of Pediatric Plastic Surgeons N2 - The human face shows individual features and features that are characteristic for sex and age (the loss of childlike characteristics during maturation). The analysis of facial dimensions is essential for identifying individual features also for forensic issues. The analysis of facial proportions was performed on photogrammetric data from front views of 125 children. The data were pooled from 2 different studies. The children's data were obtained from a longitudinal study and reduced by random generator to ensure the data of adults from a separate cross-sectional study. We applied principal component analysis on photogrammetric facial proportions of 169 individuals: 125 children (63 boys and 62 girls) aged 2-7 years and 44 adults (18 men and 26 women) aged 18-65 years. Facial proportions depend on age and sex. Three components described age: (1) proportions of facial height to head height, (2) proportions that involve endocanthal breadth, and (3) bigonial to bizygonial proportions. Proportions that associate with sex are connected with nasal distances and nasal to bizygonial distances. Twenty-three percent of the variance, particularly variance that are connected with proportions of lower and middle face heights to head height, do neither depend on sex nor on age and thus appear useful for screening purposes, eg, for dysmorphic genetic syndromes. KW - Human face KW - face proportions KW - ontogenesis KW - principal component analysis Y1 - 2013 U6 - https://doi.org/10.1097/SCS.0b013e31826d07a3 SN - 1049-2275 VL - 24 IS - 1 SP - 237 EP - 241 PB - Lippincott Williams & Wilkins CY - Philadelphia ER - TY - JOUR A1 - Carregari, Victor Corasolla A1 - Floriano, Rafael Stuani A1 - Rodrigues-Simioni, Lea A1 - Winck, Flavia V. A1 - Baldasso, Paulo Aparecido A1 - Ponce-Soto, Luis Alberto A1 - Marangoni, Sergio T1 - Biochemical, Pharmacological, and Structural Characterization of New Basic PLA(2) Bbil-TX from Bothriopsis bilineata Snake Venom JF - BioMed research international N2 - Bbil-TX, a PLA(2), was purified from Bothriopsis bilineata snake venom after only one chromatographic step using RP-HPLC on mu-Bondapak C-18 column. A molecular mass of 14243.8 Da was confirmed by -Tof ltima API ESI/ MS (TOF MS mode) mass spectrometry. The partial protein sequence obtained was then submitted to BLASTp, with the search restricted to PLA(2) from snakes and shows high identity values when compared to other PLA(2)s. PLA(2) activity was presented in the presence of a synthetic substrate and showed a minimum sigmoidal behavior, reaching its maximal activity at pH 8.0 and 25-37 degrees C. Maximum PLA(2) activity required Ca2+ and in the presence of Cd2+, Zn2+, Mn2+, and Mg2+ it was reduced in the presence or absence of Ca2+. Crotapotin from Crotalus durissus cascavella rattlesnake venom and antihemorrhagic factor DA2-II from Didelphis albiventris opossum sera under optimal conditions significantly inhibit the enzymatic activity. Bbil-TX induces myonecrosis in mice. The fraction does not show a significant cytotoxic activity in myotubes and myoblasts (C2C12). The infiammatory events induced in the serum of mice by Bbil-TX isolated from Bothriopsis bilineata snake venom were investigated. An increase in vascular permeability and in the levels of TNF-a, IL-6, and IL-1 was was induced. Since Bbil-TX exerts a stronger proinfiammatory effect, the phospholipid hydrolysis may be relevant for these phenomena. Y1 - 2013 U6 - https://doi.org/10.1155/2013/612649 SN - 2314-6133 SN - 2314-6141 PB - Hindawi Publishing Corp. CY - New York ER - TY - JOUR A1 - Messerschmidt, Katrin A1 - Heilmann, Katja T1 - Toxin-antigen conjugates as selection tools for antibody producing cells JF - Journal of immunological methods N2 - The generation of antibodies with designated specificity requires cost-intensive and time-consuming screening procedures. Here we present a new method by which hybridoma cells can be selected based on the specificity of the produced antibody by the use of antigen-toxin-conjugates thus eliminating the need of a screening procedure. Initial experiments were done with methotrexate as low molecular weight toxin and fluorescein as model antigen. Methotrexate and a methotrexate-fluorescein conjugate were characterized regarding their toxicity. Afterwards the effect of the fluorescein-specific antibody B13-DE1 on the toxicity of the methotrexate-fluorescein conjugate was determined. Finally, first results showed that hybridoma cells that produce fluorescein specific antibodies are able to grow in the presence of fluorescein-toxin-conjugates. KW - Monoclonal antibody KW - Hybridoma technology KW - Selection of antibody producing cells Y1 - 2013 U6 - https://doi.org/10.1016/j.jim.2012.10.010 SN - 0022-1759 VL - 387 IS - 1-2 SP - 167 EP - 172 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Pfestorf, H. A1 - Weiss, L. A1 - Müller, J. A1 - Boch, Steffen A1 - Socher, S. A. A1 - Prati, Daniel A1 - Schöning, Ingo A1 - Weisser, W. A1 - Fischer, M. A1 - Jeltsch, Florian T1 - Community mean traits as additional indicators to monitor effects of land-use intensity On grassland plant diversity JF - Perspectives in plant ecology, evolution and systematics N2 - Semi-natural grasslands, biodiversity hotspots in Central-Europe, suffer from the cessation of traditional land-use. Amount and intensity of these changes challenge current monitoring frameworks typically based on classic indicators such as selected target species or diversity indices. Indicators based on plant functional traits provide an interesting extension since they reflect ecological strategies at individual and ecological processes at community levels. They typically show convergent responses to gradients of land-use intensity over scales and regions, are more directly related to environmental drivers than diversity components themselves and enable detecting directional changes in whole community dynamics. However, probably due to their labor- and cost intensive assessment in the field, they have been rarely applied as indicators so far. Here we suggest overcoming these limitations by calculating indicators with plant traits derived from online accessible databases. Aiming to provide a minimal trait set to monitor effects of land-use intensification on plant diversity we investigated relationships between 12 community mean traits, 2 diversity indices and 6 predictors of land-use intensity within grassland communities of 3 different regions in Germany (part of the German 'Biodiversity Exploratory' research network). By standardization of traits and diversity measures, use of null models and linear mixed models we confirmed (i) strong links between functional community composition and plant diversity, (ii) that traits are closely related to land-use intensity, and (iii) that functional indicators are equally, or even more sensitive to land-use intensity than traditional diversity indices. The deduced trait set consisted of 5 traits, i.e., specific leaf area (SLA), leaf dry matter content (LDMC), seed release height, leaf distribution, and onset of flowering. These database derived traits enable the early detection of changes in community structure indicative for future diversity loss. As an addition to current monitoring measures they allow to better link environmental drivers to processes controlling community dynamics. KW - Biodiversity Exploratories KW - Biological conservation KW - (Semi-natural) Grasslands KW - Plant functional traits KW - Indicators KW - Land-use intensity Y1 - 2013 U6 - https://doi.org/10.1016/j.ppees.2012.10.003 SN - 1433-8319 VL - 15 IS - 1 SP - 1 EP - 11 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Dormann, Carsten F. A1 - Elith, Jane A1 - Bacher, Sven A1 - Buchmann, Carsten M. A1 - Carl, Gudrun A1 - Carre, Gabriel A1 - Garcia Marquez, Jaime R. A1 - Gruber, Bernd A1 - Lafourcade, Bruno A1 - Leitao, Pedro J. A1 - Münkemüller, Tamara A1 - McClean, Colin A1 - Osborne, Patrick E. A1 - Reineking, Bjoern A1 - Schröder-Esselbach, Boris A1 - Skidmore, Andrew K. A1 - Zurell, Damaris A1 - Lautenbach, Sven T1 - Collinearity a review of methods to deal with it and a simulation study evaluating their performance JF - Ecography : pattern and diversity in ecology ; research papers forum N2 - Collinearity refers to the non independence of predictor variables, usually in a regression-type analysis. It is a common feature of any descriptive ecological data set and can be a problem for parameter estimation because it inflates the variance of regression parameters and hence potentially leads to the wrong identification of relevant predictors in a statistical model. Collinearity is a severe problem when a model is trained on data from one region or time, and predicted to another with a different or unknown structure of collinearity. To demonstrate the reach of the problem of collinearity in ecology, we show how relationships among predictors differ between biomes, change over spatial scales and through time. Across disciplines, different approaches to addressing collinearity problems have been developed, ranging from clustering of predictors, threshold-based pre-selection, through latent variable methods, to shrinkage and regularisation. Using simulated data with five predictor-response relationships of increasing complexity and eight levels of collinearity we compared ways to address collinearity with standard multiple regression and machine-learning approaches. We assessed the performance of each approach by testing its impact on prediction to new data. In the extreme, we tested whether the methods were able to identify the true underlying relationship in a training dataset with strong collinearity by evaluating its performance on a test dataset without any collinearity. We found that methods specifically designed for collinearity, such as latent variable methods and tree based models, did not outperform the traditional GLM and threshold-based pre-selection. Our results highlight the value of GLM in combination with penalised methods (particularly ridge) and threshold-based pre-selection when omitted variables are considered in the final interpretation. However, all approaches tested yielded degraded predictions under change in collinearity structure and the folk lore'-thresholds of correlation coefficients between predictor variables of |r| >0.7 was an appropriate indicator for when collinearity begins to severely distort model estimation and subsequent prediction. The use of ecological understanding of the system in pre-analysis variable selection and the choice of the least sensitive statistical approaches reduce the problems of collinearity, but cannot ultimately solve them. Y1 - 2013 U6 - https://doi.org/10.1111/j.1600-0587.2012.07348.x SN - 0906-7590 SN - 1600-0587 VL - 36 IS - 1 SP - 27 EP - 46 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Petrov, Veselin A1 - Schippers, Jos A1 - Benina, Maria A1 - Minkov, Ivan A1 - Müller-Röber, Bernd A1 - Gechev, Tsanko S. T1 - In search for new players of the oxidative stress network by phenotyping an Arabidopsis T-DNA mutant collection on reactive oxygen species-eliciting chemicals JF - Plant omics N2 - The ability of some chemical compounds to cause oxidative stress offers a fast and convenient way to study the responses of plants to reactive oxygen species (ROS). In order to unveil potential novel genetic players of the ROS-regulatory network, a population of similar to 2,000 randomly selected Arabidopsis thaliana T-DNA insertion mutants was screened for ROS sensitivity/resistance by growing seedlings on agar medium supplemented with stress-inducing concentrations of the superoxide-eliciting herbicide methyl viologen or the catalase inhibitor 3-amino-triazole. A semi-robotic setup was used to capture and analyze images of the chemically treated seedlings which helped interpret the screening results by providing quantitative information on seedling area and healthy-to-chlorotic tissue ratios for data verification. A ROS-related phenotype was confirmed in three of the initially selected 33 mutant candidates, which carry T-DNA insertions in genes encoding a Ring/Ubox superfamily protein, ABI5 binding protein 1 (AFP1), previously reported to be involved in ABA signaling, and a protein of unknown function, respectively. In addition, we identified six mutants, most of which have not been described yet, that are related to growth or chloroplast development and show defects in a ROS-independent manner. Thus, semi-automated image capturing and phenotyping applied on publically available T-DNA insertion collections adds a simple means for discovering novel mutants in complex physiological processes and identifying the genes involved. KW - growth KW - image analysis KW - methyl viologen KW - LemnaTec KW - screening KW - superoxide Y1 - 2013 SN - 1836-0661 VL - 6 IS - 1 SP - 46 EP - 54 PB - Southern Cross Publ. CY - Lismore ER - TY - JOUR A1 - Nottebrock, Henning A1 - Esler, Karen J. A1 - Schurr, Frank Martin T1 - Effects of intraspecific and community density on the lifetime fecundity of long-lived shrubs JF - Perspectives in plant ecology, evolution and systematics N2 - Intra- and interspecific density dependence has profound consequences for plant population and community dynamics. In long-lived plants, however, lifetime patterns and mechanisms of density dependence are difficult to study. Here, we examine effects of intraspecific and community density on the lifetime fecundity of two long-lived shrub species from South African Fynbos: Protea repens (animal-pollinated, hermaphroditic) and Leucadendron rubrum (wind-pollinated, dioecious). Both species are serotinous, retaining seeds in cones until fire kills the mother plant. We measured lifetime fecundity as the product of cone number, proportion of cones that are not damaged by predation and seed set (fertile seeds per intact cone). Intraspecific and community densities were quantified by counting individuals of target species and all Proteaceae in small- and large-scale neighbourhoods (10 m and 50 m radius) around each focal individual. Additionally, we determined the age and size of focal individuals. We found that lifetime fecundity of the wind-pollinated L rubrum is density independent. In contrast, the lifetime fecundity of the animal-pollinated P. repens increases with large-scale intraspecific density and shows a hump-shaped relationship to large-scale community density. Community density has a hump-shaped effect on seed set (probably through partial absence of generalized pollinators at low and competition for pollinators at high densities) and negatively affects cone number per individual. For both species, plant age decreases seed set while increasing lifetime fecundity. The qualitative differences in the density dependence of lifetime fecundity may arise from differences between animal and wind pollination. In particular, interactions with generalized animal pollinators may cause community-level Allee effects with profound consequences for the future dynamics of long-lived plant populations and communities. KW - Competition KW - Community-level Allee effects KW - Facilitation KW - Fitness components KW - Interspecific interactions KW - Plant-animal interactions Y1 - 2013 U6 - https://doi.org/10.1016/j.ppees.2013.03.003 SN - 1433-8319 VL - 15 IS - 3 SP - 150 EP - 161 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Liang, Wei A1 - Heinrich, Ingo A1 - Helle, Gerhard A1 - Linan, Isabel Dorado A1 - Heinken, Thilo T1 - Applying CLSM to increment core surfaces for histometric analyses a novel advance in quantitative wood anatomy JF - Dendrochronologia : an interdisciplinary journal of tree-ring science N2 - A novel procedure has been developed to conduct cell structure measurements on increment core samples of conifers. The procedure combines readily available hardware and software equipment. The essential part of the procedure is the application of a confocal laser scanning microscope (CLSM) which captures images directly from increment cores surfaced with the advanced WSL core-microtome. Cell wall and lumen are displayed with a strong contrast due to the monochrome black and green nature of the images. Consecutive images are merged into long images representing entire increment cores which are then analysed for cell structures in suitable software. KW - Wood anatomy KW - Cell structures KW - Confocal laser scanning microscopy KW - CLSM KW - Dendrochronology KW - Surface preparation Y1 - 2013 U6 - https://doi.org/10.1016/j.dendro.2012.09.002 SN - 1125-7865 VL - 31 IS - 2 SP - 140 EP - 145 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Solly, Emily A1 - Schöning, Ingo A1 - Boch, Steffen A1 - Mueller, J. A1 - Socher, S. A. A1 - Trumbore, S. E. A1 - Schrumpf, M. T1 - Mean age of carbon in fine roots from temperate forests and grasslands with different management JF - Biogeosciences N2 - Fine roots are the most dynamic portion of a plant's root system and a major source of soil organic matter. By altering plant species diversity and composition, soil conditions and nutrient availability, and consequently belowground allocation and dynamics of root carbon (C) inputs, land-use and management changes may influence organic C storage in terrestrial ecosystems. In three German regions, we measured fine root radiocarbon (C-14) content to estimate the mean time since C in root tissues was fixed from the atmosphere in 54 grassland and forest plots with different management and soil conditions. Although root biomass was on average greater in grasslands 5.1 +/- 0.8 g (mean +/- SE, n = 27) than in forests 3.1 +/- 0.5 g (n = 27) (p < 0.05), the mean age of C in fine roots in forests averaged 11.3 +/- 1.8 yr and was older and more variable compared to grasslands 1.7 +/- 0.4 yr (p < 0.001). We further found that management affects the mean age of fine root C in temperate grasslands mediated by changes in plant species diversity and composition. Fine root mean C age is positively correlated with plant diversity (r = 0.65) and with the number of perennial species (r = 0.77). Fine root mean C age in grasslands was also affected by study region with averages of 0.7 +/- 0.1 yr (n= 9) on mostly organic soils in northern Germany and of 1.8 +/- 0.3 yr (n = 9) and 2.6 +/- 0.3 (n = 9) in central and southern Germany (p < 0.05). This was probably due to differences in soil nutrient contents and soil moisture conditions between study regions, which affected plant species diversity and the presence of perennial species. Our results indicate more long-lived roots or internal redistribution of C in perennial species and suggest linkages between fine root C age and management in grasslands. These findings improve our ability to predict and model belowground C fluxes across broader spatial scales. Y1 - 2013 U6 - https://doi.org/10.5194/bg-10-4833-2013 SN - 1726-4170 VL - 10 IS - 7 SP - 4833 EP - 4843 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - Sultanow, Eldar A1 - Weber, Edzard T1 - Pharmataxigraphie Model of a Hybrid System of RFID Technology and optical Methods JF - Die pharmazeutische Industrie Y1 - 2013 SN - 0031-711X VL - 75 IS - 7 SP - 1197 EP - + PB - Editio-Cantor-Verl. für Medizin und Naturwiss. CY - Aulendorf ER - TY - JOUR A1 - Girstmair, Hannah A1 - Saffert, Paul A1 - Rode, Sascha A1 - Czech, Andreas A1 - Holland, Gudrun A1 - Bannert, Norbert A1 - Ignatova, Zoya T1 - Depletion of Cognate Charged Transfer RNA Causes Translational Frameshifting within the Expanded CAG Stretch in Huntingtin JF - Cell reports N2 - Huntington disease (HD), a dominantly inherited neurodegenerative disorder caused by the expansion of a CAG-encoded polyglutamine (polyQ) repeat in huntingtin (Htt), displays a highly heterogeneous etiopathology and disease onset. Here, we show that the translation of expanded CAG repeats in mutant Htt exon 1 leads to a depletion of charged glutaminyl-transfer RNA (tRNA) Gln-CUG that pairs exclusively to the CAG codon. This results in translational frameshifting and the generation of various transframe-encoded species that differently modulate the conformational switch to nucleate fibrillization of the parental polyQ protein. Intriguingly, the frameshifting frequency varies strongly among different cell lines and is higher in cells with intrinsically lower concentrations of tRNA Gln-CUG. The concentration of tRNA Gln-CUG also differs among different brain areas in the mouse. We propose that translational frameshifting may act as a significant disease modifier that contributes to the cell-selective neurotoxicity and disease course heterogeneity of HD on both cellular and individual levels. Y1 - 2013 U6 - https://doi.org/10.1016/j.celrep.2012.12.019 SN - 2211-1247 VL - 3 IS - 1 SP - 148 EP - 159 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Heinken, Thilo A1 - Weber, Ewald T1 - Consequences of habitat fragmentation for plant species do we know enough? JF - Perspectives in plant ecology, evolution and systematics N2 - Habitat fragmentation is one of the most important causes for the decline of plant species. However, plants differing in phylogeny, habitat requirements and biology are likely to respond differently to habitat fragmentation. We ask whether case studies on the effects of habitat fragmentation conducted so far allow generalizations about its effects on the fitness and genetic diversity of populations of endangered plant species. We compared the characteristics of plant species endangered in Germany whose sensitivity to habitat fragmentation had been studied with those of the endangered species that had not been studied. We found strong discrepancies between the two groups with regard to their taxonomy and traits relevant to their sensitivity to habitat fragmentation. Monocots, graminoids, clonal, abiotically pollinated and self compatible species were underrepresented among the studied species, and most study species were from a few habitat types, in particular grasslands. We conclude that our current knowledge of the effects of habitat fragmentation on plant populations is not sufficient to provide widely applicable guidelines for species management. The selection of species studied so far has been biased toward species from certain habitats and species exhibiting traits that probably make them vulnerable to habitat fragmentation. Future studies should include community-wide approaches in different habitats, e.g. re-visitation studies in which the species pool is assessed at different time intervals, and population-biological studies of species from a wide range of habitats, and of different life forms and growth strategies. A more representative picture of the effects of habitat fragmentation would allow a better assessment of threats and more specific recommendations for optimally managing populations of endangered plants. KW - CSR-strategies KW - Naturally rare species KW - Plant conservation KW - Recently rare species KW - Species traits KW - Taxonomic position Y1 - 2013 U6 - https://doi.org/10.1016/j.ppees.2013.05.003 SN - 1433-8319 VL - 15 IS - 4 SP - 205 EP - 216 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Schrade, Lisa A1 - Scheffler, Christiane T1 - Assessing the applicability of the digital laser rangefinder GLM Professional (R) Bosch 250 VF for anthropometric field studies JF - Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft für Anthropologie N2 - The digital laser rangefinder GLM Professional (R) BOSCH 250 VF was tested as a modified preproduction model with regard to its applicability of quantifying humans' height. The aim of this investigation was to determine and evaluate the instrument's precision, as well as its manageability within anthropometric field studies. Data collected by the digital laser rangefinder did not show a significant difference to data of control by an anthropometer. Furthermore, more than 96% of the difference values are located within area of agreement. Nevertheless, the GLM Professional (R) is a highly sensitive instrument and mean SD within threefold data acquisition is twice as high as SD resulting from data collection by an anthropometer. However, due to the minimal percentage differences within data acquisition and compared to the standard method, the GLM Professional (R) is proved to be a reliable instrument and to be highly applicable for anthropometric field studies. Furthermore, due to its excellent manageability and compact size, the GLM Professional (R) shows a very good applicability even for less trained anthropometrists and thus ameliorates the possibilities of collecting reliable data within anthropometric field studies. KW - anthropometric field studies KW - height KW - measuring instrument KW - digital laser range finder Y1 - 2013 U6 - https://doi.org/10.1127/0003-5548/2013/0223 SN - 0003-5548 VL - 70 IS - 2 SP - 137 EP - 145 PB - Schweizerbart CY - Stuttgart ER - TY - JOUR A1 - Feger, Martina A1 - Fajol, Abul A1 - Lebedeva, Aleksandra A1 - Meissner, Adrian A1 - Michael, Diana A1 - Völkl, Jakob A1 - Alesutan, Ioana A1 - Schleicher, Erwin A1 - Reichetzeder, Christoph A1 - Hocher, Berthold A1 - Qadri, Syed M. A1 - Lang, Florian T1 - Effect of Carbon Monoxide Donor CORM-2 on Vitamin D-3 Metabolism JF - Kidney & blood pressure research : official organ of the Gesellschaft für Nephrologie N2 - Background/Aims: Carbon monoxide (CO) interferes with cytochrome-dependent cellular functions and acts as gaseous transmitter. CO is released from CO-releasing molecules (CORM) including tricarbonyl-dichlororuthenium (II) dimer (CORM-2), molecules considered for the treatment of several disorders including vascular dysfunction, inflammation, tissue ischemia and organ rejection. Cytochrome P450-sensitive function include formation of 1,25-dihydroxyvitamin D-3 (1,25(OH)(2)D-3) by renal 25-hydroxyvitamin D-3 1-alpha-hydroxylase (Cyp27b1). The enzyme is regulated by PTH, FGF23 and klotho. 1,25(OH)(2)D-3 regulates Ca2+ and phosphate transport as well as klotho expression. The present study explored, whether CORM-2 influences 1,25(OH)(2)D-3 formation and klotho expression. Methods: Mice were treated with intravenous CORM-2 (20 mg/kg body weight). Plasma 1,25(OH)(2)D-3 and FGF23 concentrations were determined by ELISA, phosphate, calcium and creatinine concentrations by colorimetric methods, transcript levels by quantitative RT-PCR and protein expression by western blotting. Fgf23 mRNA transcript levels were further determined in rat osteosarcoma UMR106 cells without or with prior treatment for 24 hours with 20 mu M CORM-2. Results: CORM-2 injection within 24 hours significantly increased FGF23 plasma levels and decreased 1,25(OH)(2)D-3 plasma levels, renal Cyp27b1 gene expression as well as renal klotho protein abundance and transcript levels. Moreover, treatment of UMR106 cells with CORM-2 significantly increased Fgf23 transcript levels. Conclusion: CO-releasing molecule CORM-2 enhances FGF23 expression and release and decreases klotho expression and 1,25(OH)(2)D-3 synthesis. KW - CORM-2 KW - 1,25-Dihydroxyvitamin D-3 KW - Klotho KW - FGF23 KW - Phosphate KW - Calcium Y1 - 2013 U6 - https://doi.org/10.1159/000355730 SN - 1420-4096 SN - 1423-0143 VL - 37 IS - 4-5 SP - 496 EP - 505 PB - Karger CY - Basel ER - TY - JOUR A1 - Hocher, Berthold A1 - Oberthür, Dominik A1 - Slowinski, Torsten A1 - Querfeld, Uwe A1 - Schäfer, Franz A1 - Doyon, Anke A1 - Tepel, Martin A1 - Roth, Heinz J. A1 - Grön, Hans J. A1 - Reichetzeder, Christoph A1 - Betzel, Christian A1 - Armbruster, Franz Paul T1 - Modeling of Oxidized PTH (oxPTH) and Non-oxidized PTH (n-oxPTH) Receptor Binding and Relationship of Oxidized to Non-Oxidized PTH in Children with Chronic Renal Failure, Adult Patients on Hemodialysis and Kidney Transplant Recipients JF - Kidney & blood pressure research : official organ of the Gesellschaft für Nephrologie N2 - Background: The biological properties of oxidized and non-oxidized PTH are substantially different. Oxidized PTH (oxPTH) loses its PTH receptor-stimulating properties, whereas non-oxidized PTH (n-oxPTH) is a full agonist of the receptor. This was described in more than 20 well published studies in the 1970(s) and 80(s). However, PTH oxidation has been ignored during the development of PTH assays for clinical use so far. Even the nowadays used third generation assay systems do not consider oxidation of PTH. We recently developed an assay to differentiate between oxPTH and n-oxPTH. In the current study we established normal values for this assay system. Furthermore, we compare the ratio of oxPTH to n-oxPTH in different population with chronic renal failure: 620 children with renal failure stage 2-4 of the 4C study, 342 adult patients on dialysis, and 602 kidney transplant recipients. In addition, we performed modeling of the interaction of either oxPTH or n-oxPTH with the PTH receptor using biophysical structure approaches. Results: The children had the highest mean as well as maximum n-oxPTH concentrations as compared to adult patients (both patients on dialysis as well as kidney transplant recipients). The relationship between oxPTH and n-oxPTH of individual patients varied substantially in all three populations with renal impairment. The analysis of n-oxPTH in 89 healthy control subjects revealed that n-oxPTH concentrations in patient with renal failure were higher as compared to healthy adult controls (2.25-fold in children with renal failure, 1.53-fold in adult patients on dialysis, and 1.56-fold in kidney transplant recipients, respectively). Computer assisted biophysical structure modeling demonstrated, however, minor sterical- and/or electrostatic changes in oxPTH and n-oxPTH. This indicated that PTH oxidation may induce refolding of PTH and hence alters PTH-PTH receptor interaction via oxidation induced three-dimensional structure alteration of PTH. Conclusion: A huge proportion of circulating PTH measured by current state-of-the-art assay systems is oxidized and thus not biologically active. The relationship between oxPTH and n-oxPTH of individual patients varied substantially. Non-oxidized PTH concentrations are 1.5 - 2.25 fold higher in patients with renal failure as compared to health controls. Measurements of n-oxPTH may reflect the hormone status more precise. The iPTH measures describes most likely oxidative stress in patients with renal failure rather than the PTH hormone status. This, however, needs to be demonstrated in further clinical studies. KW - n-oxPTH KW - Chronic Renal Failure KW - Kidney Transplantation KW - Hemodialysis KW - Oxidation KW - PTH KW - Chronic Renal Failure in Children Y1 - 2013 U6 - https://doi.org/10.1159/000350149 SN - 1420-4096 SN - 1423-0143 VL - 37 IS - 4-5 SP - 240 EP - 251 PB - Karger CY - Basel ER - TY - JOUR A1 - Burgold, Julia A1 - Rolfes, Manfred T1 - Of voyeuristic safari tours and responsible tourism with educational value observing moral communication in slum and township tourism in Cape Town and Mumbai JF - Die Erde : journal of the Geographical Society of Berlin ; Zeitschrift der Gesellschaft für Erdkunde zu Berlin N2 - Sightseeing in the poorest quarters of southern hemisphere cities has been observed occurring in Cape Town, Rio de Janeiro, Mumbai and many other cities. The increasing global interest in touring poor urban environments is accompanied by a strong morally charged debate; so far, this debate has not been critically addressed. This article avoids asking if slum tourism is good or bad, but instead seeks a second-order observation, i.e. to investigate under what conditions the social praxis of slum tourism is considered as good or bad, by processing information on esteem or dis-esteem among tourists and tour providers. Special attention is given to any relation between morality and place, and the thesis posited is that the moral charging of slum tourism is dependent on the presence of specific preconceived notions of slums and poverty. This shall be clarified by means of references to two empirical case studies carried out in (1) Cape Town in 2007 and 2008 and (2) Mumbai in 2009. KW - Slum tourism KW - township tourism KW - morality KW - place Y1 - 2013 SN - 0013-9998 VL - 144 IS - 2 SP - 161 EP - 174 PB - Gesellschaft für Erdkunde CY - Berlin ER - TY - JOUR A1 - Wang, Jing A1 - Fritzsch, Claire A1 - Bernarding, Johannes A1 - Krause, Thomas A1 - Mauritz, Karl-Heinz A1 - Brunetti, Maddalena A1 - Dohle, Christian T1 - Cerebral activation evoked by the mirror illusion of the hand in stroke patients compared to normal subjects JF - Neurorehabilitation : an interdisciplinary journal N2 - BACKGROUND: Mirror therapy (MT) was found to improve motor function after stroke, but its neural mechanisms remain unclear, especially in single stroke patients. OBJECTIVES: The following imaging study was designed to compare brain activation patterns evoked by the mirror illusion in single stroke patients with normal subjects. METHODS: Fifteen normal volunteers and five stroke patients with severe arm paresis were recruited. Cerebral activations during movement mirroring by means of a video chain were recorded with functional magnetic resonance imaging (fMRI). Single-subject analysis was performed using SPM 8. RESULTS: For normal subjects, ten and thirteen subjects displayed lateralized cerebral activations evoked by the mirror illusion while moving their right and left hand respectively. The magnitude of this effect in the precuneus contralateral to the seen hand was not dependent on movement speed or subjective experience. Negative correlation of activation strength with age was found for the right hand only. The activation pattern in stroke patients is comparable to that of normal subjects and present in four out of five patients. CONCLUSIONS: In summary, the mirror illusion can elicit cerebral activation contralateral to the perceived hand in the majority of single normal subjects, but not in all of them. This is similar even in stroke patients with severe hemiparesis. KW - Movement KW - mirror illusion KW - imaging KW - mirror therapy KW - stroke Y1 - 2013 U6 - https://doi.org/10.3233/NRE-130999 SN - 1053-8135 SN - 1878-6448 VL - 33 IS - 4 SP - 593 EP - 603 PB - IOS Press CY - Amsterdam ER - TY - JOUR A1 - May, Felix A1 - Giladi, Itamar A1 - Ristow, Michael A1 - Ziv, Yaron A1 - Jeltsch, Florian T1 - Plant functional traits and community assembly along interacting gradients of productivity and fragmentation JF - Perspectives in plant ecology, evolution and systematics N2 - Quantifying the association of plant functional traits to environmental gradients is a promising approach for understanding and projecting community responses to land use and climatic changes. Although habitat fragmentation and climate are expected to affect plant communities interactively, there is a lack of empirical studies addressing trait associations to fragmentation in different climatic regimes. In this study, we analyse data on the key functional traits: specific leaf area (SLA), plant height, seed mass and seed number. First, we assess the evidence for the community assembly mechanisms habitat filtering and competition at different spatial scales, using several null-models and a comprehensive set of community-level trait convergence and divergence indices. Second, we analyse the association of community-mean traits with patch area and connectivity along a south-north productivity gradient. We found clear evidence for trait convergence due to habitat filtering. In contrast, the evidence for trait divergence due to competition fundamentally depended on the null-model used. When the null-model controlled for habitat filtering, there was only evidence for trait divergence at the smallest sampling scale (0.25 m x 0.25 m). All traits varied significantly along the S-N productivity gradient. While plant height and SLA were consistently associated with fragmentation, the association of seed mass and seed number with fragmentation changed along the S-N gradient. Our findings indicate trait convergence due to drought stress in the arid sites and due to higher productivity in the mesic sites. The association of plant traits to fragmentation is likely driven by increased colonization ability in small and/or isolated patches (plant height, seed number) or increased persistence ability in isolated patches (seed mass). Our study provides the first empirical test of trait associations with fragmentation along a productivity gradient. We conclude that it is crucial to study the interactive effects of different ecological drivers on plant functional traits. KW - Connectivity KW - Drought-stress KW - Habitat filtering KW - Limiting similarity KW - Null models KW - Plant height KW - Seed mass KW - Seed number KW - Specific leaf area (SLA) Y1 - 2013 U6 - https://doi.org/10.1016/j.ppees.2013.08.002 SN - 1433-8319 VL - 15 IS - 6 SP - 304 EP - 318 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Rüder, Constantin A1 - Sauter, Tilman A1 - Kratz, Karl A1 - Haase, Tobias A1 - Peter, Jan A1 - Jung, Friedrich A1 - Lendlein, Andreas A1 - Zohlnhöfer, Dietlind T1 - Influence of fibre diameter and orientation of electrospun copolyetheresterurethanes on smooth muscle and endothelial cell behaviour JF - Clinical hemorheology and microcirculation : blood flow and vessels N2 - Polymers exhibiting cell-selective effects represent an extensive research field with high relevance for biomedical applications e.g. in the cardiovascular field supporting re-endothelialization while suppressing smooth muscle cell overgrowth. Such an endothelial cell-selective effect could be recently demonstrated for a copolyetheresterurethane (PDC) containing biodegradable poly(p-dioxanone) and poly(epsilon-caprolactone) segments, which selectively enhanced the adhesion of human umbilical vein endothelial cells (HUVEC) while suppressing the attachment of smooth muscle cells (SMC). In this study we investigated the influence of the fibre orientation (random and aligned) and fibre diameter (2 mu m and 500 nm) of electrospun PDC scaffolds on the adhesion, proliferation and apoptosis of HUVEC and SMC. Adhesion, viability and proliferation of HUVEC was diminished when the fibre diameter was reduced to a submicron scale, while the orientation of the microfibres did only slightly influence the cellular behaviour. In contrast, a submicron fibre diameter improved SMC viability. In conclusion, PDC scaffolds with micron-sized single fibres could be promising candidate materials for cell-selective stent coatings. KW - Endothelialization KW - drug eluting stent KW - degradable polymer KW - electrospinning KW - cell selectivity Y1 - 2013 U6 - https://doi.org/10.3233/CH-131787 SN - 1386-0291 SN - 1875-8622 VL - 55 IS - 4 SP - 513 EP - 522 PB - IOS Press CY - Amsterdam ER - TY - JOUR A1 - Drygala, Frank A1 - Werner, Ulrike A1 - Zoller, Hinrich T1 - Diet composition of the invasive raccoon dog (Nyctereutes procyonoides) and the native red fox (Vulpes vulpes) in north-east Germany JF - Hystrix : the Italian journal of mammalogy N2 - Invasive alien species pose a great threat to the integrity of natural communities by competition with and predation on native species. In Germany the invasive raccoon dog (Nyctereutes procyonoides) and the native red fox (Vulpes vulpes) occupy a similar ecological niche. Therefore, the aim of our study was to discover the extent of exploitative diet competition between these two generalist carnivores. Carcasses of red foxes (n=256) and raccoon dogs (n=253) were collected throughout Mecklenburg Western-Pomerania (north-east Germany) and stomachs contains were analysed. Frequency of occurrence and biomass share indicate that both canids are omnivorous and pursue opportunistic feeding strategies. Small mammals and edible plant material were the most important food resources for red foxes and raccoon dogs. Nonetheless, interspecies differences were recorded for edible plant material, small mammals and insects. While red foxes mostly feed on voles, raccoon dogs consumed mice and shrews as often as voles. Only raccoon dogs preyed on amphibians. There were no differences in carrion consumption, both species scavenged on wild boar and we found clear competition for carrion year-round. Moreover, there was evidence that two red foxes foraged on raccoon dogs and vice versa. The mean annual interspecies diet overlap index was relatively high. The diets determined for raccoon dogs and red foxes were quite similar and a similar food niche breadth was recorded. However, only minor competition is assumed to take place since differences in feeding habits do exist. KW - Nyctereutes procyonoides KW - Vulpes vulpes KW - invasive species KW - diet competition KW - feeding strategies Y1 - 2013 U6 - https://doi.org/10.4404/hystrix.-24.2-8867 SN - 0394-1914 SN - 1825-5272 VL - 24 IS - 2 SP - 190 EP - 194 PB - Associazione Teriologica Romana CY - Roma ER - TY - JOUR A1 - Mahler, B. A1 - Schneider, A. R. R. A1 - Di Giacomo, A. S. A1 - Di Giacomo, A. G. A1 - Reboreda, Juan C. A1 - Tiedemann, Ralph T1 - Microsatellite usefulness is independent of phylogenetic distance in Tyrant flycatchers (Aves: Tyrannidae) - a test using two globally threatened species JF - Genetics and molecular research N2 - Tyrant flycatchers (Aves: Tyrannidae) are endemic to the New World, and many species of this group are threatened or near-threatened at the global level. The aim of this study was to test the 18 microsatellite markers that have been published for other Tyrant flycatchers in the Strange-tailed Tyrant (Alectrurus risora) and the Sharp-tailed Tyrant (Culicivora caudacuta), two endemic species of southern South American grasslands that are classified as vulnerable. We also analyzed the usefulness of loci in relation to phylogenetic distance to the source species. Amplification success was high in both species (77 to 83%) and did not differ between the more closely and more distantly related species to the source species. Polymorphism success was also similar for both species, with 9 and 8 loci being polymorphic, respectively. An increased phylogenetic distance thus does not gradually lead to allelic or locus dropouts, implying that in Tyrant flycatchers, the published loci are useful independent of species relatedness. KW - Alectrurus risora KW - Culicivora caudacuta KW - Microsatellites KW - Tyrannidae Y1 - 2013 U6 - https://doi.org/10.4238/2013.August.12.12 SN - 1676-5680 VL - 12 IS - 3 SP - 2966 EP - 2972 PB - FUNPEC CY - Ribeirao Preto ER - TY - JOUR A1 - von der Lippe, Moritz A1 - Bullock, James M. A1 - Kowarik, Ingo A1 - Knopp, Tatjana A1 - Wichmann, Matthias T1 - Human-mediated dispersal of seeds by the airflow of vehicles JF - PLoS one N2 - Human-mediated dispersal is known as an important driver of long-distance dispersal for plants but underlying mechanisms have rarely been assessed. Road corridors function as routes of secondary dispersal for many plant species but the extent to which vehicles support this process remains unclear. In this paper we quantify dispersal distances and seed deposition of plant species moved over the ground by the slipstream of passing cars. We exposed marked seeds of four species on a section of road and drove a car along the road at a speed of 48 km/h. By tracking seeds we quantified movement parallel as well as lateral to the road, resulting dispersal kernels, and the effect of repeated vehicle passes. Median distances travelled by seeds along the road were about eight meters for species with wind dispersal morphologies and one meter for species without such adaptations. Airflow created by the car lifted seeds and resulted in longitudinal dispersal. Single seeds reached our maximum measuring distance of 45 m and for some species exceeded distances under primary dispersal. Mathematical models were fit to dispersal kernels. The incremental effect of passing vehicles on longitudinal dispersal decreased with increasing number of passes as seeds accumulated at road verges. We conclude that dispersal by vehicle airflow facilitates seed movement along roads and accumulation of seeds in roadside habitats. Dispersal by vehicle airflow can aid the spread of plant species and thus has wide implications for roadside ecology, invasion biology and nature conservation. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0052733 SN - 1932-6203 VL - 8 IS - 1 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Liu, Chun A1 - Sibly, Richard M. A1 - Grimm, Volker A1 - Thorbek, Pernille T1 - Linking pesticide exposure and spatial dynamics an individual-based model of wood mouse (Apodemus sylvaticus) populations in agricultural landscapes JF - Ecological modelling : international journal on ecological modelling and engineering and systems ecolog N2 - The wood mouse is a common and abundant species in agricultural landscape and is a focal species in pesticide risk assessment. Empirical studies on the ecology of the wood mouse have provided sufficient information for the species to be modelled mechanistically. An individual-based model was constructed to explicitly represent the locations and movement patterns of individual mice. This together with the schedule of pesticide application allows prediction of the risk to the population from pesticide exposure. The model included life-history traits of wood mice as well as typical landscape dynamics in agricultural farmland in the UK. The model obtains a good fit to the available population data and is fit for risk assessment purposes. It can help identify spatio-temporal situations with the largest potential risk of exposure and enables extrapolation from individual-level endpoints to population-level effects. Largest risk of exposure to pesticides was found when good crop growth in the "sink" fields coincided with high "source" population densities in the hedgerows. KW - Population dynamics KW - Pesticides KW - Ecological risk assessment KW - Habitat choice KW - Agent-based model KW - NetLogo Y1 - 2013 U6 - https://doi.org/10.1016/j.ecolmodel.2012.09.016 SN - 0304-3800 VL - 248 IS - 2 SP - 92 EP - 102 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Neigenfind, Jost A1 - Grimbs, Sergio A1 - Nikoloski, Zoran T1 - On the relation between reactions and complexes of (bio)chemical reaction networks JF - Journal of theoretical biology N2 - Robustness of biochemical systems has become one of the central questions in systems biology although it is notoriously difficult to formally capture its multifaceted nature. Maintenance of normal system function depends not only on the stoichiometry of the underlying interrelated components, but also on the multitude of kinetic parameters. Invariant flux ratios, obtained within flux coupling analysis, as well as invariant complex ratios, derived within chemical reaction network theory, can characterize robust properties of a system at steady state. However, the existing formalisms for the description of these invariants do not provide full characterization as they either only focus on the flux-centric or the concentration-centric view. Here we develop a novel mathematical framework which combines both views and thereby overcomes the limitations of the classical methodologies. Our unified framework will be helpful in analyzing biologically important system properties. KW - Metabolic network KW - Mass action system KW - Flux coupling analysis KW - Chemical reaction network theory Y1 - 2013 U6 - https://doi.org/10.1016/j.jtbi.2012.10.016 SN - 0022-5193 VL - 317 IS - 2 SP - 359 EP - 365 PB - Elsevier CY - London ER - TY - JOUR A1 - Klingstrom, Tomas A1 - Soldatova, Larissa A1 - Stevens, Robert A1 - Roos, T. Erik A1 - Swertz, Morris A. A1 - Müller, Kristian M. A1 - Kalas, Matus A1 - Lambrix, Patrick A1 - Taussig, Michael J. A1 - Litton, Jan-Eric A1 - Landegren, Ulf A1 - Bongcam-Rudloff, Erik T1 - Workshop on laboratory protocol standards for the molecular methods database JF - New biotechnology N2 - Management of data to produce scientific knowledge is a key challenge for biological research in the 21st century. Emerging high-throughput technologies allow life science researchers to produce big data at speeds and in amounts that were unthinkable just a few years ago. This places high demands on all aspects of the workflow: from data capture (including the experimental constraints of the experiment), analysis and preservation, to peer-reviewed publication of results. Failure to recognise the issues at each level can lead to serious conflicts and mistakes; research may then be compromised as a result of the publication of non-coherent protocols, or the misinterpretation of published data. In this report, we present the results from a workshop that was organised to create an ontological data-modelling framework for Laboratory Protocol Standards for the Molecular Methods Database (MolMeth). The workshop provided a set of short- and long-term goals for the MolMeth database, the most important being the decision to use the established EXACT description of biomedical ontologies as a starting point. Y1 - 2013 U6 - https://doi.org/10.1016/j.nbt.2012.05.019 SN - 1871-6784 VL - 30 IS - 2 SP - 109 EP - 113 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Gechev, Tsanko S. A1 - Benina, Maria A1 - Obata, Toshihiro A1 - Tohge, Takayuki A1 - Neerakkal, Sujeeth A1 - Minkov, Ivan A1 - Hille, Jacques A1 - Temanni, Mohamed-Ramzi A1 - Marriott, Andrew S. A1 - Bergström, Ed A1 - Thomas-Oates, Jane A1 - Antonio, Carla A1 - Müller-Röber, Bernd A1 - Schippers, Jos H. M. A1 - Fernie, Alisdair R. A1 - Toneva, Valentina T1 - Molecular mechanisms of desiccation tolerance in the resurrection glacial relic Haberlea rhodopensis JF - Cellular and molecular life sciences N2 - Haberlea rhodopensis is a resurrection plant with remarkable tolerance to desiccation. Haberlea exposed to drought stress, desiccation, and subsequent rehydration showed no signs of damage or severe oxidative stress compared to untreated control plants. Transcriptome analysis by next-generation sequencing revealed a drought-induced reprogramming, which redirected resources from growth towards cell protection. Repression of photosynthetic and growth-related genes during water deficiency was concomitant with induction of transcription factors (members of the NAC, NF-YA, MADS box, HSF, GRAS, and WRKY families) presumably acting as master switches of the genetic reprogramming, as well as with an upregulation of genes related to sugar metabolism, signaling, and genes encoding early light-inducible (ELIP), late embryogenesis abundant (LEA), and heat shock (HSP) proteins. At the same time, genes encoding other LEA, HSP, and stress protective proteins were constitutively expressed at high levels even in unstressed controls. Genes normally involved in tolerance to salinity, chilling, and pathogens were also highly induced, suggesting a possible cross-tolerance against a number of abiotic and biotic stress factors. A notable percentage of the genes highly regulated in dehydration and subsequent rehydration were novel, with no sequence homology to genes from other plant genomes. Additionally, an extensive antioxidant gene network was identified with several gene families possessing a greater number of antioxidant genes than most other species with sequenced genomes. Two of the transcripts most abundant during all conditions encoded catalases and five more catalases were induced in water-deficient samples. Using the pharmacological inhibitor 3-aminotriazole (AT) to compromise catalase activity resulted in increased sensitivity to desiccation. Metabolome analysis by GC or LC-MS revealed accumulation of sucrose, verbascose, spermidine, and gamma-aminobutyric acid during drought, as well as particular secondary metabolites accumulating during rehydration. This observation, together with the complex antioxidant system and the constitutive expression of stress protective genes suggests that both constitutive and inducible mechanisms contribute to the extreme desiccation tolerance of H. rhodopensis. KW - Antioxidant genes KW - Catalase KW - Desiccation tolerance KW - Drought stress KW - Metabolome analysis KW - Resurrection plants Y1 - 2013 U6 - https://doi.org/10.1007/s00018-012-1155-6 SN - 1420-682X VL - 70 IS - 4 SP - 689 EP - 709 PB - Springer CY - Basel ER - TY - JOUR A1 - Seifan, Merav A1 - Seifan, Tal A1 - Schiffers, Katja A1 - Jeltsch, Florian A1 - Tielboerger, Katja T1 - Beyond the competition-colonization trade-off - linking multiple trait response to disturbance characteristics JF - The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences N2 - Disturbances' role in shaping communities is well documented but highly disputed. We suggest replacing the overused two-trait trade-off approach with a functional group scheme, constructed from combinations of four key traits that represent four classes of species' responses to disturbances. Using model results and field observations from sites affected by two highly different disturbances, we demonstrated that popular dichotomous trade-offs are not sufficient to explain community dynamics, even if some emerge under certain conditions. Without disturbances, competition was only sufficient to predict species survival but not relative success, which required some escape mechanism (e.g., long-term dormancy). With highly predictable and large-scale disturbances, successful species showed a combination of high individual tolerance to disturbance and, more surprisingly, high competitive ability. When disturbances were less predictable, high individual tolerance and long-term seed dormancy were favored, due to higher environmental uncertainty. Our study demonstrates that theories relying on a small number of predefined trade-offs among traits (e.g., competition-colonization trade-off) may lead to unrealistic results. We suggest that the understanding of disturbance-community relationships can be significantly improved by employing sets of relevant trait assemblies instead of the currently common approach in which trade-offs are assumed in advance. KW - competition resistance trade-off KW - functional types KW - intermediate disturbance hypothesis KW - plant communities KW - species assemblies Y1 - 2013 U6 - https://doi.org/10.1086/668844 SN - 0003-0147 VL - 181 IS - 2 SP - 151 EP - 160 PB - Univ. of Chicago Press CY - Chicago ER - TY - JOUR A1 - Milinkovitch, Michel C. A1 - Kanitz, Ricardo A1 - Tiedemann, Ralph A1 - Tapia, Washington A1 - Llerena, Fausto A1 - Caccone, Adalgisa A1 - Gibbs, James P. A1 - Powell, Jeffrey R. T1 - Recovery of a nearly extinct Galapagos tortoise despite minimal genetic variation JF - Evolutionary applications N2 - A species of Galapagos tortoise endemic to Espanola Island was reduced to just 12 females and three males that have been bred in captivity since 1971 and have produced over 1700 offspring now repatriated to the island. Our molecular genetic analyses of juveniles repatriated to and surviving on the island indicate that none of the tortoises sampled in 1994 had hatched on the island versus 3% in 2004 and 24% in 2007, which demonstrates substantial and increasing reproduction in situ once again. This recovery occurred despite the parental population having an estimated effective population size <8 due to a combination of unequal reproductive success of the breeders and nonrandom mating in captivity. These results provide guidelines for adapting breeding regimes in the parental captive population and decreasing inbreeding in the repatriated population. Using simple morphological data scored on the sampled animals, we also show that a strongly heterogeneous distribution of tortoise sizes on Espanola Island observed today is due to a large variance in the number of animals included in yearly repatriation events performed in the last 40years. Our study reveals that, at least in the short run, some endangered species can recover dramatically despite a lack of genetic variation and irregular repatriation efforts. KW - captive populations KW - conservation biology KW - conservation genetics Y1 - 2013 U6 - https://doi.org/10.1111/eva.12014 SN - 1752-4571 VL - 6 IS - 2 SP - 377 EP - 383 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Fechner, Lennart A1 - Baumann, Otto A1 - Walz, Bernd T1 - Activation of the cyclic AMP pathway promotes serotonin-induced Ca2+ oscillations in salivary glands of the blowfly Calliphora vicina JF - Cell calcium N2 - Ca2+ and cAMP signalling pathways interact in a complex manner at multiple sites. This crosstalk fine-tunes the spatiotemporal patterns of Ca2+ and cAMP signals. In salivary glands of the blowfly Calliphora vicina fluid secretion is stimulated by serotonin (5-hydroxytryptamine, 5-HT) via activation of two different 5-HT receptors coupled to the InsP(3)/Ca2+ (Cv5-HT2 alpha) or the cAMP pathway (Cv5-HT7), respectively. We have shown recently in permeabilized gland cells that cAMP sensitizes InsP(3)-induced Ca2+ release to InsP(3). Here we study the effects of the CAMP signalling pathway on 5-HT-induced oscillations in transepithelial potential (TEP) and in intracellular [Ca2+]. We show: (1) Blocking the activation of the cAMP pathway by cinanserin suppresses the generation of TEP and Ca2+ oscillations, (2) application of 8-CPT-cAMP in the presence of cinanserin restores 5-HT-induced TEP and Ca2+ oscillations, (3) 8-CPT-cAMP sensitizes the InsP(3)/Ca2+ signalling pathway to 5-HT and the Cv5-HT2 alpha, receptor agonist 5-MeOT, (4) 8-CPT-cAMP induces Ca2+ oscillations in cells loaded with subthreshold concentrations of InsP(3), (5) inhibition of protein kinase A by H-89 abolishes 5-HT-induced TEP and Ca2+ spiking and mimics the effect of cinanserin. These results suggest that activation of the cyclic AMP pathway promotes the generation of 5-HT-induced Ca2+ oscillations in blowfly salivary glands. KW - Calcium KW - Ca2+ KW - Calcium oscillations KW - cAMP KW - Signalling KW - Crosstalk KW - Salivary gland KW - Calliphora KW - Blowfly KW - Insect Y1 - 2013 U6 - https://doi.org/10.1016/j.ceca.2012.10.004 SN - 0143-4160 VL - 53 IS - 2 SP - 94 EP - 101 PB - Churchill Livingstone CY - Edinburgh ER - TY - JOUR A1 - Gläser, Stefanie P. A1 - Bolte, Kathrin A1 - Martin, Karin A1 - Busse, Hans-Jürgen A1 - Grossart, Hans-Peter A1 - Kämpfer, Peter A1 - Gläser, Jens T1 - Novosphingobium fuchskuhlense sp nov., isolated from the north-east basin of Lake Grosse Fuchskuhle JF - International journal of systematic and evolutionary microbiology N2 - A yellow pigmented, Gram-negative, rod-shaped bacterium designated FNE08-7(T) was isolated from subsurface water of the north-east basin of the bog lake Grosse Fuchskuhle (Brandenburg, Germany). A first analysis of the nearly full-length 16S rRNA gene sequence analysis including environmental 16S rRNA gene sequences derived from freshwater ecosystems showed that strain FNE08-7(T) is the first cultured representative, to our knowledge, of the freshwater tribe Novo-A2. Further analysis indicates highest 16S rRNA gene sequence similarities to the type strains of Novosphingobium stygium (98.0%) and Novosphingobium taihuense (97.4%) and between 94.0% and 96.9% sequence similarity to other members of the genus Novosphingobium. Reconstruction of phylogenetic trees showed that strain FNE08-7(T) formed a distinct cluster with the type strains of N. stygium and N. taihuense supported by high bootstrap values. DNA DNA hybridization of strain FNE08-7(T) with N. stygium SMCC B0712(T) and N. taihuense DSM 17507(T) revealed low similarity values of 18.4% (reciprocal: 11.4%) and 23.1% (reciprocal: 54.2%), respectively. The predominant fatty acid of the isolate is C-18:1 omega 7c (56.4%) and two characteristic 2-hydroxy fatty acids, C-14:0 2-OH (16.5%) and C-15:0 2-OH (3.3%) occur. Ubiquinone Q-10 is the major respiratory quinone. The predominant polar lipids are phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, sphingoglycolipid, phosphatidylcholine and minor amounts of diphosphatidylglycerol. Spermidine is the predominant polyamine. Characterization by genotypic, chemotaxonomic and phenotypic analysis indicate that strain FNE08-7(T) represents a novel species of the genus Novosphingobium within the Alphaproteobacteria. Therefore, we propose the species Novosphingobium fuchskuhlense sp. nov., with FNE08-7(T) (=DSM 25065(T)=CCM 7978(T)=CCUG 61508(T)) as the type strain. Y1 - 2013 U6 - https://doi.org/10.1099/ijs.0.043083-0 SN - 1466-5026 VL - 63 SP - 586 EP - 592 PB - Society for General Microbiology CY - Reading ER - TY - JOUR A1 - Meli, Mattia A1 - Auclerc, Apolline A1 - Palmqvist, Annemette A1 - Forbes, Valery E. A1 - Grimm, Volker T1 - Population-level consequences of spatially heterogeneous exposure to heavy metals in soil an individual-based model of springtails JF - Ecological modelling : international journal on ecological modelling and engineering and systems ecolog N2 - Contamination of soil with toxic heavy metals poses a major threat to the environment and human health. Anthropogenic sources include smelting of ores, municipal wastes, fertilizers, and pesticides. In assessing soil quality and the environmental and ecological risk of contamination with heavy metals, often homogeneous contamination of the soil is assumed. However, soils are very heterogeneous environments. Consequently, both contamination and the response of soil organisms can be assumed to be heterogeneous. This might have consequences for the exposure of soil organisms and for the extrapolation of risk from the individual to the population level. Therefore, to explore how soil contamination of different spatial heterogeneity affects population dynamics of soil invertebrates, we developed a spatially explicit individual-based model of the springtail, Folsomia candida, a standard test species for ecotoxicological risk assessment. In the model, individuals were assumed to sense and avoid contaminated habitat with a certain probability that depends on contamination level. Avoidance of contaminated areas thus influenced the individuals' movement and feeding, their exposure, and in turn all other biological processes underlying population dynamics. Model rules and parameters were based on data from the literature, or were determined via pattern-oriented modelling. The model correctly predicted several patterns that were not used for model design and calibration. Simulation results showed that the ability of the individuals to detect and avoid the toxicant, combined with the presence of clean habitat patches which act as "refuges", made equilibrium population size due to toxic effects less sensitive to increases in toxicant concentration. Additionally, the level of heterogeneity among patches of soil (i.e. the difference in concentration) was important: at the same average concentration, a homogeneously contaminated scenario was the least favourable habitat, while higher levels of heterogeneity corresponded to higher population growth rate and equilibrium size. Our model can thus be used as a tool for extrapolating from short-term effects at the individual level to long-term effects at the population level under more realistic conditions. It can thus be used to develop and extrapolate from standard ecotoxicological tests in the laboratory to ecological risk assessments. KW - Avoidance KW - Folsomia candida KW - Copper KW - Heterogeneity KW - Pattern-oriented modelling KW - Soil ecology Y1 - 2013 U6 - https://doi.org/10.1016/j.ecolmodel.2012.11.010 SN - 0304-3800 VL - 250 IS - 1 SP - 338 EP - 351 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Bhabak, Krishna P. A1 - Kleuser, Burkhard A1 - Huwiler, Andrea A1 - Arenz, Christoph T1 - Effective inhibition of acid and neutral ceramidases by novel B-13 and LCL-464 analogues JF - Bioorganic & medicinal chemistry : a Tetrahedron publication for the rapid dissemination of full original research papers and critical reviews on biomolecular chemistry, medicinal chemistry and related disciplines N2 - Induction of apoptosis mediated by the inhibition of ceramidases has been shown to enhance the efficacy of conventional chemotherapy in several cancer models. Among the inhibitors of ceramidases reported in the literature, B-13 is considered as a lead compound having good in vitro potency towards acid ceramidase. Furthermore, owing to the poor activity of B-13 on lysosoamal acid ceramidase in living cells, LCL-464 a modified derivative of B-13 containing a basic omega-amino group at the fatty acid was reported to have higher potency towards lysosomal acid ceramidase in living cells. In a search for more potent inhibitors of ceramidases, we have designed a series of compounds with structural modifications of B-13 and LCL-464. In this study, we show that the efficacy of B-13 in vitro as well as in intact cells can be enhanced by suitable modification of functional groups. Furthermore, a detailed SAR investigation on LCL-464 analogues revealed novel promising inhibitors of aCDase and nCDase. In cell culture studies using the breast cancer cell line MDA-MB-231, some of the newly developed compounds elevated endogenous ceramide levels and in parallel, also induced apoptotic cell death. In summary, this study shows that structural modification of the known ceramidase inhibitors B-13 and LCL-464 generates more potent ceramidase inhibitors that are active in intact cells and not only elevates the cellular ceramide levels, but also enhances cell death. KW - Sphingolipids KW - Ceramide KW - Ceramidase inhibitors KW - Structure-activity-relationship Y1 - 2013 U6 - https://doi.org/10.1016/j.bmc.2012.12.014 SN - 0968-0896 VL - 21 IS - 4 SP - 874 EP - 882 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Dahl, Jan-Ulrik A1 - Radon, Christin A1 - Bühning, Martin A1 - Nimtz, Manfred A1 - Leichert, Lars I. A1 - Denis, Yann A1 - Jourlin-Castelli, Cecile A1 - Iobbi-Nivol, Chantal A1 - Mejean, Vincent A1 - Leimkühler, Silke T1 - The Sulfur Carrier Protein TusA Has a Pleiotropic Role in Escherichia coli That Also Affects Molybdenum Cofactor Biosynthesis JF - JOURNAL OF BIOLOGICAL CHEMISTRY N2 - The Escherichia coli L-cysteine desulfurase IscS mobilizes sulfur from L-cysteine for the synthesis of several biomolecules such as iron-sulfur (FeS) clusters, molybdopterin, thiamin, lipoic acid, biotin, and the thiolation of tRNAs. The sulfur transfer from IscS to various biomolecules is mediated by different interaction partners (e.g. TusA for thiomodification of tRNAs, IscU for FeS cluster biogenesis, and ThiI for thiamine biosynthesis/tRNA thiolation), which bind at different sites of IscS. Transcriptomic and proteomic studies of a Delta tusA strain showed that the expression of genes of the moaABCDE operon coding for proteins involved in molybdenum cofactor biosynthesis is increased under aerobic and anaerobic conditions. Additionally, under anaerobic conditions the expression of genes encoding hydrogenase 3 and several molybdoenzymes such as nitrate reductase were also increased. On the contrary, the activity of all molydoenzymes analyzed was significantly reduced in the Delta tusA mutant. Characterization of the Delta tusA strain under aerobic conditions showed an overall low molybdopterin content and an accumulation of cyclic pyranopterin monophosphate. Under anaerobic conditions the activity of nitrate reductase was reduced by only 50%, showing that TusA is not essential for molybdenum cofactor biosynthesis. We present a model in which we propose that the direction of sulfur transfer for each sulfur-containing biomolecule is regulated by the availability of the interaction partner of IscS. We propose that in the absence of TusA, more IscS is available for FeS cluster biosynthesis and that the overproduction of FeS clusters leads to a modified expression of several genes. Y1 - 2013 U6 - https://doi.org/10.1074/jbc.M112.431569 SN - 0021-9258 VL - 288 IS - 8 SP - 5426 EP - 5442 PB - AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC CY - BETHESDA ER - TY - JOUR A1 - Lin, Yue A1 - Berger, Uta A1 - Grimm, Volker A1 - Huth, Franka A1 - Weiner, Jacob T1 - Plant interactions alter the predictions of metabolic scaling theory JF - PLoS one N2 - Metabolic scaling theory (MST) is an attempt to link physiological processes of individual organisms with macroecology. It predicts a power law relationship with an exponent of -4/3 between mean individual biomass and density during density-dependent mortality (self-thinning). Empirical tests have produced variable results, and the validity of MST is intensely debated. MST focuses on organisms' internal physiological mechanisms but we hypothesize that ecological interactions can be more important in determining plant mass-density relationships induced by density. We employ an individual-based model of plant stand development that includes three elements: a model of individual plant growth based on MST, different modes of local competition (size-symmetric vs. -asymmetric), and different resource levels. Our model is consistent with the observed variation in the slopes of self-thinning trajectories. Slopes were significantly shallower than -4/3 if competition was size-symmetric. We conclude that when the size of survivors is influenced by strong ecological interactions, these can override predictions of MST, whereas when surviving plants are less affected by interactions, individual-level metabolic processes can scale up to the population level. MST, like thermodynamics or biomechanics, sets limits within which organisms can live and function, but there may be stronger limits determined by ecological interactions. In such cases MST will not be predictive. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0057612 SN - 1932-6203 VL - 8 IS - 2 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Bauer, Barbara A1 - Sommer, Ulrich A1 - Gaedke, Ursula T1 - High predictability of spring phytoplankton biomass in mesocosms at the species, functional group and community level JF - Freshwater biology N2 - 1. Models aim to predict phytoplankton dynamics based on observed initial conditions and a set of equations and parameters. However, our knowledge about initial conditions in nature is never perfect. Thus, if phytoplankton dynamics are sensitive to small variations in initial conditions, they are difficult to predict. 2. We used time-series data from indoor mesocosm experiments with natural phyto- and zooplankton communities to quantify the extent to which small initial differences in the species, functional group and community biomass in parallel treatments were amplified or buffered over time. We compared the differences in dynamics between replicates and among all mesocosms of 1year. 3. Temperature-sensitive grazing during the exponential growth phase of phytoplankton caused divergence. In contrast, negative density dependence caused convergence. 4. Mean differences in biomass between replicates were similar for all hierarchical levels. This indicates that differences in their initial conditions were amplified to the same extent. Even though large differences in biomass occasionally occurred between replicates for a short time, dynamics returned to the same path at all hierarchical levels. This suggests that internal feedback mechanisms make the spring development of phytoplankton highly predictable. KW - divergence KW - hierarchical level KW - mesocosms KW - predictability KW - replicates Y1 - 2013 U6 - https://doi.org/10.1111/j.1365-2427.2012.02780.x SN - 0046-5070 VL - 58 IS - 3 SP - 588 EP - 596 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Zakharova, A. A1 - Nikoloski, Zoran A1 - Koseska, Aneta T1 - Dimensionality reduction of bistable biological systems JF - Bulletin of mathematical biology : official journal of the Society for Mathematical Biology N2 - Time hierarchies, arising as a result of interactions between system's components, represent a ubiquitous property of dynamical biological systems. In addition, biological systems have been attributed switch-like properties modulating the response to various stimuli across different organisms and environmental conditions. Therefore, establishing the interplay between these features of system dynamics renders itself a challenging question of practical interest in biology. Existing methods are suitable for systems with one stable steady state employed as a well-defined reference. In such systems, the characterization of the time hierarchies has already been used for determining the components that contribute to the dynamics of biological systems. However, the application of these methods to bistable nonlinear systems is impeded due to their inherent dependence on the reference state, which in this case is no longer unique. Here, we extend the applicability of the reference-state analysis by proposing, analyzing, and applying a novel method, which allows investigation of the time hierarchies in systems exhibiting bistability. The proposed method is in turn used in identifying the components, other than reactions, which determine the systemic dynamical properties. We demonstrate that in biological systems of varying levels of complexity and spanning different biological levels, the method can be effectively employed for model simplification while ensuring preservation of qualitative dynamical properties (i.e., bistability). Finally, by establishing a connection between techniques from nonlinear dynamics and multivariate statistics, the proposed approach provides the basis for extending reference-based analysis to bistable systems. KW - Bistability KW - Time-scales hierarchy KW - Similarity transformation KW - Canonical correlation analysis KW - Dimensionality reduction Y1 - 2013 U6 - https://doi.org/10.1007/s11538-013-9807-8 SN - 0092-8240 VL - 75 IS - 3 SP - 373 EP - 392 PB - Springer CY - New York ER - TY - JOUR A1 - Speck, Janina A1 - Räuber, Christina A1 - Kükenshöner, Tim A1 - Niemöller, Christoph A1 - Mueller, Katelyn J. A1 - Schleberger, Paula A1 - Dondapati, Padmarupa A1 - Hecky, Jochen A1 - Arndt, Katja Maren A1 - Müller, Kristian M. T1 - TAT hitchhiker selection expanded to folding helpers, multimeric interactions and combinations with protein fragment complementation JF - Protein engineering design & selection N2 - The twin-arginine translocation (TAT) pathway of the bacterial cytoplasmic membrane mediates translocation only of proteins that accomplished a native-like conformation. We deploy this feature in modular selection systems for directed evolution, in which folding helpers as well as dimeric or oligomeric proteinprotein interactions enable TAT-dependent translocation of the resistance marker TEM -lactamase (L). Specifically, we demonstrate and analyze selection of (i) enhancers for folding by direct TAT translocation selection of a target protein interposed between the TorA signal sequence and L, (ii) dimeric or oligomeric proteinprotein interactions by hitchhiker translocation (HiT) selection of proteins fused to the TorA signal sequence and to the L, respectively and (iii) heterotrimeric proteinprotein interactions by combining HiT with protein fragment complementation selection of proteins fused to two split L fragments and TorA, respectively. The lactamase fragments were additionally engineered for improved activity and stability. Applicability was benchmarked with interaction partners of known affinity and multimerization whereby cellular fitness correlated well with biophysical protein properties. Ultimately, the HiT selection was employed to identify peptides, which specifically bind to leukemia- and melanoma-relevant target proteins (MITF and ETO) by coiled-coil or tetra-helix-bundle formation with high affinity. The various versions of TAT selection led to inhibiting peptides (iPEPs) of disease-promoting interactions and enabled so far difficult to achieve selections. KW - HiT selection KW - NHR2 KW - TAT selection KW - three hybrid KW - two hybrid Y1 - 2013 U6 - https://doi.org/10.1093/protein/gzs098 SN - 1741-0126 VL - 26 IS - 3 SP - 225 EP - 242 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Linklater, Wayne L. A1 - Mayer, Katharina A1 - Swaisgood, Ronald R. T1 - Chemical signals of age, sex and identity in black rhinoceros JF - Animal behaviour N2 - Olfactory communication may be particularly important to black rhinoceros, Diceros bicornis, because they are solitary living and have comparatively poor eyesight but their populations are structured by inter-and intrasexual relationships. Understanding olfactory functions and processes might achieve better conservation management but their study in rhinoceros remains anecdotal or descriptive. Experimental approaches are required but rarely possible as rhinoceros are difficult to observe and manipulate. We measured the olfactory investigation behaviour (duration and frequency of sniffing) of black rhinoceros in four experiments designed to determine the function of chemosignals in dung and urine. A habituationedishabituation trial demonstrated that black rhinoceros discriminated individually distinctive odours from faecal signals (experiment 1). When adults (>6 years old) were presented with dung from conspecifics of different sex and age classes (adult, and subadult from 2 to 4 years old), male dung was investigated more by both sexes, and females investigated subadult dung more (experiment 2). Both dung and urine from the same adult donors were investigated by both sexes, but male dung was investigated more than female dung and female urine more than male urine, although differences were statistically weak (experiment 3). Lastly, fresh faecal samples and those aged 1, 2, 4, 16 and 32 days were similarly investigated, indicating that they still function as olfactory signals. Together the results indicate that dung or urine signalled age, sex and identity to conspecifics and signals may persist as dung decays. Chemosignals are likely to be important to the social and spatial organization of black rhinoceros. KW - black rhinoceros KW - Diceros bicornis var. minor KW - dung KW - faeces KW - hook-lipped rhinoceros KW - individual discrimination KW - olfactory communication KW - signal KW - urine Y1 - 2013 U6 - https://doi.org/10.1016/j.anbehav.2012.12.034 SN - 0003-3472 VL - 85 IS - 3 SP - 671 EP - 677 PB - Elsevier CY - London ER -