BetaDock: Shape-Priority Docking Method Based on Beta-Complex

Abstract

This paper presents an approach and a software, BetaDock, to the docking problem by putting the priority on shape complementarity between a receptor and a ligand. The approach is based on the theory of the β-complex. Given the Voronoi diagram of the receptor whose topology is stored in the quasi-triangulation, the β-complex corresponding to water molecule is computed. Then, the boundary of the β-complex defines the β-shape which has the complete proximity information among all atoms on the receptor boundary. From the β-shape, we first compute pockets where the ligand may bind. Then, we quickly place the ligand within each pocket by solving the singular value decomposition problem and the assignment problem. Using the conformations of the ligands within the pockets as the initial solutions, we run the genetic algorithm to find the optimal solution for the docking problem. The performance of the proposed algorithm was verified through a benchmark test and showed that BetaDock is superior to a popular docking software AutoDock 4.     

Spatial memory deficits in maternal iron deficiency paradigms are associated with altered glucocorticoid levels

"The goal of this study was to examine the effect of maternal iron deficiency on the developing hippocampus in order to define a developmental window for this effect, and to see whether iron deficiency causes changes in glucocorticoid levels. The study was carried out using pre-natal, post-natal, and pre + post-natal iron deficiency paradigm. Iron deficient pregnant dams and their pups displayed elevated corticosterone which, in turn, differentially affected glucocorticoid receptor (GR) expression in the CA1 and the dentate gyrus. Brain Derived Neurotrophic Factor (BDNF) was reduced in the hippocampi of pups following elevated corticosterone levels. Reduced neurogenesis at P7 was seen in pups born to iron deficient mothers, and these pups had reduced numbers of hippocampal pyramidal and granule cells as adults. Hippocampal subdivision volumes also were altered. The structural and molecular defects in the pups were correlated with radial arm maze performance; reference memory function was especially affected. Pups from dams that were iron deficient throughout pregnancy and lactation displayed the complete spectrum of defects, while pups from dams that were iron deficient only during pregnancy or during lactation displayed subsets of defects. These findings show that maternal iron deficiency is associated with altered levels of corticosterone and GR expression, and with spatial memory deficits in their pups."     

Old‐male paternity advantage is a function of accumulating sperm and last‐male precedence in a butterfly

Old‐male mating advantage has been convincingly demonstrated in Bicyclus anynana butterflies. This intriguing pattern may be explained by two alternative hypotheses: (i) an increased aggressiveness and persistence of older males during courtship, being caused by the older males' low residual reproductive value; and (ii) an active preference of females towards older males what reflects a good genes hypothesis. Against this background, we here investigate postcopulatory sexual selection by double‐mating Bicyclus anynana females to older and younger males, thus allowing for sperm competition and cryptic mate choice, and by genotyping the resulting offspring. Virgin females were mated with a younger virgin (2–3 days old) and afterwards an older virgin male (12–13 days old) or vice versa. Older males had a higher paternity success than younger ones, but only when being the second (=last) mating partner, while paternity success was equal among older and younger males when older males were the first mating partner. Older males produced larger spermatophores with much higher numbers of fertile sperm than younger males. Thus, we found no evidence for cryptic female mate choice. Rather, the findings reported here seem to result from a combination of last‐male precedence and the number of sperm transferred upon mating, both increasing paternity success.     

光核桃遗传资源的经济价值评估与保护

本文将光核桃遗传资源的经济价值划分为直接利用价值、间接利用价值和潜在利用价值,采用市场价格法、旅行费用法、防护费用法及类比分析法等方法对光核桃遗传资源的经济价值进行估算,并提出该资源保护与管理建议。光核桃遗传资源经济价值的评估,将为具有潜在巨大经济价值的生物遗传资源管理提供价值评估方法,同时为维护国家利益、制订生物多样性保护与管理政策及建立生物遗传资源惠益分享制度提供技术支持。     

马尾松和苦槠林根际土壤矿化和根系分解CO2释放的温度敏感性

以中亚热带马尾松林和苦槠林为对象,原位收集根际和非根际土壤、树木不同生态功能的根系,开展15℃、25℃、35℃和45℃恒温培养模拟试验,采用密闭气室碱液吸收法测定53 d内CO2释放的动态变化.结果表明:两种森林类型不同温度下土壤矿化CO2释放速率的根际效应介于1.12 ～3.09,且培养前期高于培养后期;15℃下马尾松林和苦槠林差异不显著,25℃和35℃下前者低于后者,45℃下则相反.不同培养温度下两树种吸收根分解的CO2释放速率均高于过渡根和贮存根,且马尾松均低于苦槠.两种森林类型CO2释放的Q10值均为土壤(1.21 ～1.83)显著高于根系(0.96 ～1.36).两种森林类型土壤矿化CO2释放的Q10值差异不显著,而马尾松根系分解CO2释放的Q10值高于苦槠.推断全球变暖导致的土壤矿化CO2释放的增量将远远高于根系分解,且马尾松林高于苦槠林;地带性顶极群落应对气候变化的抵抗力强于先锋树种群落.     

南方红壤区3年生茶园土壤呼吸特征

为探讨南方红壤区茶园的土壤呼吸特征,采用LI-Cor8100开路式土壤碳通量测定系统观测3年生茶园系统的土壤呼吸速率,对茶园土壤呼吸速率的季节变化和在茶行尺度上的空间异质性进行了研究。结果表明,茶园土壤呼吸速率的月动态变化呈明显的单峰曲线特征,峰值出现在8月;茶园土壤呼吸速率的月动态变化与温度呈极显著相关(P<0.01),土壤10 cm的温度能够解释茶园不同观测区域土壤呼吸速率月动态变化的67.79%~88.52%;用指数方程计算的茶园不同观测区域土壤呼吸Q10值为1.58~1.86。在茶行尺度上,茶园土壤呼吸速率存在明显的空间异质性,土壤呼吸速率通常在距离茶树基部较近的位置较高;根系生物量能够解释茶园土壤呼吸速率在茶行尺度上空间变异的82.68%。因此,根系分布的空间差异是造成茶园土壤呼吸速率空间异质性的主要原因。     

Decreasing the Roughage: Concentrate Ratio of a Diet to Determine the Critical Roughage Part for Beef Cattle

The critical roughage part (CRP) of 2 diet types was determined in a cross-over design with 6 double-muscled and 6 normally conformated Belgian Blue bulls fitted with rumen cannulae. The roughage:concentrate ratio was lowered weekly until signs of a lack of physical structure were observed. For diet 1, consisting of maize silage and concentrates, the initial proportion of maize silage was 25% of DM but it decreased weekly with 5% units of DM. For the second diet, consisting of wheat straw and concentrate, 12% straw (DM basis) was provided during the first week and thereafter the proportion of straw decreased weekly with 3% units of DM. Several directly observable parameters (rumen pH, feed intake, bloat, faecal consistency) were evaluated weekly for each bull. Apart from these direct indicators of acidosis, also other parameters, whose results were only available after the end of the trial, were determined (volatile fatty acid profile, lactic acid concentration, chewing time). The roughage part between the part fed when signs of a lack of physical structure was first observed and the part that was fed the week before, was considered as the CRP. Most animals showed no acute signs of clinical acidosis (directly observable parameters) and finished the trial on a 100% concentrate diet. However, in sacco rumen DM-degradabilities of maize silage, grass silage and wheat grain was depressed considerably when low roughage diets were fed. Based on all observed parameters, the mean CRP was calculated to be 14.7% for diet 1 and 8.1% for diet 2. The beef type (double-muscled or not) had no influence on the CRP.     

Grazing effects on plant diversity in the endemic Erica mackayana heathland community of north-west Spain

Background: Large areas of heathland landscapes in Galicia, north-west Spain, have traditionally been extensively grazed by free-ranging cattle and wild ponies. Recently, a large reduction in the number of these larger herbivores has been observed, with unknown consequences for the habitat.

Aims: To evaluate the effects of grazing and herbivore density on plant diversity, community composition and vegetation structure of the endemic wet heathlands dominated by Erica mackayana in Galicia.

Methods: Field sampling of vascular plants, generalised linear models (GLMs), non-metric multidimensional distance scaling (NMDS).

Results: Grazed sites had significantly higher total and rare species richness and diversity than ungrazed sites. Higher densities of cattle resulted in lower numbers of rare species, while wild pony density had no effect on rare species richness. In grazed sites, vegetation was lower with greater variation in height, resulting in greater heterogeneity of the habitat. Precipitation and summer temperatures were related to plant diversity, mainly beta diversity. Soil organic matter negatively correlated with rare species.

Discussion: Grazing, mostly by wild ponies, was demonstrated to be positively related to plant diversity and vegetation structure. Lack of grazing or high cattle densities resulted in a negative effect on total and rare species richness and diversity. Future climate change may negatively affect heathland plant diversity. Galician wild ponies represent a unique case of sustainable management of a wild species and an invaluable cultural heritage. Moreover, they have a significant role in maintaining the endemic E. mackayana heathlands, what would justify specific conservation actions for these large herbivores.     

Territory Availability at Different Spatial Scales does not Affect Fighting Investment in Males of the Lycaenid Butterfly Strymon mulucha

In territorial species, rivals investment in fights over territories may increase when the availability of suitable areas for defense is low. This should occur because low territory availability may increase the costs to maintain and acquire territories. Although such process occurs in small spatial scales (local scale), territory availability in larger scales (regional scale) may also affect fighting investment, as losers should incur additional dispersing costs to find new territories. In this study, we used males of the hilltopping butterfly Strymon mulucha to evaluate the hypothesis that males should invest more in territorial fights when the costs to find new territories are higher (both at local and at regional scale). We timed male–male contests for territories located in 12 hilltops and measured male density per territory in each hilltop (local scale). We also quantified the distance between hilltops containing suitable areas for territories (regional scale). Male–male contests lasted 21 s on average, and copulations did not occur during the observations. The duration of contests was unrelated to the male density per territory or to the distance among hilltops, indicating that the investment in fights was unaffected by the availability of territorial sites, independent of the spatial scale. As male–male contests in S. mulucha are longer than the mean contest duration in other butterfly species and mating is extremely rare, we suggest that the value of each territory may be high enough to favor males that always invest as much as possible in contests.