Extended rat liver slice survival and stability monitored using clinical biomarkers

Precision-cut liver slices are reportedly limited as toxicity models by their short half-life in culture. We used traditional clinical chemistry biomarkers and histology to assess a newer procedure for improved liver slice maintenance. Slices from Sprague-Dawley rat livers were well maintained in a roller culture system for up to 10 days based on protein content (60-70% or higher of initial values) and biomarker retention and verified by histological examination of the tissues showing morphological integrity and viability of hepatocyte and biliary regions. Exposure of the slices to geldanamycin (GEL) resulted in loss of slice LDH and transaminase content, with associated depression in ALP and GGT levels and elevated bilirubin, indicating that GEL affects both cell types as occurs in vivo with this hepatobiliary toxicant. Thus, we conclude that liver slices merit further investigation as a general model for chronic as well as acute toxicity studies.     

Exploring the concept of interaction computing through the discrete algebraic analysis of the Belousov–Zhabotinsky reaction

Interaction computing (IC) aims to map the properties of integrable low-dimensional non-linear dynamical systems to the discrete domain of finite-state automata in an attempt to reproduce in software the self-organizing and dynamically stable properties of sub-cellular biochemical systems. As the work reported in this paper is still at the early stages of theory development it focuses on the analysis of a particularly simple chemical oscillator, the Belousov–Zhabotinsky (BZ) reaction. After retracing the rationale for IC developed over the past several years from the physical, biological, mathematical, and computer science points of view, the paper presents an elementary discussion of the Krohn–Rhodes decomposition of finite-state automata, including the holonomy decomposition of a simple automaton, and of its interpretation as an abstract positional number system. The method is then applied to the analysis of the algebraic properties of discrete finite-state automata derived from a simplified Petri net model of the BZ reaction. In the simplest possible and symmetrical case the corresponding automaton is, not surprisingly, found to contain exclusively cyclic groups. In a second, asymmetrical case, the decomposition is much more complex and includes five different simple non-abelian groups whose potential relevance arises from their ability to encode functionally complete algebras. The possible computational relevance of these findings is discussed and possible conclusions are drawn.     

Development and validation of an experimental and theoretical method for the chiral discrimination of dinotefuran

Dinotefuran is a low-cost agrochemical considered a highly toxic product. In this sense, there is a need for its constant environmental, biological, and food control, aiming to ensure its use to humans as well as to preserve biodiversity and ecosystems. In the present work, we developed an experimental and theoretical method for dinotefuran chiral discrimination. According to the main results, the dinotefuran enantioselective separation was efficiently optimized by high-performance liquid chromatography evaluating the influence of different percentage compositions in the mobile phase to improve the resolution of the peaks in the chromatogram. The novelty of this work was the proposition of a reduced molecular model for the chiral selector amylose-Tris-(3,5-dimethylphenylcarbamate) polysaccharide that was able to adequately describe at the molecular level its interaction with the dinotefuran enantiomers. Besides, the thermodynamic and structural parameters obtained via density functional theory calculations pointed out the chiral discrimination as well as the enantiomeric elution order of the analyte studied, confirming the experimental data, thus validating our proposed method. Finally, hydrogen bonds and repulsive interactions played a key role in the discrimination between the diastereomeric complexes, and consequently, for the dinotefuran enantioselective separation.     

A continuum theoretical model and finite elements simulation of bacterial flagellar filament phase transition

The Bacterial flagellar filament can undergo a polymorphic phase transition in response to both mechanical and chemical variations in vitro and in vivo environments. Under mechanical stimuli, such as viscous flow or forces induced by motor rotation, the filament changes its phase from left-handed normal (N) to right-handed semi-coiled (SC) via phase nucleation and growth. Our detailed mechanical analysis of existing experiments shows that both torque and bending moment contribute to the filament phase transition. In this paper, we establish a non-convex and non-local continuum model based on the Ginzburg-Landau theory to describe main characteristics of the filament phase transition such as new-phase nucleation, growth, propagation and the merging of neighboring interfaces. The finite element method (FEM) is adopted to simulate the phase transition under a displacement-controlled loading condition (rotation angle and bending deflection). We show that new-phase nucleation corresponds to the maximum torque and bending moment at the stuck end of the filament. The hysteresis loop in the loading and unloading curves indicates energy dissipation. When the new phase grows and propagates, torque and bending moment remain static. We also find that there is a drop in load when the two interfaces merge, indicating a concomitant reduction in the interfacial energy. Finally, the interface thickness is governed by the coefficients of the gradient of order parameters in the non-local interface energy. Our continuum theory and the finite element method provide a method to study the mechanical behavior of such biomaterials.     

Demographic trade-offs determine species abundance and diversity

Aims Much recent theory has focused on the role of neutral processes in assembling communities, but the basic assumption that all species are demographically identical has found little empirical support. Here, we show that the framework of the current neutral theory can easily be generalized to incorporate species differences so long as fitness equivalence among individuals is maintained through trade-offs between birth and death.Methods Our theory development is based on a careful reformulation of the Moran model of metacommunity dynamics in terms of a non-linear one-step stochastic process, which is described by a master equation.Important findings We demonstrate how fitness equalization through demographic trade-offs can generate significant macroecological diversity patterns, leading to a very different interpretation of the relation between Fisher's α and Hubbell's fundamental biodiversity number. Our model shows that equal fitness (not equal demographics) significantly promotes species diversity through strong selective sieving of community membership against high-mortality species, resulting in a positive association between species abundance and per capita death rate. An important implication of demographic trade-off is that it can partly explain the excessively high speciation rates predicted by the neutral theory of the stronger symmetry. Fitness equalization through demographic trade-offs generalizes neutral theory by considering heterospecific demographic difference, thus representing a significant step toward integrating the neutral and niche paradigms of biodiversity.     

Does organic farming benefit farmland birds in winter?

The generally higher biodiversity on organic farms may be influenced by management features such as no synthetic pesticide and fertilizer inputs and/or by differences in uncropped habitat at the site and landscape scale. We analysed bird and habitat data collected on 48 paired organic and conventional farms over two winters to determine the extent to which broad-scale habitat differences between systems could explain overall differences in farmland bird abundance. Density was significantly higher on organic farms for six out of 16 species, and none on conventional. Total abundance of all species combined was higher on organic farms in both years. Analyses using an information-theoretic approach suggested that both habitat extent and farm type were important predictors only for starling and greenfinch. Organic farming as currently practised may not provide significant benefits to those bird species that are limited by winter food resources, in particular, several declining granivores.     

Consequences of adaptive foraging in diverse communities

1.  Selective pressures acting on foraging activities constrain the strength of interaction, hence the stability and energetic availability in food webs.
2.  Because such selective pressures are usually measured at the individual level and because most experimental and theoretical works focus on simple settings, linking adaptive foraging with community scale patterns is still a far stretch.
3.  Some recent models incorporate foraging adaptation in diverse communities. The models vary in the way they incorporate adaptation, via evolutionary or behavioural changes, and define individual fitness in various ways.
4.  In spite of these differences, some general results linking adaptation to community structure and functioning emerge. In the present article, I introduce these different models and highlight their common results.
5.  Adaptive foraging provides stability to large food web models and predicts successfully interaction patterns within food webs as well as other topological features such as food chain length.
6.  The relationships between adaptive foraging and other structuring factors particularly depend on how well connected the local community is with surrounding communities (metacommunity aspect).     

A neutral model of edge effects

In this paper a spatially implicit neutral model for explaining the edge effects between habitats is proposed. To analyze this model we use two different approaches: a discrete approach that is based on the Master equation for a one step jump process and a continuous approach based on the approximation of the discrete jump process with the Kolmogorov-Fokker-Planck forward and backward equations. The discrete and continuous approaches are applied to analyze the species abundance distributions and the time to species extinction. Moreover, with the aid of the continuous approach a realistic classification of the behavior of species in local communities is developed. The species abundance dynamics at the edge between two distinct habitats is compared with those located in the homogeneous interior habitats using species abundance distributions and the first time to species extinction. We show that the structure of the links between local community and the metacommunity plays an important role on species persistence. Specifically, species at the edge between two distinct metacommunities have higher extinction rate than those in the interior habitats connected only to one metacommunity. Moreover, the same species might be persistent in the homogeneous interior habitat, but its probability of extinction from the edge local community could be very high.