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Background: Much of the organismal variation we observe in nature is due to differences in organ size. The observation that even closely related species can show large, stably inherited differences in organ size indicates a strong genetic component to the control of organ size. Despite recent progress in identifying factors controlling organ growth in plants, our overall understanding of this process remains limited, partly because the individual factors have not yet been connected into larger regulatory pathways or networks. To begin addressing this aim, we have studied the upstream regulation of expression of BIG BROTHER (BB), a central growth-control gene in Arabidopsis thaliana that prevents overgrowth of organs. Final organ size and BB expression levels are tightly correlated, implying the need for precise control of its expression. BB expression mirrors proliferative activity, yet the gene functions to limit proliferation, suggesting that it acts in an incoherent feedforward loop downstream of growth activators to prevent over-proliferation. Results: To investigate the upstream regulation of BB we combined a promoter deletion analysis with a phylogenetic footprinting approach. We were able to narrow down important, highly conserved, cis-regulatory elements within the BB promoter. Promoter sequences of other Brassicaceae species were able to partially complement the A. thaliana bb-1 mutant, suggesting that at least within the Brassicaceae family the regulatory pathways are conserved. Conclusions: This work underlines the complexity involved in precise quantitative control of gene expression and lays the foundation for identifying important upstream regulators that determine BB expression levels and thus final organ size.
Background: Detection of immunogenic proteins remains an important task for life sciences as it nourishes the understanding of pathogenicity, illuminates new potential vaccine candidates and broadens the spectrum of biomarkers applicable in diagnostic tools. Traditionally, immunoscreenings of expression libraries via polyclonal sera on nitrocellulose membranes or screenings of whole proteome lysates in 2-D gel electrophoresis are performed. However, these methods feature some rather inconvenient disadvantages. Screening of expression libraries to expose novel antigens from bacteria often lead to an abundance of false positive signals owing to the high cross reactivity of polyclonal antibodies towards the proteins of the expression host. A method is presented that overcomes many disadvantages of the old procedures.
Results: Four proteins that have previously been described as immunogenic have successfully been assessed immunogenic abilities with our method. One protein with no known immunogenic behaviour before suggested potential immunogenicity. We incorporated a fusion tag prior to our genes of interest and attached the expressed fusion proteins covalently on microarrays. This enhances the specific binding of the proteins compared to nitrocellulose. Thus, it helps to reduce the number of false positives significantly. It enables us to screen for immunogenic proteins in a shorter time, with more samples and statistical reliability. We validated our method by employing several known genes from Campylobacter jejuni NCTC 11168.
Conclusions: The method presented offers a new approach for screening of bacterial expression libraries to illuminate novel proteins with immunogenic features. It could provide a powerful and attractive alternative to existing methods and help to detect and identify vaccine candidates, biomarkers and potential virulence-associated factors with immunogenic behaviour furthering the knowledge of virulence and pathogenicity of studied bacteria.zeige weniger
Inheritance is an important and widely spread concept enabling the elegant expression of hierarchy in object-oriented software programs or models. It has been defined for graphs and graph transformations enhancing the applicability of this formal technique. Up to now, for the analysis of transformations with inheritance a flattening construction has been used, which yields all the well-known results for graph transformation but results in a large number of graphs and rules that have to be analyzed. In this paper, we introduce a new category of typed attributed graphs with inheritance. For the detection of conflicts between graph transformations on these graphs, the notion of abstract critical pairs is defined. This allows us to perform the analysis on polymorphic rules and transformations without the need for flattening, which significantly increases the efficiency of the analysis and eases the interpretation of the analysis results. The new main result is the Local Confluence Theorem for typed attributed graph transformation with inheritance using abstract critical pairs. All constructions and results are demonstrated on an example for the analysis of refactorings. (C) 2012 Elsevier B.V. All rights reserved.
We introduce the idea of actually cooling quantum systems by means of incoherent thermal light, hence giving rise to a counterintuitive mechanism of "cooling by heating." In this effect, the mere incoherent occupation of a quantum mechanical mode serves as a trigger to enhance the coupling between other modes. This notion of effectively rendering states more coherent by driving with incoherent thermal quantum noise is applied here to the optomechanical setting, where this effect occurs most naturally. We discuss two ways of describing this situation, one of them making use of stochastic sampling of Gaussian quantum states with respect to stationary classical stochastic processes. The potential of experimentally demonstrating this counterintuitive effect in optomechanical systems with present technology is sketched.
Analyzing insurance-loss data we derive stochastic storm-damage functions for residential buildings. On district level we fit power-law relations between daily loss and maximum wind speed, typically spanning more than 4 orders of magnitude. The estimated exponents for 439 German districts roughly range from 8 to 12. In addition, we find correlations among the parameters and socio-demographic data, which we employ in a simplified parametrization of the damage function with just 3 independent parameters for each district. A Monte Carlo method is used to generate loss estimates and confidence bounds of daily and annual storm damages in Germany. Our approach reproduces the annual progression of winter storm losses and enables to estimate daily losses over a wide range of magnitudes. Citation: Prahl, B. F., D. Rybski, J. P. Kropp, O. Burghoff, and H. Held (2012), Applying stochastic small-scale damage functions to German winter storms, Geophys. Res. Lett., 39, L06806, doi: 10.1029/2012GL050961.
Febuxostat, a drug recently approved in the US, European Union and Japan for treatment of gout, inhibits xanthine oxidoreductase (XOR)-mediated generation of uric acid during purine catabolism. It inhibits bovine milk XOR with a K-i in the picomolar-order, but we found that it is a much weaker inhibitor of Rhodobacter capsulatus XOR, even though the substrate-binding pockets of mammalian and bacterial XOR are well-conserved as regards to catalytically important residues and three-dimensional structure, and both permit the inhibitor to be accommodated in the active site, as indicated by computational docking studies. To clarify the reason for the difference of inhibitory potency towards the two XORs, we performed molecular dynamics simulations. The results indicate that differences in mobility of hydrophobic residues that do not directly interact with the substrate account for the difference in inhibitory potency.
Nanogradient polymer brushes
(2012)
A transient two-dimensional model describing degenerate four-wave mixing inside saturable gain media is presented. The new model is compared to existing one-dimensional models with their qualitative results confirmed. Large quantitative differences with respect to peak reflectivity and optimum pump fluence are observed. Furthermore, the influence of the beam focus size, the transverse position and the crossing angle on the reflectivity of the grating is investigated using the improved model. It is demonstrated that the phase conjugate reflectivity depends sensitively on the transverse features of the interacting beams with a transverse shift in the position of the pump beams yielding a threefold improvement in reflectivity. (C) 2012 Optical Society of America
Forests seem to represent low-erosion systems, according to most, but not all, studies of suspended-sediment yield. We surmised that this impression reflects an accidental bias in the selection of monitoring sites towards those with prevailing vertical hydrological flowpaths, rather than a tight causal link between vegetation cover and erosion alone. To evaluate this conjecture, we monitored, over a 2-year period, a 3.3 ha old-growth rainforest catchment prone to frequent and widespread overland flow. We sampled stream flow at two and overland flow at three sites in a nested arrangement on a within-event basis, and monitored the spatial and temporal frequency of overland flow. Suspended-sediment concentrations were modeled with Random Forest and Quantile Regression Forest to be able to estimate the annual yields for the 2 years, which amounted to 1 t ha(-1) and 2 t ha(-1) in a year with below-average and with average precipitation, respectively. These estimates place our monitoring site near the high end of reported suspended-sediment yields and lend credence to the notion that low yields reflect primarily the dominance of vertical flowpaths and not necessarily and exclusively the kind of vegetative cover. Undisturbed forest and surface erosion are certainly no contradiction in terms even in the absence of mass movements.
The use of nanoparticles in polymer composite dielectrics has promised great improvements, but useful results have been elusive. Here, the importance of the interfacial interactions between the nanoparticles and the polymer matrix are investigated in TiO2 nanocomposites for dielectric materials using surface functionalisation. The interface is observed to dominate the nanocomposite properties and leads to a threefold increase in permittivity at volume fractions as low as 10%. Surface functionalisation of the filler nanoparticles with silanes allows control of this interface, avoiding significant degradation of the other important material properties, particularly electrical breakdown strength, and resulting in a material that is demonstrated successfully as an active material in a dielectric elastomer actuator application with increased work output compared to the pure polymer. Although further permittivity increases are observed when the interface regions have formed a percolation network, the other material properties deteriorate. The observation of percolation behaviour allows the interface thickness to be estimated.
This Letter describes four new 4-trimethylammonio-2,2,6,6-tetramethylpiperidine-1-yloxyls bearing camphorsulfonate, triflate, tosylate, or lactate as counter ions. These spin probes were made by anion metathesis of 4-trimethylammonio-2,2,6,6-tetramethylpiperidine-1-yloxyl iodide using the corresponding silver salts. The latter is made by the alkylation of 4-amino-2,2,6,6-tetramethylpiperidine-1-yloxyl. Furthermore, the Letter gives an improved synthetic way to 4-sulfonamido-2,2,6,6-tetramethylpiperidine-1-yloxyl using chlorosulfuric acid trimethylsilylester and 4-amino-2,2,6,6-tetramethylpiperidine-1-yloxyl. All the spin probes are highly interesting for the investigation of ionic liquids.
Background: There are alternative substrates to the mitochondrial respiration.
Results: Data-driven model-based analysis renders predictions of alternative substrates to the mitochondrial respiration.
Conclusion: Metabolomics data in conjunction with flux-based models can discriminate among hypotheses based on enzymology alone.
Significance: This analysis provides a basic framework for in silico studies of alternative pathways in metabolism.
The large scale production of a monoclonal anti-progesterone antibody in serum free medium followed by affinity chromatography on protein G lead to a contamination of the antibody sample with a protein of about 14 kDa. This protein was identified by mass spectrometry as secretory leukocyte protease inhibitor (SLPI). This SLPI contamination lead to a failure of the fiber-optic based competitive fluorescence assay to detect progesterone in milk. Purification of the monoclonal antibody using protein A columns circumvented this problem.
Process-aware information systems typically involve various kinds of process stakeholders. That, in turn, leads to multiple process models that capture a common process from different perspectives and at different levels of abstraction. In order to guarantee a certain degree of uniformity, the consistency of such related process models is evaluated using formal criteria. However, it is unclear how modelling experts assess the consistency between process models, and which kind of notion they perceive to be appropriate.
In this paper, we focus on control flow aspects and investigate the adequacy of consistency notions. In particular, we report findings from an online experiment, which allows us to compare in how far trace equivalence and two notions based on behavioural profiles approximate expert perceptions on consistency. Analysing 69 expert statements from process analysts, we conclude that trace equivalence is not suited to be applied as a consistency notion, whereas the notions based on behavioural profiles approximate the perceived consistency of our subjects significantly. Therefore, our contribution is an empirically founded answer to the correlation of behaviour consistency notions and the consistency perception by experts in the field of business process modelling.
Management and engineering of process-aware information systems:
Introduction to the special issue
(2012)
We compare standard and inverted bulk heterojunction solar cells composed of PCPDTBT:PC70BM blends. Inverted devices comprising 100 nm thick active layers exhibited short circuit currents of 15 mA/cm(2), 10% larger than in corresponding standard devices. Modeling of the optical field distribution in the different device stacks proved that this enhancement originates from an increased absorption of incident light in the active layer. Internal quantum efficiencies (IQEs) were obtained from the direct comparison of experimentally derived and modeled currents for different layer thicknesses, yielding IQEs of similar to 70% for a layer thickness of 100 nm. Simulations predict a significant increase of the light harvesting efficiency upon increasing the layer thickness to 270 nm. However, a continuous deterioration of the photovoltaic properties with layer thickness was measured for both device architectures, attributed to incomplete charge extraction. On the other hand, our optical modeling suggests that inverted devices based on PCPDTBT should be able to deliver high power conversion efficiencies (PCEs) of more than 7% provided that recombination losses can be reduced.
Background: Recently, first evidence has been reported for a geneparenting interaction (G x E) with regard to adolescent alcohol use. The present investigation set out to extend this research using the catechol-O-methyltransferase (COMT) Val158Met polymorphism as a genetic susceptibility factor. Moreover, the current study examined whether a potential G x E would be consistent with one of two models of geneenvironment interplay (genetic vulnerability vs. differential susceptibility). Methods: Data were collected as part of an ongoing epidemiological cohort study following the outcome of early risk factors from birth into adulthood. Two hundred and eighty-five participants (130 males, 155 females) were genotyped for the COMT Val(158) Met polymorphism and were administered an alcohol interview, providing measures of current frequency and amount of drinking at ages 15 and 19 years. Information on three dimensions of perceived parenting behavior was obtained from the 15-year-olds. Results: Adolescents homozygous for the Met allele showed higher drinking activity at age 19 years when their parents had engaged in less supervision or were less involved, while their drinking activity was reduced under conditions of favorable parenting. No such relationship was found in individuals carrying the Val allele. Conclusions: The present findings correspond with the pattern of results predicted by the differential susceptibility hypothesis, suggesting that environmental variation would have a greater impact in individuals carrying a genetic susceptibility such that, in this group, exposure to negative environmental conditions would result in more adverse outcomes and the experience of favorable conditions would lead to more positive outcomes.
A temporary seismic network composed of 11 stations was installed in the city of Potenza (Southern Italy) to record local and regional seismicity within the context of a national project funded by the Italian Department of Civil Protection (DPC). Some stations were moved after a certain time in order to increase the number of measurement points, leading to a total of 14 sites within the city by the end of the experiment. Recordings from 26 local earthquakes (M-l 2.2-3.8 ) were analyzed to compute the site responses at the 14 sites by applying both reference and non-reference site techniques. Furthermore, the Spectral Intensity (SI) for each local earthquake, as well as their ratios with respect to the values obtained at a reference site, were also calculated. In addition, a field survey of 233 single station noise measurements within the city was carried out to increase the information available at localities different from the 14 monitoring sites. By using the results of the correlation analysis between the horizontal-to-vertical spectral ratios computed from noise recordings (NHV) at the 14 selected sites and those derived by the single station noise measurements within the town as a proxy, the spectral intensity correction factors for site amplification obtained from earthquake analysis were extended to the entire city area. This procedure allowed us to provide a microzonation map of the urban area that can be directly used when calculating risk scenarios for civil defence purposes. The amplification factors estimated following this approach show values increasing along the main valley toward east where the detrital and alluvial complexes reach their maximum thickness.
Honey bees (Apis mellifera) are well known for their excellent learning abilities. Although most age groups learn quickly to associate an odor with a sucrose reward, newly emerged bees and old foragers often perform poorly. For a long time, the reason for the poor learning performance of these age groups was unclear. We show that reduced sensitivity for sucrose is the cause for poor associative learning in newly emerged bees but not in old foragers. By increasing the sensitivity for sucrose through octopamine, we selectively improved the learning performance of insensitive newly emerged bees. Interestingly, the learning performance of foragers experiencing the same treatment remained low, despite the observed increase in sensitivity for the reward. We thus demonstrate that increasing sensitivity for the reward can improve the associative learning performance of bees when they are young but not when they had foraged for a long time. Importantly, octopamine can have very different effects on bees, depending on their initial sensory sensitivity. These differential effects of octopamine have important consequences for interpreting the action of biogenic amines on insect behavior.
We show that it is possible to approximate the zeta-function of a curve over a finite field by meromorphic functions which satisfy the same functional equation and moreover satisfy (respectively do not satisfy) an analog of the Riemann hypothesis. In the other direction, it is possible to approximate holomorphic functions by simple manipulations of such a zeta-function. No number theory is required to understand the theorems and their proofs, for it is known that the zeta-functions of curves over finite fields are very explicit meromorphic functions. We study the approximation properties of these meromorphic functions.