Resetting biological oscillators—A stochastic approach

We present a stochastic approach to phase-resetting of an ensemble of oscillators. In order to describe stimulation-induced dynamical phenomena we develop a stochastic model which consists of an ensemble of phase oscillators interacting via random forces. Every single oscillator is submitted to a phase stimulus. The ensemble's dynamics is determined by a Fokker-Planck equation. The stationary states are calculated explicitly, whereas the transients are analysed numerically. If the stimulus of a given (non-vanishing) intensity is administered at a critical initial cluster phase for a critical duration T _crit the ensemble's synchronized oscillation is annihilated. A transition from type 1 resetting to type 0 resetting occurs when the stimulation duration exceeds T _crit. Stimulation causes a shift of the mean frequency of every single oscillator. This frequency shift is explicitly calculated by deriving the mean first passage time. The model shows that there is a subcritical intensity which is connected with an enhanced vulnerability to stimulation. The desynchronized states, the so-called black holes, are typically associated with a double peak in the ensemble's phase distribution. This is important for analysing experimental data because simple peak-detection algorithms are not able to extract the underlying dynamics.Our results are discussed from the experimentator's point of view so that the insights derived from our model can improve data analysis and design of stimulation experiments.     

Growth ring analysis of multiple dicotyledonous herb species—A novel community-wide approach

Longevity is a key demographic characteristic of herbaceous plants, but often unknown. While root or rhizome growth ring analysis may allow assessment plant longevity directly and conveniently, so far it has only been used in a few case studies of herbaceous dicotyledonous species. To evaluate whether growth ring analysis is applicable to a large spectrum of herbaceous dicotyledonous plant species, we used plant communities of varying species richness in a 12-year-old grassland biodiversity experiment (Jena Experiment). Cross-sections of the oldest available part of the plants were analysed for all available dicotyledonous perennial herb species (S = 37), which represented three functional groups: legumes, small herbs and tall herbs. We studied 1664 individuals representing the genet in clearly distinguishable plant individuals, and the ramet in clonally growing plant species.Roots of eleven species with permanent primary root were harvested. They showed clearly visible growth rings. Longevity was extended with a mean age of 4.0 years (SE = 0.3). Seven species, which also had a permanent primary root, showed less distinct growth rings. They were shorter-lived (mean age 3.0 years (SE = 0.3)). In six species with obligate clonal growth mostly rhizomes were sampled, but individuals were still identifiable due to their growth habit. For these species growth rings were clearly visible. Longevity of rhizomes was extended (mean age 3.3 years (SE = 0.5)). In 13 species with obligate clonal growth also rhizomes were sampled, but plant individuals were not identifiable. For these species longevity was low (mean age 2.1 years (SE = 0.2)). Community mean age was significantly lower when small herbs were present and higher when tall herbs were present, while legumes had no effect on community mean age. In summary, anatomical analysis of roots and rhizomes is a suitable tool to study the population age structure of a large spectrum of perennial dicotyledonous herbaceous species and therefore opens new perspectives for demographic studies at the community level.     

Polyphasic approach of bacterial classification — An overview of recent advances

Classification of microorganisms on the basis of traditional microbiological methods (morphological, physiological and biochemical) creates a blurred image about their taxonomic status and thus needs further clarification. It should be based on a more pragmatic approach of deploying a number of methods for the complete characterization of microbes. Hence, the methods now employed for bacterial systematics include, the complete 16S rRNA gene sequencing and its comparative analysis by phylogenetic trees, DNA-DNA hybridization studies with related organisms, analyses of molecular markers and signature pattern(s), biochemical assays, physiological and morphological tests. Collectively these genotypic, chemotaxonomic and phenotypic methods for determining taxonomic position of microbes constitute what is known as the ‘polyphasic approach’ for bacterial systematics. This approach is currently the most popular choice for classifying bacteria and several microbes, which were previously placed under invalid taxa have now been resolved into new genera and species. This has been possible owing to rapid development in molecular biological techniques, automation of DNA sequencing coupled with advances in bioinformatic tools and access to sequence databases. Several DNA-based typing methods are known; these provide information for delineating bacteria into different genera and species and have the potential to resolve differences among the strains of a species. Therefore, newly isolated strains must be classified on the basis of the polyphasic approach. Also previously classified organisms, as and when required, can be reclassified on this ground in order to obtain information about their accurate position in the microbial world. Thus, current techniques enable microbiologists to decipher the natural phylogenetic relationships between microbes.     

Prodrugs of fumarate esters for the treatment of psoriasis and multiple sclerosis—a computational approach

Density functional theory (DFT) calculations at B3LYP/6-31 G (d,p) and B3LYP/6-311?+?G(d,p) levels for the substituted pyridine-catalyzed isomerization of monomethyl maleate revealed that isomerization proceeds via four steps, with the rate-limiting step being proton transfer from the substituted pyridinium ion to the C=C double bond in INT1. In addition, it was found that the isomerization rate (maleate to fumarate) is solvent dependent. Polar solvents, such as water, tend to accelerate the isomerization rate, whereas apolar solvents, such as chloroform, act to slow down the reaction. A linear correlation was obtained between the isomerization activation energy and the dielectric constant of the solvent. Furthermore, linearity was achieved when the activation energy was plotted against the pK _a value of the catalyst. Substituted-pyridine derivatives with high pK _a values were able to catalyze isomerization more efficiently than those with low pK _a values. The calculated relative rates for prodrugs 1–6 were: 1 (406.7), 2 (7.6?×?10⁶), 3 (1.0), 4 (20.7), 5 (13.5) and 6 (2.2?×?10³). This result indicates that isomerizations of prodrugs 1 and 3–5 are expected to be slow and that of prodrugs 2 and 6 are expected to be relatively fast. Hence, prodrugs 2 and 3–5 have the potential to be utilized as prodrugs for the slow release of monomethylfumarate in the treatment of psoriasis and multiple sclerosis.

A UNEP/SETAC approach towards a life cycle sustainability assessment—our contribution to Rio+20

Purpose

To contribute to the upcoming United Nations Conference on Sustainable Development (Rio+20) in 2012 by introducing a life cycle sustainability assessment (LCSA) and showing how it can play a crucial role in moving towards sustainable consumption and production. The publication, titled Towards a Life Cycle Sustainability Assessment, and published by the UNEP/SETAC Life Cycle Initiative aims to show how three life cycle techniques—(environmental) LCA, S-LCA and LCC—can be combined as part of an over-arching LCSA.

Methods

The method was demonstrated by evaluating the characteristics of each phase for each life cycle technique. In defining the goal and scope of an LCSA, for example, different aspects should be taken into account to establish the aim of the study as well as the functional unit, system boundaries, impact category and allocation. Then, the data to be collected for the life cycle sustainability inventory can be either in a unit process or on an organisational level. They can also be quantitative or qualitative. Life cycle sustainability impact assessment should consider the relevance of the impacts as well as the perspective of stakeholders. The interpretation should not add up the results, but rather evaluate them jointly. In order to clarify the approach, a case study is presented to evaluate three types of marble according to the proposed method.

Results and discussion

The authors have identified that while LCSA is feasible, following areas need more development: data production and acquisition, methodological development, discussion about LCSA criteria (e.g. cutoff rules), definitions and formats of communication and dissemination of LCSA results and the expansion of research and applications combining (environmental) LCA, LCC and S-LCA. The authors also indicate that it is necessary to develop more examples and cases to improve user capacity to analyse the larger picture and therefore address the three dimensions or pillars of sustainability in a systematic way. Software and database providers are called for in order to facilitate user-friendly and accessible tools to promote LCSAs.

Conclusions

The application demonstrated that, although methodological improvements are still needed, important steps towards an overarching sustainability assessment have been accomplished. LCSA is possible and should be pursued; however, more efforts should be made to improve the technique and facilitate the studies in order to contribute to a greener economy.     

Expansion and contraction of the cytotoxic T lymphocyte response—An optimal control approach

The kinetics of the cytotoxic T lymphocyte (CTL) response against intracellular pathogens has been found to have many stereotypical features that appear to be programmed early in the infection. We explain these findings here in terms of CTL response kinetics that minimize the probability that a pathological symptom will occur in association with the infection and its eradication. We assume that both the infection and the CTLs contribute to this pathology. We find that contraction kinetics is influenced by the relative pathogenicities of infection and CTLs, as well as on the virulence of the infection and the efficiency of the CTLs, but not by the magnitude of expansion or the dose and duration of infection. Our analysis explains the finding that the duration of the CTL expansion is highly stereotypical, with the maximum expansion of the CTL response dependent on the dose of the infection. Finally, we show that the stereotypical nature of CTL kinetics relies upon stringent regulation of the rates at which CTLs proliferate and die.     

Which future for the French Pyrenean brown bear (Ursus arctos) population? An approach using stage-structured deterministic and stochastic models

The Pyrenean brown bear (Ursus arctos) population is considered as one of the most seriously threatened with extinction in Western Europe. To assess its viability and possible needs of augmentation, we develop deterministic and stochastic stage-structured demographic models. The deterministic model reveals that a bear population cannot have a high annual growth rate and is particularly sensitive to breeder survival. High demographic parameters appear to be crucial to population persistence, especially for a small population that remains vulnerable to demographic and environmental stochasticities. The Pyrenean population cannot therefore be considered as viable. Successful conservation strategies for this population would require releasing more bears in both sub-populations in the near future.     

The mitochondrial permeability transition pore (PTP) — An example of multiple molecular exaptation?

The mitochondrial permeability transition (PT) is a well-recognized phenomenon that allows mitochondria to undergo a sudden increase of permeability to solutes with molecular mass ≤ 1500 Da, leading to organelle swelling and structural modifications. The relevance of PT relies on its master role in the manifestation of programmed cell death (PCD). This function is performed by a mega-channel (in some cases inhibited by cyclosporin A) named permeability transition pore (PTP), whose function could derive from the assembly of different mitochondrial proteins.In this paper we examine the distribution and characteristics of PTP in mitochondria of eukaryotic organisms so far investigated in order to draw a hypothesis on the mechanism of its evolution. As a result, we suggest that PTP may have arisen as a new function linked to a multiple molecular exaptation of different mitochondrial proteins, even though they could nevertheless still play their original role.Furthermore, we suggest that the early appearance of PTP could have had a crucial role in the establishment of endosymbiosis in eukaryotic cells, by the coordinated balancing of ATP production by glycolysis (performed by the primary phagocyte) and oxidative phosphorylation (accomplished by the endosymbiont). Indeed, we argue on the possibility that this new energetic equilibrium could have opened the way to the subsequent evolution toward metazoans.     

Biological modeling of complex chemotaxis behaviors for C. elegans under speed regulation—a dynamic neural networks approach

In this paper, the modeling of several complex chemotaxis behaviors of C. elegans is explored, which include food attraction, toxin avoidance, and locomotion speed regulation. We first model the chemotaxis behaviors of food attraction and toxin avoidance separately. Then, an integrated chemotaxis behavioral model is proposed, which performs the two chemotaxis behaviors simultaneously. The novelty and the uniqueness of the proposed chemotaxis behavioral models are characterized by several attributes. First, all the chemotaxis behavioral model sare on biological basis, namely, the proposed chemotaxis behavior models are constructed by extracting the neural wire diagram from sensory neurons to motor neurons, where sensory neurons are specific for chemotaxis behaviors. Second, the chemotaxis behavioral models are able to perform turning and speed regulation. Third, chemotaxis behaviors are characterized by a set of switching logic functions that decide the orientation and speed. All models are implemented using dynamic neural networks (DNN) and trained using the real time recurrent learning (RTRL) algorithm. By incorporating a speed regulation mechanism, C. elegans can stop spontaneously when approaching food source or leaving away from toxin. The testing results and the comparison with experiment results verify that the proposed chemotaxis behavioral models can well mimic the chemotaxis behaviors of C. elegans in different environments.     

Fibre digestibility in large herbivores as related to digestion type and body mass — An in vitro approach

The coexistence of different ungulate species in a given ecosystem has been the focus of many studies. Differences between ruminant foregut fermenters and hindgut fermenters were remarkable for example in the way they ingest and digest high fibre diets. Digestion trials based on total collections are difficult to conduct or are sometimes even not possible for wild animals in the field or in zoos. To gain information on the fibre digestion achieved by these animals and the influence of body mass (BM) thereon, a method using spot sampling is desirable. In this study, in vitro fermentation of faecal neutral detergent fibre (NDF) was used as a measure of fibre digestion in large ungulates. Food and faecal samples of 10 ruminant foregut fermenting and 7 hindgut fermenting species/breeds were collected. All animals received 100% grass hay with ad libitum access. The NDF of food and faeces was fermented in vitro in a Hohenheim gas test (HGT) for 96 h. The digestion type generally had an effect on the gas production (GP) of faecal NDF in the HGT with hindgut fermenters showing higher values than ruminant foregut fermenters. At any time interval of incubation, BM had no influence on GP. The results are in accordance with both findings that ruminant foregut fermenters have longer mean retention times and more comprehensive particle reduction and findings of a lack of influence of BM on digesta mean retention time. It can be stated that the HGT (96 h) is a useful and quick method to show also small differences within groups in fibre digestion.     

Satellite Ecology (SATECO)—linking ecology,remote sensing and micrometeorology,from plot to regional scale,for the study of ecosystem structure and function

There is a growing requirement for ecosystem science to help inform a deeper understanding of the effects of global climate change and land use change on terrestrial ecosystem structure and function, from small area (plot) to landscape, regional and global scales. To meet these requirements, ecologists have investigated plant growth and carbon cycling processes at plot scale, using biometric methods to measure plant carbon accumulation, and gas exchange (chamber) methods to measure soil respiration. Also at the plot scale, micrometeorologists have attempted to measure canopy- or ecosystem-scale CO₂ flux by the eddy covariance technique, which reveals diurnal, seasonal and annual cycles. Mathematical models play an important role in integrating ecological and micrometeorological processes into ecosystem scales, which are further useful in interpreting time-accumulated information derived from biometric methods by comparing with CO₂ flux measurements. For a spatial scaling of such plot-level understanding, remote sensing via satellite is used to measure land use/vegetation type distribution and temporal changes in ecosystem structures such as leaf area index. However, to better utilise such data, there is still a need for investigations that consider the structure and function of ecosystems and their processes, especially in mountainous areas characterized by complex terrain and a mosaic distribution of vegetation. For this purpose, we have established a new interdisciplinary approach named ‘Satellite Ecology’, which aims to link ecology, remote sensing and micrometeorology to facilitate the study of ecosystem function, at the plot, landscape, and regional scale. This article was contributed at the invitation of the Editorial Committee.     

Stratification of density in dry deciduous forest using satellite remote sensing digital data—An approach based on spectral indices

Forest density expressing the stocking status constitutes the major stand physiognomic parameter of Indian forest. Density and age are often taken as surrogate to structural and compositional changes that occur with the forest succession. Satellite remote sensing spectral response is reported to provide information on structure and composition of forest stands. The various vegetation indices are also correlated with forest canopy closure. The paper presents a three way crown density model utilizing the vegetation indices viz., advanced vegetation index, bare soil index and canopy shadow index for classification of forest crown density. The crop and water classes which could not be delineated by the model were finally masked from normalized difference vegetation index and TM band 7 respectively. The rule based approach has been implemented for land use and forest density classification. The broad land cover classification accuracy has been found to be 91.5%. In the higher forest density classes the classification accuracy ranged between 93 and 95%, whereas in the lower density classes it was found to be between 82 and 85%.