Research of population with impulsive perturbations based on dynamics of a neutral delay equation and ecological quality system

This paper studies the global behaviors of a nonlinear autonomous neutral delay differential population model with impulsive perturbation. This model may be suitable for describing the dynamics of population with long larval and short adult phases. It is shown that the system may have global stability of the extinction and positive equilibria, or grow without being bounded under some conditions.     

A management policy for sika deer based on sex-specific hunting

We consider here a management policy for a sika deer (Cervus nippon) population in the eastern part of Hokkaido. Deer populations are characterized by a large intrinsic rate of population increase, no significant density effects on population growth before population crash, and a relatively simple life history. Our goals of management for the deer population are (1) to avoid irruption with severe damage to agriculture and forestry, (2) to avoid the risk of extinction of the deer population, and (3) to maintain a sustainable yield of deer. To make a robust program on the basis of uncertain information about the deer population, we consider three levels of relative population size and four levels of hunting pressures. We also take into consideration a critical level for extinction, an optimal level, and an irruption level. The hunting pressure for females is set to increase with the population size. We also recommend catching males if the population size is between the critical and optimal levels and catching females and males if the population size is larger than the optimal level. We must avoid cases of irruption or threatened population under various sets of uncertain parameter values. The simulation results suggest that management based on sex-specific hunting is effective to diminish the annual variation in hunting yield. Received: April 8, 1998 / Accepted: December 25, 1998     

Perturbation of maize rhizosphere microflora following seed bacterization with Burkholderia cepacia MCI 7

Introduction of a large quantity of exogenous microorganisms may disrupt a local ecosystem and affect the natural microflora. In this work we investigated the effects of the introduction of a plant growth promoting strain of Burkholderia cepacia into the rhizosphere of maize on both indigenous B. cepacia populations and microbial community structure of total culturable bacteria using the concept of r/K strategy. Moreover we studied the distribution of bacterial populations in the root system at various soil depths. Seed bacterization was used as application method. Root colonization of the introduced strain occurred mainly on roots close to the plant stem, whereas indigenous B. cepacia was recovered at higher amounts from the lower parts of root systems of mature plants. As far as total culturable bacteria are concerned, an almost uniform distribution in the root system of mature plants was observed. The release of the exogenous bacterial strain affected mainly the microbial populations of young growing plants rather than mature plants. Indeed it caused only short-term perturbations in the microbial community of maize rhizosphere. Colonization of maize roots by indigenous B. cepacia was not significantly affected by the presence of the exogenous strain.     

Simulating the fidelity and the three Mg mechanism of pol η and clarifying the validity of transition state theory in enzyme catalysis

Pol η belongs to the important Y family of DNA polymerases that can catalyze translesion synthesis across sites of damaged DNA. This activity involves the reduced fidelity of Pol η for 8‐oxo‐7,8‐dhyedro‐2′‐deoxoguanosin(8‐oxoG). The fundamental interest in Pol η has grown recently with the demonstration of the importance of a 3rd Mg2+ ion. The current work explores both the fidelity of Pol η and the role of the 3rd metal ion, by using empirical valence bond (EVB) simulations. The simulations reproduce the observed trend in fidelity and shed a new light on the role of the 3rd metal ion. It is found that this ion does not lead to a major catalytic effect, but most probably plays an important role in reducing the product release barrier. Furthermore, it is concluded, in contrast to some implications, that the effect of this metal does not violate transition state theory, and the evaluation of the catalytic effect must conserve the molecular composition upon moving from the reactant to the transition state. Proteins 2017; 85:1446–1453. © 2017 Wiley Periodicals, Inc.     

Numerical Approaches to Life Cycle Interpretation - The case of the Ecoinvent’96 database (10 pp)

Goal, Scope and Background To strengthen the evaluative power of LCA, life cycle interpretation should be further developed. A previous contribution (Heijungs & Kleijn 2001) elaborated five examples of concrete methods within the subset of numerical approaches towards interpretation. These methods were: contribution analysis, perturbation analysis, uncertainty analysis, comparative analysis, and discernibility analysis. Developments in software have enabled the possibility to apply the five example methods to explore the much-used Ecoinvent”96 database.Discussion of Methods The numerical approaches implemented in this study include contribution analysis, perturbation analysis, uncertainty analysis, comparative analysis, discernibility analysis and the newly developed key issue analysis. The data used comes from a very large process database: Ecoinvent’96, containing 1163 processes, 1181 economic flows and 571 environmental flows. Conclusions Results are twofold: they serve as a benchmark to the usefulness and feasibility of these numerical approaches, and they shed light on the question of stability and structure in an often-used large system of interconnected processes. Most of the approaches perform quite well: computation time on a moderate PC is between a few seconds a few minutes. Only Monte Carlo analyses may require much longer, but even then it appears that most questions can be answered within a few hours. Moreover, analytical expressions for error propagation are much faster than Monte Carlo analyses, while giving almost identical results. Despite the fact that many processes are connected to each other, leading to the possibility of a very unstable system and very sensitive coefficients, the overall results show that most results are not extremely uncertain. There are, however, some exceptions to this positive message.     

Osmolyte perturbation reveals conformational equilibria in spin‐labeled proteins

Recent evidence suggests that proteins at equilibrium can exist in a manifold of conformational substates, and that these substates play important roles in protein function. Therefore, there is great interest in identifying regions in proteins that are in conformational exchange. Electron paramagnetic resonance spectra of spin‐labeled proteins containing the nitroxide side chain (R1) often consist of two (or more) components that may arise from slow exchange between conformational substates (lifetimes > 100 ns). However, crystal structures of proteins containing R1 have shown that multicomponent spectra can also arise from equilibria between rotamers of the side chain itself. In this report, it is shown that these scenarios can be distinguished by the response of the system to solvent perturbation with stabilizing osmolytes such as sucrose. Thus, site‐directed spin labeling (SDSL) emerges as a new tool to explore slow conformational exchange in proteins of arbitrary size, including membrane proteins in a native‐like environment. Moreover, equilibrium between substates with even modest differences in conformation is revealed, and the simplicity of the method makes it suitable for facile screening of multiple proteins. Together with previously developed strategies for monitoring picosecond to millisecond backbone dynamics, the results presented here expand the timescale over which SDSL can be used to explore protein flexibility.     

ent-Steroids: Novel tools for studies of signaling pathways

Membrane receptors are often modulated by steroids and it is necessary to distinguish the effects of steroids at these receptors from effects occurring at nuclear receptors. Additionally, it may also be mechanistically important to distinguish between direct effects caused by binding of steroids to membrane receptors and indirect effects on membrane receptor function caused by steroid perturbation of the membrane containing the receptor. In this regard, ent-steroids, the mirror images of naturally occurring steroids, are novel tools for distinguishing between these various actions of steroids. The review provides a background for understanding the different actions that can be expected of steroids and ent-steroids in biological systems, references for the preparation of ent-steroids, a short discussion about relevant forms of stereoisomerism and the requirements that need to be fulfilled for the interaction between two molecules to be enantioselective. The review then summarizes results of biophysical, biochemical and pharmacological studies published since 1992 in which ent-steroids have been used to investigate the actions of steroids in membranes and/or receptor-mediated signaling pathways.