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Background
More than in other domains the heterogeneous services world in bioinformatics demands for a methodology to classify and relate resources in a both human and machine accessible manner. The Semantic Web, which is meant to address exactly this challenge, is currently one of the most ambitious projects in computer science. Collective efforts within the community have already led to a basis of standards for semantic service descriptions and meta-information. In combination with process synthesis and planning methods, such knowledge about types and services can facilitate the automatic composition of workflows for particular research questions.
Results
In this study we apply the synthesis methodology that is available in the Bio-jETI workflow management framework for the semantics-based composition of EMBOSS services. EMBOSS (European Molecular Biology Open Software Suite) is a collection of 350 tools (March 2010) for various sequence analysis tasks, and thus a rich source of services and types that imply comprehensive domain models for planning and synthesis approaches. We use and compare two different setups of our EMBOSS synthesis domain: 1) a manually defined domain setup where an intuitive, high-level, semantically meaningful nomenclature is applied to describe the input/output behavior of the single EMBOSS tools and their classifications, and 2) a domain setup where this information has been automatically derived from the EMBOSS Ajax Command Definition (ACD) files and the EMBRACE Data and Methods ontology (EDAM). Our experiments demonstrate that these domain models in combination with our synthesis methodology greatly simplify working with the large, heterogeneous, and hence manually intractable EMBOSS collection. However, they also show that with the information that can be derived from the (current) ACD files and EDAM ontology alone, some essential connections between services can not be recognized.
Conclusions
Our results show that adequate domain modeling requires to incorporate as much domain knowledge as possible, far beyond the mere technical aspects of the different types and services. Finding or defining semantically appropriate service and type descriptions is a difficult task, but the bioinformatics community appears to be on the right track towards a Life Science Semantic Web, which will eventually allow automatic service composition methods to unfold their full potential.
Many organisms have developed defences to avoid predation by species at higher trophic levels. The capability of primary producers to defend themselves against herbivores affects their own survival, can modulate the strength of trophic cascades and changes rates of competitive exclusion in aquatic communities. Algal species are highly flexible in their morphology, growth form, biochemical composition and production of toxic and deterrent compounds. Several of these variable traits in phytoplankton have been interpreted as defence mechanisms against grazing. Zooplankton feed with differing success on various phytoplankton species, depending primarily on size, shape, cell wall structure and the production of toxins and deterrents. Chemical cues associated with (i) mechanical damage, (ii) herbivore presence and (iii) grazing are the main factors triggering induced defences in both marine and freshwater phytoplankton, but most studies have failed to disentangle the exact mechanism(s) governing defence induction in any particular species. Induced defences in phytoplankton include changes in morphology (e.g. the formation of spines, colonies and thicker cell walls), biochemistry (such as production of toxins, repellents) and in life history characteristics (formation of cysts, reduced recruitment rate). Our categorization of inducible defences in terms of the responsible induction mechanism provides guidance for future work, as hardly any of the available studies on marine or freshwater plankton have performed all the treatments that are required to pinpoint the actual cue(s) for induction. We discuss the ecology of inducible defences in marine and freshwater phytoplankton with a special focus on the mechanisms of induction, the types of defences, their costs and benefits, and their consequences at the community level.
Fusarium spp. infection of cereal grain is a common problem, which leads to a dramatic loss of grain quality. The aim of the present study was to investigate the effect of Fusarium infection on the wheat storage protein gluten and its fractions, the gliadins and glutenins, in an in vitro model system. Gluten proteins were digested by F. graminearum proteases for 2, 4, 8 and 24 h, separated by Osborne fractionation and characterised by chromatographic (RP-HPLC) and electrophoretic analysis (SDS-Page). Gluten digestion by F. graminearum proteases showed in comparison with gliadins a preference for the glutenins whereas the HMW subfraction was at most affected. In comparison with a untreated control, the HMW subfraction was degraded of about 97% after 4 h incubation with Fusarium proteases. Separate digestion of gliadin and glutenin underlined the preference for HMW-GS. Analogue to the observed change in the gluten composition, the yield of the proteins extracted changed. A higher amount of glutenin fragments was found in the gliadin extraction solution after digestion and could mask a gliadin destruction at the same time. This observation can contribute to explain the frequently reported reduced glutenin amount parallel to an increase in gliadin quantity after Fusarium infection in grains.
Background
Riociguat is the first of a new class of drugs, the soluble guanylate cyclase (sGC) stimulators. Riociguat has a dual mode of action: it sensitizes sGC to the body’s own NO and can also increase sGC activity in the absence of NO. The NO-sGC-pathway is impaired in many cardiovascular diseases such as heart failure, pulmonary hypertension and diabetic nephropathy (DN). DN leads to high cardiovascular morbidity and mortality. There is still a high unmet medical need. The urinary albumin excretion rate is a predictive biomarker for these clinical events. Therefore, we investigated the effect of riociguat, alone and in combination with the angiotensin II receptor antagonist (ARB) telmisartan on the progression of DN in diabetic eNOS knock out mice, a new model closely resembling human pathology.
Methods
Seventy-six male eNOS knockout C57BL/6J mice were divided into 4 groups after receiving intraperitoneal high-dose streptozotocin: telmisartan (1 mg/kg), riociguat (3 mg/kg), riociguat+telmisartan (3 and 1 mg/kg), and vehicle. Fourteen mice were used as non-diabetic controls. After 12 weeks, urine and blood were obtained and blood pressure measured. Glucose concentrations were highly increased and similar in all diabetic groups.
Results
Riociguat, alone (105.2 ± 2.5 mmHg; mean±SEM; n = 14) and in combination with telmisartan (105.0 ± 3.2 mmHg; n = 12), significantly reduced blood pressure versus diabetic controls (117.1 ± 2.2 mmHg; n = 14; p = 0.002 and p = 0.004, respectively), whereas telmisartan alone (111.2 ± 2.6 mmHg) showed a modest blood pressure lowering trend (p = 0.071; n = 14). The effects of single treatment with either riociguat (97.1 ± 15.7 µg/d; n = 13) or telmisartan (97.8 ± 26.4 µg/d; n = 14) did not significantly lower albumin excretion on its own (p = 0.067 and p = 0.101, respectively). However, the combined treatment led to significantly lower urinary albumin excretion (47.3 ± 9.6 µg/d; n = 12) compared to diabetic controls (170.8 ± 34.2 µg/d; n = 13; p = 0.004), and reached levels similar to non-diabetic controls (31.4 ± 10.1 µg/d, n = 12).
Conclusion
Riociguat significantly reduced urinary albumin excretion in diabetic eNOS knock out mice that were refractory to treatment with ARB’s alone. Patients with diabetic nephropathy refractory to treatment with ARB’s have the worst prognosis among all patients with diabetic nephropathy. Our data indicate that additional stimulation of sGC on top of standard treatment with ARB`s may offer a new therapeutic approach for patients with diabetic nephropathy resistant to ARB treatment.
Due to their optical and electro-conductive attributes, carbazole derivatives are interesting materials for a large range of biosensor applications. In this study, we present the synthesis routes and fluorescence evaluation of newly designed carbazole fluorosensors that, by modification with uracil, have a special affinity for antiretroviral drugs via either Watson–Crick or Hoogsteen base pairing. To an N-octylcarbazole-uracil compound, four different groups were attached, namely thiophene, furane, ethylenedioxythiophene, and another uracil; yielding four different derivatives. Photophysical properties of these newly obtained derivatives are described, as are their interactions with the reverse transcriptase inhibitors such as abacavir, zidovudine, lamivudine and didanosine. The influence of each analyte on biosensor fluorescence was assessed on the basis of the Stern–Volmer equation and represented by Stern–Volmer constants. Consequently we have demonstrated that these structures based on carbazole, with a uracil group, may be successfully incorporated into alternative carbazole derivatives to form biosensors for the molecular recognition of antiretroviral drugs.
Saccades move objects of interest into the center of the visual field for high-acuity visual analysis. White, Stritzke, and Gegenfurtner (Current Biology, 18, 124–128, 2008) have shown that saccadic latencies in the context of a structured background are much shorter than those with an unstructured background at equal levels of visibility. This effect has been explained by possible preactivation of the saccadic circuitry whenever a structured background acts as a mask for potential saccade targets. Here, we show that background textures modulate rates of microsaccades during visual fixation. First, after a display change, structured backgrounds induce a stronger decrease of microsaccade rates than do uniform backgrounds. Second, we demonstrate that the occurrence of a microsaccade in a critical time window can delay a subsequent saccadic response. Taken together, our findings suggest that microsaccades contribute to the saccadic facilitation effect, due to a modulation of microsaccade rates by properties of the background.
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.
Restoration of semi-natural grassland communities
involves a combination of (1) sward disturbance to
create a temporal window for establishment, and (2)
target species introduction, the latter usually by seed
sowing. With great regularity, particular species
establish only poorly. More reliable establishment
could improve outcome of restoration projects and
increase cost-effectiveness. We investigated the
abiotic germination niche of ten poorly establishing
calcareous grassland species by simultaneously
exploring the effects of moisture and light availability
and temperature fluctuation on percentage germina-
tion and speed of germination. We also investigated
the effects of three different pre-treatments used to
enhance seed germination – cold-stratification, osmo-
tic priming and priming in combination with gibberellic
acid (GA 3 ) – and how these affected abiotic
germination niches. Species varied markedly in width
of abiotic germination niche, ranging from Carex flacca
with very strict abiotic requirements, to several species
reliably germinating across the whole range of abiotic
conditions. Our results suggest pronounced differ-
ences between species in gap requirements for
establishment. Germination was improved in most
species by at least one pre-treatment. Evidence for
positive effects of adding GA 3 to seed priming
solutions was limited. In several species, pre-treated
seeds germinated under a wider range of abiotic
conditions than untreated seeds. Improved knowledge
of species-specific germination niches and the effects
of seed pre-treatments may help to improve species
establishment by sowing, and to identify species for
which sowing at a later stage of restoration or
introduction as small plants may represent a more
viable strategy.
We show that the residue density of the logarithm of a generalized Laplacian on a closed manifold defines an invariant polynomial-valued differential form. We express it in terms of a finite sum of residues of
classical pseudodifferential symbols. In the case of the square of a Dirac operator, these formulas provide a pedestrian proof of the Atiyah–Singer formula for a pure Dirac operator in four dimensions and for a
twisted Dirac operator on a flat space of any dimension. These correspond to special cases of a more general formula by Scott and Zagier. In our approach, which is of perturbative nature, we use either a Campbell–Hausdorff formula derived by Okikiolu or a noncommutative Taylor-type formula.
X-ray observations of young Planetary Nebulæ (PNe) have revealed diffuse emission in extended regions around both H-rich and H-deficient central stars. In order to also repro-duce physical properties of H-deficient objects, we have, at first, extended our time-dependent radiation-hydrodynamic models with heat conduction for such conditions. Here we present some of the important physical concepts, which determine how and when a hot wind-blown bubble forms. In this study we have had to consider the, largely unknown, evolution of the CSPN, the slow (AGB) wind, the fast hot-CSPN wind, and the chemical composition. The main conclusion of our work is that heat conduction is needed to explain X-ray properties of wind-blown bubbles also in H-deficient objects.
We study pattern-forming instabilities in reaction-advection-diffusion systems. We develop an approach based on Lyapunov-Bloch exponents to figure out the impact of a spatially periodic mixing flow on the stability of a spatially homogeneous state. We deal with the flows periodic in space that may have arbitrary time dependence. We propose a discrete in time model, where reaction, advection, and diffusion act as successive operators, and show that a mixing advection can lead to a pattern-forming instability in a two-component system where only one of the species is advected. Physically, this can be explained as crossing a threshold of Turing instability due to effective increase of one of the diffusion constants.
The space missions Voyager and Cassini together with earthbound observations re-vealed a wealth of structures in Saturn’s rings. There are, for example, waves being excited at ring positions which are in orbital resonance with Saturn’s moons. Other structures can be assigned to embedded moons like empty gaps, moon induced wakes or S-shaped propeller features. Further-more, irregular radial structures are observed in the range from 10 meters until kilometers. Here some of these structures will be discussed in the frame of hydrodynamical modeling of Saturn’s dense rings. For this purpose we will characterize the physical properties of the ring particle ensemble by mean field quantities and point to the special behavior of the transport coefficients. We show that unperturbed rings can become unstable and how diffusion acts in the rings. Additionally, the alternative streamline formalism is introduced to describe perturbed regions of dense rings with applications to the wake damping and the dispersion relation of the density waves.
The main thread of this review article is to identify the reasons of how to account for the trajectory of American power in the region. Leaving behind the vast amount of highly politicised and hastily compiled volumes of recent years (notwithstanding valuable exceptions), the monographs composed by Lawrence Freedman, Trita Parsi and Oliver Roy attempt to subtly disentangle the intricacies of US involvement in the region from highly distinct perspectives. One caveat for International Relations theorists is that none of the
aforementioned authors intends to provide theoretical frameworks for his examination. However, since IR theory has damagingly neglected history in the last decades, the works under review here, at least in part, compensate for this disciplinary and intellectual failure. In conclusion, Freedman’s in-depth approach as a diplomatic historian, with its under-lying reference to the various traditions in US foreign policy thinking, is most illuminating, while Parsi’s contestable account focuses too narrowly on the Iran-Israel relationship. Roy’s explications fail to show how and why the ‘ideological’ element in US foreign policy came to carry exceedingly more weight after 2001 than it did in the 1990s.
Increased antioxidant capacity in the plasma of dogs after a single oral dosage of tocotrienols
(2011)
The intestinal absorption of tocotrienols (TCT) in dogs is, to our knowledge, so far unknown. Adult Beagle dogs (n 8) were administered a single oral dosage of a TCT-rich fraction (TRF; 40 mg/kg body weight) containing 32 % a-TCT, 2 % b-TCT, 27 % g-TCT, 14 % d-TCT and 25 % a-tocopherol (a-TCP). Blood was sampled at baseline (fasted), 1, 2, 3, 4, 5, 6, 8 and 12 h after supplementation. Plasma and chylomicron concentrations of TCT and a-TCP were measured at each time point. Plasma TAG were measured enzymatically, and plasma antioxidant capacity was assessed by the Trolox equivalent antioxidant capacity assay. In fasted dogs, levels of TCT were 0·07 ( SD 0·03) mmol/l. Following the administration of the TRF, total plasma TCT peaked at 2 h (7·16 ( SD 3·88) mmol/l; P, 0·01) and remained above baseline levels (0·67 ( SD 0·44) mmol/l; P, 0·01) at 12 h. The TCT response in chylomicrons paralleled the increase in TCT in plasma with a maximum peak (3·49 ( SD 2·06) mmol/l; P, 0·01) at 2 h post-dosage. a-TCP was the major vitamin E detected in plasma and unaffected by TRF supplementation. The Trolox equivalent values increased from 2 h (776 ( SD 51·2) mmol/l) to a maximum at 12 h (1130 ( SD 7·72) mmol/l; P,0·01). The results show that TCT are detected in postprandial plasma of dogs. The increase in antioxidant capacity suggests a potential beneficial role of TCT supplementation in the prevention or treatment of several diseases in dogs.
We asked whether invariant phonetic indices for syllable structure can be identified in a language where word-initial consonant clusters, regardless of their sonority profile, are claimed to be parsed heterosyllabically. Four speakers of Moroccan Arabic were recorded, using Electromagnetic Articulography. Pursuing previous work, we employed temporal diagnostics for syllable structure, consisting of static correspondences between any given phonological organisation and its presumed phonetic indices. We show that such correspondences offer only a partial understanding of the relation between syllabic organisation and continuous indices of that organisation. We analyse the failure of the diagnostics and put forth a new approach in which different phonological organisations prescribe different ways in which phonetic indices change as phonetic parameters are scaled. The main finding is that invariance is found in these patterns of change, rather than in static correspondences between phonological constructs and fixed values for their phonetic indices.
Although horses and donkeys belong to the same genus, their genetic characteristics probably result in specific proteomes and post-translational modifications (PTM) of proteins. Since PTM can alter protein properties, specific PTM may contribute to species-specific characteristics. Therefore, the aim of the present study was to analyse differences in serum protein profiles of horses and donkeys as well as mules, which combine the genetic backgrounds of both species. Additionally, changes in PTM of the protein transthyretin (TTR) were analysed. Serum protein profiles of each species (five animals per species) were determined using strong anion exchanger ProteinChips (R) (Bio-Rad, Munich, Germany) in combination with surface-enhanced laser desorption ionisation-time of flight MS. The PTM of TTR were analysed subsequently by immunoprecipitation in combination with matrix-assisted laser desorption ionisation-time of flight MS. Protein profiling revealed species-specific differences in the proteome, with some protein peaks present in all three species as well as protein peaks that were unique for donkeys and mules, horses and mules or for horses alone. The molecular weight of TTR of horses and donkeys differed by 30Da, and both species revealed several modified forms of TTR besides the native form. The mass spectra of mules represented a merging of TTR spectra of horses and donkeys. In summary, the present study indicated that there are substantial differences in the proteome of horses and donkeys. Additionally, the results probably indicate that the proteome of mules reveal a higher similarity to donkeys than to horses.
Using the notion of an elementary loop, Gebser and Schaub (2005. Proceedings of the Eighth International Conference on Logic Programming and Nonmonotonic Reasoning (LPNMR’05 ), 53–65) refined the theorem on loop formulas attributable to Lin and Zhao (2004) by considering loop formulas of elementary loops only. In this paper, we reformulate the definition of an elementary loop, extend it to disjunctive programs, and study several properties of elementary loops, including how maximal elementary loops are related to minimal unfounded sets. The results provide useful insights into the stable model semantics in terms of elementary loops. For a nondisjunctive program, using a graph-theoretic characterization of an elementary loop, we show that the problem of recognizing an elementary loop is tractable. On the other hand, we also show that the corresponding problem is coNP-complete for a disjunctive program. Based on the notion of an elementary loop, we present the class of Head-Elementary-loop-Free (HEF) programs, which strictly generalizes the class of Head-Cycle-Free (HCF) programs attributable to Ben-Eliyahu and Dechter (1994. Annals of Mathematics and Artificial Intelligence 12, 53–87). Like an HCF program, an HEF program can be turned into an equivalent nondisjunctive program in polynomial time by shifting head atoms into the body.
We present XMM-Newton and Chandra observations of the born-again planetary nebula A 30. These X-ray observations reveal a bright unresolved source at the position of the central star whose X-ray luminosity exceeds by far the model expectations for photospheric emission and for shocks within the stellar wind. We suggest that a “born-again hot bubble” may be responsible for this X-ray emission. Diffuse X-ray emission associated with the petal-like features and one of the H-poor knots seen in the optical is also found. The weakened emission of carbon lines in the spectrum of the diffuse emission can be interpreted as the dilution of stellar wind by mass-loading or as the detection of material ejected during a very late thermal pulse.
We introduce an approach to detecting inconsistencies in large biological networks by using answer set programming. To this end, we build upon a recently proposed notion of consistency between biochemical/genetic reactions and high-throughput profiles of cell activity. We then present an approach based on answer set programming to check the consistency of large-scale data sets. Moreover, we extend this methodology to provide explanations for inconsistencies by determining minimal representations of conflicts. In practice, this can be used to identify unreliable data or to indicate missing reactions.
Building biological models by inferring functional dependencies from experimental data is an important issue in Molecular Biology. To relieve the biologist from this traditionally manual process, various approaches have been proposed to increase the degree of automation. However, available approaches often yield a single model only, rely on specific assumptions, and/or use dedicated, heuristic algorithms that are intolerant to changing circumstances or requirements in the view of the rapid progress made in Biotechnology. Our aim is to provide a declarative solution to the problem by appeal to Answer Set Programming (ASP) overcoming these difficulties. We build upon an existing approach to Automatic Network Reconstruction proposed by part of the authors. This approach has firm mathematical foundations and is well suited for ASP due to its combinatorial flavor providing a characterization of all models explaining a set of experiments. The usage of ASP has several benefits over the existing heuristic algorithms. First, it is declarative and thus transparent for biological experts. Second, it is elaboration tolerant and thus allows for an easy exploration and incorporation of biological constraints. Third, it allows for exploring the entire space of possible models. Finally, our approach offers an excellent performance, matching existing, special-purpose systems.
Preference handling and optimization are indispensable means for addressing nontrivial applications in Answer Set Programming (ASP). However, their implementation becomes difficult whenever they bring about a significant increase in computational complexity. As a consequence, existing ASP systems do not offer complex optimization capacities, supporting, for instance, inclusion-based minimization or Pareto efficiency. Rather, such complex criteria are typically addressed by resorting to dedicated modeling techniques, like saturation. Unlike the ease of common ASP modeling, however, these techniques are rather involved and hardly usable by ASP laymen. We address this problem by developing a general implementation technique by means of meta-prpogramming, thus reusing existing ASP systems to capture various forms of qualitative preferences among answer sets. In this way, complex preferences and optimization capacities become readily available for ASP applications.
The armed conflict in Afghanistan since 2001 has raised manifold questions pertaining to the humanitarian rules relative to the conduct of hostilities. In Afghanistan, as is often the case in so-called asymmetric conflicts, the geographical and temporal boundaries of the battlefield, and the distinction between civilians and fighters, are increasingly blurred. As a result, the risks for both civilians and soldiers operating in Afghanistan are high. The objective of this article is to assess whether - and if so how much - the armed conflict in Afghanistan has affected the application and interpretation of the principles of distinction, proportionality, and precaution - principles that form the core of legal rules pertaining to the conduct of hostilities.
Urbanity and literature
(2011)
Transarea studies focus upon spaces as created by the movements that criss-cross them. From this point of view, from its very beginnings, literature is closely interrelated with a vectorial (and much less with a purely spatial) conception of history - and with urbanity, which plays a decisive role in Gilgamesh's travels through a (narrative) cosmos centered upon the city of Uruk. This article explores the city as a transareal space of movement in three examples of literature, with no fixed abode, around the turn of the millennium, i.e. Assia Djebar's Les Nuits de Strasbourg, Emine Sevgi Oezdamar's Istanbul-Berlin Trilogy, and Cecile Wajsbrot's L'ile aux musees. These three writers project, in a very specific way, cities in motion as anagrammatic and fractal structures.
To understand the evolution and morphology of planetary nebulae, a detailed knowledge of their central stars is required. Central stars that exhibit emission lines in their spectra, indicating stellar mass-loss allow to study the evolution of planetary nebulae in action. Emission line central stars constitute about 10 % of all central stars. Half of them are practically hydrogen-free Wolf-Rayet type central stars of the carbon sequence, [WC], that show strong emission lines of carbon and oxygen in their spectra. In this contribution we address the weak emission-lines central stars (wels). These stars are poorly analyzed and their hydrogen content is mostly unknown. We obtained optical spectra, that include the important Balmer lines of hydrogen, for four weak emission line central stars. We present the results of our analysis, provide spectral classification and discuss possible explanations for their formation and evolution.
The Karaburun Peninsula, which is considered part of the Anatolide-Tauride Block of Turkey, contains clastic and carbonate sequences deposited on the northern margin of Gondwana. The Palaeozoic clastic sequence, which is intruded by the Early Triassic granitoid and tectonically overlies a Mesozoic melange sequence, can be divided into three subunits: a lower clastic subunit consisting of a sandstone-shale alternation, an upper clastic subunit consisting of black chert-bearing shales, sandstone and conglomerate, and a Permo-Carboniferous carbonate subunit. The lower Triassic Karaburun I-type granitoid has a high initial Sr-87/Sr-86 ratio (0.709021-0.709168), and low Nd-143/Nd-144 ratio (0.512004-0.512023) and epsilon Nd (-5.34 to -5.70) isotopic values. Geochronological data indicate a crystallization (intrusion) age of 247.1 +/- 2.0 Ma (Scythian). Geochemically, the acidic magmatism reflects a subduction-related continental-arc basin tectonic setting, which can be linked to the opening of the northern branch of Neo-Tethys as a continental back-arc rifting basin on the northern margin of Gondwana. This can be related to the closure through southward subduction of the Palaeotethys Ocean beneath Gondwana.
The analysis of palaeoclimate time series is usually affected by severe methodological problems, resulting primarily from non-equidistant sampling and uncertain age models. As an alternative to existing methods of time series analysis, in this paper we argue that the statistical properties of recurrence networks - a recently developed approach - are promising candidates for characterising the system's nonlinear dynamics and quantifying structural changes in its reconstructed phase space as time evolves. In a first order approximation, the results of recurrence network analysis are invariant to changes in the age model and are not directly affected by non-equidistant sampling of the data. Specifically, we investigate the behaviour of recurrence network measures for both paradigmatic model systems with non-stationary parameters and four marine records of long-term palaeoclimate variations. We show that the obtained results are qualitatively robust under changes of the relevant parameters of our method, including detrending, size of the running window used for analysis, and embedding delay. We demonstrate that recurrence network analysis is able to detect relevant regime shifts in synthetic data as well as in problematic geoscientific time series. This suggests its application as a general exploratory tool of time series analysis complementing existing methods.
The aim of this paper is to estimate the Hurst parameter of Fractional Gaussian Noise (FGN) using Bayesian inference. We propose an estimation technique that takes into account the full correlation structure of this process. Instead of using the integrated time series and then applying an estimator for its Hurst exponent, we propose to use the noise signal directly. As an application we analyze the time series of the Nile River, where we find a posterior distribution which is compatible with previous findings. In addition, our technique provides natural error bars for the Hurst exponent.
We study pattern-forming instabilities in reaction-advection-diffusion systems. We develop an approach based on Lyapunov-Bloch exponents to figure out the impact of a spatially periodic mixing flow on the stability of a spatially homogeneous state. We deal with the flows periodic in space that may have arbitrary time dependence. We propose a discrete in time model, where reaction, advection, and diffusion act as successive operators, and show that a mixing advection can lead to a pattern-forming instability in a two-component system where only one of the species is advected. Physically, this can be explained as crossing a threshold of Turing instability due to effective increase of one of the diffusion constants.
Soil moisture at the plot or hill-slope scale is an important link between local vadose zone hydrology and catchment hydrology. However, so far only a few methods are on the way to close this gap between point measurements and remote sensing. One new measurement methodology that could determine integral soil moisture at this scale is the aboveground sensing of cosmic-ray neutrons, more precisely of ground albedo neutrons. The present study performed ground albedo neutron sensing (GANS) at an agricultural field in northern Germany. To test the method it was accompanied by other soil moisture measurements for a summer period with corn crops growing on the field and a later autumn-winter period without crops and a longer period of snow cover. Additionally, meteorological data and aboveground crop biomass were included in the evaluation. Hourly values of ground albedo neutron sensing showed a high statistical variability. Six-hourly values corresponded well with classical soil moisture measurements, after calibration based on one reference dry period and three wet periods of a few days each. Crop biomass seemed to influence the measurements only to minor degree, opposed to snow cover which has a more substantial impact on the measurements. The latter could be quantitatively related to a newly introduced field neutron ratio estimated from neutron counting rates of two energy ranges. Overall, our study outlines a procedure to apply the ground albedo neutron sensing method based on devices now commercially available, without the need for accompanying numerical simulations and suited for longer monitoring periods after initial calibration.
Quantification of subsurface water fluxes based on the one dimensional solution to the heat transport equation depends on the accuracy of measured subsurface temperatures. The influence of temperature probe setup on the accuracy of vertical water flux calculation was systematically evaluated in this experimental study. Four temperature probe setups were installed into a sand box experiment to measure temporal highly resolved vertical temperature profiles under controlled water fluxes in the range of +/- 1.3 md(-1). Pass band filtering provided amplitude differences and phase shifts of the diurnal temperature signal varying with depth depending on water flux. Amplitude ratios of setups directly installed into the saturated sediment significantly varied with sand box hydraulic gradients. Amplitude ratios provided an accurate basis for the analytical calculation of water flow velocities, which matched measured flow velocities. Calculated flow velocities were sensitive to thermal properties of saturated sediment and to temperature sensor spacing, but insensitive to thermal dispersivity equal to solute dispersivity. Amplitude ratios of temperature probe setups indirectly installed into piezometer pipes were influenced by thermal exchange processes within the pipes and significantly varied with water flux direction only. Temperature time lags of small sensor distances of all setups were found to be insensitive to vertical water flux.
The need to increase food production for a growing world population makes an assessment of global agricultural water productivities and virtual water flows important. Using the hydrology and agro-biosphere model LPJmL, we quantify at 0.5 degrees resolution the amount of blue and green water (irrigation and precipitation water) needed to produce one unit of crop yield, for 11 of the world's major crop types. Based on these, we also quantify the agricultural water footprints (WFP) of all countries, for the period 1998-2002, distinguishing internal and external WFP (virtual water imported from other countries) and their blue and green components, respectively. Moreover, we calculate water savings and losses, and for the first time also land savings and losses, through international trade with these products. The consistent separation of blue and green water flows and footprints shows that green water globally dominates both the internal and external WFP (84% of the global WFP and 94% of the external WFP rely on green water). While no country ranks among the top ten with respect to all water footprints calculated here, Pakistan and Iran demonstrate high absolute and per capita blue WFP, and the US and India demonstrate high absolute green and blue WFPs. The external WFPs are relatively small (6% of the total global blue WFP, 16% of the total global green WFP). Nevertheless, current trade of the products considered here saves significant water volumes and land areas (similar to 263 km(3) and similar to 41 Mha, respectively, equivalent to 5% of the sowing area of the considered crops and 3.5% of the annual precipitation on this area). Relating the proportions of external to internal blue/green WFP to the per capita WFPs allows recognizing that only a few countries consume more water from abroad than from their own territory and have at the same time above-average WFPs. Thus, countries with high per capita water consumption affect mainly the water availability in their own country. Finally, this study finds that flows/savings of both virtual water and virtual land need to be analysed together, since they are intrinsically related.
Genome sequencing of closely related individuals has yielded valuable insights that link genome evolution to phenotypic variations. However, advancement in sequencing technology has also led to an escalation in the number of poor quality-drafted genomes assembled based on reference genomes that can have highly divergent or haplotypic regions. The self-fertilizing nature of Arabidopsis thaliana poses an advantage to sequencing projects because its genome is mostly homozygous. To determine the accuracy of an Arabidopsis drafted genome in less conserved regions, we performed a resequencing experiment on a similar to 371-kb genomic interval in the Landsberg erecta (Ler-0) accession. We identified novel structural variations (SVs) between Ler-0 and the reference accession Col-0 using a long-range polymerase chain reaction approach to generate an Illumina data set that has positional information, that is, a data set with reads that map to a known location. Positional information is important for accurate genome assembly and the resolution of SVs particularly in highly duplicated or repetitive regions. Sixty-one regions with misassembly signatures were identified from the Ler-0 draft, suggesting the presence of novel SVs that are not represented in the draft sequence. Sixty of those were resolved by iterative mapping using our data set. Fifteen large indels (> 100 bp) identified from this study were found to be located either within protein-coding regions or upstream regulatory regions, suggesting the formation of novel alleles or altered regulation of existing genes in Ler-0. We propose future genome-sequencing experiments to follow a clone-based approach that incorporates positional information to ultimately reveal haplotype-specific differences between accessions.
Speech perception requires rapid extraction of the linguistic content from the acoustic signal. The ability to efficiently process rapid changes in auditory information is important for decoding speech and thereby crucial during language acquisition. Investigating functional networks of speech perception in infancy might elucidate neuronal ensembles supporting perceptual abilities that gate language acquisition. Interhemispheric specializations for language have been demonstrated in infants. How these asymmetries are shaped by basic temporal acoustic properties is under debate. We recently provided evidence that newborns process non-linguistic sounds sharing temporal features with language in a differential and lateralized fashion. The present study used the same material while measuring brain responses of 6 and 3 month old infants using simultaneous recordings of electroencephalography (EEG) and near-infrared spectroscopy (NIRS). NIRS reveals that the lateralization observed in newborns remains constant over the first months of life. While fast acoustic modulations elicit bilateral neuronal activations, slow modulations lead to right-lateralized responses. Additionally, auditory-evoked potentials and oscillatory EEG responses show differential responses for fast and slow modulations indicating a sensitivity for temporal acoustic variations. Oscillatory responses reveal an effect of development, that is, 6 but not 3 month old infants show stronger theta-band desynchronization for slowly modulated sounds. Whether this developmental effect is due to increasing fine-grained perception for spectrotemporal sounds in general remains speculative. Our findings support the notion that a more general specialization for acoustic properties can be considered the basis for lateralization of speech perception. The results show that concurrent assessment of vascular based imaging and electrophysiological responses have great potential in the research on language acquisition.
Linear mixed models (LMMs) provide a still underused methodological perspective on combining experimental and individual-differences research. Here we illustrate this approach with two-rectangle cueing in visual attention (Egly et al., 1994). We replicated previous experimental cue-validity effects relating to a spatial shift of attention within an object (spatial effect), to attention switch between objects (object effect), and to the attraction of attention toward the display centroid (attraction effect), also taking into account the design-inherent imbalance of valid and other trials. We simultaneously estimated variance/covariance components of subject-related random effects for these spatial, object, and attraction effects in addition to their mean reaction times (RTs). The spatial effect showed a strong positive correlation with mean RT and a strong negative correlation with the attraction effect. The analysis of individual differences suggests that slow subjects engage attention more strongly at the cued location than fast subjects. We compare this joint LMM analysis of experimental effects and associated subject-related variances and correlations with two frequently used alternative statistical procedures.
Spatial numerical associations (SNAs) are prevalent yet their origin is poorly understood. We first consider the possible prime role of reading habits in shaping SNAs and list three observations that argue against a prominent influence of this role: (1) directional reading habits for numbers may conflict with those for non-numerical symbols, (2) short-term experimental manipulations can overrule the impact of decades of reading experience, (3) SNAs predate the acquisition of reading. As a promising alternative, we discuss behavioral, neuroscientific, and neuropsychological evidence in support of finger counting as the most likely initial determinant of SNAs. Implications of this "manumerical cognition" stance for the distinction between grounded, embodied, and situated cognition are discussed.
SLocX predicting subcellular localization of Arabidopsis proteins leveraging gene expression data
(2011)
Despite the growing volume of experimentally validated knowledge about the subcellular localization of plant proteins, a well performing in silico prediction tool is still a necessity. Existing tools, which employ information derived from protein sequence alone, offer limited accuracy and/or rely on full sequence availability. We explored whether gene expression profiling data can be harnessed to enhance prediction performance. To achieve this, we trained several support vector machines to predict the subcellular localization of Arabidopsis thaliana proteins using sequence derived information, expression behavior, or a combination of these data and compared their predictive performance through a cross-validation test. We show that gene expression carries information about the subcellular localization not available in sequence information, yielding dramatic benefits for plastid localization prediction, and some notable improvements for other compartments such as the mito-chondrion, the Golgi, and the plasma membrane. Based on these results, we constructed a novel subcellular localization prediction engine, SLocX, combining gene expression profiling data with protein sequence-based information. We then validated the results of this engine using an independent test set of annotated proteins and a transient expression of GFP fusion proteins. Here, we present the prediction framework and a website of predicted localizations for Arabidopsis. The relatively good accuracy of our prediction engine, even in cases where only partial protein sequence is available (e.g., in sequences lacking the N-terminal region), offers a promising opportunity for similar application to non-sequenced or poorly annotated plant species. Although the prediction scope of our method is currently limited by the availability of expression information on the ATH1 array, we believe that the advances in measuring gene expression technology will make our method applicable for all Arabidopsis proteins.
Large-scale co-expression approach to dissect secondary cell wall formation across plant species
(2011)
Plant cell walls are complex composites largely consisting of carbohydrate-based polymers, and are generally divided into primary and secondary walls based on content and characteristics. Cellulose microfibrils constitute a major component of both primary and secondary cell walls and are synthesized at the plasma membrane by cellulose synthase (CESA) complexes. Several studies in Arabidopsis have demonstrated the power of co-expression analyses to identify new genes associated with secondary wall cellulose biosynthesis. However, across-species comparative co-expression analyses remain largely unexplored. Here, we compared co-expressed gene vicinity networks of primary and secondary wall CESAsin Arabidopsis, barley, rice, poplar, soybean, Medicago, and wheat, and identified gene families that are consistently co-regulated with cellulose biosynthesis. In addition to the expected polysaccharide acting enzymes, we also found many gene families associated with cytoskeleton, signaling, transcriptional regulation, oxidation, and protein degradation. Based on these analyses, we selected and biochemically analyzed T-DNA insertion lines corresponding to approximately twenty genes from gene families that re-occur in the co-expressed gene vicinity networks of secondary wall CESAs across the seven species. We developed a statistical pipeline using principal component analysis and optimal clustering based on silhouette width to analyze sugar profiles. One of the mutants, corresponding to a pinoresinol reductase gene, displayed disturbed xylem morphology and held lower levels of lignin molecules. We propose that this type of large-scale co-expression approach, coupled with statistical analysis of the cell wall contents, will be useful to facilitate rapid knowledge transfer across plant species.
Hydrocarbons can be found in many different habitats and represent an important carbon source for microbes. As fossil fuels, they are also an important economical resource and through natural seepage or accidental release they can be major pollutants. DNA-specific stains and molecular probes bind to hydrocarbons, causing massive background fluorescence, thereby hampering cell enumeration. The cell extraction procedure of Kallmeyer et al. (2008) separates the cells from the sediment matrix. In principle, this technique can also be used to separate cells from oily sediments, but it was not originally optimized for this application. Here we present a modified extraction method in which the hydrocarbons are removed prior to cell extraction. Due to the reduced background fluorescence the microscopic image becomes clearer, making cell identification, and enumeration much easier. Consequently, the resulting cell counts from oily samples treated according to our new protocol are significantly higher than those treated according to Kallmeyer et al. (2008). We tested different amounts of a variety of solvents for their ability to remove hydrocarbons and found that n-hexane and in samples containing more mature oils methanol, delivered the best results. However, as solvents also tend to lyse cells, it was important to find the optimum solvent to sample ratio, at which hydrocarbon extraction is maximized and cell lysis minimized. A volumetric ratio of 1:2-1:5 between a formalin-fixed sediment slurry and solvent delivered highest cell counts. Extraction efficiency was around 30-50% and was checked on both oily samples spiked with known amounts of E. coli cells and oil-free samples amended with fresh and biodegraded oil. The method provided reproducible results on samples containing very different kinds of oils with regard to their degree of biodegradation. For strongly biodegraded oil MeOH turned out to be the most appropriate solvent, whereas for less biodegraded samples n-hexane delivered best results.
In order to provide probabilistic projections of the future evolution of the Atlantic Meridional Overturning Circulation (AMOC), we calibrated a simple Stommel-type box model to emulate the output of fully coupled three-dimensional atmosphere-ocean general circulation models (AOGCMs) of the Coupled Model Intercomparison Project (CMIP). Based on this calibration to idealised global warming scenarios with and without interactive atmosphere-ocean fluxes and freshwater perturbation simulations, we project the future evolution of the AMOC mean strength within the covered calibration range for the lower two Representative Concentration Pathways (RCPs) until 2100 obtained from the reduced complexity carbon cycle-climate model MAGICC 6. For RCP3-PD with a global mean temperature median below 1.0 degrees C warming relative to the year 2000, we project an ensemble median weakening of up to 11% compared to 22% under RCP4.5 with a warming median up to 1.9 degrees C over the 21st century. Additional Greenland meltwater of 10 and 20 cm of global sea-level rise equivalent further weakens the AMOC by about 4.5 and 10 %, respectively. By combining our outcome with a multi-model sea-level rise study we project a dynamic sea-level rise along the New York City coastline of 4 cm for the RCP3-PD and of 8 cm for the RCP4.5 scenario over the 21st century. We estimate the total steric and dynamic sea-level rise for New York City to be about 24 cm until 2100 for the RCP3-PD scenario, which can hold as a lower bound for sea-level rise projections in this region, as it does not include ice sheet and mountain glacier contributions.
We present climatic consequences of the Representative Concentration Pathways (RCPs) using the coupled climate model CLIMBER-3 alpha, which contains a statistical-dynamical atmosphere and a three-dimensional ocean model. We compare those with emulations of 19 state-of-the-art atmosphere-ocean general circulation models (AOGCM) using MAGICC6. The RCPs are designed as standard scenarios for the forthcoming IPCC Fifth Assessment Report to span the full range of future greenhouse gas (GHG) concentrations pathways currently discussed. The lowest of the RCP scenarios, RCP3-PD, is projected in CLIMBER-3 alpha to imply a maximal warming by the middle of the 21st century slightly above 1.5 degrees C and a slow decline of temperatures thereafter, approaching today's level by 2500. We identify two mechanisms that slow down global cooling after GHG concentrations peak: The known inertia induced by mixing-related oceanic heat uptake; and a change in oceanic convection that enhances ocean heat loss in high latitudes, reducing the surface cooling rate by almost 50%. Steric sea level rise under the RCP3-PD scenario continues for 200 years after the peak in surface air temperatures, stabilizing around 2250 at 30 cm. This contrasts with around 1.3 m of steric sea level rise by 2250, and 2 m by 2500, under the highest scenario, RCP8.5. Maximum oceanic warming at intermediate depth (300-800 m) is found to exceed that of the sea surface by the second half of the 21st century under RCP3-PD. This intermediate-depth warming persists for centuries even after surface temperatures have returned to present-day values, with potential consequences for marine ecosystems, oceanic methane hydrates, and ice-shelf stability. Due to an enhanced land-ocean temperature contrast, all scenarios yield an intensification of monsoon rainfall under global warming.
A parameterization for the motion of ice-shelf fronts on a Cartesian grid in finite-difference land-ice models is presented. The scheme prevents artificial thinning of the ice shelf at its edge, which occurs due to the finite resolution of the model. The intuitive numerical implementation diminishes numerical dispersion at the ice front and enables the application of physical boundary conditions to improve the calculation of stress and velocity fields throughout the ice-sheet-shelf system. Numerical properties of this subgrid modification are assessed in the Potsdam Parallel Ice Sheet Model (PISM-PIK) for different geometries in one and two horizontal dimensions and are verified against an analytical solution in a flow-line setup.
Greenland ice sheet model parameters constrained using simulations of the Eemian Interglacial
(2011)
Using a new approach to force an ice sheet model, we performed an ensemble of simulations of the Greenland Ice Sheet evolution during the last two glacial cycles, with emphasis on the Eemian Interglacial. This ensemble was generated by perturbing four key parameters in the coupled regional climate-ice sheet model and by introducing additional uncertainty in the prescribed "background" climate change. The sensitivity of the surface melt model to climate change was determined to be the dominant driver of ice sheet instability, as reflected by simulated ice sheet loss during the Eemian Interglacial period. To eliminate unrealistic parameter combinations, constraints from present-day and paleo information were applied. The constraints include (i) the diagnosed present-day surface mass balance partition between surface melting and ice discharge at the margin, (ii) the modeled present-day elevation at GRIP; and (iii) the modeled elevation reduction at GRIP during the Eemian. Using these three constraints, a total of 360 simulations with 90 different model realizations were filtered down to 46 simulations and 20 model realizations considered valid. The paleo constraint eliminated more sensitive melt parameter values, in agreement with the surface mass balance partition assumption. The constrained simulations resulted in a range of Eemian ice loss of 0.4-4.4m sea level equivalent, with a more likely range of about 3.7-4.4m sea level if the GRIP delta O-18 isotope record can be considered an accurate proxy for the precipitation-weighted annual mean temperatures.
Identifying the chemical mechanisms behind soil carbon bound in organo-mineral complexes is necessary to determine the degree to which soil organic carbon is stabilized belowground. Analysis of delta C-13 and delta N-15 isotopic signatures of stabilized OM fractions along with soil mineral characteristics may yield important information about OM-mineral associations and their processing history. We anlayzed the delta C-13 and delta N-15 isotopic signatures from two organic matter (OM) fractions along with soil mineral proxies to identify the likely binding mechanisms involved. We analyzed OM fractions hypothesized to contain carbon stabilized through organo-mineral complexes: (1) OM separated chemically with sodium pyrophosphate (OM(PY)) and (2) OM occluded in micro-structures found in the chemical extraction residue (OM(ER)). Because the OM fractions were separated from five different soils with paired forest and arable land use histories, we could address the impact of land use change on carbon binding and processing mechanisms. We used partial least squares regression to analyze patterns in the isotopic signature of OM with established mineral and chemical proxies indicative for certain binding mechanisms. We found different mechanisms predominate in each land use type. For arable soils, the formation of OM(PY)-Ca-mineral associations was identified as an important OM binding mechanism. Therefore, we hypothesize an increased stabilization of microbial processed OM(PY) through Ca2+ interactions. In general, we found the forest soils to contain on average 10% more stabilized carbon relative to total carbon stocks, than the agricultural counter part. In forest soils, we found a positive relationship between isotopic signatures of OM(PY) and the ratio of soil organic carbon content to soil surface area (SOC/SSA). This indicates that the OM(PY) fractions of forest soils represent layers of slower exchange not directly attached to mineral surfaces. From the isotopic composition of the OM(ER) fraction, we conclude that the OM in this fraction from both land use types have undergone a different pathway to stabilization that does not involve microbial processing, which may include OM which is highly protected within soil micro-structures.
Coastal uplift and tsunami effects associated to the 2010 M(w)8.8 Maule earthquake in Central Chile
(2011)
On February 27, 2010 at 03:34:08 AM an M(w)8.8 earthquake, with epicenter located off Cobquecura (73.24 degrees W; 36.29 degrees S), severely hit Central Chile. The tsunami waves that followed this event affected the coastal regions between the cities of Valparaiso and Valdivia, with minor effects as far as Coquimbo. The earthquake occurred along the subduction of the Nazca oceanic plate beneath the South American plate. Coseismic coastal uplift was estimated through observations of bleached lithothamnioids crustose coralline algae, which were exposed after the mainshock between 34.13 degrees S and 38.34 degrees S, suggesting the latitudinal distribution of the earthquake rupture. The measured coastal uplift values varied between 240 +/- 20 cm at sites closer to the trench along the western coast of the Arauco peninsula and 15 +/- 10 cm at sites located farther east. A maximum value of 260 +/- 50 cm was observed at the western coast of Santa Maria Island, which is similar to the reported uplift associated with the 1835 earthquake at Concepcion. Land subsidence values on the order of 0.5 m to 1 m evidenced a change in polarity and position of the coseismic hinge at 110-120 km from the trench. In four sites along the coast we observed a close match between coastal uplift values deduced from bleached lithothamnioids algae and GPS measurements. According to field observations tsunami heights reached ea. 14 m in the coastal area of the Maule Region immediately north of the epicenter, and diminished progressively northwards to 4-2 m near Valparaiso. Along the coast of Cobquecura, tsunami height values were inferior to 2-4 m. More variable tsunami heights of 6-8 m were measured at Dichato-Talcahuano and Tirua-Puerto Saavedra, in the Biobio and Arauco regions, respectively, to the south of the epicenter. According to eyewitnesses, the tsunami reached the coast between 12 to 20 and 30 to 45 minutes in areas located closer and faraway from the earthquake rupture zone, respectively. Destructive tsunami waves arrived also between 2.5 and 4.5 hours after the mainshock, especially along the coast of the Biobio and Arauco regions. The tsunami effects were highly variable along the coast, as a result of geomorphological and bathymetric local conditions, besides potential complexities induced by the main shock.
We present a dynamic equilibrium simulation of the ice sheet-shelf system on Antarctica with the Potsdam Parallel Ice Sheet Model (PISM-PIK). The simulation is initialized with present-day conditions for bed topography and ice thickness and then run to steady state with constant present-day surface mass balance. Surface temperature and sub-shelf basal melt distribution are parameterized. Grounding lines and calving fronts are free to evolve, and their modeled equilibrium state is compared to observational data. A physically-motivated calving law based on horizontal spreading rates allows for realistic calving fronts for various types of shelves. Steady-state dynamics including surface velocity and ice flux are analyzed for whole Antarctica and the Ronne-Filchner and Ross ice shelf areas in particular. The results show that the different flow regimes in sheet and shelves, and the transition zone between them, are captured reasonably well, supporting the approach of superposition of SIA and SSA for the representation of fast motion of grounded ice. This approach also leads to a natural emergence of sliding-dominated flow in stream-like features in this new 3-D marine ice sheet model.
We present the Potsdam Parallel Ice Sheet Model (PISM-PIK), developed at the Potsdam Institute for Climate Impact Research to be used for simulations of large-scale ice sheet-shelf systems. It is derived from the Parallel Ice Sheet Model (Bueler and Brown, 2009). Velocities are calculated by superposition of two shallow stress balance approximations within the entire ice covered region: the shallow ice approximation (SIA) is dominant in grounded regions and accounts for shear deformation parallel to the geoid. The plug-flow type shallow shelf approximation (SSA) dominates the velocity field in ice shelf regions and serves as a basal sliding velocity in grounded regions. Ice streams can be identified diagnostically as regions with a significant contribution of membrane stresses to the local momentum balance. All lateral boundaries in PISM-PIK are free to evolve, including the grounding line and ice fronts. Ice shelf margins in particular are modeled using Neumann boundary conditions for the SSA equations, reflecting a hydrostatic stress imbalance along the vertical calving face. The ice front position is modeled using a subgrid-scale representation of calving front motion (Albrecht et al., 2011) and a physically-motivated calving law based on horizontal spreading rates. The model is tested in experiments from the Marine Ice Sheet Model Intercomparison Project (MISMIP). A dynamic equilibrium simulation of Antarctica under present-day conditions is presented in Martin et al. (2011).
Memory, history, knowledges of the living together on to know living together of the literature
(2011)
Cultures and societies develop in a certain moment and within a certain context an awareness of how to live together, which not only has to be enriched continuously, but can also be lost or destroyed to a greater or smaller measure. Literature is, in its capacity as highly dynamic and interactive heritage and generator of life knowledge, that multilingual wisdom, which in dense form can find basic gnosemes of a good living, knowing how to survive and how to live together, which are crucial for the future of our planet and its very different manifestations of life.
Background: Although nowaday it is broadly accepted that mitochondrial DNA (mtDNA) may undergo recombination, the frequency of such recombination remains controversial. Its estimation is not straightforward, as recombination under homoplasmy (i.e., among identical mt genomes) is likely to be overlooked. In species with tandem duplications of large mtDNA fragments the detection of recombination can be facilitated, as it can lead to gene conversion among duplicates. Although the mechanisms for concerted evolution in mtDNA are not fully understood yet, recombination rates have been estimated from "one per speciation event" down to 850 years or even "during every replication cycle".
Results: Here we present the first complete mt genome of the avian family Bucerotidae, i.e., that of two Philippine hornbills, Aceros waldeni and Penelopides panini. The mt genomes are characterized by a tandemly duplicated region encompassing part of cytochrome b, 3 tRNAs, NADH6, and the control region. The duplicated fragments are identical to each other except for a short section in domain I and for the length of repeat motifs in domain III of the control region. Due to the heteroplasmy with regard to the number of these repeat motifs, there is some size variation in both genomes; with around 21,657 bp (A. waldeni) and 22,737 bp (P. panini), they significantly exceed the hitherto longest known avian mt genomes, that of the albatrosses. We discovered concerted evolution between the duplicated fragments within individuals. The existence of differences between individuals in coding genes as well as in the control region, which are maintained between duplicates, indicates that recombination apparently occurs frequently, i. e., in every generation.
Conclusions: The homogenised duplicates are interspersed by a short fragment which shows no sign of recombination. We hypothesize that this region corresponds to the so-called Replication Fork Barrier (RFB), which has been described from the chicken mitochondrial genome. As this RFB is supposed to halt replication, it offers a potential mechanistic explanation for frequent recombination in mitochondrial genomes.
Background: Recent studies using transcript and metabolite profiles of wild-type and gene deletion mutants revealed that photorespiratory pathways are essential for the growth of Synechocystis sp. PCC 6803 under atmospheric conditions. Pool size changes of primary metabolites, such as glycine and glycolate, indicated a link to photorespiration.
Methodology/Principal Findings: The (13)C labelling kinetics of primary metabolites were analysed in photoautotrophically grown cultures of Synechocystis sp. PCC 6803 by gas chromatography-mass spectrometry (GC-MS) to demonstrate the link with photorespiration. Cells pre-acclimated to high CO(2) (5%, HC) or limited CO(2) (0.035%, LC) conditions were pulse-labelled under very high (2% w/w) (13)C-NaHCO(3) (VHC) conditions followed by treatment with ambient (12)C at HC and LC conditions, respectively. The (13)C enrichment, relative changes in pool size, and (13)C flux of selected metabolites were evaluated. We demonstrate two major paths of CO(2) assimilation via Rubisco in Synechocystis, i.e., from 3PGA via PEP to aspartate, malate and citrate or, to a lesser extent, from 3PGA via glucose-6-phosphate to sucrose. The results reveal evidence of carbon channelling from 3PGA to the PEP pool. Furthermore, (13)C labelling of glycolate was observed under conditions thought to suppress photorespiration. Using the glycolate-accumulating Delta glcD1 mutant, we demonstrate enhanced (13)C partitioning into the glycolate pool under conditions favouring photorespiration and enhanced (13)C partitioning into the glycine pool of the glycine-accumulating Delta gcvT mutant. Under LC conditions, the photorespiratory mutants Delta glcD1 and Delta gcvT showed enhanced activity of the additional carbon-fixing PEP carboxylase pathway.
Conclusions/Significance: With our approach of non-steady-state (13)C labelling and analysis of metabolite pool sizes with respective (13)C enrichments, we identify the use and modulation of major pathways of carbon assimilation in Synechocystis in the presence of high and low inorganic carbon supplies.
Quantum correlations exhibit behaviour that cannot be resolved with a local hidden variable picture of the world. In quantum information, they are also used as resources for information processing tasks, such as measurement-based quantum computation (MQC). In MQC, universal quantum computation can be achieved via adaptive measurements on a suitable entangled resource state. In this paper, we look at a version of MQC in which we remove the adaptivity of measurements and aim to understand what computational abilities remain in the resource. We show that there are explicit connections between this model of computation and the question of non-classicality in quantum correlations. We demonstrate this by focusing on deterministic computation of Boolean functions, in which natural generalizations of the Greenberger-Horne-Zeilinger paradox emerge; we then explore probabilistic computation via, which multipartite Bell inequalities can be defined. We use this correspondence to define families of multi-party Bell inequalities, which we show to have a number of interesting contrasting properties.
Fluid intelligence is the ability to think flexibly and to understand abstract relations. People with high fluid intelligence (hi-fluIQ) perform better in analogical reasoning tasks than people with average fluid intelligence (ave-fluIQ). Although previous neuroimaging studies reported involvement of parietal and frontal brain regions in geometric analogical reasoning (which is a prototypical task for fluid intelligence), however, neuroimaging findings on geometric analogical reasoning in hi-fluIQ are sparse. Furthermore, evidence on the relation between brain activation and intelligence while solving cognitive tasks is contradictory. The present study was designed to elucidate the cerebral correlates of geometric analogical reasoning in a sample of hi-fluIQ and ave-fluIQ high school students. We employed a geometric analogical reasoning task with graded levels of task difficulty and confirmed the involvement of the parieto-frontal network in solving this task. In addition to characterizing the brain regions involved in geometric analogical reasoning in hi-fluIQ and ave-fluIQ, we found that blood oxygenation level dependency (BOLD) signal changes were greater for hi-fluIQ than for ave-fluIQ in parietal brain regions. However, ave-fluIQ showed greater BOLD signal changes in the anterior cingulate cortex and medial frontal gyrus than hi-fluIQ. Thus, we showed that a similar network of brain regions is involved in geometric analogical reasoning in both groups. Interestingly, the relation between brain activation and intelligence is not mono-directional, but rather, it is specific for each brain region. The negative brain activation-intelligence relationship in frontal brain regions in hi-fluIQ goes along with a better behavioral performance and reflects a lower demand for executive monitoring compared to ave-fluIQ individuals. In conclusion, our data indicate that flexibly modulating the extent of regional cerebral activity is characteristic for fluid intelligence.
Liver cirrhosis is often complicated by an impaired renal excretion of water and sodium. Diuretics tend to further deteriorate renal function. It is unknown whether chronic selective adenosine A(1) receptor blockade, via inhibition of the hepatorenal reflex and the tubuloglomerular feedback, might exert diuretic and natriuretic effects without a reduction of the glomerular filtration rate. In healthy animals intravenous treatment with the novel A(1) receptor antagonist SLV329 resulted in a strong dose-dependent diuretic (up to 3.4-fold) and natriuretic (up to 13.5-fold) effect without affecting creatinine clearance. Male Wistar rats with thioacetamide-induced liver cirrhosis received SLV329, vehicle or furosemide for 12 weeks. The creatinine clearance of cirrhotic animals decreased significantly (-36.5%, p < 0.05), especially in those receiving furosemide (-41.9%, p < 0.01). SLV329 was able to prevent this decline of creatinine clearance. Mortality was significantly lower in cirrhotic animals treated with SLV329 in comparison to animals treated with furosemide (17% vs. 54%, p < 0.05). SLV329 did not relevantly influence the degree of liver fibrosis, kidney histology or expression of hepatic or renal adenosine receptors. In conclusion, chronic treatment with SLV329 prevented the decrease of creatinine clearance in a rat model of liver cirrhosis. Further studies will have to establish whether adenosine A(1) receptor antagonists are clinically beneficial at different stages of liver cirrhosis.
Microcystins are cyanobacterial toxins that represent a serious threat to drinking water and recreational lakes worldwide. Here, we show that microcystin fulfils an important function within cells of its natural producer Microcystis. The microcystin deficient mutant Delta mcyB showed significant changes in the accumulation of proteins, including several enzymes of the Calvin cycle, phycobiliproteins and two NADPH-dependent reductases. We have discovered that microcystin binds to a number of these proteins in vivo and that the binding is strongly enhanced under high light and oxidative stress conditions. The nature of this binding was studied using extracts of a microcystin-deficient mutant in vitro. The data obtained provided clear evidence for a covalent interaction of the toxin with cysteine residues of proteins. A detailed investigation of one of the binding partners, the large subunit of RubisCO showed a lower susceptibility to proteases in the presence of microcystin in the wild type. Finally, the mutant defective in microcystin production exhibited a clearly increased sensitivity under high light conditions and after hydrogen peroxide treatment. Taken together, our data suggest a protein-modulating role for microcystin within the producing cell, which represents a new addition to the catalogue of functions that have been discussed for microbial secondary metabolites.
The human immunodeficiency virus (HIV) can be suppressed by highly active anti-retroviral therapy (HAART) in the majority of infected patients. Nevertheless, treatment interruptions inevitably result in viral rebounds from persistent, latently infected cells, necessitating lifelong treatment. Virological failure due to resistance development is a frequent event and the major threat to treatment success. Currently, it is recommended to change treatment after the confirmation of virological failure. However, at the moment virological failure is detected, drug resistant mutants already replicate in great numbers. They infect numerous cells, many of which will turn into latently infected cells. This pool of cells represents an archive of resistance, which has the potential of limiting future treatment options. The objective of this study was to design a treatment strategy for treatment-naive patients that decreases the likelihood of early treatment failure and preserves future treatment options. We propose to apply a single, pro-active treatment switch, following a period of treatment with an induction regimen. The main goal of the induction regimen is to decrease the abundance of randomly generated mutants that confer resistance to the maintenance regimen, thereby increasing subsequent treatment success. Treatment is switched before the overgrowth and archiving of mutant strains that carry resistance against the induction regimen and would limit its future re-use. In silico modelling shows that an optimal trade-off is achieved by switching treatment at & 80 days after the initiation of antiviral therapy. Evaluation of the proposed treatment strategy demonstrated significant improvements in terms of resistance archiving and virological response, as compared to conventional HAART. While continuous pro-active treatment alternation improved the clinical outcome in a randomized trial, our results indicate that a similar improvement might also be reached after a single pro-active treatment switch. The clinical validity of this finding, however, remains to be shown by a corresponding trial.
Background: Soil biota effects are increasingly accepted as an important driver of the abundance and distribution of plants. While biogeographical studies on alien invasive plant species have indicated coevolution with soil biota in their native distribution range, it is unknown whether adaptation to soil biota varies among populations within the native distribution range. The question of local adaptation between plants and their soil biota has important implications for conservation of biodiversity and may justify the use of seed material from local provenances in restoration campaigns.
Methodology/Principal Findings: We studied soil biota effects in ten populations of the steppe grass Stipa capillata from two distinct regions, Europe and Asia. We tested for local adaptation at two different scales, both within (ca. 10-80 km) and between (ca. 3300 km) regions, using a reciprocal inoculation experiment in the greenhouse for nine months. Generally, negative soil biota effects were consistent. However, we did not find evidence for local adaptation: both within and between regions, growth of plants in their 'home soil' was not significantly larger relative to that in soil from other, more distant, populations.
Conclusions/Significance: Our study suggests that negative soil biota effects can prevail in different parts of a plant species' range. Absence of local adaptation points to the possibility of similar rhizosphere biota composition across populations and regions, sufficient gene flow to prevent coevolution, selection in favor of plasticity, or functional redundancy among different soil biota. From the point of view of plant - soil biota interactions, our findings indicate that the current practice of using seeds exclusively from local provenances in ecosystem restoration campaigns may not be justified.
The effect of tannins on mediterranean ruminant ingestive behavior the role of the oral cavity
(2011)
Sheep, cattle and goat are domestic ruminants of significant economic interest in the Mediterranean region. Although sharing the same pasture ranges, they ingest different plants and plant parts and, consequently different levels of tannins. This suggests an ability to detect and adapt ingestion according to animal physiological limits of tolerance for plant secondary metabolites. This review will detail the effects of dietary tannins on feeding behavior, and the role of the oral cavity in this process, with focus on such ruminant species. The role of salivary protein profile in tannin perception in the oral cavity, and as a defense mechanism, will be discussed.
In eukaryotes, the transcription of tRNA genes is initiated by the concerted action of transcription factors IIIC (TFIIIC) and IIIB (TFIIIB) which direct the recruitment of polymerase III. While TFIIIC recognizes highly conserved, intragenic promoter elements, TFIIIB binds to the non-coding 5'-upstream regions of the tRNA genes. Using a systematic bioinformatic analysis of 11 multicellular eukaryotic genomes we identified a highly conserved TATA motif followed by a CAA-motif in the tRNA upstream regions of all plant genomes. Strikingly, the 5'-flanking tRNA regions of the animal genomes are highly heterogeneous and lack a common conserved sequence signature. Interestingly, in the animal genomes the tRNA species that read the same codon share conserved motifs in their upstream regions. Deep-sequencing analysis of 16 human tissues revealed multiple splicing variants of two of the TFIIIB subunits, Bdp1 and Brf1, with tissue-specific expression patterns. These multiple forms most likely modulate the TFIIIB-DNA interactions and explain the lack of a uniform signature motif in the tRNA upstream regions of animal genomes. The anticodon-dependent 5'-flanking motifs provide a possible mechanism for independent regulation of the tRNA transcription in various human tissues.
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.
Copper(I)-Catalyzed [3+2] Cycloaddition of 3-Azidoquinoline-2,4(1H,3H)-diones with terminal alkynes
(2011)
3-Azidoquinoline-2,4(1H,3H)-diones 1, which are readily available from 4-hydroxyquinolin-2(1H)-ones 4 via 3-chloroquinoline-2,4(1H, 3H)-diones 5, afford, in copper(I)-catalyzed [3 + 2] cycloaddition reaction with terminal acetylenes, 1,4-disubstituted 1,2,3-triazoles 3 in moderate to excellent yields. The structures of compounds 3 were confirmed by (1)H and (13)C-NMR spectroscopy, combustion analyses and mass spectrometry.
The title compound was prepared by the reaction of 1,4,10,13-tetraoxa-7,16-diazacyclo-octadecane with 4-chloro-2-methyl-phenoxyacetic acid in a ratio of 1:2. The structure has been proved by the data of elemental analysis, IR spectroscopy, NMR ((1)H, (13)C) technique and by X-ray diffraction analysis. Intermolecular hydrogen bonds between the azonium protons and oxygen atoms of the carboxylate groups were found. Immunoactive properties of the title compound have been screened. The compound has the ability to suppress spontaneous and Con A-stimulated cell proliferation in vitro and therefore can be considered as immunodepressant.
The dynamical structure of genetic networks determines the occurrence of various biological mechanisms, such as cellular differentiation. However, the question of how cellular diversity evolves in relation to the inherent stochasticity and intercellular communication remains still to be understood. Here, we define a concept of stochastic bifurcations suitable to investigate the dynamical structure of genetic networks, and show that under stochastic influence, the expression of given proteins of interest is defined via the probability distribution of the phase variable, representing one of the genes constituting the system. Moreover, we show that under changing stochastic conditions, the probabilities of expressing certain concentration values are different, leading to different functionality of the cells, and thus to differentiation of the cells in the various types.
Background: The elderly need strength training more and more as they grow older to stay mobile for their everyday activities. The goal of training is to reduce the loss of muscle mass and the resulting loss of motor function. The dose-response relationship of training intensity to training effect has not yet been fully elucidated.
Methods: PubMed was selectively searched for articles that appeared in the past 5 years about the effects and dose-response relationship of strength training in the elderly.
Results: Strength training in the elderly (> 60 years) increases muscle strength by increasing muscle mass, and by improving the recruitment of motor units, and increasing their firing rate. Muscle mass can be increased through training at an intensity corresponding to 60% to 85% of the individual maximum voluntary strength. Improving the rate of force development requires training at a higher intensity (above 85%), in the elderly just as in younger persons. It is now recommended that healthy old people should train 3 or 4 times weekly for the best results; persons with poor performance at the outset can achieve improvement even with less frequent training. Side effects are rare.
Conclusion: Progressive strength training in the elderly is efficient, even with higher intensities, to reduce sarcopenia, and to retain motor function.
Quantum theory (QT) is usually formulated in terms of abstract mathematical postulates involving Hilbert spaces, state vectors and unitary operators. In this paper, we show that the full formalism of QT can instead be derived from five simple physical requirements, based on elementary assumptions regarding preparations, transformations and measurements. This is very similar to the usual formulation of special relativity, where two simple physical requirements-the principles of relativity and light speed invariance-are used to derive the mathematical structure of Minkowski space-time. Our derivation provides insights into the physical origin of the structure of quantum state spaces (including a group-theoretic explanation of the Bloch ball and its three dimensionality) and suggests several natural possibilities to construct consistent modifications of QT.
We present a lexicon-based approach to extracting sentiment from text. The Semantic Orientation CALculator (SO-CAL) uses dictionaries of words annotated with their semantic orientation (polarity and strength), and incorporates intensification and negation. SO-CAL is applied to the polarity classification task, the process of assigning a positive or negative label to a text that captures the text's opinion towards its main subject matter. We show that SO-CAL's performance is consistent across domains and on completely unseen data. Additionally, we describe the process of dictionary creation, and our use of Mechanical Turk to check dictionaries for consistency and reliability.
The outcomes of measurements on entangled quantum systems can be nonlocally correlated. However, while it is easy to write down toy theories allowing arbitrary nonlocal correlations, those allowed in quantum mechanics are limited. Quantum correlations cannot, for example, violate a principle known as macroscopic locality, which implies that they cannot violate Tsirelson's bound. This paper shows that there is a connection between the strength of nonlocal correlations in a physical theory and the structure of the state spaces of individual systems. This is illustrated by a family of models in which local state spaces are regular polygons, where a natural analogue of a maximally entangled state of two systems exists. We characterize the nonlocal correlations obtainable from such states. The family allows us to study the transition between classical, quantum and super-quantum correlations by varying only the local state space. We show that the strength of nonlocal correlations-in particular whether the maximally entangled state violates Tsirelson's bound or not-depends crucially on a simple geometric property of the local state space, known as strong self-duality. This result is seen to be a special case of a general theorem, which states that a broad class of entangled states in probabilistic theories-including, by extension, all bipartite classical and quantum states-cannot violate macroscopic locality. Finally, our results show that models exist that are locally almost indistinguishable from quantum mechanics, but can nevertheless generate maximally nonlocal correlations.
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/.
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.
Background: A direct pharmacological stimulation of soluble guanylate cyclase (sGC) is an emerging therapeutic approach to the management of various cardiovascular disorders associated with endothelial dysfunction. Novel sGC stimulators, including riociguat (BAY 63-2521), have a dual mode of action: They sensitize sGC to endogenously produced nitric oxide (NO) and also directly stimulate sGC independently of NO. Little is known about their effects on tissue remodeling and degeneration and survival in experimental malignant hypertension.
Methods and Results: Mortality, hemodynamics and biomarkers of tissue remodeling and degeneration were assessed in Dahl salt-sensitive rats maintained on a high salt diet and treated with riociguat (3 or 10 mg/kg/d) for 14 weeks. Riociguat markedly attenuated systemic hypertension, improved systolic heart function and increased survival from 33% to 85%. Histological examination of the heart and kidneys revealed that riociguat significantly ameliorated fibrotic tissue remodeling and degeneration. Correspondingly, mRNA expression of the pro-fibrotic biomarkers osteopontin (OPN), tissue inhibitor of matrix metalloproteinase-1 (TIMP-1) and plasminogen activator inhibitor-1 (PAI-1) in the myocardium and the renal cortex was attenuated by riociguat. In addition, riociguat reduced plasma and urinary levels of OPN, TIMP-1, and PAI-1.
Conclusions: Stimulation of sGC by riociguat markedly improves survival and attenuates systemic hypertension and systolic dysfunction, as well as fibrotic tissue remodeling in the myocardium and the renal cortex in a rodent model of pressure and volume overload. These findings suggest a therapeutic potential of sGC stimulators in diseases associated with impaired cardiovascular and renal functions.
Background: Inferring regulatory interactions between genes from transcriptomics time-resolved data, yielding reverse engineered gene regulatory networks, is of paramount importance to systems biology and bioinformatics studies. Accurate methods to address this problem can ultimately provide a deeper insight into the complexity, behavior, and functions of the underlying biological systems. However, the large number of interacting genes coupled with short and often noisy time-resolved read-outs of the system renders the reverse engineering a challenging task. Therefore, the development and assessment of methods which are computationally efficient, robust against noise, applicable to short time series data, and preferably capable of reconstructing the directionality of the regulatory interactions remains a pressing research problem with valuable applications.
Results: Here we perform the largest systematic analysis of a set of similarity measures and scoring schemes within the scope of the relevance network approach which are commonly used for gene regulatory network reconstruction from time series data. In addition, we define and analyze several novel measures and schemes which are particularly suitable for short transcriptomics time series. We also compare the considered 21 measures and 6 scoring schemes according to their ability to correctly reconstruct such networks from short time series data by calculating summary statistics based on the corresponding specificity and sensitivity. Our results demonstrate that rank and symbol based measures have the highest performance in inferring regulatory interactions. In addition, the proposed scoring scheme by asymmetric weighting has shown to be valuable in reducing the number of false positive interactions. On the other hand, Granger causality as well as information-theoretic measures, frequently used in inference of regulatory networks, show low performance on the short time series analyzed in this study.
Conclusions: Our study is intended to serve as a guide for choosing a particular combination of similarity measures and scoring schemes suitable for reconstruction of gene regulatory networks from short time series data. We show that further improvement of algorithms for reverse engineering can be obtained if one considers measures that are rooted in the study of symbolic dynamics or ranks, in contrast to the application of common similarity measures which do not consider the temporal character of the employed data. Moreover, we establish that the asymmetric weighting scoring scheme together with symbol based measures (for low noise level) and rank based measures (for high noise level) are the most suitable choices.
The meadow grasshopper, Chorthippus parallelus (Zetterstedt), is common and widespread in Central Europe, with a low dispersal range per generation. A population study in Central Germany (Frankenwald and Thuringer Schiefergebirge) showed strong interpopulation differences in abundance and individual fitness. We examined genetic variability using microsatellite markers within and between 22 populations in a short-to long-distance sampling (19 populations, Frankenwald, Schiefergebirge, as well as a southern transect), and in the Erzgebirge region (three populations), with the latter aiming to check for effects as a result of historical forest cover. Of the 671 C. parallelus captured, none was macropterous (functionally winged). All populations showed a high level of expected and observed heterozygosity (mean 0.80-0.90 and 0.60-0.75, respectively), whereas there was evidence of inbreeding (F(IS) values all positive). Allelic richness for all locus-population combinations was high (mean 9.3-11.2), whereas alleles per locus ranged from 15-62. At a local level, genic and genotypic differences were significant. Pairwise F(ST) values were in the range 0.00-0.04, indicating little interpopulation genetic differentiation. Similarly, the calculated gene flow was very high, based on the respective F(ST) (19.5) and using private alleles (7.7). A Neighbour-joining tree using Nei's D(A) and principal coordinate analysis separated two populations that were collected in the Erzgebirge region. Populations from this region may have escaped the effects of the historical forest cover. The visualization of the spatial arrangement of genotypes revealed one geographical barrier to gene flow in the short-distance sampling.
The chemical composition of eclogites, found as boulders in a Tertiary conglomerate from the Guajira Peninsula, Colombia suggests that these rocks are mainly metamorphosed basaltic andesites. They are depleted in LILE elements compared to MORB, have a negative Nb-anomaly and flat to enriched REE patterns, suggesting that their protoliths evolved in a subduction related tectonic setting. They show island-arc affinities and are similar to primitive island-arc rocks described in the Caribbean. The geochemical characteristics are comparable to low-grade greenschists from the nearby Etpana Terrane, which are interpreted as part of a Cretaceous intra-oceanic arc. These data support evidence that the eclogites and the Etpana terrane rocks formed from the same volcano-sedimentary sequence. Part of this sequence was accreted onto the margin and another was incorporated into the subduction channel and metamorphosed at eclogite facies conditions. Ar-40-Ar-39 ages of 79.2 +/- 1.1Ma and 82.2 +/- 2.5Ma determined on white micas, separated from two eclogite samples, are interpreted to be related to the cooling of the main metamorphic event. The formation of a common volcano-sedimentary protolith and subsequent metamorphism of these units record the ongoing Late Cretaceous continental subduction of the South American margin within the Caribbean intra-oceanic arc subduction zone. This gave way to an arc-continent collision between the Caribbean and the South American plates, where this sequence was exhumed after the Campanian.
We report on synchrotron-based high-repetition rate ultrafast x-ray diffraction (UXRD) experiments monitoring the transport of heat from an epitaxial La(0.7)Sr(0.3)MnO(3)/SrTiO(3) superlattice (SL) into the substrate on timescales from 100 ps to 4 mu s. Transient thermal lattice expansion was determined with an accuracy of 10(-7), corresponding to a sensitivity to temperature changes down to 0.01 K. We follow the heat flow within the SL and into the substrate after the impulsive laser heating leads to a small temperature rise of Delta T = 6 K. The transient lattice temperature can be simulated very well using the bulk heat conductivities. This contradicts the interpretation of previous UXRD measurements, which predicted a long-lasting expansion of SrRuO(3) for more than 200 ps. The disagreement could be resolved by assuming that the heat conductivity changes in the first hundred picoseconds.
Forster resonance energy transfer (FRET) from luminescent terbium complexes (LTC) as donors to semiconductor quantum dots (QDs) as acceptors allows extraordinary large FRET efficiencies due to the long Forster distances afforded. Moreover, time-gated detection permits an efficient suppression of autofluorescent background leading to sub-picomolar detection limits even within multiplexed detection formats. These characteristics make FRET-systems with LTC and QDs excellent candidates for clinical diagnostics. So far, such proofs of principle for highly sensitive multiplexed biosensing have only been performed under optimized buffer conditions and interactions between real-life clinical media such as human serum or plasma and LTC-QD-FRET-systems have not yet been taken into account. Here we present an extensive spectroscopic analysis of absorption, excitation and emission spectra along with the luminescence decay times of both the single components as well as the assembled FRET-systems in TRIS-buffer, TRIS-buffer with 2% bovine serum albumin, and fresh human plasma. Moreover, we evaluated homogeneous LTC-QD FRET assays in QD conjugates assembled with either the well-known, specific biotin-streptavidin biological interaction or, alternatively, the metal-affinity coordination of histidine to zinc. In the case of conjugates assembled with biotin-streptavidin no significant interference with the optical and binding properties occurs whereas the histidine-zinc system appears to be affected by human plasma.
Glycans comprise ubiquitous and essential biopolymers, which usually occur as highly diverse mixtures. The myriad different structures are generated by a limited number of carbohydrate-active enzymes (CAZymes), which are unusual in that they catalyze multiple reactions by being relatively unspecific with respect to substrate size. Existing experimental and theoretical descriptions of CAZyme-mediated reaction systems neither comprehensively explain observed action patterns nor suggest biological functions of polydisperse pools in metabolism. Here, we overcome these limitations with a novel theoretical description of this important class of biological systems in which the mixing entropy of polydisperse pools emerges as an important system variable. In vitro assays of three CAZymes essential for central carbon metabolism confirm the power of our approach to predict equilibrium distributions and non-equilibrium dynamics. A computational study of the turnover of the soluble heteroglycan pool exemplifies how entropy-driven reactions establish a metabolic buffer in vivo that attenuates fluctuations in carbohydrate availability. We argue that this interplay between energy- and entropy-driven processes represents an important regulatory design principle of metabolic systems.
Many of our daily decisions are memory based, that is, the attribute information about the decision alternatives has to be recalled. Behavioral studies suggest that for such decisions we often use simple strategies (heuristics) that rely on controlled and limited information search. It is assumed that these heuristics simplify decision-making by activating long-term memory representations of only those attributes that are necessary for the decision. However, from behavioral studies alone, it is unclear whether using heuristics is indeed associated with limited memory search. The present study tested this assumption by monitoring the activation of specific long-term-memory representations with fMRI while participants made memory-based decisions using the "take-the-best" heuristic. For different decision trials, different numbers and types of information had to be retrieved and processed. The attributes consisted of visual information known to be represented in different parts of the posterior cortex. We found that the amount of information required for a decision was mirrored by a parametric activation of the dorsolateral PFC. Such a parametric pattern was also observed in all posterior areas, suggesting that activation was not limited to those attributes required for a decision. However, the posterior increases were systematically modulated by the relative importance of the information for making a decision. These findings suggest that memory-based decision-making is mediated by the dorsolateral PFC, which selectively controls posterior storage areas. In addition, the systematic modulations of the posterior activations indicate a selective boosting of activation of decision-relevant attributes.
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.
The NFX1-LIKE1 (NFXL1) and NFXL2 genes were identified as regulators of salt stress responses. The NFXL1 protein is a nuclear factor that positively affects adaptation to salt stress. The nfxl1-1 loss-of-function mutant displayed reduced survival rates under salt and high light stress. In contrast, the nfxl2-1 mutant, defective in the NFXL2 gene, and NFXL2-antisense plants exhibited enhanced survival under these conditions. We show here that the loss of NFXL2 function results in abscisic acid (ABA) overaccumulation, reduced stomatal conductance, and enhanced survival under drought stress. The nfxl2-1 mutant displayed reduced stomatal aperture under all conditions tested. Fusicoccin treatment, exposition to increasing light intensities, and supply of decreasing CO2 concentrations demonstrated full opening capacity of nfxl2-1 stomata. Reduced stomatal opening presumably is a consequence of elevated ABA levels. Furthermore, seedling growth, root growth, and stomatal closure were hypersensitive to exogenous ABA. The enhanced ABA responses may contribute to the improved drought stress resistance of the mutant. Three NFXL2 splice variants were cloned and named NFXL2-78, NFXL2-97, and NFXL2-100 according to the molecular weight of the putative proteins. Translational fusions to the green fluorescent protein suggest nuclear localisation of the NFXL2 proteins. Stable expression of the NFXL2-78 splice variant in nfxl2-1 plants largely complemented the mutant phenotype. Our data show that NFXL2 controls ABA levels and suppresses ABA responses. NFXL2 may prevent unnecessary and costly stress adaptation under favourable conditions.
Neglecting the naturally existing functional diversity of communities and the resulting potential to respond to altered conditions may strongly reduce the realism and predictive power of ecological models. We therefore propose and study a predator-prey model that describes mutual feedback via species shifts in both predator and prey, using a dynamic trait approach. Species compositions of the two trophic levels were described by mean functional traits-prey edibility and predator food-selectivity- and functional diversities by the variances. Altered edibility triggered shifts in food-selectivity so that consumers continuously respond to the present prey composition, and vice versa. This trait-mediated feedback mechanism resulted in a complex dynamic behavior with ongoing oscillations in the mean trait values, reflecting continuous reorganization of the trophic levels. The feedback was only possible if sufficient functional diversity was present in both trophic levels. Functional diversity was internally maintained on the prey level as no niche existed in our system, which was ideal under any composition of the predator level due to the trade-offs between edibility, growth and carrying capacity. The predators were only subject to one trade-off between food-selectivity and grazing ability and in the absence of immigration, one predator type became abundant, i.e., functional diversity declined to zero. In the lack of functional diversity the system showed the same dynamics as conventional models of predator-prey interactions ignoring the potential for shifts in species composition. This way, our study identified the crucial role of trade-offs and their shape in physiological and ecological traits for preserving diversity.
Background: Uremic cardiomyopathy contributes substantially to mortality in chronic kidney disease (CKD) patients. Glucagon-like peptide-1 (GLP-1) may improve cardiac function, but is mainly degraded by dipeptidyl peptidase-4 (DPP-4).
Methodology/Principal Findings: In a rat model of chronic renal failure, 5/6-nephrectomized [5/6N] rats were treated orally with DPP-4 inhibitors (linagliptin, sitagliptin, alogliptin) or placebo once daily for 4 days from 8 weeks after surgery, to identify the most appropriate treatment for cardiac dysfunction associated with CKD. Linagliptin showed no significant change in blood level AUC(0-infinity) in 5/6N rats, but sitagliptin and alogliptin had significantly higher AUC(0-infinity) values; 41% and 28% (p=0.0001 and p=0.0324), respectively. No correlation of markers of renal tubular and glomerular function with AUC was observed for linagliptin, which required no dose adjustment in uremic rats. Linagliptin 7 mu mol/kg caused a 2-fold increase in GLP-1 (AUC 201.0 ng/l*h) in 5/6N rats compared with sham-treated rats (AUC 108.6 ng/l*h) (p=0.01). The mRNA levels of heart tissue fibrosis markers were all significantly increased in 5/6N vs control rats and reduced/normalized by linagliptin.
Conclusions/Significance: DPP-4 inhibition increases plasma GLP-1 levels, particularly in uremia, and reduces expression of cardiac mRNA levels of matrix proteins and B-type natriuretic peptides (BNP). Linagliptin may offer a unique approach for treating uremic cardiomyopathy in CKD patients, with no need for dose-adjustment.
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.
The pathway of molybdenum cofactor biosynthesis has been studied in detail by using proteins from Mycobacterium species, which contain several homologs associated with the first steps of Moco biosynthesis. While all Mycobacteria species contain a MoeZR, only some strains have acquired an additional homolog, MoeBR, by horizontal gene transfer. The role of MoeBR and MoeZR was studied in detail for the interaction with the two MoaD-homologs involved in Moco biosynthesis, MoaD1 and MoaD2, in addition to the CysO protein involved in cysteine biosynthesis. We show that both proteins have a role in Moco biosynthesis, while only MoeZR, but not MoeBR, has an additional role in cysteine biosynthesis. MoeZR and MoeBR were able to complement an E. coli moeB mutant strain, but only in conjunction with the Mycobacterial MoaD1 or MoaD2 proteins. Both proteins were able to sulfurate MoaD1 and MoaD2 in vivo, while only MoeZR additionally transferred the sulfur to CysO. Our in vivo studies show that Mycobacteria have acquired several homologs to maintain Moco biosynthesis. MoeZR has a dual role in Moco- and cysteine biosynthesis and is involved in the sulfuration of MoaD and CysO, whereas MoeBR only has a role in Moco biosynthesis, which is not an essential function for Mycobacteria.
Simultaneous limitation of plant growth by two or more nutrients is increasingly acknowledged as a common phenomenon in nature, but its cellular mechanisms are far from understood. We investigated the uptake kinetics of CO(2) and phosphorus of the algae Chlamydomonas acidophila in response to growth at limiting conditions of CO(2) and phosphorus. In addition, we fitted the data to four different Monod-type models: one assuming Liebigs Law of the minimum, one assuming that the affinity for the uptake of one nutrient is not influenced by the supply of the other (independent colimitation) and two where the uptake affinity for one nutrient depends on the supply of the other (dependent colimitation). In addition we asked whether the physiological response under colimitation differs from that under single nutrient limitation. We found no negative correlation between the affinities for uptake of the two nutrients, thereby rejecting a dependent colimitation. Kinetic data were supported by a better model fit assuming independent uptake of colimiting nutrients than when assuming Liebigs Law of the minimum or a dependent colimitation. Results show that cell nutrient homeostasis regulated nutrient acquisition which resulted in a trade-off in the maximum uptake rates of CO(2) and phosphorus, possibly driven by space limitation on the cell membrane for porters for the different nutrients. Hence, the response to colimitation deviated from that to a single nutrient limitation. In conclusion, responses to single nutrient limitation cannot be extrapolated to situations where multiple nutrients are limiting, which calls for colimitation experiments and models to properly predict growth responses to a changing natural environment. These deviations from single nutrient limitation response under colimiting conditions and independent colimitation may also hold for other nutrients in algae and in higher plants.
Cyanobacteria are prolific producers of natural products. Investigations into the biochemistry responsible for the formation of these compounds have revealed fascinating mechanisms that are not, or only rarely, found in other microorganisms. In this article, we survey the biosynthetic pathways of cyanobacteria isolated from freshwater, marine and terrestrial habitats. We especially emphasize modular nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) pathways and highlight the unique enzyme mechanisms that were elucidated or can be anticipated for the individual products. We further include ribosomal natural products and UV-absorbing pigments from cyanobacteria. Mechanistic insights obtained from the biochemical studies of cyanobacterial pathways can inspire the development of concepts for the design of bioactive compounds by synthetic-biology approaches in the future.
Vitamin A metabolism is changed in donors after living-kidney transplantation an observational study
(2011)
Background: The kidneys are essential for the metabolism of vitamin A (retinol) and its transport proteins retinol-binding protein 4 (RBP4) and transthyretin. Little is known about changes in serum concentration after living donor kidney transplantation (LDKT) as a consequence of unilateral nephrectomy; although an association of these parameters with the risk of cardiovascular diseases and insulin resistance has been suggested. Therefore we analyzed the concentration of retinol, RBP4, apoRBP4 and transthyretin in serum of 20 living-kidney donors and respective recipients at baseline as well as 6 weeks and 6 months after LDKT.
Results: As a consequence of LDKT, the kidney function of recipients was improved while the kidney function of donors was moderately reduced within 6 weeks after LDKT. With regard to vitamin A metabolism, the recipients revealed higher levels of retinol, RBP4, transthyretin and apoRBP4 before LDKT in comparison to donors. After LDKT, the levels of all four parameters decreased in serum of the recipients, while retinol, RBP4 as well as apoRBP4 serum levels of donors increased and remained increased during the follow-up period of 6 months.
Conclusion: LDKT is generally regarded as beneficial for allograft recipients and not particularly detrimental for the donors. However, it could be demonstrated in this study that a moderate reduction of kidney function by unilateral nephrectomy, resulted in an imbalance of components of vitamin A metabolism with a significant increase of retinol and RBP4 and apoRBP4 concentration in serum of donors.
Der Beitrag konzentriert sich auf die neue einheitliche Behördenrufnummer D115, als aktuelles, innovatives eGovernment-Projekt der deutschen Verwaltungsmodernisierung. Als theoretische Grundlage der hier vorliegenden empirischen verwaltungswissen schaftlichen Analyse sekundiert der Multilevel-Governance-Ansatz, welcher die Mehrebenenverflechtung der politisch-administrativen Strukturen, die Vielschichtigkeit und die besondere Governancestruktur des Reformvorhabens am besten erfassen dürfte. Die Analyse der Funktionsweise der Behördenrufnummer D115, der beteiligten Akteure und deren institutionell bedingter Motivation kommt insgesamt zum Ergebnis, dass der Ansatz für das Modernisierungsprojekt als geradezu exemplarisch zu betrachten ist. Die Berücksichtigung des Mehrebenencharakters sowie der dabei zur Anwendung kommen den Netzwerk- und Steuerungsmechanismen sind bei einem solchen Projekt und künftigen eGovernment-Projekten unverzichtbar.
Der Beitrag konzentriert sich auf die neue einheitliche Behördenrufnummer D115, als aktuelles, innovatives eGovernment-Projekt der deutschen Verwaltungsmodernisierung. Als theoretische Grundlage der hier vorliegenden empirischen verwaltungswissen schaftlichen Analyse sekundiert der Multilevel-Governance-Ansatz, welcher die Mehrebenenverflechtung der politisch-administrativen Strukturen, die Vielschichtigkeit und die besondere Governancestruktur des Reformvorhabens am besten erfassen dürfte. Die Analyse der Funktionsweise der Behördenrufnummer D115, der beteiligten Akteure und deren institutionell bedingter Motivation kommt insgesamt zum Ergebnis, dass der Ansatz für das Modernisierungsprojekt als geradezu exemplarisch zu betrachten ist. Die Berücksichtigung des Mehrebenencharakters sowie der dabei zur Anwendung kommen den Netzwerk- und Steuerungsmechanismen sind bei einem solchen Projekt und künftigen eGovernment-Projekten unverzichtbar.
The selection of ‘good’ pictures has increasingly become a crucial factor when transmitting news to the recipients. Every day thousands of events are happening and millions of pictures are taken. By choosing photographs for newspapers and magazines, photographic editorial departments want to attract the recipients’ attention, evoke emotions and get them to read their stories. But what exactly is a good picture that meets these expectations? Which criteria are decisive for selecting pictures and what effects of this selection can be measured on the recipients’ side? This article presents the results of a research project carried out at the University of Erfurt in 2008 and conducted in collaboration with the German weekly magazine stern. It deals with the selection and impact of press photography by introducing the concept ‘photo news factors’. Applying the traditional news value theory to pictures, photo news factors are defined as selection criteria that, on the part of the communicator, decide whether the press photos are worth publishing. Furthermore, they are assumed to exert an influence on the intensity of attention that a picture arouses.
This article presents several acceptability rating experiments concerned with crossing wh-movement in German multiple questions. Our results show that there is no general superiority effect in German, thus refuting claims to the contrary by Featherston (2005). However, acceptability is reduced when a whphrase crosses a wh-subject with which it agrees in animacy. We explain this finding in terms of the availability of different sorting keys for the answers to the multiple questions.
The article provides an overview of the grammatical realization of focus in four West Chadic languages (Chadic, Afro-Asiatic). The languages discussed exhibit an intriguing crosslinguistic variation in the realization of focus, both among themselves as well as compared to European intonation languages. They also display language-internal variation in the formal realization of focus. The West Chadic languages differ widely in their ways of expressing focus, which range from syntactic over prosodic to morphological devices. In contrast to European intonation languages, the focus marking systems of the West Chadic languages are inconsistent in that focus is often not grammatically expressed, but these inconsistencies are shown to be systematic. Subject foci (contrastive or not) and contrastive nonsubject foci are always grammatically marked, whereas information focus on nonsubjects need not be marked as such. The absence of formal focus marking supports pragmatic theories of focus in terms of contextual resolution. The special status of focused subjects and contrastive foci is derived from the Contrastive Focus Hypothesis, which requires unexpected foci and unexpected focus contents to be marked as such, together with the assumption that canonical subjects in West Chadic receive a default interpretation as topics. Finally, I discuss certain focus ambiguities which are not attested in intonation languages, nor do they follow on standard accounts of focus marking, but which can be accounted for in terms of constraint interaction in the formal expression of focus.
This paper discusses a hitherto undescribed usage of the particle so as a dedicated focus marker in contemporary German. I discuss grammatical and pragmatic characteristics of this focus marker, supporting my account with natural linguistic data and with controlled experimental evidence showing that so has a significant influence on speakers’ understanding of what the focus expression in a sentence is. Against this background, I sketch a possible pragmaticalization path from referential usages of so via hedging to a semantically bleached focus marker, which, unlike particles such as auch ‘also’/‘too’ or nur ‘only’, does not contribute any additional meaning.
Der Aufsatz umreißt die Wirkung von Averroes’ Bearbeitung der aristotelischen ‚Poetik‘ als argumentativer Disziplin. Beginnend mit Al-Farabi und Al-Gazali im zehnten Jahrhundert wird die ‚Poetik‘ den logischen Disziplinen des ‚Organon‘ zugerechnet. Während die Theorie eines ‚poetischen Syllogismus‘ nicht rezipiert worden ist, wurde der argumentative Status der Dichtung vom zwölften Jahrhundert an auch im lateinischen Westen bekannt. Mit unterschiedlichen Begründungen übernahmen Dominicus Gundissalinus, Vincenz von Beauvais, Albertus Magnus, Roger Bacon und Thomas von Aquin die Klassifizierung der Poetik als argumentative Disziplin. Am Ende des Aufsatzes steht ein Ausblick auf Coluccio Salutatis ‚De laboribus Herculis‘ und die humanistische Rezeption dieser Tradition.
Der Aufsatz zeigt, dass es sich bei der averroischen Bearbeitung der aristotelischen ‚Poetik‘ um eine in sich konsistente Theorie der Dichtung handelt, die allerdings mit der aristotelischen Konzeption der Dichtung nur wenig zu tun hat. Ausgehend von der Übersetzung von ‚Tragödie‘ und ‚Komödie‘ mit ‚Lob‘ und ‚Tadel‘ entwickelt Averroes einen Begriff von Dichtung als moralphilosophisches Argument zum Lob der Tugend und zum Tadel des Lasters. Im Mittelpunkt steht die Interpretation des aristotelischen Begriffs der mimesis als similitudo, das heißt als Gleichnis. Als gleichnishaftes Argument ist Dichtung nur graduell von anderen argumentativen Formen wie der demonstrativen Logik und der Rhetorik unterschieden.
Über die Autoren
(2011)