用于蛋白质同源模建及三维结构预测的结构比较方法

继前面的工作把测试蛋白从三族扩大到十一族,寻求联配参数的普适“缺省值“;比较不同的主链曲率和挠率的计算方法,进一步确认主链的折红红分几何刻划方法的有效性;寻找有效的可变缺失突变惩罚函数的形式。结果表明,编制的蛋白质多重联配软件系统是满意的,可用于蛋白质三维结构预测。     

Compartmental modelling of photorespiration and carbon metabolism of water stressed leaves

Abstract Carbon fluxes in photosynthesis and photorespiration of water stressed leaves have been analysed in a steady state model based on the ribulose diphosphate carboxylase (RuDP carboxylase) and RuDP oxygenase enzyme activities and the CO₂ and O₂ concentrations in the leaf. Agreement between predicted and observed photorespiration (Lawlor & Fock, 1975) and C flux in the glycollate pathway is good over much of the range of water stress, but not at severe stress. An alternative source of respiratory CO₂ is suggested to explain the discrepancy. The model suggests that resistance to CO₂ fixation is mainly in the carboxylation reactions, not in CO₂ transport. Using the steady state model, the kinetics of ¹⁴C incorporation into photosynthetic and photorespiratory intermediates are simulated. The predicted rate of ¹⁴C incorporation is faster than observed and delay terms in the model are used to simulate the slow rates of mixing and metabolic reactions. Inactive pools of glycine and serine are suggested to explain the observed specific activities of glycine and serine. Three models of carbon flux between the glycollate pathway, the photosynthetic carbon reduction cycle and sucrose synthesis are considered. The most satisfactory simulation is for glycollate pathway carbon feeding into the PCR cycle pool of 3-phosphoglyceric acid which provides the carbon for sucrose synthesis. Simulation of the specific activity of CO₂ released in photorespiration suggests that a source of unlabelled carbon may contribute to photorespiration.     

A systematic approach to the simulation of short-term processes in the plant-environment complex

Abstract. A conceptual framework is presented for modelling short-term processes in the plant and its environment as an integrated system. Flows of water, water vapour, heat, momentum, CO₂, soluble carbohydrate and phosphorus are all described by equations of the same general type, i.e. in terms of diffusivity-type parameters, capacities and potential gradients. A representative volume of the crop is divided horizontally into layers and vertically between crop and environment for treatment by a finite-difference method. Vertical flow occurs in the atmosphere, soil, stems and larger roots, andilateral flow between leaves and air, and between finer roots and soil. The interception of direct sunlight and the flux densities of downward and upward diffuse radiation within layers are calculated by a step-wise procedure.
The conversions of materials within the plant are treated as functions of appropriate state variables. Schemes for carbon and phosphorus provide for flow to and from the translocation system, and for photosynthesis, respiration and growth.
A model of a fully-established lucerne crop is described and the sensitivity of model performance to changes in a number of parameter values explored. Simulation runs under varying conditions indicate realistic prediction of diurnal trends.     

Degree-day Models for Predicting Egg Hatch and Population Increase of Criconemella xenoplax

A degree-day model was derived to predict egg hatch for Criconemella xenoplax. Eggs collected from gravid females were incubated in distilled water at constant temperatures of 10-35 C. Sixty-six percent of all eggs hatched between 13 and 32 C, and 42% hatched at 10 C. All eggs aborted above 32.5 C. Between 25 and 32 C, 8.5 ± 0.5 days were required for egg hatch. Degree-day requirement for egg hatch at 10-30 C was estimated to be 154 ± 5 with a base of 9.03 ± 0.04 C. This base of 9 C was adopted in studies of the relationship between degree-days and nematode population increase on Prunus seedlings grown 9-11 weeks in a greenhouse. Degree-day accumulations were based upon daily averages from maximum and minimum air temperatures. Ratios of final to initial population densities exhibited an exponential pattern in relation to degree-day accumulations with proportionate doubling increment of 0.100 ± 0.049 every 139 ± 8 degree-days. These results provide a means of predicting nematode population increase under greenhouse conditions and a basis for choosing sampling intervals when evaluating nematode multiplication.     

基于实码遗传算法的湖泊水质模型参数优化

参数的合理取值决定着模型的模拟效果,因此确定研究区域的模型结构后,需要对模型的参数进行优化.湖泊水质模型(Simulation by means of an Analytical Lake Model,SALMO)利用常微分方程描述湖泊的营养物质循环和食物链动态,考虑了多个生态过程,包含104个参数.由于参数较多,不适宜采用传统参数优化方法进行优化.利用太湖梅梁湾2005年数据,采用实码遗传算法优化了SALMO模型中相对敏感的参数,运用优化后的模型,模拟了梅梁湾2006年的水质.对比分析参数优化前后模型的效果表明遗传算法能高效地对SALMO进行参数优化,优化后的模拟精度得到了显著提高,能更好地模拟梅梁湾的水质变化.     

Modelling the Human Immune System by Combining Bioinformatics and Systems Biology Approaches

Over the past decade a number of bioinformatics tools have been developed that use genomic sequences as input to predict to which parts of a microbe the immune system will react, the so-called epitopes. Many predicted epitopes have later been verified experimentally, demonstrating the usefulness of such predictions. At the same time, simulation models have been developed that describe the dynamics of different immune cell populations and their interactions with microbes. These models have been used to explain experimental findings where timing is of importance, such as the time between administration of a vaccine and infection with the microbe that the vaccine is intended to protect against. In this paper, we outline a framework for integration of these two approaches. As an example, we develop a model in which HIV dynamics are correlated with genomics data. For the first time, the fitness of wild type and mutated virus are assessed by means of a sequence-dependent scoring matrix, derived from a BLOSUM matrix, that links protein sequences to growth rates of the virus in the mathematical model. A combined bioinformatics and systems biology approach can lead to a better understanding of immune system-related diseases where both timing and genomic information are of importance.     

Northern richness and southern poverty: contrasting genetic footprints of glacial refugia in the relictual tree Sciadopitys verticillata (Coniferales: Sciadopityaceae)

Sciadopitys verticillata is amongst the most relictual of all plants, being the last living member of an ancient conifer lineage, the Sciadopityaceae, and is distributed in small and disjunct populations in high rainfall regions of Japan. Although mega‐fossils indicate the persistence of the species within Japan through the Pleistocene glacial–interglacial cycles, how the species withstood the colder and drier climates of the glacials is not well known. The present study utilized phylogeography and palaeodistribution modelling to test whether the species survived within pollen‐based coastal temperate forest glacial refugia or within previously unidentified refugia close to its current range. Sixteen chloroplast haplotypes were found that displayed significant geographical structuring. Unexpectedly, northern populations in central Honshu most distant from coastal refugia had the highest chloroplast diversity and were differentiated from the south, a legacy of glacial populations possibly in inland river valleys close to its current northern range. By contrast, populations near putative coastal refugia in southern Japan, harboured the lower chloroplast diversity and were dominated by a single haplotype. Fragment size polymorphism at a highly variable and homoplasious mononucleotide repeat region in the trnT‐trnL intergenic spacer reinforced the contrasting patterns of diversity observed between northern and southern populations. The divergent histories of northern and southern populations revealed in the present study will inform the management of this globally significant conifer. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 108 , 263–277.     

作物生长模拟模型研究和应用

作物生长模拟模型研究和应用宇振荣（北京农业大学农业生态环境系,１０００９４）ＳｔｕｄｉｅｓｏｎＣｒｏｐＧｒｏｗｔｈＭｏｄｅｌｌｉｎｇａｎｄＩｔｓＡｐｐｌｉｃａｔｉｏｎ．￥ＹｕＺｈｅｎｒｏｎｇ（ＤｅｐａｒｔｍｅｎｔｏｆＡｇｒｏ－Ｅ－ｃｏｌｏｇｉｃａｌＥ...