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The preparation of porous, i.e., high surface area electrodes from transparent conducting oxides, is a valuable goal in materials chemistry as such electrodes can enable further development of optoelectronic, electrocatalytic, or bioelectronic devices. In this work the first tin-rich mesoporous indium tin oxide is prepared using the molecular heterobimetallic single-source precursor, indium tin tris-tert-butoxide, together with an appropriate structure-directing template, yielding materials with high surface areas and tailorable pore size. The resulting mesoporous tin-rich ITO films show a high and durable electrical conductivity and transparency, making them interesting materials for hosting electroactive biomolecules such as proteins. In fact, its unique performance in bioelectronic applications has been demonstrated by immobilization of high amounts of cytochrome c into the mesoporous film which undergo redox processes directly with the conductive electrode material.
Trait-based studies have become extremely common in plant ecology. Trait-based approaches often rely on the tacit assumption that intraspecific trait variability (ITV) is negligible compared to interspecific variability, so that species can be characterized by mean trait values. Yet, numerous recent studies have challenged this assumption by showing that ITV significantly affects various ecological processes. Accounting for ITV may thus strengthen trait-based approaches, but measuring trait values on a large number of individuals per species and site is not feasible. Therefore, it is important and timely to synthesize existing knowledge on ITV in order to (1) decide critically when ITV should be considered, and (2) establish methods for incorporating this variability. Here we propose a practical set of rules to identify circumstances under which ITV should be accounted for. We formulate a spatial trait variance partitioning hypothesis to highlight the spatial scales at which ITV cannot be ignored in ecological studies. We then refine a set of four consecutive questions on the research question, the spatial scale, the sampling design, and the type of studied traits, to determine case-by-case if a given study should quantify ITV and test its effects. We review methods for quantifying ITV and develop a step-by-step guideline to design and interpret simulation studies that test for the importance of ITV. Even in the absence of quantitative knowledge on ITV, its effects can be assessed by varying trait values within species within realistic bounds around the known mean values. We finish with a discussion of future requirements to further incorporate ITV within trait-based approaches. This paper thus delineates a general framework to account for ITV and suggests a direction towards a more quantitative trait-based ecology.
The Aquatic Warbler Acrocephalus paludicola was once a common breeding bird in mesotrophic fen mires all over Central and Western Europe. In the last century large parts of its habitat have been destroyed by wetland drainage and agricultural intensification. Besides protecting the remaining breeding habitats, it is of great importance to preserve suitable migration stopover habitats and wintering grounds to avert the extinction of the species.
We determined home-range size and the use of vegetation associations of Aquatic Warblers on the wintering grounds in a flooded plain north of the Djoudj National Park in Senegal. Individual birds (11) were caught in mist nets and equipped with radio transmitters. Locations were assessed by radiotelemetry and a compositional analysis was conducted to determine which vegetation types were preferred within home ranges.
Similar to their behaviour on the breeding grounds, the Aquatic Warblers showed no territorial behaviour in their winter quarters. They used home ranges that averaged 4 ha in size, which they shared with conspecifics and other warblers. The home ranges overlapped 54% on average, with a maximum of 90% in an area used by four individuals. The vegetation structure of the wintering habitat is similar to breeding grounds and stopover sites of the species. Preferential vegetation had 80% to 100% cover and consisted of 60 to 90 cm high stands of Oryza longistaminata, Scirpus maritimus or Eleocharis mutata. Most birds stayed more often near the edge of open water, probably for foraging. A constant inundation seems essential, because Aquatic Warblers never occurred in desiccated parts of the study site.
To gain a deeper understanding of the mechanisms behind biomass accumulation, it is important to study plant growth behavior. Manually phenotyping large sets of plants requires important human resources and expertise and is typically not feasible for detection of weak growth phenotypes. Here, we established an automated growth phenotyping pipeline for Arabidopsis thaliana to aid researchers in comparing growth behaviors of different genotypes.
The analysis pipeline includes automated image analysis of two-dimensional digital plant images and evaluation of manually annotated information of growth stages. It employs linear mixed-effects models to quantify genotype effects on total rosette area and relative leaf growth rate (RLGR) and ANOVAs to quantify effects on developmental times.
Using the system, a single researcher can phenotype up to 7000 plants d(-1). Technical variance is very low (typically < 2%). We show quantitative results for the growth-impaired starch-excessmutant sex4-3 and the growth-enhancedmutant grf9.
We show that recordings of environmental and developmental variables reduce noise levels in the phenotyping datasets significantly and that careful examination of predictor variables (such as d after sowing or germination) is crucial to avoid exaggerations of recorded phenotypes and thus biased conclusions.
The new pi-conjugated 1,2,3-triazol-1,4-diyl fluoroionophore 1 generated via Cu(I) catalyzed [3 + 2] cycloaddition shows high fluorescence enhancement factors (FEF) in the presence of Na+ (FEF = 58) and K+ (FEF = 27) in MeCN and high selectivity towards K+ under simulated physiological conditions (160 mM K+ or Na+, respectively) with a FEF of 2.5 for K+.
ORS1, an H2O2-Responsive NAC Transcription Factor, Controls Senescence in Arabidopsis thaliana
(2011)
We report here that ORS1, a previously uncharacterized member of the NAC transcription factor family, controls leaf senescence in Arabidopsis thaliana. Overexpression of ORS1 accelerates senescence in transgenic plants, whereas its inhibition delays it. Genes acting downstream of ORS1 were identified by global expression analysis using transgenic plants producing dexamethasone-inducible ORS1-GR fusion protein. Of the 42 up-regulated genes, 30 (similar to 70%) were previously shown to be up-regulated during age-dependent senescence. We also observed that 32 (similar to 76%) of the ORS1-dependent genes were induced by long-term (4 d), but not short-term (6 h) salinity stress (150 mM NaCl). Furthermore, expression of 16 and 24 genes, respectively, was induced after 1 and 5 h of treatment with hydrogen peroxide (H2O2), a reactive oxygen species known to accumulate during salinity stress. ORS1 itself was found to be rapidly and strongly induced by H2O2 treatment in both leaves and roots. Using in vitro binding site selection, we determined the preferred binding motif of ORS1 and found it to be present in half of the ORS1-dependent genes. ORS1 is a paralog of ORE1/ANAC092/AtNAC2, a previously reported regulator of leaf senescence. Phylogenetic footprinting revealed evolutionary conservation of the ORS1 and ORE1 promoter sequences in different Brassicaceae species, indicating strong positive selection acting on both genes. We conclude that ORS1, similarly to ORE1, triggers expression of senescence-associated genes through a regulatory network that may involve cross-talk with salt- and H2O2-dependent signaling pathways.
The selaginella genome identifies genetic changes associated with the evolution of vascular plants
(2011)
Vascular plants appeared similar to 410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.
Motivation: Network-centered studies in systems biology attempt to integrate the topological properties of biological networks with experimental data in order to make predictions and posit hypotheses. For any topology-based prediction, it is necessary to first assess the significance of the analyzed property in a biologically meaningful context. Therefore, devising network null models, carefully tailored to the topological and biochemical constraints imposed on the network, remains an important computational problem.
Results: We first review the shortcomings of the existing generic sampling scheme-switch randomization-and explain its unsuitability for application to metabolic networks. We then devise a novel polynomial-time algorithm for randomizing metabolic networks under the (bio)chemical constraint of mass balance. The tractability of our method follows from the concept of mass equivalence classes, defined on the representation of compounds in the vector space over chemical elements. We finally demonstrate the uniformity of the proposed method on seven genome-scale metabolic networks, and empirically validate the theoretical findings. The proposed method allows a biologically meaningful estimation of significance for metabolic network properties.
Analysis of biological networks requires assessing the statistical significance of network-based predictions by using a realistic null model. However, the existing network null model, switch randomization, is unsuitable for metabolic networks, as it does not include physical constraints and generates unrealistic reactions. We present JMassBalance, a tool for mass-balanced randomization and analysis of metabolic networks. The tool allows efficient generation of large sets of randomized networks under the physical constraint of mass balance. In addition, various structural properties of the original and randomized networks can be calculated, facilitating the identification of the salient properties of metabolic networks with a biologically meaningful null model.
Mate choice copying was mostly described as a strategy employed by females to assess the quality of potential mates, but also males can copy other males' mate choice. An open question in this context is whether and how copying males evaluate sperm competition risk, as mating with a female that has already copulated with another male obviously sets the stage for intense sperm competition (i.e., in species with internal fertilization). Using the livebearing Atlantic molly (Poecilia mexicana) as a model, we asked (a) whether males of that species indeed copy other males' choices, and if they do so, (b) whether copying males strategically adjust their behavior to sperm competition risk. We used an approach where focal males could first choose to associate with a large or a small stimulus female. Mate choice tests were then repeated after an "observation phase" during which either no model male was present (treatment 1, control) or the previously non-preferred female could be seen associating (treatment 2) or physically interacting (treatment 3) with a model male. We found that, after the observation phase, males spent considerably more time with the previously non-preferred female in treatment (2), i.e., they copied the model male's choice. This effect was much weaker during treatment (3) where sexual interactions between the model male and the formerly non-preferred female were allowed. Males, therefore, seem to adjust their copying behavior strategically to the perceived risk of sperm competition.
Background: In many species males face a higher predation risk than females because males display elaborate traits that evolved under sexual selection, which may attract not only females but also predators. Females are, therefore, predicted to avoid such conspicuous males under predation risk. The present study was designed to investigate predator-induced changes of female mating preferences in Atlantic mollies (Poecilia mexicana). Males of this species show a pronounced polymorphism in body size and coloration, and females prefer large, colorful males in the absence of predators.
Results: In dichotomous choice tests predator-naive (lab-reared) females altered their initial preference for larger males in the presence of the cichlid Cichlasoma salvini, a natural predator of P. mexicana, and preferred small males instead. This effect was considerably weaker when females were confronted visually with the non-piscivorous cichlid Vieja bifasciata or the introduced non-piscivorous Nile tilapia (Oreochromis niloticus). In contrast, predator experienced (wild-caught) females did not respond to the same extent to the presence of a predator, most likely due to a learned ability to evaluate their predators' motivation to prey.
Conclusions: Our study highlights that (a) predatory fish can have a profound influence on the expression of mating preferences of their prey (thus potentially affecting the strength of sexual selection), and females may alter their mate choice behavior strategically to reduce their own exposure to predators. (b) Prey species can evolve visual predator recognition mechanisms and alter their mate choice only when a natural predator is present. (c) Finally, experiential effects can play an important role, and prey species may learn to evaluate the motivational state of their predators.
Despite the fact that the loss of a species from a community has the potential to cause a dramatic decline in biodiversity, for example through cascades of secondary extinctions, little is known about the factors contributing to the extinction risk of any particular species. Here we expand earlier modeling approaches using a dynamic food-web model that accounts for bottom-up as well as top-down effects. We investigate what factors influence a species' extinction risk and time to extinction of the non-persistent species.
We identified three basic properties that affect a species' risk of extinction. The highest extinction risk is born by species with (1) low energy input (e.g. high trophic level), (2) susceptibility to the loss of energy pathways (e.g. specialists with few prey species) and (3) dynamic instability (e.g. low Hill exponent and reliance on homogeneous energy channels when feeding on similarly sized prey).
Interestingly, and different from field studies, we found that the trophic level and not the body mass of a species influences its extinction risk. On the other hand, body mass is the single most important factor determining the time to extinction of a species, resulting in small species dying first. This suggests that in the field the trophic level might have more influence on the extinction risk than presently recognized.
Edaphic fauna contributes to important ecosystem functions in grassland soils such as decomposition and nutrient mineralization. Since this functional role is likely to be altered by global change and associated shifts in plant communities, a thorough understanding of large scale drivers on below-ground processes independent of regional differences in soil type or climate is essential. We investigated the relationship between abiotic (soil properties, management practices) and biotic (plant functional group composition, vegetation characteristics, soil fauna abundance) predictors and feeding activity of soil fauna after accounting for sample year and study region. Our study was carried out over a period of two consecutive years in 92 agricultural grasslands in three regions of Germany, spanning a latitudinal gradient of more than 500 km. A structural equation model suggests that feeding activity of soil fauna as measured by the bait-lamina test was positively related to legume and grass species richness in both years. Most probably, a diverse vegetation promotes feeding activity of soil fauna via alterations of both microclimate and resource availability. Feeding activity of soil fauna also increased with earthworm biomass via a pathway over Collembola abundance. The effect of earthworms on the feeding activity in soil may be attributed to their important role as ecosystem engineers. As no additional effects of agricultural management such as fertilization, livestock density or number of cuts on bait consumption were observed, our results suggest that the positive effect of legume and grass species richness on the feeding activity in soil fauna is a general one that will not be overruled by regional differences in management or environmental conditions. We thus suggest that agri-environment schemes aiming at the protection of belowground activity and associated ecosystem functions in temperate grasslands may generally focus on maintaining plant diversity, especially with regard to the potential effects of climate change on future vegetation structure.
Permanent genetic resources added to molecular ecology resources database 1 April 2011-31 May 2011
(2011)
This article documents the addition of 92 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Anopheles minimus, An. sinensis, An. dirus, Calephelis mutica, Lutjanus kasmira, Murella muralis and Orchestia montagui. These loci were cross-tested on the following species: Calephelis arizonensi, Calephelis borealis, Calephelis nemesis, Calephelis virginiensis and Lutjanus bengalensis.
In response to stress small organic compounds termed osmolytes are ubiquitously accumulated in all cell types to regulate the intracellular solvent quality and to counteract the deleterious effect on the stability and function of cellular proteins. Given the evidence that destabilization of the native state of a protein either by mutation or by environmental changes triggers the aggregation in the neurodegenerative pathologies, the modulation of the intracellular solute composition with osmolytes is an attractive strategy to stabilize an aggregating protein. Here we report the effect of three natural osmolytes on the in vivo and in vitro aggregation landscape of huntingtin exon 1 implicated in the Huntington's disease. Trimethylamine N-oxide (TMAO) and proline redirect amyloid fibrillogenesis of the pathological huntingtin exon 1 to nonamyloidogenic amorphous assemblies via two dissimilar molecular mechanisms. TMAO causes a rapid formation of bulky amorphous aggregates with minimally exposed surface area, whereas proline solubilizes the monomer and suppresses the accumulation of early transient aggregates. Conversely, glycine betaine enhances fibrillization in a fashion reminiscent of the genesis of functional amyloids. Strikingly, none of the natural osmolytes can completely abrogate the aggregate formation; however, they redirect the amyloidogenesis into alternative, nontoxic aggregate species. Our study reveals new insights into the complex interactions of osmoprotectants with polyQaggregates.
Background: The ability to create nanostructures with biomolecules is one of the key elements in nanobiotechnology. One of the problems is the expensive and mostly custom made equipment which is needed for their development. We intended to reduce material costs and aimed at miniaturization of the necessary tools that are essential for nanofabrication. Thus we combined the capabilities of molecular ink lithography with DNA-self-assembling capabilities to arrange DNA in an independent array which allows addressing molecules in nanoscale dimensions.
Results: For the construction of DNA based nanostructures a method is presented that allows an arrangement of DNA strands in such a way that they can form a grid that only depends on the spotted pattern of the anchor molecules. An atomic force microscope (AFM) has been used for molecular ink lithography to generate small spots. The sequential spotting process allows the immobilization of several different functional biomolecules with a single AFM-tip. This grid which delivers specific addresses for the prepared DNA-strand serves as a two-dimensional anchor to arrange the sequence according to the pattern. Once the DNA-nanoarray has been formed, it can be functionalized by PNA (peptide nucleic acid) to incorporate advanced structures.
Conclusions: The production of DNA-nanoarrays is a promising task for nanobiotechnology. The described method allows convenient and low cost preparation of nanoarrays. PNA can be used for complex functionalization purposes as well as a structural element.
Understanding and predicting the composition and spatial structure of communities is a central challenge in ecology. An important structural property of animal communities is the distribution of individual home ranges. Home range formation is controlled by resource heterogeneity, the physiology and behaviour of individual animals, and their intra- and interspecific interactions. However, a quantitative mechanistic understanding of how home range formation influences community composition is still lacking. To explore the link between home range formation and community composition in heterogeneous landscapes we combine allometric relationships for physiological properties with an algorithm that selects optimal home ranges given locomotion costs, resource depletion and competition in a spatially-explicit individual-based modelling framework. From a spatial distribution of resources and an input distribution of animal body mass, our model predicts the size and location of individual home ranges as well as the individual size distribution (ISD) in an animal community. For a broad range of body mass input distributions, including empirical body mass distributions of North American and Australian mammals, our model predictions agree with independent data on the body mass scaling of home range size and individual abundance in terrestrial mammals. Model predictions are also robust against variation in habitat productivity and landscape heterogeneity. The combination of allometric relationships for locomotion costs and resource needs with resource competition in an optimal foraging framework enables us to scale from individual properties to the structure of animal communities in heterogeneous landscapes. The proposed spatially-explicit modelling concept not only allows for detailed investigation of landscape effects on animal communities, but also provides novel insights into the mechanisms by which resource competition in space shapes animal communities.
Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony (GTP) is a phylogenetic optimization criterion in which a species tree that minimizes the number of gene duplications induced among a set of gene trees is selected. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic advances to examine the performance of GTP on a plant data set consisting of 18,896 gene trees containing 510,922 protein sequences from 136 plant taxa (giving a combined alignment length of >2.9 million characters). The relationships inferred from the GTP analysis were largely consistent with previous large-scale studies of backbone plant phylogeny and resolved some controversial nodes. The placement of taxa that were present in few gene trees generally varied the most among GTP bootstrap replicates. Excluding these taxa either before or after the GTP analysis revealed high levels of phylogenetic support across plants. The analyses supported magnoliids sister to a eudicot + monocot clade and did not support the eurosid I and II clades. This study presents a nuclear genomic perspective on the broad-scale phylogenic relationships among plants, and it demonstrates that nuclear genes with a history of duplication and loss can be phylogenetically informative for resolving the plant tree of life.
The loss of species from ecological communities can unleash a cascade of secondary extinctions, the risk and extent of which are likely to depend on the traits of the species that are lost from the community. To identify species traits that have the greatest impact on food web robustness to species loss we here subject allometrically scaled, dynamical food web models to several deletion sequences based on species' connectivity, generality, vulnerability or body mass. Further, to evaluate the relative importance of dynamical to topological effects we compare robustness between dynamical and purely topological models. This comparison reveals that the topological approach overestimates robustness in general and for certain sequences in particular. Top-down directed sequences have no or very low impact on robustness in topological analyses, while the dynamical analysis reveals that they may be as important as high-impact bottom-up directed sequences. Moreover, there are no deletion sequences that result, on average, in no or very few secondary extinctions in the dynamical approach. Instead, the least detrimental sequence in the dynamical approach yields an average robustness similar to the most detrimental (non-basal) deletion sequence in the topological approach. Hence, a topological analysis may lead to erroneous conclusions concerning both the relative and the absolute importance of different species traits for robustness. The dynamical sequential deletion analysis shows that food webs are least robust to the loss of species that have many trophic links or that occupy low trophic levels. In contrast to previous studies we can infer, albeit indirectly, that secondary extinctions were triggered by both bottom-up and top-down cascades.
Background: In Moco biosynthesis, sulfur is transferred from L-cysteine to MPT synthase, catalyzing the conversion of cPMP to MPT.
Results: The rhodanese-like protein YnjE is a novel protein involved in Moco biosynthesis.
Conclusion: YnjE enhances the rate of conversion of cPMP to MPT and interacts with MoeB and IscS. S
ignificance: To understand the mechanism of sulfur transfer and the role of rhodaneses in the cell.
Functional aspects of water soluble chlorophyll-binding protein (WSCP) in plants were investigated during the courses of leaf senescence, chlorophyll biogenesis, stress response and photoprotection. The cDNA sequence encoding WSCP from cauliflower was cloned into a binary vector to facilitate Agrobacterium tumefaciens mediated transformation of Nicotiana tabacum. The resultant transgenic tobacco plants overexpressed the CauWSCP gene under the control of a 35S-promoter. Analyses of protein and pigment contents indicate that WSCP overexpression does not enhance chlorophyll catabolism in vivo, thus rendering a role of WSCP in Chl degradation unlikely. Accumulation of higher levels of protochlorophyllide in WSCP overexpressor plants corroborates a proposed temporary storage and carrier function of WSCP for chlorophyll and late precursors. Although WSCP overexpressor plants did not show significant differences in non-photochemical quenching of chlorophyll fluorescence, they are characterized by significantly lower zeaxanthin accumulation and peroxidase activity at different light intensities, even at high light intensities of 700-900 mu mol photons m(-2) s(-1). These results suggest a photoprotective function of the functional chlorophyll binding-WSCP tetramer by shielding of chlorophylls from molecular oxygen.
Background: Flux coupling analysis (FCA) is a useful method for finding dependencies between fluxes of a metabolic network at steady-state. FCA classifies reactions into subsets (called coupled reaction sets) in which activity of one reaction implies activity of another reaction. Several approaches for FCA have been proposed in the literature.
Results: We introduce a new FCA algorithm, FFCA (Feasibility-based Flux Coupling Analysis), which is based on checking the feasibility of a system of linear inequalities. We show on a set of benchmarks that for genome-scale networks FFCA is faster than other existing FCA methods.
Conclusions: We present FFCA as a new method for flux coupling analysis and prove it to be faster than existing approaches. A corresponding software tool is freely available for non-commercial use at http://www.bioinformatics.org/ffca/.
Control over molecular architectures obtained via ADMET polymerization is limited by the step-growth nature of this technique. A new approach to this polycondensation method is described allowing for the synthesis of diblock and star-shaped polymers with molecular weight control by using the selectivity of olefin cross-metathesis between acrylates and terminal olefins.
The nutrient concentration in seeds determines many aspects of potential success of the sexual reproductive phase of plants, including the seed predation probability, efficiency of seed dispersal and seedling performance. Despite considerable research interest in latitudinal gradients of foliar nutrients, a similar gradient for seeds remains unexplored. We investigated a potential latitudinal gradient in seed nutrient concentrations within the widespread European understorey forest herb Anemone nemorosa L. We sampled seeds of A. nemorosa in 15 populations along a 1900-km long latitudinal gradient at three to seven seed collection dates post-anthesis and investigated the relative effects of growing degree-hours > 5 degrees C, soil characteristics and latitude on seed nutrient concentrations. Seed nitrogen, nitrogen:phosphorus ratio and calcium concentration decreased towards northern latitudes, while carbon:nitrogen ratios increased. When taking differences in growing degree-hours and measured soil characteristics into account and only considering the most mature seeds, the latitudinal decline remained particularly significant for seed nitrogen concentration. We argue that the decline in seed nitrogen concentration can be attributed to northward decreasing seed provisioning due to lower soil nitrogen availability or greater investment in clonal reproduction. This pattern may have large implications for the reproductive performance of this forest herb as the degree of seed provisioning ultimately co-determines seedling survival and reproductive success.
1. Worldwide, the floristic composition of temperate forests bears the imprint of past land use for decades to centuries as forests regrow on agricultural land. Many species, however, display significant interregional variation in their ability to (re)colonize post-agricultural forests. This variation in colonization across regions and the underlying factors remain largely unexplored.
2. We compiled data on 90 species and 812 species x study combinations from 18 studies across Europe that determined species' distribution patterns in ancient (i.e. continuously forested since the first available land use maps) and post-agricultural forests. The recovery rate (RR) of species in each landscape was quantified as the log-response ratio of the percentage occurrence in post-agricultural over ancient forest and related to the species-specific life-history traits and local (soil characteristics and light availability) and regional factors (landscape properties as habitat availability, time available for colonization, and climate).
3. For the herb species, we demonstrate a strong (interactive) effect of species' life-history traits and forest habitat availability on the RR of post-agricultural forest. In graminoids, however, none of the investigated variables were significantly related to the RR.
4. The better colonizing species that mainly belonged to the short-lived herbs group showed the largest interregional variability. Their recovery significantly increased with the amount of forest habitat within the landscape, whereas, surprisingly, the time available for colonization, climate, soil characteristics and light availability had no effect.
5. Synthesis. By analysing 18 independent studies across Europe, we clearly showed for the first time on a continental scale that the recovery of short-lived forest herbs increased with the forest habitat availability in the landscape. Small perennial forest herbs, however, were generally unsuccessful in colonizing post-agricultural forest even in relatively densely forested landscapes. Hence, our results stress the need to avoid ancient forest clearance to preserve the typical woodland flora.
Slow-colonizing forest understorey plants are probably not able to rapidly adjust their distribution range following large-scale climate change. Therefore, the acclimation potential to climate change within their actual occupied habitats will likely be key for their short-and long-term persistence. We combined transplant experiments along a latitudinal gradient with open-top chambers to assess the effects of temperature on phenology, growth and reproductive performance of multiple populations of slow-colonizing understorey plants, using the spring flowering geophytic forb Anemone nemorosa and the early summer flowering grass Milium effusum as study species. In both species, emergence time and start of flowering clearly advanced with increasing temperatures. Vegetative growth (plant height, aboveground biomass) and reproductive success (seed mass, seed germination and germinable seed output) of A. nemorosa benefited from higher temperatures. Climate warming may thus increase future competitive ability and colonization rates of this species. Apart from the effects on phenology, growth and reproductive performance of M. effusum generally decreased when transplanted southwards (e. g., plant size and number of individuals decreased towards the south) and was probably more limited by light availability in the south. Specific leaf area of both species increased when transplanted southwards, but decreased with open-top chamber installation in A. nemorosa. In general, individuals of both species transplanted at the home site performed best, suggesting local adaptation. We conclude that contrasting understorey plants may display divergent plasticity in response to changing temperatures which may alter future understorey community dynamics.
We measured LHS traits in 41 Anemone nemorosa and 44 Milium effusum populations along a 1900-2300 km latitudinal gradient from N France to N Sweden. We then applied multilevel models to identify the effects of regional (temperature, latitude) and local (soil fertility and acidity, overstorey canopy cover) environmental factors on LHS traits.
Both species displayed a significant 4% increase in plant height with every degree northward shift (almost a two-fold plant height difference between the southernmost and northernmost populations). Neither seed mass nor SLA showed a significant latitudinal cline. Temperature had a large effect on the three LHS traits of Anemone. Latitude, canopy cover and soil nutrients were related to the SLA and plant height of Milium. None of the investigated variables appeared to be related to the seed mass of Milium.
The variation in LHS traits indicates that the ecological strategy determined by the position of each population in this three-factor triangle is not constant along the latitudinal gradient. The significant increase in plant height suggests greater competitive abilities for both species in the northernmost populations. We also found that the studied environmental factors affected the LHS traits of the two species on various scales: spring-flowering Anemone was affected more by temperature, whereas early-summer flowering Milium was affected more by local and other latitude-related factors. Finally, previously reported cross-species correlations between LHS traits and latitude were generally unsupported by our within-species approach.
Protein expression in heterologous hosts for functional studies is a cumbersome effort. Here, we report a superior platform for parallel protein expression in vivo and in vitro. The platform combines highly efficient ligation-independent cloning (LIC) with instantaneous detection of expressed proteins through N- or C-terminal fusions to infrared fluorescent protein (IFP). For each open reading frame, only two PCR fragments are generated (with three PCR primers) and inserted by LIC into ten expression vectors suitable for protein expression in microbial hosts, including Escherichia coli, Kluyveromyces lactis, Pichia pastoris, the protozoon Leishmania tarentolae, and an in vitro transcription/translation system. Accumulation of IFP-fusion proteins is detected by infrared imaging of living cells or crude protein extracts directly after SDS-PAGE without additional processing. We successfully employed the LIC-IFP platform for in vivo and in vitro expression of ten plant and fungal proteins, including transcription factors and enzymes. Using the IFP reporter, we additionally established facile methods for the visualisation of protein-protein interactions and the detection of DNA-transcription factor interactions in microtiter and gel-free format. We conclude that IFP represents an excellent reporter for high-throughput protein expression and analysis, which can be easily extended to numerous other expression hosts using the setup reported here.
With its homo-pentameric structure and calcium-dependent specificity for phosphocholine (PCh), human c-reactive protein (CRP) is produced by the liver and secreted in elevated quantities in response to inflammation. CRP is widely accepted as a cardiac marker, e.g. in point-of-care diagnostics, however, its heterologous expression has proven difficult. Here, we demonstrate the expression of CRP in different Escherichia coli strains as well as by in vitro transcription/translation. Although expression in these systems was straightforward, most of the protein that accumulated was insoluble. We therefore expanded our study to include the expression of CRP in two eukaryotic hosts, namely the yeast Kluyveromyces lactis and the protozoon Leishmania tarentolae. Both expression systems are optimized for secretion of recombinant proteins and here allowed successful expression of soluble CRP. We also demonstrate the purification of recombinant CRP from Leishmania growth medium; the purification of protein expressed from K. lactis was not successful. Functional and intact CRP pentamer is known to interact with PCh in Ca(2+)-dependent manner. In this report we verify the binding specificity of recombinant CRP from L tarentolae (2 mu g/mL culture medium) for PCh.
Under natural conditions, plants are exposed to rapidly changing light intensities. To acclimate to such fluctuations, plants have evolved adaptive mechanisms that optimally exploit available light energy and simultaneously minimise damage of the photosynthetic apparatus through excess light. An important mechanism is the dissipation of excess excitation energy as heat which can be measured as nonphotochemical quenching of chlorophyll fluorescence (NPQ). In this paper, we present a highly simplified mathematical model that captures essential experimentally observed features of the short term adaptive quenching dynamics. We investigate the stationary and dynamic behaviour of the model and systematically analyse the dependence of characteristic system properties on key parameters such as rate constants and pool sizes. Comparing simulations with experimental data allows to derive conclusions about the validity of the simplifying assumptions and we further propose hypotheses regarding the role of the xanthophyll cycle in NPQ. We envisage that the presented theoretical description of the light reactions in conjunction with short term adaptive processes serves as a basis for the development of more detailed mechanistic models by which the molecular mechanisms of NPQ can be theoretically studied.
Indirect resource competition and interference are widely occurring mechanisms of interspecific interactions. We have studied the seasonal expression of these two interaction types within a two-species, boreal small mammal system. Seasons differ by resource availability, individual breeding state and intraspecific social system. Live-trapping methods were used to monitor space use and reproduction in 14 experimental populations of bank voles Myodes glareolus in large outdoor enclosures with and without a dominant competitor, the field vole Microtus agrestis. We further compared vole behaviour using staged dyadic encounters in neutral arenas in both seasons. Survival of the non-breeding overwintering bank voles was not affected by competition. In the spring, the numbers of male bank voles, but not of females, were reduced significantly in the competition populations. Bank vole home ranges expanded with vole density in the presence of competitors, indicating food limitation. A comparison of behaviour between seasons based on an analysis of similarity revealed an avoidance of costly aggression against opponents, independent of species. Interactions were more aggressive during the summer than during the winter, and heterospecific encounters were more aggressive than conspecific encounters. Based on these results, we suggest that interaction types and their respective mechanisms are not either-or categories and may change over the seasons. During the winter, energy constraints and thermoregulatory needs decrease direct aggression, but food constraints increase indirect resource competition. Direct interference appears in the summer, probably triggered by each individual's reproductive and hormonal state and the defence of offspring against conspecific and heterospecific intruders. Both interaction forms overlap in the spring, possibly contributing to spring declines in the numbers of subordinate species.
A number of short-lived, iteroparous animal species have small broods in the early breeding season and larger broods in later breeding season. Brood size affects not only offspring size, but as recent results suggest, may also affect offspring's temperament, hormonal status, and aggression as adults. Most populations of short-lived, iteroparous mammals fluctuate predictably over the season, with low densities in winter, increasing densities in summer and a population peak in late summer followed by a population breakdown. If animals live only through parts of the season, possibly such differences in density and hence also in social environments among seasons require different personality types to increase individual fitness. We present data on behavior of European rabbits from a field enclosure study. These data clearly show that aggressiveness is higher in young from smaller litters than in young from larger litters, and smaller litters are usually born during the early breeding season. Moreover, our data suggest that behavioral types of the young rabbits are stable over time, at least during their subadult life. We suggest, that changes in mean litter size over the course of the breeding season may not only be a product of mothers' age or food availability, but may also have an adaptive function by preparing offspring characteristics for adulthood in a social environment undergoing predictable density changes within the season.
Ex situ collections in botanic gardens have great potential in contributing to the conservation of rare plants. However, little is known about the effects of cultivation on the genetic diversity and fitness of garden populations, about genetic changes due to unconscious selection and potential adaptation to the artificial conditions. We compared the genetic variability and fitness of the rare, short-lived perennial Cynoglossum officinale from 12 botanic gardens and five natural populations in Germany. Genetic variability was assessed with eight nuclear microsatellites. Plants were grown in a common garden and performance was measured over 2 years. Mean genetic diversity was very similar in botanic garden and natural populations. However, four of the garden populations exhibited no genetic variability at all. Moreover, the genetic diversity of garden populations decreased with increasing duration of cultivation, indicating genetic drift. Plant performance from natural and garden populations in terms of growth, flowering and seed production was similar and in garden populations only seed mass was strongly related to genetic diversity. Several lines of evidence indicated genetic changes in garden populations in response to cultivation. Seed dormancy was strongly reduced in garden populations, and in response to nutrient addition garden plants increased the size of their main inflorescence, while wild plants increased the number of inflorescences. These changes could be maladaptive in nature and reduce the suitability of garden populations as a source for reintroductions. We suggest that botanic gardens should pay more attention to the problem of potential genetic changes in their plant collections.
Low-dimensional trade-offs fail to explain richness and structure in species-rich plant communities
(2011)
Mathematical models and ecological theory suggest that low-dimensional life history trade-offs (i.e. negative correlation between two life history traits such as competition vs. colonisation) may potentially explain the maintenance of species diversity and community structure. In the absence of trade-offs, we would expect communities to be dominated by 'super-types' characterised by mainly positive trait expressions. However, it has proven difficult to find strong empirical evidence for such trade-offs in species-rich communities. We developed a spatially explicit, rule-based and individual-based stochastic model to explore the importance of low-dimensional trade-offs. This model simulates the community dynamics of 288 virtual plant functional types (PFTs), each of which is described by seven life history traits. We consider trait combinations that fit into the trade-off concept, as well as super-types with little or no energy constraints or resource limitations, and weak PFTs, which do not exploit resources efficiently. The model is parameterised using data from a fire-prone, species-rich Mediterranean-type shrubland in southwestern Australia. We performed an exclusion experiment, where we sequentially removed the strongest PFT in the simulation and studied the remaining communities. We analysed the impact of traits on performance of PFTs in the exclusion experiment with standard and boosted regression trees. Regression tree analysis of the simulation results showed that the trade-off concept is necessary for PFT viability in the case of weak trait expression combinations such as low seed production or small seeds. However, species richness and diversity can be high despite the presence of super-types. Furthermore, the exclusion of super-types does not necessarily lead to a large increase in PFT richness and diversity. We conclude that low-dimensional trade-offs do not provide explanations for multi-species co-existence contrary to the prediction of many conceptual models.
We consider a sessile hemispherical bubble sitting on the transversally oscillating bottom of a deep liquid layer and focus on the interplay of the compressibility of the bubble and the contact angle hysteresis. In the presence of contact angle hysteresis, the compressible bubble exhibits two kinds of terminal oscillations: either with the stick-slip motion of the contact line or with the completely immobile contact line. For the stick-slip oscillations, we detect a double resonance, when the external frequency is close to eigenfrequencies of both the breathing mode and shape oscillations. For the regimes evolving to terminal oscillations with the fixed contact line, we find an unusual transient resembling modulated oscillations.
Random matrix theory (RMT) is well suited to describing the emergent properties of systems with complex interactions amongst their constituents through their eigenvalue spectrums. Some RMT results are applied to the problem of clustering high dimensional biological data with complex dependence structure amongst the variables. It will be shown that a gene relevance or correlation network can be constructed by choosing a correlation threshold in a principled way, such that it corresponds to a block diagonal structure in the correlation matrix, if such a structure exists. The structure is then found using community detection algorithms, but with parameter choice guided by RMT predictions. The resulting clustering is compared to a variety of hierarchical clustering outputs and is found to the most generalised result, in that it captures all the features found by the other considered methods.
Synergistic in vitro anti-HIV type 1 activity of tenofovir with carbohydrate-binding agents (CBAs)
(2011)
Tenofovir, a well-known and highly prescribed anti-HIV-1 drug for the treatment of HIV/AIDS infections, has recently also shown its effectiveness as a potential microbicide drug in the prevention of HIV transmission.
Here, we evaluated the combination of tenofovir with various members of the class of carbohydrate-binding agents (CBAs) targeting the glycans on the viral envelope gp120 for their anti-HIV efficacy. The tenofovir/CBA combinations predominantly showed synergistic antiviral activity using the median effect principle.
These findings illustrate that combination of tenofovir with CBAs may increase the antiviral potency of the individual drugs and reducing the risk on potential side-effects.
Almost all glucosyl transfer reactions rely on glucose-1-phosphate (Glc-1-P) that either immediately acts as glucosyl donor or as substrate for the synthesis of the more widely used Glc dinucleotides, ADPglucose or UDPglucose. In this communication, we have analyzed two Glc-1-P-related processes: the carbon flux from externally supplied Glc-1-P to starch by either mesophyll protoplasts or intact chloroplasts from Arabidopsis (Arabidopsis thaliana). When intact protoplasts or chloroplasts are incubated with [U-C-14]Glc-1-P, starch is rapidly labeled. Incorporation into starch is unaffected by the addition of unlabeled Glc-6-P or Glc, indicating a selective flux from Glc-1-P to starch. However, illuminated protoplasts incorporate less C-14 into starch when unlabeled bicarbonate is supplied in addition to the C-14-labeled Glc-1-P. Mesophyll protoplasts incubated with [U-C-14] Glc-1-P incorporate C-14 into the plastidial pool of adenosine diphosphoglucose. Protoplasts prepared from leaves of mutants of Arabidopsis that lack either the plastidial phosphorylase or the phosphoglucomutase isozyme incorporate C-14 derived from external Glc-1-P into starch, but incorporation into starch is insignificant when protoplasts from a mutant possessing a highly reduced ADPglucose pyrophosphorylase activity are studied. Thus, the path of assimilatory starch biosynthesis initiated by extraplastidial Glc-1-P leads to the plastidial pool of adenosine diphosphoglucose, and at this intermediate it is fused with the Calvin cycle-driven route. Mutants lacking the plastidial phosphoglucomutase contain a small yet significant amount of transitory starch.
Identification of a novel heteroglycan-interacting protein, HIP 1.3, from Arabidopsis thaliana
(2011)
Plastidial degradation of transitory starch yields mainly maltose and glucose. Following the export into the cytosol, maltose acts as donor for a glucosyl transfer to cytosolic heteroglycans as mediated by a cytosolic transglucosidase (DPE2; EC 2.4.1.25) and the second glucosyl residue is liberated as glucose. The cytosolic phosphorylase (Pho2/PHS2; EC 2.4.1.1) also interacts with heteroglycans using the same intramolecular sites as DPE2. Thus, the two glucosyl transferases interconnect the cytosolic pools of glucose and glucose 1-phosphate. Due to the complex monosaccharide pattern, other heteroglycan-interacting proteins (Hips) are expected to exist.
Identification of those proteins was approached by using two types of affinity chromatography. Heteroglycans from leaves of Arabidopsis thaliana (Col-0) covalently bound to Sepharose served as ligands that were reacted with a complex mixture of buffer-soluble proteins from Arabidopsis leaves. Binding proteins were eluted by sodium chloride. For identification, SDS-PAGE, tryptic digestion and MALDI-TOF analyses were applied. A strongly interacting polypeptide (approximately 40 kDa; designated as HIP1.3) was observed as product of locus At1g09340. Arabidopsis mutants deficient in HIP1.3 were reduced in growth and contained heteroglycans displaying an altered monosaccharide pattern. Wild type plants express HIP1.3 most strongly in leaves. As revealed by immuno fluorescence, HIP1.3 is located in the cytosol of mesophyll cells but mostly associated with the cytosolic surface of the chloroplast envelope membranes. In an HIP1.3-deficient mutant the immunosignal was undetectable. Metabolic profiles from leaves of this mutant and wild type plants as well were determined by GC-MS. As compared to the wild type control, more than ten metabolites, such as ascorbic acid, fructose, fructose bisphosphate, glucose, glycine, were elevated in darkness but decreased in the light. Although the biochemical function of HIP1.3 has not yet been elucidated, it is likely to possess an important function in the central carbon metabolism of higher plants.
The maximum population, also called Earth's carrying capacity, is the maximum number of people that can live on the food and other resources available on planet Earth. Previous investigations estimated the maximum carrying capacity as large as about 1 trillion people under the assumption that photosynthesis is the limiting process. Here we use a present state-of-the-art dynamic global vegetation model with managed planetary land surface, Lund-Potsdam-Jena managed Land (LPJmL), to calculate the yields of the most productive crops on a global 0.5 degrees x 0.5 degrees grid. Using the 2005 crop distribution the model predicts total harvested calories that are sufficient for the nutrition of 11.4 billion people. We define scenarios where humankind uses the whole land area for agriculture, saves the rain forests and the boreal evergreen forests or cultivates only pasture to feed animals. Every scenario is run in an extreme version with no allowance for urban and recreational needs and in two soft versions with a certain area per person for non-agricultural use. We find that there are natural limits of the maximum carrying capacity which are independent of any increase in agricultural productivity, if non-agricultural land use is accounted for. Using all land planet Earth can sustain 282 billion people. The save-forests-scenario yields 150 billion people. The scenario that cultivates only pasture to feed animals yields 96 billion people. Nevertheless, we should always have in mind that all our calculated numbers for the carrying capacity refer to extreme scenarios where humankind may only vegetate on this planet. Our numbers are considerably higher than the general median estimate of upper bounds of human population found in the literature in the order of 10 billion.
The present work contributes to the development of reusable sensing systems with a visual evaluation of the detection process related to an analyte. An electrochemical switchable protein-based optical device was designed with the core part composed of cytochrome c immobilized in a mesoporous indium tin oxide film. A color-developing redox-sensitive dye was used as switchable component of the system. The cytochrome c-catalyzed oxidation of the dye by hydrogen peroxide is spectroscopically investigated. When the dye is co-immobilized with the protein, its redox state is easily controlled by application of an electrical potential at the supporting material. This enables to electrochemically reset the system to the initial state and repetitive signal generation. The implemented reset function of the color forming reaction will make calibration of small test devices possible. The principle can be extended to other color forming redox reactions and to coupled enzyme systems, such as rapid food testing and indication of critical concentrations of metabolites for health care.
The essential mineral nutrient potassium (K(+)) is the most important inorganic cation for plants and is recognized as a limiting factor for crop yield and quality. Nonetheless, it is only partially understood how K(+) contributes to plant productivity. K(+) is used as a major active solute to maintain turgor and to drive irreversible and reversible changes in cell volume. K(+) also plays an important role in numerous metabolic processes, for example, by serving as an essential cofactor of enzymes. Here, we provide evidence for an additional, previously unrecognized role of K(+) in plant growth. By combining diverse experimental approaches with computational cell simulation, we show that K(+) circulating in the phloem serves as a decentralized energy storage that can be used to overcome local energy limitations. Posttranslational modification of the phloem-expressed Arabidopsis K(+) channel AKT2 taps this "potassium battery," which then efficiently assists the plasma membrane H(+)-ATPase in energizing the transmembrane phloem (re) loading processes.
Conservation actions need to account for and be adapted to address changes that will occur under global climate change. The identification of stresses on biological diversity (as defined in the Convention on Biological Diversity) is key in the process of adaptive conservation management. We considered any impact of climate change on biological diversity a stress because such an effect represents a change (negative or positive) in key ecological attributes of an ecosystem or parts of it. We applied a systemic approach and a hierarchical framework in a comprehensive classification of stresses to biological diversity that are caused directly by global climate change. Through analyses of 20 conservation sites in 7 countries and a review of the literature, we identified climate-change-induced stresses. We grouped the identified stresses according to 3 levels of biological diversity: stresses that affect individuals and populations, stresses that affect biological communities, and stresses that affect ecosystem structure and function. For each stress category, we differentiated 3 hierarchical levels of stress: stress class (thematic grouping with the coarsest resolution, 8); general stresses (thematic groups of specific stresses, 21); and specific stresses (most detailed definition of stresses, 90). We also compiled an overview of effects of climate change on ecosystem services using the categories of the Millennium Ecosystem Assessment and 2 additional categories. Our classification may be used to identify key climate-change-related stresses to biological diversity and may assist in the development of appropriate conservation strategies. The classification is in list format, but it accounts for relations among climate-change-induced stresses.
Scale-dependent determinants of plant species richness in a semi-arid fragmented agro-ecosystem
(2011)
Aims: (1) Understanding how the relationship between species richness and its determinants depends on the interaction between scales at which the response and explanatory variables are measured. (2) Quantifying the relative contributions of local, intermediate and large-scale determinants of species richness in a fragmented agro-ecosystem. (3) Testing the hypothesis that the relative contribution of these determinants varies with the grain size at which species richness is measured.
Location: A fragmented agro-ecosystem in the Southern Judea Lowland, Israel, within a desert-Mediterranean transition zone.
Methods: Plant species richness was estimated using hierarchical nested sampling in 81 plots, positioned in 38 natural vegetation patches within an agricultural matrix (mainly wheat fields) among three land units along a sharp precipitation gradient. Explanatory variables included position along that gradient, patch area, patch isolation, habitat heterogeneity and overall plant density. We used general linear models and hierarchical partitioning of variance to test and quantify the effect of each explanatory variable on species richness at four grain sizes (0.0625, 1, 25 and 225m(2)).
Results: Species richness was mainly affected by position along a precipitation gradient and overall plant density, and to a lesser extent by habitat heterogeneity. It was also significantly affected by patch area and patch isolation, but only for small grain sizes. The contribution of each explanatory variable to explained variance in species richness varied with grain size, i.e. scale-dependent. The influence of geographic position and habitat heterogeneity on species richness increased with grain size, while the influence of plant density decreased with grain size.
Main conclusions: Species richness is determined by the combined effect of several scale-dependent determinants. Ability to detect an effect and effect size of each determinant varies with the scale (grain size) at which it is measured. The combination of a multi-factorial approach and multi-scale sampling reveals that conclusions drawn from studies that ignore these dimensions are restricted and potentially misleading.
During the last decade microarrays have become a powerful analytical tool. Commonly microarrays are produced in a non-contact manner using silicone printheads. However, silicone printheads are expensive and not able to be used as a disposable. Here, we show the development and functional characterization of 8-channel plastic microarray printheads that overcome both disadvantages of their conventional silicone counterparts. A combination of injection-molding and laser processing allows us to produce a high quantity of cheap, customizable and disposable microarray printheads. The use of plastics (e.g., polystyrene) minimizes the need for surface modifications required previously for proper printing results. Time-consuming regeneration processes, cleaning procedures and contaminations caused by residual samples are avoided. The utilization of plastic printheads for viscous liquids, such as cell suspensions or whole blood, is possible. Furthermore, functional parts within the plastic printhead (e.g., particle filters) can be included. Our printhead is compatible with commercially available TopSpot devices but provides additional economic and technical benefits as compared to conventional TopSpot printheads, while fulfilling all requirements demanded on the latter. All in all, this work describes how the field of traditional microarray spotting can be extended significantly by low cost plastic printheads.
Spatiotemporal dynamics of the Calvin cycle multistationarity and symmetry breaking instabilities
(2011)
The possibility of controlling the Calvin cycle has paramount implications for increasing the production of biomass. Multistationarity, as a dynamical feature of systems, is the first obvious candidate whose control could find biotechnological applications. Here we set out to resolve the debate on the multistationarity of the Calvin cycle. Unlike the existing simulation-based studies, our approach is based on a sound mathematical framework, chemical reaction network theory and algebraic geometry, which results in provable results for the investigated model of the Calvin cycle in which we embed a hierarchy of realistic kinetic laws. Our theoretical findings demonstrate that there is a possibility for multistationarity resulting from two sources, homogeneous and inhomogeneous instabilities, which partially settle the debate on multistability of the Calvin cycle. In addition, our tractable analytical treatment of the bifurcation parameters can be employed in the design of validation experiments.
The prevailing paradigm in aquatic science is that microbial methanogenesis happens primarily in anoxic environments. Here, we used multiple complementary approaches to show that microbial methane production could and did occur in the well-oxygenated water column of an oligotrophic lake (Lake Stechlin, Germany). Oversaturation of methane was repeatedly recorded in the well-oxygenated upper 10 m of the water column, and the methane maxima coincided with oxygen oversaturation at 6 m. Laboratory incubations of unamended epilimnetic lake water and inoculations of photoautotrophs with a lake-enrichment culture both led to methane production even in the presence of oxygen, and the production was not affected by the addition of inorganic phosphate or methylated compounds. Methane production was also detected by in-lake incubations of lake water, and the highest production rate was 1.8-2.4 nM.h(-1) at 6 m, which could explain 33-44% of the observed ambient methane accumulation in the same month. Temporal and spatial uncoupling between methanogenesis and methanotrophy was supported by field and laboratory measurements, which also helped explain the oversaturation of methane in the upper water column. Potentially methanogenic Archaea were detected in situ in the oxygenated, methane-rich epilimnion, and their attachment to photoautotrophs might allow for anaerobic growth and direct transfer of substrates for methane production. Specific PCR on mRNA of the methyl coenzyme M reductase A gene revealed active methanogenesis. Microbial methane production in oxygenated water represents a hitherto overlooked source of methane and can be important for carbon cycling in the aquatic environments and water to air methane flux.
Target-distance computation by cortical neurons sensitive to echo delay is an essential characteristic of the auditory system of insectivorous bats. To assess if functional requirements such as detection of small insects versus larger stationary surfaces of plants are reflected in cortical properties, we compare delay-tuned neurons in a frugivorous (C. perspicillata, CP) and an insectivorous (P. parnellii, PP) bat species that belong to related families within the superfamily of Noctilionoidea. The bandwidth and shape of delay-tuning curves and the range of characteristic delays are similar in both species and hence are not related to different echolocation strategies. Most units respond at 2-6 ms echo delay with most sensitive thresholds of 20-30 dB SPL. In CP, units tuned to delays > 12 ms are slightly more abundant and are more sensitive than in PP. All delay-tuned neurons in CP reliably respond to single pure-tone stimuli, whereas such responses are only observed in 49% of delay-tuned units in PP. The cortical representation of echo delay (chronotopy) covers a larger area in CP but is less precise than described in PP. Since chronotopy is absent in certain other insectivorous bat species, it is open if these differences in topography are related to echolocation behaviour.
Estimating large herbivore density has been a major area of research in recent decades. Previous studies monitoring ungulate density, however, focused mostly on determining animal abundance, and did not interpret animal distribution in relation to habitat parameters. We surveyed large ungulates in the Biodiversity Exploratory Schorfheide-Chorin using faecal pellet group counts. This allowed us to explore the link between relative ungulate abundance, habitat use, and browsing damage on trees in a region with several types of forest, including unharvested and age-class beech forests, as well as age-class pine forests. Our results demonstrate that roe deer and fallow deer relative abundance is negatively correlated with large tree cover, and positively correlated with the cover of small shrubs (Rubus spec., Vaccinium spec.), and winter food supply. Habitat use of roe deer and fallow deer, as estimated by counting faecal pellet groups, revealed a preference for mature pine forests, and avoidance of deciduous forests. This differential habitat use is explained by different distributions of high quality food resources during winter. The response of deer to understory cover differed between roe deer and fallow deer at high cover percentages. The amount of browsing damage we observed on coniferous trees was not consistent with the relative deer abundance. Browsing damage was consistently higher on most deciduous trees, except for beech saplings which sustained less damage when roe deer density was low. Because roe deer is a highly selective feeder, it was reported to affect tree diversity by feeding only on trees with high nutritional value. Consequently, we propose that managing the number of all deer species by hunting is necessary to allow successful forest regeneration. Such an adjustment to deer numbers would need to account for both current tree diversity and alternative food resources. Our findings may be applicable to other forest landscapes in northeastern Germany including mature pine stands and differently harvested deciduous forests.
Potassium (K(+)) channel function is fundamental to many physiological processes. However, components and mechanisms regulating the activity of plant K(+) channels remain poorly understood. Here, we show that the calcium (Ca(2+)) sensor CBL4 together with the interacting protein kinase CIPK6 modulates the activity and plasma membrane (PM) targeting of the K(+) channel AKT2 from Arabidopsis thaliana by mediating translocation of AKT2 to the PM in plant cells and enhancing AKT2 activity in oocytes. Accordingly, akt2, cbl4 and cipk6 mutants share similar developmental and delayed flowering phenotypes. Moreover, the isolated regulatory C-terminal domain of CIPK6 is sufficient for mediating CBL4- and Ca(2+)-dependent channel translocation from the endoplasmic reticulum membrane to the PM by a novel targeting pathway that is dependent on dual lipid modifications of CBL4 by myristoylation and palmitoylation. Thus, we describe a critical mechanism of ion-channel regulation where a Ca(2+) sensor modulates K(+) channel activity by promoting a kinase interaction-dependent but phosphorylation-independent translocation of the channel to the PM.