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Over the last two decades, macroecology the analysis of large-scale, multi-species ecological patterns and processes has established itself as a major line of biological research. Analyses of statistical links between environmental variables and biotic responses have long and successfully been employed as a main approach, but new developments are due to be utilized. Scanning the horizon of macroecology, we identified four challenges that will probably play a major role in the future. We support our claims by examples and bibliographic analyses. 1) Integrating the past into macroecological analyses, e.g. by using paleontological or phylogenetic information or by applying methods from historical biogeography, will sharpen our understanding of the underlying reasons for contemporary patterns. 2) Explicit consideration of the local processes that lead to the observed larger-scale patterns is necessary to understand the fine-grain variability found in nature, and will enable better prediction of future patterns (e.g. under environmental change conditions). 3) Macroecology is dependent on large-scale, high quality data from a broad spectrum of taxa and regions. More available data sources need to be tapped and new, small-grain large-extent data need to be collected. 4) Although macroecology already lead to mainstreaming cutting-edge statistical analysis techniques, we find that more sophisticated methods are needed to account for the biases inherent to sampling at large scale. Bayesian methods may be particularly suitable to address these challenges. To continue the vigorous development of the macroecological research agenda, it is time to address these challenges and to avoid becoming too complacent with current achievements.
Indoor mesocosm experiments were conducted to test for potential climate change effects on the spring succession of Baltic Sea plankton. Two different temperature (Delta 0 A degrees C and Delta 6 A degrees C) and three light scenarios (62, 57 and 49 % of the natural surface light intensity on sunny days), mimicking increasing cloudiness as predicted for warmer winters in the Baltic Sea region, were simulated. By combining experimental and modeling approaches, we were able to test for a potential dietary mismatch between phytoplankton and zooplankton. Two general predator-prey models, one representing the community as a tri-trophic food chain and one as a 5-guild food web were applied to test for the consequences of different temperature sensitivities of heterotrophic components of the plankton. During the experiments, we observed reduced time-lags between the peaks of phytoplankton and protozoan biomass in response to warming. Microzooplankton peak biomass was reached by 2.5 day A degrees C-1 earlier and occurred almost synchronously with biomass peaks of phytoplankton in the warm mesocosms (Delta 6 A degrees C). The peak magnitudes of microzooplankton biomass remained unaffected by temperature, and growth rates of microzooplankton were higher at Delta 6 A degrees C (mu(a dagger 0 A degrees C) = 0.12 day(-1) and mu(a dagger 6 A degrees C) = 0.25 day(-1)). Furthermore, warming induced a shift in microzooplankton phenology leading to a faster species turnover and a shorter window of microzooplankton occurrence. Moderate differences in the light levels had no significant effect on the time-lags between autotrophic and heterotrophic biomass and on the timing, biomass maxima and growth rate of microzooplankton biomass. Both models predicted reduced time-lags between the biomass peaks of phytoplankton and its predators (both microzooplankton and copepods) with warming. The reduction of time-lags increased with increasing Q(10) values of copepods and protozoans in the tritrophic food chain. Indirect trophic effects modified this pattern in the 5-guild food web. Our study shows that instead of a mismatch, warming might lead to a stronger match between protist grazers and their prey altering in turn the transfer of matter and energy toward higher trophic levels.
1. The polyunsaturated fatty acid eicosapentaenoic acid (EPA) plays an important role in aquatic food webs, in particular at the primary producerconsumer interface where keystone species such as daphnids may be constrained by its dietary availability. Such constraints and their seasonal and interannual changes may be detected by continuous measurements of EPA concentrations. However, such EPA measurements became common only during the last two decades, whereas long-term data sets on plankton biomass are available for many well-studied lakes. Here, we test whether it is possible to estimate EPA concentrations from abiotic variables (light and temperature) and the biomass of prey organisms (e.g. ciliates, diatoms and cryptophytes) that potentially provide EPA for consumers. 2. We used multiple linear regression to relate size- and taxonomically resolved plankton biomass data and measurements of temperature and light intensity to directly measured EPA concentrations in Lake Constance during a whole year. First, we tested the predictability of EPA concentrations from the biomass of EPA-rich organisms (diatoms, cryptophytes and ciliates). Secondly, we included the variables mean temperature and mean light intensity over the sampling depth (020 m) and depth (08 and 820 m) as factors in our model to check for large-scale seasonal- and depth-dependent effects on EPA concentrations. In a third step, we included the deviations of light and temperature from mean values in our model to allow for their potential influence on the biochemical composition of plankton organisms. We used the Akaike Information Criterion to determine the best models. 3. All approaches supported our proposition that the biomasses of specific plankton groups are variables from which seston EPA concentrations can be derived. The importance of ciliates as an EPA source in the seston was emphasised by their high weight in our models, although ciliates are neglected in most studies that link fatty acids to seston taxonomic composition. The large-scale seasonal variability of light intensity and its interaction with diatom biomass were significant predictors of EPA concentrations. The deviation of temperature from mean values, accounting for a depth-dependent effect on EPA concentrations, and its interaction with ciliate biomass were also variables with high predictive power. 4. The best models from the first and second approaches were validated with measurements of EPA concentrations from another year (1997). The estimation with the best model including only biomass explained 80%, and the best model from the second approach including mean temperature and depth explained 87% of the variability in EPA concentrations in 1997. 5. We show that it is possible to predict EPA concentrations reliably from plankton biomass, while the inclusion of abiotic factors led to results that were only partly consistent with expectations from laboratory studies. Our approach of including biotic predictors should be transferable to other systems and allow checking for biochemical constraints on primary consumers.
Leaf senescence is an active process required for plant survival, and it is flexibly controlled, allowing plant adaptation to environmental conditions. Although senescence is largely an age-dependent process, it can be triggered by environmental signals and stresses. Leaf senescence coordinates the breakdown and turnover of many cellular components, allowing a massive remobilization and recycling of nutrients from senescing tissues to other organs (e.g., young leaves, roots, and seeds), thus enhancing the fitness of the plant. Such metabolic coordination requires a tight regulation of gene expression. One important mechanism for the regulation of gene expression is at the transcriptional level via transcription factors (TFs). The NAC TF family (NAM, ATAF, CUC) includes various members that show elevated expression during senescence, including ORE1 (ANAC092/AtNAC2) among others. ORE1 was first reported in a screen for mutants with delayed senescence (oresara1, 2, 3, and 11). It was named after the Korean word “oresara,” meaning “long-living,” and abbreviated to ORE1, 2, 3, and 11, respectively. Although the pivotal role of ORE1 in controlling leaf senescence has recently been demonstrated, the underlying molecular mechanisms and the pathways it regulates are still poorly understood. To unravel the signaling cascade through which ORE1 exerts its function, we analyzed particular features of regulatory pathways up-stream and down-stream of ORE1. We identified characteristic spatial and temporal expression patterns of ORE1 that are conserved in Arabidopsis thaliana and Nicotiana tabacum and that link ORE1 expression to senescence as well as to salt stress. We proved that ORE1 positively regulates natural and dark-induced senescence. Molecular characterization of the ORE1 promoter in silico and experimentally suggested a role of the 5’UTR in mediating ORE1 expression. ORE1 is a putative substrate of a calcium-dependent protein kinase named CKOR (unpublished data). Promising data revealed a positive regulation of putative ORE1 targets by CKOR, suggesting the phosphorylation of ORE1 as a requirement for its regulation. Additionally, as part of the ORE1 up-stream regulatory pathway, we identified the NAC TF ATAF1 which was able to transactivate the ORE1 promoter in vivo. Expression studies using chemically inducible ORE1 overexpression lines and transactivation assays employing leaf mesophyll cell protoplasts provided information on target genes whose expression was rapidly induced upon ORE1 induction. First, a set of target genes was established and referred to as early responding in the ORE1 regulatory network. The consensus binding site (BS) of ORE1 was characterized. Analysis of some putative targets revealed the presence of ORE1 BSs in their promoters and the in vitro and in vivo binding of ORE1 to their promoters. Among these putative target genes, BIFUNCTIONAL NUCLEASE I (BFN1) and VND-Interacting2 (VNI2) were further characterized. The expression of BFN1 was found to be dependent on the presence of ORE1. Our results provide convincing data which support a role for BFN1 as a direct target of ORE1. Characterization of VNI2 in age-dependent and stress-induced senescence revealed ORE1 as a key up-stream regulator since it can bind and activate VNI2 expression in vivo and in vitro. Furthermore, VNI2 was able to promote or delay senescence depending on the presence of an activation domain located in its C-terminal region. The plasticity of this gene might include alternative splicing (AS) to regulate its function in different organs and at different developmental stages, particularly during senescence. A model is proposed on the molecular mechanism governing the dual role of VNI2 during senescence.
Unique properties of eukaryote-type actin and profilin horizontally transferred to cyanobacteria
(2012)
A eukaryote-type actin and its binding protein profilin encoded on a genomic island in the cyanobacterium Microcystis aeruginosa PCC 7806 co-localize to form a hollow, spherical enclosure occupying a considerable intracellular space as shown by in vivo fluorescence microscopy. Biochemical and biophysical characterization reveals key differences between these proteins and their eukaryotic homologs. Small-angle X-ray scattering shows that the actin assembles into elongated, filamentous polymers which can be visualized microscopically with fluorescent phalloidin. Whereas rabbit actin forms thin cylindrical filaments about 100 mu m in length, cyanobacterial actin polymers resemble a ribbon, arrest polymerization at 510 lam and tend to form irregular multi-strand assemblies. While eukaryotic profilin is a specific actin monomer binding protein, cyanobacterial profilin shows the unprecedented property of decorating actin filaments. Electron micrographs show that cyanobacterial profilin stimulates actin filament bundling and stabilizes their lateral alignment into heteropolymeric sheets from which the observed hollow enclosure may be formed. We hypothesize that adaptation to the confined space of a bacterial cell devoid of binding proteins usually regulating actin polymerization in eukaryotes has driven the co-evolution of cyanobacterial actin and profilin, giving rise to an intracellular entity.
Parenchyma cells from tubers of Solanum tuberosum L. convert several externally supplied sugars to starch but the rates vary largely. Conversion of glucose 1-phosphate to starch is exceptionally efficient. In this communication, tuber slices were incubated with either of four solutions containing equimolar [U-C-14]glucose 1-phosphate, [U-C-14]sucrose, [U-C-14]glucose 1-phosphate plus unlabelled equimolar sucrose or [U-C-14]sucrose plus unlabelled equimolar glucose 1-phosphate. C-14-incorporation into starch was monitored. In slices from freshly harvested tubers each unlabelled compound strongly enhanced C-14 incorporation into starch indicating closely interacting paths of starch biosynthesis. However, enhancement disappeared when the tubers were stored. The two paths (and, consequently, the mutual enhancement effect) differ in temperature dependence. At lower temperatures, the glucose 1-phosphate-dependent path is functional, reaching maximal activity at approximately 20 degrees C but the flux of the sucrose-dependent route strongly increases above 20 degrees C. Results are confirmed by in vitro experiments using [U-C-14]glucose 1-phosphate or adenosine-[U-C-14]glucose and by quantitative zymograms of starch synthase or phosphorylase activity. In mutants almost completely lacking the plastidial phosphorylase isozyme(s), the glucose 1-phosphate-dependent path is largely impeded. Irrespective of the size of the granules, glucose 1-phosphate-dependent incorporation per granule surface area is essentially equal. Furthermore, within the granules no preference of distinct glucosyl acceptor sites was detectable. Thus, the path is integrated into the entire granule biosynthesis. In vitro C-14-incorporation into starch granules mediated by the recombinant plastidial phosphorylase isozyme clearly differed from the in situ results. Taken together, the data clearly demonstrate that two closely but flexibly interacting general paths of starch biosynthesis are functional in potato tuber cells.
Clusters of codons pairing to low-abundance tRNAs synchronize the translation with co-translational folding of single domains in multidomain proteins. Although proven with some examples, the impact of the ribosomal speed on the folding and solubility on a global, cell-wide level remains elusive. Here we show that upregulation of three low-abundance tRNAs in Escherichia coil increased the aggregation propensity of several cellular proteins as a result of an accelerated elongation rate. Intriguingly, alterations in the concentration of the natural tRNA pool compromised the solubility of various chaperones consequently rendering the solubility of some chaperone-dependent proteins.
Translatome and metabolome effects triggered by gibberellins during rosette growth in Arabidopsis
(2012)
Although gibberellins (GAs) are well known for their growth control function, little is known about their effects on primary metabolism. Here the modulation of gene expression and metabolic adjustment in response to changes in plant (Arabidopsis thaliana) growth imposed on varying the gibberellin regime were evaluated. Polysomal mRNA populations were profiled following treatment of plants with paclobutrazol (PAC), an inhibitor of GA biosynthesis, and gibberellic acid (GA(3)) to monitor translational regulation of mRNAs globally. Gibberellin levels did not affect levels of carbohydrates in plants treated with PAC and/or GA(3). However, the tricarboxylic acid cycle intermediates malate and fumarate, two alternative carbon storage molecules, accumulated upon PAC treatment. Moreover, an increase in nitrate and in the levels of the amino acids was observed in plants grown under a low GA regime. Only minor changes in amino acid levels were detected in plants treated with GA(3) alone, or PAC plus GA(3). Comparison of the molecular changes at the transcript and metabolite levels demonstrated that a low GA level mainly affects growth by uncoupling growth from carbon availability. These observations, together with the translatome changes, reveal an interaction between energy metabolism and GA-mediated control of growth to coordinate cell wall extension, secondary metabolism, and lipid metabolism.
Die Strahlentherapie ist neben der Chemotherapie und einer operativen Entfernung die stärkste Waffe für die Bekämpfung bösartiger Tumore in der Krebsmedizin. Nach Herz-Kreislauf-Erkrankungen ist Krebs die zweithäufigste Todesursache in der westlichen Welt, wobei Prostatakrebs heutzutage die häufigste, männliche Krebserkrankung darstellt. Trotz technologischer Fortschritte der radiologischen Verfahren kann es noch viele Jahre nach einer Radiotherapie zu einem Rezidiv kommen, was zum Teil auf die hohe Resistenzfähigkeit einzelner, entarteter Zellen des lokal vorkommenden Tumors zurückgeführt werden kann. Obwohl die moderne Strahlenbiologie viele Aspekte der Resistenzmechanismen näher beleuchtet hat, bleiben Fragestellungen, speziell über das zeitliche Ansprechen eines Tumors auf ionisierende Strahlung, größtenteils unbeantwortet, da systemweite Untersuchungen nur begrenzt vorliegen. Als Zellmodelle wurden vier Prostata-Krebszelllinien (PC3, DuCaP, DU-145, RWPE-1) mit unterschiedlichen Strahlungsempfindlichkeiten kultiviert und auf ihre Überlebensfähigkeit nach ionisierender Bestrahlung durch einen Trypanblau- und MTT-Vitalitätstest geprüft. Die proliferative Kapazität wurde mit einem Koloniebildungstest bestimmt. Die PC3 Zelllinie, als Strahlungsresistente, und die DuCaP Zelllinie, als Strahlungssensitive, zeigten dabei die größten Differenzen bezüglich der Strahlungsempfindlichkeit. Auf Grundlage dieser Ergebnisse wurden die beiden Zelllinien ausgewählt, um anhand ihrer transkriptomweiten Genexpressionen, eine Identifizierung potentieller Marker für die Prognose der Effizienz einer Strahlentherapie zu ermöglichen. Weiterhin wurde mit der PC3 Zelllinie ein Zeitreihenexperiment durchgeführt, wobei zu 8 verschiedenen Zeitpunkten nach Bestrahlung mit 1 Gy die mRNA mittels einer Hochdurchsatz-Sequenzierung quantifiziert wurde, um das dynamisch zeitversetzte Genexpressionsverhalten auf Resistenzmechanismen untersuchen zu können. Durch das Setzen eines Fold Change Grenzwertes in Verbindung mit einem P-Wert < 0,01 konnten aus 10.966 aktiven Genen 730 signifikant differentiell exprimierte Gene bestimmt werden, von denen 305 stärker in der PC3 und 425 stärker in der DuCaP Zelllinie exprimiert werden. Innerhalb dieser 730 Gene sind viele stressassoziierte Gene wiederzufinden, wie bspw. die beiden Transmembranproteingene CA9 und CA12. Durch Berechnung eines Netzwerk-Scores konnten aus den GO- und KEGG-Datenbanken interessante Kategorien und Netzwerke abgeleitet werden, wobei insbesondere die GO-Kategorien Aldehyd-Dehydrogenase [NAD(P)+] Aktivität (GO:0004030) und der KEGG-Stoffwechselweg der O-Glykan Biosynthese (hsa00512) als relevante Netzwerke auffällig wurden. Durch eine weitere Interaktionsanalyse konnten zwei vielversprechende Netzwerke mit den Transkriptionsfaktoren JUN und FOS als zentrale Elemente identifiziert werden. Zum besseren Verständnis des dynamisch zeitversetzten Ansprechens der strahlungsresistenten PC3 Zelllinie auf ionisierende Strahlung, konnten anhand der 10.840 exprimierten Gene und ihrer Expressionsprofile über 8 Zeitpunkte interessante Einblicke erzielt werden. Während es innerhalb von 30 min (00:00 - 00:30) nach Bestrahlung zu einer schnellen Runterregulierung der globalen Genexpression kommt, folgen in den drei darauffolgenden Zeitabschnitten (00:30 - 01:03; 01:03 - 02:12; 02:12 - 04:38) spezifische Expressionserhöhungen, die eine Aktivierung schützender Netzwerke, wie die Hochregulierung der DNA-Reparatursysteme oder die Arretierung des Zellzyklus, auslösen. In den abschließenden drei Zeitbereichen (04:38 - 09:43; 09:43 - 20:25; 20:25 - 42:35) liegt wiederum eine Ausgewogenheit zwischen Induzierung und Supprimierung vor, wobei die absoluten Genexpressionsveränderungen ansteigen. Beim Vergleich der Genexpressionen kurz vor der Bestrahlung mit dem letzten Zeitpunkt (00:00 - 42:53) liegen mit 2.670 die meisten verändert exprimierten Gene vor, was einer massiven, systemweiten Genexpressionsänderung entspricht. Signalwege wie die ATM-Regulierung des Zellzyklus und der Apoptose, des NRF2-Signalwegs nach oxidativer Stresseinwirkung und die DNA-Reparaturmechanismen der homologen Rekombination, des nicht-homologen End Joinings, der MisMatch-, der Basen-Exzision- und der Strang-Exzision-Reparatur spielen bei der zellulären Antwort eine tragende Rolle. Äußerst interessant sind weiterhin die hohen Aktivitäten RNA-gesteuerter Ereignisse, insbesondere von small nucleolar RNAs und Pseudouridin-Prozessen. Demnach scheinen diese RNA-modifizierenden Netzwerke einen bisher unbekannten funktionalen und schützenden Einfluss auf das Zellüberleben nach ionisierender Bestrahlung zu haben. All diese schützenden Netzwerke mit ihren zeitspezifischen Interaktionen sind essentiell für das Zellüberleben nach Einwirkung von oxidativem Stress und zeigen ein komplexes aber im Einklang befindliches Zusammenspiel vieler Einzelkomponenten zu einem systemweit ablaufenden Programm.
Transcription factor OsHsfC1b regulates salt tolerance and development in Oryza sativa ssp japonica
(2012)
Background and aims Salt stress leads to attenuated growth and productivity in rice. Transcription factors like heat shock factors (HSFs) represent central regulators of stress adaptation. Heat shock factors of the classes A and B are well established as regulators of thermal and non-thermal stress responses in plants; however, the role of class C HSFs is unknown. Here we characterized the function of the OsHsfC1b (Os01g53220) transcription factor from rice.
Methodology We analysed the expression of OsHsfC1b in the rice japonica cultivars Dongjin and Nipponbare exposed to salt stress as well as after mannitol, abscisic acid (ABA) and H2O2 treatment. For functional characterization of OsHsfC1b, we analysed the physiological response of a T-DNA insertion line (hsfc1b) and two artificial micro-RNA (amiRNA) knock-down lines to salt, mannitol and ABA treatment. In addition, we quantified the expression of small Heat Shock Protein (sHSP) genes and those related to signalling and ion homeostasis by quantitative real-time polymerase chain reaction in roots exposed to salt. The subcellular localization of OsHsfC1b protein fused to green fluorescent protein (GFP) was determined in Arabidopsis mesophyll cell protoplasts.
Principal results Expression of OsHsfC1b was induced by salt, mannitol and ABA, but not by H2O2. Impaired function of OsHsfC1b in the hsfc1b mutant and the amiRNA lines led to decreased salt and osmotic stress tolerance, increased sensitivity to ABA, and temporal misregulation of salt-responsive genes involved in signalling and ion homeostasis. Furthermore, sHSP genes showed enhanced expression in knock-down plants under salt stress. We observed retarded growth of hsfc1b and knock-down lines in comparison with control plants under non-stress conditions. Transient expression of OsHsfC1b fused to GFP in protoplasts revealed nuclear localization of the transcription factor.
Conclusions OsHsfC1b plays a role in ABA-mediated salt stress tolerance in rice. Furthermore, OsHsfC1b is involved in the response to osmotic stress and is required for plant growth under non-stress conditions.
Silvicultural practices lead to changes in forest composition and structure and may impact species diversity from the overall regional species pool to stand-level species occurrence. We explored to what extent fine-scale occupancy patterns in differently managed forest stands are driven by environment and ecological traits in three regions in Germany using a multi-species hierarchical model. We tested for the possible impact of environmental variables and ecological traits on occupancy dynamics in a joint modelling exercise while taking possible variation in coefficient estimates over years and plots into account. Bird species richness differed across regions and years, and trends in species richness across years were different in the three regions. On the species level, forest management affected occupancy of species in all regions, but only 35% of the total assemblage-level variation in occurrence probability was explained by either forest type and successional stage and <?1% by forest edge. On the assemblage level, bird occurrence decreased with body mass in all regions. Species with smaller breeding ranges had lower occurrence probabilities in one region, while later spring arrival decreased occurrence probabilities in the two other regions. Spatial variation in the effect size of trait covariates such as species phylogeny and breeding strata showed that variation in patch occupancy due to fine-scale differences in forest management is, to some extent, predictable from ecological traits. Our results show that environmental factors and ecological traits jointly predict variation in bird occupancy patterns and their response to forest management. Observations at the fine scale of forest stands, at which conservation efforts can be arranged along with forest management practices in heterogeneous environments, have been shown to provide meaningful insights despite the difficulties involved in monitoring mobile organisms such as birds at the plot level.
Aim Biotic interactions within guilds or across trophic levels have widely been ignored in species distribution models (SDMs). This synthesis outlines the development of species interaction distribution models (SIDMs), which aim to incorporate multispecies interactions at large spatial extents using interaction matrices. Location Local to global. Methods We review recent approaches for extending classical SDMs to incorporate biotic interactions, and identify some methodological and conceptual limitations. To illustrate possible directions for conceptual advancement we explore three principal ways of modelling multispecies interactions using interaction matrices: simple qualitative linkages between species, quantitative interaction coefficients reflecting interaction strengths, and interactions mediated by interaction currencies. We explain methodological advancements for static interaction data and multispecies time series, and outline methods to reduce complexity when modelling multispecies interactions. Results Classical SDMs ignore biotic interactions and recent SDM extensions only include the unidirectional influence of one or a few species. However, novel methods using error matrices in multivariate regression models allow interactions between multiple species to be modelled explicitly with spatial co-occurrence data. If time series are available, multivariate versions of population dynamic models can be applied that account for the effects and relative importance of species interactions and environmental drivers. These methods need to be extended by incorporating the non-stationarity in interaction coefficients across space and time, and are challenged by the limited empirical knowledge on spatio-temporal variation in the existence and strength of species interactions. Model complexity may be reduced by: (1) using prior ecological knowledge to set a subset of interaction coefficients to zero, (2) modelling guilds and functional groups rather than individual species, and (3) modelling interaction currencies and species effect and response traits. Main conclusions There is great potential for developing novel approaches that incorporate multispecies interactions into the projection of species distributions and community structure at large spatial extents. Progress can be made by: (1) developing statistical models with interaction matrices for multispecies co-occurrence datasets across large-scale environmental gradients, (2) testing the potential and limitations of methods for complexity reduction, and (3) sampling and monitoring comprehensive spatio-temporal data on biotic interactions in multispecies communities.
We use substituted polyanilines for the construction of new polymer electrodes for interaction studies with the redox protein cytochrome c (cyt c) and the enzyme sulfite oxidase (SO). For these purposes four different polyaniline copolymers are chemically synthesized. Three of them are copolymers, containing 2-methoxyaniline-5-sulfonic acid with variable ratios of aniline; the fourth copolymer consists of 3-amino-benzoic acid and aniline. The results show that all polymers are suitable for being immobilized as thin stable films on gold wire and indium tin oxide (ITO) electrode surfaces from DMSO solution. This can be demonstrated by cyclic voltammetry and UV-Vis spectroscopy measurements. Moreover, cyt c can be electrochemically detected not only in solution, but also immobilized on top of the polymer films. Furthermore, the appearance of a significant catalytic current has been demonstrated for the sulfonated polyanilines, when the polymer-coated protein electrode is being measured upon addition of sulfite oxidase, confirming the establishment of a bioanalytical signal chain. Best results have been obtained for the polymer with highest sulfonation grade. The redox switching of the polymer by the enzymatic reaction can also be analyzed by following the spectral properties of the polymer electrode.
The response of forest plant regeneration to temperature variation along a latitudinal gradient
(2012)
The response of forest herb regeneration from seed to temperature variations across latitudes was experimentally assessed in order to forecast the likely response of understorey community dynamics to climate warming.
Seeds of two characteristic forest plants (Anemone nemorosa and Milium effusum) were collected in natural populations along a latitudinal gradient from northern France to northern Sweden and exposed to three temperature regimes in growth chambers (first experiment). To test the importance of local adaptation, reciprocal transplants were also made of adult individuals that originated from the same populations in three common gardens located in southern, central and northern sites along the same gradient, and the resulting seeds were germinated (second experiment). Seedling establishment was quantified by measuring the timing and percentage of seedling emergence, and seedling biomass in both experiments.
Spring warming increased emergence rates and seedling growth in the early-flowering forb A. nemorosa. Seedlings of the summer-flowering grass M. effusum originating from northern populations responded more strongly in terms of biomass growth to temperature than southern populations. The above-ground biomass of the seedlings of both species decreased with increasing latitude of origin, irrespective of whether seeds were collected from natural populations or from the common gardens. The emergence percentage decreased with increasing home-away distance in seeds from the transplant experiment, suggesting that the maternal plants were locally adapted.
Decreasing seedling emergence and growth were found from the centre to the northern edge of the distribution range for both species. Stronger responses to temperature variation in seedling growth of the grass M. effusum in the north may offer a way to cope with environmental change. The results further suggest that climate warming might differentially affect seedling establishment of understorey plants across their distribution range and thus alter future understorey plant dynamics.
The permeation pore of K+ channels is formed by four copies of the pore domain. AtKCO3 is the only putative voltage-independent K+ channel subunit of Arabidopsis thaliana with a single pore domain. KCO3-like proteins recently emerged in evolution and, to date, have been found only in the genus Arabidopsis (A. thaliana and A. lyrata). We show that the absence of KCO3 does not cause marked changes in growth under various conditions. Only under osmotic stress we observed reduced root growth of the kco3-1 null-allele line. This phenotype was complemented by expressing a KCO3 mutant with an inactive pore, indicating that the function of KCO3 under osmotic stress does not depend on its direct ability to transport ions. Constitutively overexpressed AtKCO3 or AtKCO3::G FP are efficiently sorted to the tonoplast indicating that the protein is approved by the endoplasmic reticulum quality control. However, vacuoles isolated from transgenic plants do not have significant alterations in current density. Consistently, both AtKCO3 and AtKCO3::GFP are detected as homodimers upon velocity gradient centrifugation, an assembly state that would not allow for activity. We conclude that if AtKCO3 ever functions as a K+ channel, active tetramers are held by particularly weak interactions, are formed only in unknown specific conditions and may require partner proteins.
The plant genome encodes at least two distinct and evolutionary conserved plastidial starch-related dikinases that phosphorylate a low percentage of glucosyl residues at the starch granule surface. Esterification of starch favours the transition of highly ordered a-glucans to a less ordered state and thereby facilitates the cleavage of interglucose bonds by hydrolases. Metabolically most important is the phosphorylation at position C6, which is catalysed by the glucan, water dikinase (GWD). The reactions mediated by recombinant wild-type GWD from Arabidopsis thaliana (AtGWD) and from Solanum tuberosum (StGWD) were studied. Two mutated proteins lacking the conserved histidine residue that is indispensible for glucan phosphorylation were also included. The wild-type GWDs consume approximately 20% more ATP than is required for glucan phosphorylation. Similarly, although incapable of phosphorylating a-glucans, the two mutated dikinase proteins are capable of degrading ATP. Thus, consumption of ATP and phosphorylation of a-glucans are not strictly coupled processes but, to some extent, occur as independent phosphotransfer reactions. As revealed by incubation of the GWDs with [gamma-33P]ATP, the consumption of ATP includes the transfer of the gamma-phosphate group to the GWD protein but this autophosphorylation does not require the conserved histidine residue. Thus, the GWD proteins possess two vicinal phosphorylation sites, both of which are transiently phosphorylated. Following autophosphorylation at both sites, native dikinases flexibly use various terminal phosphate acceptors, such as water, alpha-glucans, AMP and ADP. A model is presented describing the complex phosphotransfer reactions of GWDs as affected by the availability of the various acceptors.
The uptake of potassium ions (K+) accompanied by an acidification of the apoplasm is a prerequisite for stomatal opening. The acidification (approximately 2-2.5 pH units) is perceived by voltage-gated inward potassium channels (K-in) that then can open their pores with lower energy cost. The sensory units for extracellular pH in stomatal K-in channels are proposed to be histidines exposed to the apoplasm. However, in the Arabidopsis thaliana stomatal K-in channel KAT1, mutations in the unique histidine exposed to the solvent (His(267)) do not affect the pH dependency. We demonstrate in the present study that His(267) of the KAT1 channel cannot sense pH changes since the neighbouring residue Phe(266) shifts its pK(a) to undetectable values through a cation-pi interaction. Instead, we show that Glu(240) placed in the extracellular loop between transmembrane segments S5 and S6 is involved in the extracellular acid activation mechanism. Based on structural models we propose that this region may serve as a molecular link between the pH- and the voltage-sensor. Like Glu(240), several other titratable residues could contribute to the pH-sensor of KAT1, interact with each other and even connect such residues far away from the voltage-sensor with the gating machinery of the channel.
Nuclear proteins play a central role in regulating gene expression. Their identification is important for understanding how the nuclear repertoire changes over time under different conditions. Nuclear proteins are often underrepresented in proteomic studies due to the frequently low abundance of proteins involved in regulatory processes. So far, only few studies describing the nuclear proteome of plant species have been published. Recently, the genome sequence of the unicellular green alga Chlamydomonas reinhardtii has been obtained and annotated, allowing the development of further detailed studies for this organism. However, a detailed description of its nuclear proteome has not been reported so far. Here, we present an analysis of the nuclear proteome of the sequenced Chlamydomonas strain cc503. Using LC-MS/MS, we identified 672 proteins from nuclei isolates with a maximum 1% peptide spectrum false discovery rate. Besides well-known proteins (e.g. histones), transcription factors and other transcriptional regulators (e.g. tubby and HMG) were identified. The presence of protein motifs in nuclear proteins was investigated by computational tools, and specific over-represented protein motifs were identified. This study provides new insights into the complexity of the nuclear environment and reveals novel putative protein targets for further studies of nuclear mechanisms.
Application of crab shell chitin or pentamer chitin oligosaccharide to Arabidopsis seedlings increased tolerance to salinity in wild-type but not in knockout mutants of the LysM Receptor-Like Kinase1 (CERK1/LysM RLK1) gene, known to play a critical role in signaling defense responses induced by exogenous chitin. Arabidopsis plants overexpressing the endochitinase chit36 and hexoaminidase excy1 genes from the fungus Trichoderma asperelleoides T203 showed increased tolerance to salinity, heavy-metal stresses, and Botrytis cinerea infection. Resistant lines, overexpressing fungal chitinases at different levels, were outcrossed to lysm rlk1 mutants. Independent homozygous hybrids lost resistance to biotic and abiotic stresses, despite enhanced chitinase activity. Expression analysis of 270 stress-related genes, including those induced by reactive oxygen species (ROS) and chitin, revealed constant up-regulation (at least twofold) of 10 genes in the chitinase-overexpressing line and an additional 76 salt-induced genes whose expression was not elevated in the lysm rlk1 knockout mutant or the hybrids harboring the mutation. These findings elucidate that chitin-induced signaling mediated by LysM RLK1 receptor is not limited to biotic stress response but also encompasses abiotic-stress signaling and can be conveyed by ectopic expression of chitinases in plants.
Although intensification of toxic cyanobacterial blooms over the last decade is a matter of growing concern due to bloom impact on water quality, the biological role of most of the toxins produced is not known. In this critical review we focus primarily on the biological role of two toxins, microcystins and cylindrospermopsin, in inter- and intra-species communication and in nutrient acquisition. We examine the experimental evidence supporting some of the dogmas in the field and raise several open questions to be dealt with in future research. We do not discuss the health and environmental implications of toxin presence in the water body.
Aldehyde oxidase (AO) is a complex molybdo-flavoprotein that belongs to the xanthine oxidase family. AO is active as a homodimer, and each 150-kDa monomer binds two distinct [2Fe2S] clusters, FAD, and the molybdenum cofactor. AO has an important role in the metabolism of drugs based on its broad substrate specificity oxidizing aromatic aza-heterocycles, for example, N-1-methylnicotinamide and N-methylphthalazinium, or aldehydes, such as benzaldehyde, retinal, and vanillin. Sequencing the 35 coding exons of the human AOX1 gene in a sample of 180 Italian individuals led to the identification of relatively frequent, synonymous, missense and nonsense single-nucleotide polymorphisms (SNPs). Human aldehyde oxidase (hAOX1) was purified after heterologous expression in Escherichia coli. The recombinant protein was obtained with a purity of 95% and a yield of 50 mu g/l E. coli culture. Site-directed mutagenesis of the hAOX1 cDNA allowed the purification of protein variants bearing the amino acid changes R802C, R921H, N1135S, and H1297R, which correspond to some of the identified SNPs. The hAOX1 variants were purified and compared with the wild-type protein relative to activity, oligomerization state, and metal content. Our data show that the mutation of each amino acid residue has a variable impact on the ability of hAOX1 to metabolize selected substrates. Thus, the human population is characterized by the presence of functionally inactive hAOX1 allelic variants as well as variants encoding enzymes with different catalytic activities. Our results indicate that the presence of these allelic variants should be considered for the design of future drugs.
Effects of food quality and quantity on consumers are neither independent nor interchangeable. Although consumer growth and reproduction show strong variation in relation to both food quality and quantity, the effects of food quality or food quantity have usually been studied in isolation. In two experiments, we studied the growth and reproduction in three filter-feeding freshwater zooplankton species, i.e. Daphnia galeata x hyalina, D. pulicaria and D. magna, on their algal food (Scenedesmus obliquus), varying in carbon to phosphorus (C:P) ratios and quantities (concentrations). In the first experiment, we found a strong positive effect of the phosphorus content of food on growth of Daphnia, both in their early and late juvenile development. Variation in the relationship between the P-content of animals and their growth rate reflected interspecific differences in nutrient requirements. Although growth rates typically decreased as development neared maturation, this did not affect these species-specific couplings between growth rate and Daphnia P-content. In the second experiment, we examined the effects of food quality on Daphnia growth at different levels of food quantity. With the same decrease in P-content of food, species with higher estimated P-content at zero growth showed a larger increase in threshold food concentrations (i.e. food concentration sufficient to meet metabolic requirements but not growth). These results suggest that physiological processes such as maintenance and growth may in combination explain effects of food quality and quantity on consumers. Our study shows that differences in response to variation in food quality and quantity exist between species. As a consequence, species-specific effects of food quality on consumer growth will also determine how species deal with varying food levels, which has implications for resource-consumer interactions.
Aldehyde oxidases (AOXs) are homodimeric proteins belonging to the xanthine oxidase family of molybdenum-containing enzymes. Each 150-kDa monomer contains a FAD redox cofactor, two spectroscopically distinct [2Fe-2S] clusters, and a molybdenum cofactor located within the protein active site. AOXs are characterized by broad range substrate specificity, oxidizing different aldehydes and aromatic N-heterocycles. Despite increasing recognition of its role in the metabolism of drugs and xenobiotics, the physiological function of the protein is still largely unknown. We have crystallized and solved the crystal structure of mouse liver aldehyde oxidase 3 to 2.9 angstrom. This is the first mammalian AOX whose structure has been solved. The structure provides important insights into the protein active center and further evidence on the catalytic differences characterizing AOX and xanthine oxidoreductase. The mouse liver aldehyde oxidase 3 three-dimensional structure combined with kinetic, mutagenesis data, molecular docking, and molecular dynamics studies make a decisive contribution to understand the molecular basis of its rather broad substrate specificity.
The blowfly salivary gland - A model system for analyzing the regulation of plasma membrane V-ATPase
(2012)
Vacuolar H+-ATPases (V-ATPases) are heteromultimeric proteins that use the energy of ATP hydrolysis for the electrogenic transport of protons across membranes. They are common to all eukaryotic cells and are located in the plasma membrane or in membranes of acid organelles. In many insect epithelia, V-ATPase molecules reside in large numbers in the apical plasma membrane and create an electrochemical proton gradient that is used for the acidification or alkalinization of the extracellular space, the secretion or reabsorption of ions and fluids, the import of nutrients, and diverse other cellular activities. Here, we summarize our results on the functions and regulation of V-ATPase in the tubular salivary gland of the blowfly Calliphora vicina. In this gland, V-ATPase activity energizes the secretion of a KCl-rich saliva in response to the neurohormone serotonin (5-HT). Because of particular morphological and physiological features, the blowfly salivary glands are a superior and exemplary system for the analysis of the intracellular signaling pathways and mechanisms that modulate V-ATPase activity and solute transport in an insect epithelium.
The aromatic peroxygenase (APO; EC 1.11.2.1) from the agraric basidomycete Marasmius rotula (MroAPO) immobilized at the chitosan-capped gold-nanoparticle-modified glassy carbon electrode displayed a pair of redox peaks with a midpoint potential of -278.5 mV vs. AgCl/AgCl (1 M KCl) for the Fe(2+)/Fe(3+) redox couple of the heme-thiolate-containing protein. MroAPO oxidizes aromatic substrates such as aniline, p-aminophenol, hydroquinone, resorcinol, catechol, and paracetamol by means of hydrogen peroxide. The substrate spectrum overlaps with those of cytochrome P450s and plant peroxidases which are relevant in environmental analysis and drug monitoring. In M. rotula peroxygenase-based enzyme electrodes, the signal is generated by the reduction of electrode-active reaction products (e.g., p-benzoquinone and p-quinoneimine) with electro-enzymatic recycling of the analyte. In these enzyme electrodes, the signal reflects the conversion of all substrates thus representing an overall parameter in complex media. The performance of these sensors and their further development are discussed.
In the light of ongoing land use changes, it is important to understand how multitrophic communities perform at different land use intensities. The paradox of enrichment predicts that fertilization leads to destabilization and extinction of predator-prey systems. We tested this prediction for a land use intensity gradient from natural to highly fertilized agricultural ecosystems. We included multiple aboveground and belowground trophic levels and land use-dependent searching efficiencies of insects. To overcome logistic constraints of field experiments, we used a successfully validated simulation model to investigate plant responses to removal of herbivores and their enemies. Consistent with our predictions, instability measured by herbivore-induced plant mortality increased with increasing land use intensity. Simultaneously, the balance between herbivores and natural enemies turned increasingly towards herbivore dominance and natural enemy failure. Under natural conditions, there were more frequently significant effects of belowground herbivores and their natural enemies on plant performance, whereas there were more aboveground effects in agroecosystems. This result was partly due to the "boom-bust'' behavior of the shoot herbivore population. Plant responses to herbivore or natural enemy removal were much more abrupt than the imposed smooth land use intensity gradient. This may be due to the presence of multiple trophic levels aboveground and belowground. Our model suggests that destabilization and extinction are more likely to occur in agroecosystems than in natural communities, but the shape of the relationship is nonlinear under the influence of multiple trophic interactions. Citation: Meyer KM, Vos M, Mooij WM, Hol WHG, Termorshuizen AJ, et al. (2012) Testing the Paradox of Enrichment along a Land Use Gradient in a Multitrophic Aboveground and Belowground Community.
1. Poikilothermic animals incorporate more polyunsaturated fatty acids (PUFAs) into their cellular membranes as temperature declines, suggesting an increased sensitivity to PUFA limitation in cool conditions. To test this we raised Daphnia magna at different temperatures and investigated the effect of varying dietary PUFA on life history parameters (i.e. growth, reproduction) and the PUFA composition of body tissue and eggs.
2. Upon a PUFA-rich diet (Cryptomonas sp.) females showed higher concentrations of several omega 3 PUFAs in their body tissue at 15 degrees C than at 20 degrees C and 25 degrees C, indicating a greater structural requirement for omega 3 PUFAs at low temperature. Their eggs had an equal but higher concentration of omega 3 PUFAs than their body tissue.
3. In a life history experiment at 15 and 20 degrees C we supplemented a diet of a PUFA-free cyanobacterium with the omega 3 PUFA eicosapentaenoic acid (EPA). The growth of D. magna was more strongly EPA limited at low temperature. A greater requirement for structural EPA at 15 degrees C was indicated by a steeper increase in somatic EPA content with dietary EPA compared to 20 degrees C.
4. At 20 degrees C the development of eggs to successful hatching was high when EPA was supplied to the mothers. At 15 degrees C the hatching success was generally poor, despite of a higher maternal provision of EPA to eggs, compared to that at 20 degrees C, suggesting that EPA alone was insufficient for proper neonatal development at the low temperature. The growth of offspring from mothers raised at 20 degrees C without EPA supplementation was very low, indicating that the negative effects of EPA deficiency can be carried on to the next generation.
5. The fatty acid composition of Daphnia sp. in published field studies shows increasing proportions of saturated fatty acids with increasing environmental temperature, whereas omega 3 PUFAs and EPA show no clear pattern, suggesting that variations in dietary PUFA may mask temperature-dependent adjustments in omega 3 PUFA concentrations of cladocerans in nature.
To identify copper homeostasis genes in Rhodobacter capsulatus, we performed random transposon Tn5 mutagenesis. Screening of more than 10,000 Tn5 mutants identified tellurite resistance gene trgB as a so far unrecognized major copper tolerance determinant. The trgB gene is flanked by tellurite resistance gene trgA and cysteine synthase gene cysK2. While growth of trgA mutants was only moderately restricted by tellurite, trgB and cysK2 mutants were severely affected by tellurite, which implies that viability under tellurite stress requires increased cysteine levels. Mutational analyses revealed that trgB was the only gene in this chromosomal region conferring cross-tolerance towards copper. Expression of the monocistronic trgB gene required promoter elements overlapping the trgA coding region as shown by nested deletions. Neither copper nor tellurite affected trgB transcription as demonstrated by reverse transcriptase PCR and trgB-lacZ fusions. Addition of tellurite or copper gave rise to increased cellular tellurium and copper concentrations, respectively, as determined by inductively coupled plasma-optical emission spectroscopy. By contrast, cellular iron concentrations remained fairly constant irrespective of tellurite or copper addition. This is the first study demonstrating a direct link between copper and tellurite response in bacteria.
Coastal regions of the North East Atlantic and Mediterranean Seas have four known species of driftwood talitrids. Records are extremely scanty, often limited to the type locality and dating to 1950. We were able to study three of them, all belonging to the genus Macarorchestia, using fresh and archived samples including type material. Allometric and molecular analyses support: (1) a close relationship among all the three classically defined Macarorchestia species, (2) Macarorchestia was well separated from non-driftwood taxa, and (3) a putative new driftwood talitrid discovered during this study was not closely related to Macarorchestia. Genetic divergence between the new species and Macarorchestia remyi is as high as the average distance among a number of talitrid species included in the study for comparison. A key is provided to identify all three of the presently known species of Macarorchestia, using morphological characters employed in the allometric study.
Bacteriophages use specific tail proteins to recognize host cells. It is still not understood to molecular detail how the signal is transmitted over the tail to initiate infection. We have analysed in vitro DNA ejection in long-tailed siphovirus 9NA and short-tailed podovirus P22 upon incubation with Salmonella typhimurium lipopolysaccharide (LPS). We showed for the first time that LPS alone was sufficient to elicit DNA release from a siphovirus in vitro. Crystal structure analysis revealed that both phages use similar tailspike proteins for LPS recognition. Tailspike proteins hydrolyse LPS O antigen to position the phage on the cell surface. Thus we were able to compare in vitro DNA ejection processes from two phages with different morphologies with the same receptor under identical experimental conditions. Siphovirus 9NA ejected its DNA about 30 times faster than podovirus P22. DNA ejection is under control of the conformational opening of the particle and has a similar activation barrier in 9NA and P22. Our data suggest that tail morphology influences the efficiencies of particle opening given an identical initial receptor interaction event.
Metabolic networks are characterized by complex interactions and regulatory mechanisms between many individual components. These interactions determine whether a steady state is stable to perturbations. Structural kinetic modeling (SKM) is a framework to analyze the stability of metabolic steady states that allows the study of the system Jacobian without requiring detailed knowledge about individual rate equations. Stability criteria can be derived by generating a large number of structural kinetic models (SK-models) with randomly sampled parameter sets and evaluating the resulting Jacobian matrices. Until now, SKM experiments applied univariate tests to detect the network components with the largest influence on stability. In this work, we present an extended SKM approach relying on supervised machine learning to detect patterns of enzyme-metabolite interactions that act together in an orchestrated manner to ensure stability. We demonstrate its application on a detailed SK-model of the Calvin-Benson cycle and connected pathways. The identified stability patterns are highly complex reflecting that changes in dynamic properties depend on concerted interactions between several network components. In total, we find more patterns that reliably ensure stability than patterns ensuring instability. This shows that the design of this system is strongly targeted towards maintaining stability. We also investigate the effect of allosteric regulators revealing that the tendency to stability is significantly increased by including experimentally determined regulatory mechanisms that have not yet been integrated into existing kinetic models.
Syntheses of thiazolidine-fused heterocycles via exo-mode cyclizations of vinylogous N-acyliminium ions incorporating heteroatom-based nucleophiles have been examined and discussed. The formation of (5,6)-membered systems was feasible with all nucleophiles tried (O, S and N), while the closing of the five-membered ring was restricted to O- and S-nucleophiles. The closure of a four-membered ring failed. Instead, the bicyclic (5,6)-membered acetal derivative and the tricyclic system with an eight-membered central ring were obtained from the substrates containing O and S nucleophilic moieties, respectively. The reaction outcome and stereochemistry are rationalized using quantum chemical calculations at B3LYP/6-31G(d) level. The exclusive cis-stereoselectivity in the formation of (5,6)- and (5,5)-membered systems results from thermodynamic control, whereas the formation of the eight-membered ring was kinetically controlled.
Sustainable management of semi-arid African savannas under environmental and political change
(2012)
Drylands cover about 40% of the earth’s land surface and provide the basis for the livelihoods of 38% of the global human population. Worldwide, these ecosystems are prone to heavy degradation. Increasing levels of dryland degradation result a strong decline of ecosystem services. In addition, in highly variable semi-arid environments changing future environmental conditions will potentially have severe consequences for productivity and ecosystem dynamics. Hence, global efforts have to be made to understand the particular causes and consequences of dryland degradation and to promote sustainable management options for semi-arid and arid ecosystems in a changing world. Here I particularly address the problem of semi-arid savanna degradation, which mostly occurs in form of woody plant encroachment. At this, I aim at finding viable sustainable management strategies and improving the general understanding of semi-arid savanna vegetation dynamics under conditions of extensive livestock production. Moreover, the influence of external forces, i.e. environmental change and land reform, on the use of savanna vegetation and on the ecosystem response to this land use is assessed. Based on this I identify conditions and strategies that facilitate a sustainable use of semi-arid savanna rangelands in a changing world. I extended an eco-hydrological model to simulate rangeland vegetation dynamics for a typical semi-arid savanna in eastern Namibia. In particular, I identified the response of semi-arid savanna vegetation to different land use strategies (including fire management) also with regard to different predicted precipitation, temperature and CO2 regimes. Not only environmental but also economic and political constraints like e.g. land reform programmes are shaping rangeland management strategies. Hence, I aimed at understanding the effects of the ongoing process of land reform in southern Africa on land use and the semi-arid savanna vegetation. Therefore, I developed and implemented an agent-based ecological-economic modelling tool for interactive role plays with land users. This tool was applied in an interdisciplinary empirical study to identify general patterns of management decisions and the between-farm cooperation of land reform beneficiaries in eastern Namibia. The eco-hydrological simulations revealed that the future dynamics of semi-arid savanna vegetation strongly depend on the respective climate change scenario. In particular, I found that the capacity of the system to sustain domestic livestock production will strongly depend on changes in the amount and temporal distribution of precipitation. In addition, my simulations revealed that shrub encroachment will become less likely under future climatic conditions although positive effects of CO2 on woody plant growth and transpiration have been considered. While earlier studies predicted a further increase in shrub encroachment due to increased levels of atmospheric CO2, my contrary finding is based on the negative impacts of temperature increase on the drought sensitive seedling germination and establishment of woody plant species. Further simulation experiments revealed that prescribed fires are an efficient tool for semi-arid rangeland management, since they suppress woody plant seedling establishment. The strategies tested have increased the long term productivity of the savanna in terms of livestock production and decreased the risk for shrub encroachment (i.e. savanna degradation). This finding refutes the views promoted by existing studies, which state that fires are of minor importance for the vegetation dynamics of semi-arid and arid savannas. Again, the difference in predictions is related to the bottleneck at the seedling establishment stage of woody plants, which has not been sufficiently considered in earlier studies. The ecological-economic role plays with Namibian land reform beneficiaries showed that the farmers made their decisions with regard to herd size adjustments according to economic but not according to environmental variables. Hence, they do not manage opportunistically by tracking grass biomass availability but rather apply conservative management strategies with low stocking rates. This implies that under the given circumstances the management of these farmers will not per se cause (or further worsen) the problem of savanna degradation and shrub encroachment due to overgrazing. However, as my results indicate that this management strategy is rather based on high financial pressure, it is not an indicator for successful rangeland management. Rather, farmers struggle hard to make any positive revenue from their farming business and the success of the Namibian land reform is currently disputable. The role-plays also revealed that cooperation between farmers is difficult even though obligatory due to the often small farm sizes. I thus propose that cooperation needs to be facilitated to improve the success of land reform beneficiaries.
We have analyzed the O-antigen polysaccharide of the previously uncharacterized Escherichia coli strain TD2158 which is a host of bacteriophage HK620. This bacteriophage recognizes and cleaves the polysaccharide with its tailspike protein (TSP). The polysaccharide preparation as well as oligosaccharides obtained from HK620TSP endoglycosidase digests were analyzed with NMR spectroscopy. Additionally, sugar analysis was performed on the O-antigen polysaccharide and MALDI-TOF MS was used in oligosaccharide analysis. The present study revealed a heterogeneous polysaccharide with a hexasaccharide repeating unit of the following structure:
alpha-D-Glcp-(1 -> 6) vertical bar vertical bar 2)-alpha-L-Rhap-(1 -> 6)-alpha-D-Glcp-(1 -> 4)-alpha-D-Galp-(1 -> 3)-alpha-D-GlcpNAc- (1 ->vertical bar beta-D-Glcp/beta-D-GlcpNAc-(1 -> 3)
A repeating unit with a D-GlcNAc substitution of D-Gal has been described earlier as characteristic for serogroup O18A1. Accordingly, we termed repeating units with D-Glc substitution at D-Gal as O18A2. NMR analyses of the polysaccharide confirmed that O18A1- and O18A2-type repeats were present in a 1:1 ratio. However, HK620TSP preferentially bound the D-GlcNAc- substituted O18A1-type repeating units in its high affinity binding pocket with a dissociation constant of 140 mu M and disfavored the O18A2-type having a beta-D-Glcp-(1 -> 3)-linked group. As a result, in hexasaccharide preparations, O18A1 and O18A2 repeats were present in a 9: 1 ratio stressing the clear preference of O18A1- type repeats to be cleaved by HK620TSP.
In landscapes which are predominately characterised by agriculture, natural ecosystems are often reduced to a mosaic of scattered patches of natural vegetation. Species with formerly connected distribution ranges now have restricted gene flow among populations. This has isolating effects upon population structure, because species are often confined by their limited dispersal capabilities. In this study, we test the effects of habitat fragmentation, precipitation, and isolation of populations on the genetic structure (AFLP) and fitness of the Asteraceae Catananche lutea. Our study area is an agro-dominated ecosystem in the desert-Mediterranean transition zone of the Southern Judea Lowlands in Israel. Our analysis revealed an intermediate level of intra-population genetic diversity across the study site with reduced genetic diversity on smaller scale. Although the size of the whole study area was relatively small (20 x 45 km), we found isolation by distance to be effective. We detected a high level of genetic differentiation among populations but genetic structure did not reflect spatial patterns. Population genetic diversity was correlated neither with position along the precipitation gradient nor with different seed types or other plant fitness variables in C. lutea.
Motivation: Metabolic engineering aims at modulating the capabilities of metabolic networks by changing the activity of biochemical reactions. The existing constraint-based approaches for metabolic engineering have proven useful, but are limited only to reactions catalogued in various pathway databases.
Results: We consider the alternative of designing synthetic strategies which can be used not only to characterize the maximum theoretically possible product yield but also to engineer networks with optimal conversion capability by using a suitable biochemically feasible reaction called 'stoichiometric capacitance'. In addition, we provide a theoretical solution for decomposing a given stoichiometric capacitance over a set of known enzymatic reactions. We determine the stoichiometric capacitance for genome-scale metabolic networks of 10 organisms from different kingdoms of life and examine its implications for the alterations in flux variability patterns. Our empirical findings suggest that the theoretical capacity of metabolic networks comes at a cost of dramatic system's changes.
Background: Female sperm storage has evolved independently multiple times among vertebrates to control reproduction in response to the environment. In internally fertilising amphibians, female salamanders store sperm in cloacal spermathecae, whereas among anurans sperm storage in oviducts is known only in tailed frogs. Facilitated through extensive field sampling following historical observations we tested for sperm storing structures in the female urogenital tract of fossorial, tropical caecilian amphibians.
Findings: In the oviparous Ichthyophis cf. kohtaoensis, aggregated sperm were present in a distinct region of the posterior oviduct but not in the cloaca in six out of seven vitellogenic females prior to oviposition. Spermatozoa were found most abundantly between the mucosal folds. In relation to the reproductive status decreased amounts of sperm were present in gravid females compared to pre-ovulatory females. Sperm were absent in females past oviposition.
Conclusions: Our findings indicate short-term oviductal sperm storage in the oviparous Ichthyophis cf. kohtaoensis. We assume that in female caecilians exhibiting high levels of parental investment sperm storage has evolved in order to optimally coordinate reproductive events and to increase fitness.
We tested, in the laboratory, the influence of light intensity, temperature, and phosphorus (P) supply on fatty acid (FA) concentrations of four freshwater algae: the green algae Scenedesmus quadricauda (Turpin) Breb. and Chlamydomonas globosa J. Snow, the cryptophyte Cryptomonas ovata Ehrenb., and the diatom Cyclotella meneghiniana Kutz. We investigated the main and interactive effects of two variables on algal FA concentrations (i.e., light intensity and P supply or temperature and P supply). Interactive effects of light intensity and P supply were most pronounced in C. meneghiniana, but were also found in S. quadricauda and C. ovata. Changes in several saturated and unsaturated FA concentrations with light were more distinct in the low-P treatments than in the high-P treatments. Interactive effects of temperature and P supply on various FA concentrations were observed in all four species, but there was no consistent pattern. In lake ecosystems, P limitation often coincides with high light intensities and temperatures in summer. Therefore, it is important to examine how combinations of these environmental conditions affect FA concentrations of primary producers that are important sources of FAs for higher trophic levels.
The global warming potential of nitrous oxide (N2O) and its long atmospheric lifetime mean its presence in the atmosphere is of major concern, and that methods are required to measure and reduce emissions. Large spatial and temporal variations means, however, that simple extrapolation of measured data is inappropriate, and that other methods of quantification are required. Although process-based models have been developed to simulate these emissions, they often require a large amount of input data that is not available at a regional scale, making regional and global emission estimates difficult to achieve. The spatial extent of organic soils means that quantification of emissions from these soil types is also required, but will not be achievable using a process-based model that has not been developed to simulate soil water contents above field capacity or organic soils. The ECOSSE model was developed to overcome these limitations, and with a requirement for only input data that is readily available at a regional scale, it can be used to quantify regional emissions and directly inform land-use change decisions. ECOSSE includes the major processes of nitrogen (N) turnover, with material being exchanged between pools of SOM at rates modified by temperature, soil moisture, soil pH and crop cover. Evaluation of its performance at site-scale is presented to demonstrate its ability to adequately simulate soil N contents and N2O emissions from cropland soils in Europe. Mitigation scenarios and sensitivity analyses are also presented to demonstrate how ECOSSE can be used to estimate the impact of future climate and land-use change on N2O emissions.
1. The complex, nonlinear response of dryland systems to grazing and climatic variations is a challenge to management of these lands. Predicted climatic changes will impact the desertification of drylands under domestic livestock production. Consequently, there is an urgent need to understand the response of drylands to grazing under climate change. 2. We enhanced and parameterized an ecohydrological savanna model to assess the impacts of a range of climate change scenarios on the response of a semi-arid African savanna to grazing. We focused on the effects of temperature and CO2 level increase in combination with changes in inter- and intra-annual precipitation patterns on the long-term dynamics of three major plant functional types. 3. We found that the capacity of the savanna to sustain livestock grazing was strongly influenced by climate change. Increased mean annual precipitation and changes in intra-annual precipitation pattern have the potential to slightly increase carrying capacities of the system. In contrast, decreased precipitation, higher interannual variation and temperature increase are leading to a severe decline of carrying capacities owing to losses of the perennial grass biomass. 4. Semi-arid rangelands will be at lower risk of shrub encroachment and encroachment will be less intense under future climatic conditions. This finding holds in spite of elevated levels of atmospheric CO2 and irrespective of changes in precipitation pattern, because of the drought sensitivity of germination and establishment of encroaching species. 5. Synthesis and applications. Changes in livestock carrying capacities, both positive and negative, mainly depend on the highly uncertain future rainfall conditions. However, independent of the specific changes, shrub encroachment becomes less likely and in many cases less severe. Thus, managers of semi-arid rangelands should shift their focus from woody vegetation towards perennial grass species as indicators for rangeland degradation. Furthermore, the resulting reduced competition from woody vegetation has the potential to facilitate ecosystem restoration measures such as re-introduction of desirable plant species that are only little promising or infeasible under current climatic conditions. On a global scale, the reductions in standing biomass resulting from altered degradation dynamics of semi-arid rangelands can have negative impacts on carbon sequestration.
Shape-memory properties of polyetherurethane foams prepared by thermally induced phase separation
(2012)
In this study, we report the preparation of two structurally different shape-memory polymer foams by thermally induced phase separation (TIPS) from amorphous polyetherurethanes. Foams with either a homogeneous, monomodal, or with a hierarchically structured, bimodal, pore size distribution are obtained by adoption of the cooling protocol. The shape-memory properties have been investigated for both foam structures by cyclic, thermomechanical experiments, while the morphological changes on the micro scale (pore level) have been compared to the macro scale by an in situ micro compression device experiment. The results show that the hierarchically structured foam achieves higher shape-recovery rates and a higher total recovery as compared to the homogeneous foam, which is due to an increased energy storage capability by micro scale bending of the hierarchically structured foam compared to pure compression of the homogeneous foam.