Converting differential-equation models of biological systems to membrane computing

This paper presents a method to convert the deterministic, continuous representation of a biological system by ordinary differential equations into a non-deterministic, discrete membrane computation. The dynamics of the membrane computation is governed by rewrite rules operating at certain rates. That has the advantage of applying accurately to small systems, and to expressing rates of change that are determined locally, by region, but not necessary globally. Such spatial information augments the standard differentiable approach to provide a more realistic model. A biological case study of the ligand–receptor network of protein TGF-β is used to validate the effectiveness of the conversion method. It demonstrates the sense in which the behaviours and properties of the system are better preserved in the membrane computing model, suggesting that the proposed conversion method may prove useful for biological systems in particular.     

Non-linear molecular pattern classification using molecular beacons with multiple targets

In vitro pattern classification has been highlighted as an important future application of DNA computing. Previous work has demonstrated the feasibility of linear classifiers using DNA-based molecular computing. However, complex tasks require non-linear classification capability. Here we design a molecular beacon that can interact with multiple targets and experimentally shows that its fluorescent signals form a complex radial-basis function, enabling it to be used as a building block for non-linear molecular classification in vitro. The proposed method was successfully applied to solving artificial and real-world classification problems: XOR and microRNA expression patterns.     

A tale of two toxicities: malformed selenoproteins and oxidative stress both contribute to selenium stress in plants

Background

Despite selenium''s toxicity in plants at higher levels, crops supply most of the essential dietary selenium in humans. In plants, inorganic selenium can be assimilated into selenocysteine, which can replace cysteine in proteins. Selenium toxicity in plants has been attributed to the formation of non-specific selenoproteins. However, this paradigm can be challenged now that there is increasingly abundant evidence suggesting that selenium-induced oxidative stress also contributes to toxicity in plants.

Scope

This Botanical Briefing summarizes the evidence indicating that selenium toxicity in plants is attributable to both the accumulation of non-specific selenoproteins and selenium-induced oxidative stress. Evidence is also presented to substantiate the claim that inadvertent selenocysteine replacement probably impairs or misfolds proteins, which supports the malformed selenoprotein hypothesis. The possible physiological ramifications of selenoproteins and selenium-induced oxidative stress are discussed.

Conclusions

Malformed selenoproteins and oxidative stress are two distinct types of stress that drive selenium toxicity in plants and could impact cellular processes in plants that have yet to be thoroughly explored. Although challenging, deciphering whether the extent of selenium toxicity in plants is imparted by selenoproteins or oxidative stress could be helpful in the development of crops with fortified levels of selenium.     

Integration of Glomus mosseae with Chromolaena odorata powder for suppression of Meloidogyne incognita on maize (Zea mays L.)

Meloidogyne incognita infestation on maize results in heavy yield loss in farmers’ field. Most of the varieties adopted by subsistence farmers in Nigeria are susceptible to M. incognita. Beside these, the cost of control exceeding the profit from the crop using nematicides and the pollution risk they pose to the environment has necessitated the need for alternatives. Pot and field experiments were, therefore, conducted to investigate the effects of Chromolaena odorata powder and Glomus mosseae (a mycorrhizal fungus) on M. incognita pathogenicity on maize. Hybrid Oba super II improved maize variety adopted by local farmers was selected for the study. Maize plants were grown with G. mosseae (5 spores/g of soil) and soil amended with C. odorata powder (1% w/w) singly and in combination. Two weeks after emergence, Test plants were inoculated with 5000 M. incognita eggs. Sixty days after planting, destructive samples were assessed for root gall symptom and severity, and nematode population. Results show that G. mosseae and C. odorata powder were effective in controlling the population of M. incognita and the root knot nematode symptom and gave the highest yield parameters in combination. Single application of G. mosseae and C. odorata powder was similar in the effect on M. incognita and maize yield. Combination of G. mosseae and C. odorata powder may become a viable alternative to nematicide in managing M. incognita pathogenicity on maize as C. odorata powder may serve as a carrier medium for G. mosseae.     

Generation of initial molecular dynamics configurations in arbitrary geometries and in parallel

A computational pre-processing tool for generating initial configurations of molecules for molecular dynamics simulations in geometries described by a mesh of unstructured arbitrary polyhedra is described. The mesh is divided into separate zones and each can be filled with a single crystal lattice of atoms. Each zone is filled by creating an expanding cube of crystal unit cells, initiated from an anchor point for the lattice. Each unit cell places the appropriate atoms for the user-specified crystal structure and orientation. The cube expands until the entire zone is filled with the lattice; zones with concave and disconnected volumes may be filled. When the mesh is spatially decomposed into portions for distributed parallel processing, each portion may be filled independently, meaning that the entire molecular system never needs to fit onto a single processor, allowing very large systems to be created. The computational time required to fill a zone with molecules scales linearly with the number of cells in the zone for a fixed number of molecules, and better than linearly with the number of molecules for a fixed number of mesh cells. Our tool, molConfig, has been implemented in the open source C++ code OpenFOAM.     

Structural,catalytic and stabilizing consequences of aromatic cluster variants in human carbonic anhydrase II

The presence of aromatic clusters has been found to be an integral feature of many proteins isolated from thermophilic microorganisms. Residues found in aromatic cluster interact via π–π or C–H?π bonds between the phenyl rings, which are among the weakest interactions involved in protein stability. The lone aromatic cluster in human carbonic anhydrase II (HCA II) is centered on F226 with the surrounding aromatics F66, F95 and W97 located 12 Å posterior the active site; a location which could facilitate proper protein folding and active site construction. The role of F226 in the structure, catalytic activity and thermostability of HCA II was investigated via site-directed mutagenesis of three variants (F226I/L/W) into this position. The measured catalytic rates of the F226 variants via ¹⁸O-mass spectrometry were identical to the native enzyme, but differential scanning calorimetry studies revealed a 3–4 K decrease in their denaturing temperature. X-ray crystallographic analysis suggests that the structural basis of this destabilization is via disruption and/or removal of weak C–H?π interactions between F226 to F66, F95 and W97. This study emphasizes the importance of the delicate arrangement of these weak interactions among aromatic clusters in overall protein stability.     

The effect of the adaptor protein Isd11 on the quaternary structure of the eukaryotic cysteine desulphurase Nfs1

Small inorganic assemblies of alternating ferrous/ferric iron and sulphide ions, so-called iron–sulphur (Fe–S) clusters, are possibly nature’s most ancient prosthetic groups. One of the early actors in Fe–S cluster biosynthesis is a protein complex composed of a cysteine desulphurase, Nfs1, and its functional binding partner, Isd11. Although the essential function of Nfs1·Isd11 in the liberation of elemental sulphur from free cysteine is well established, little is known about its structure. Here, we provide evidence that shows Isd11 has a profound effect on the oligomeric state of Nfs1.     

辽宁老秃顶子自然保护区植物区系多样性

通过野外实地调查,利用植物区系谱、多样性指数、相关分析和聚类模型等方法,对辽宁老秃顶子植物区系多样性进行量化分析,揭示山地生物多样性特点、规律以及与周边植被生态的关系。结果表明:(1)辽宁老秃顶子自然保护区种子植物种类组成丰富,共有野生种子植物123科429属1 006种,且优势科现象明显,单种属和少种属占比率较高,表现出一定古老残遗性。（2）老秃顶子自然保护区植物种的区系分布型多样,区系组成复杂,来源较广泛,具有一定古老性,但植物特有现象不明显,以温带性质分布种为主,符合暖温带北部的华北植物区系特点。(3)老秃顶子山与相邻9个山地比较,植物区系Shannon-Wiener指数差异明显(1.736～2.259),其中庐山和徂徕山的Shannon-Wiener指数较高,而白石砬子和长白山的较低;10个山地的Simpson指数差异不显著(0.711 4～0.871 5)。(4)相关性分析显示,10个不同山地植物区系之间的相似程度显著,相关系数达0.617～0.995;聚类分析显示,老秃顶子山与千山、凤凰山的植物区系关系较近。本研究结果支持老秃顶子山、千山和凤凰山共同划归华北植物区系的观点,认为把老秃顶子山保护区植物区系划归于华北山地植物亚地区较为合理。