Evaluation of regression models in metabolic physiology: predicting fluxes from isotopic data without knowledge of the pathway

This study explores the ability of regression models, with no knowledge of the underlying physiology, to estimate physiological parameters relevant for metabolism and endocrinology. Four regression models were compared: multiple linear regression (MLR), principal component regression (PCR), partial least-squares regression (PLS) and regression using artificial neural networks (ANN). The pathway of mammalian gluconeogenesis was analyzed using [U−¹³C]glucose as tracer. A set of data was simulated by randomly selecting physiologically appropriate metabolic fluxes for the 9 steps of this pathway as independent variables. The isotope labeling patterns of key intermediates in the pathway were then calculated for each set of fluxes, yielding 29 dependent variables. Two thousand sets were created, allowing independent training and test data. Regression models were asked to predict the nine fluxes, given only the 29 isotopomers. For large training sets (>50) the artificial neural network model was superior, capturing 95% of the variability in the gluconeogenic flux, whereas the three linear models captured only 75%. This reflects the ability of neural networks to capture the inherent non-linearities of the metabolic system. The effect of error in the variables and the addition of random variables to the data set was considered. Model sensitivities were used to find the isotopomers that most influenced the predicted flux values. These studies provide the first test of multivariate regression models for the analysis of isotopomer flux data. They provide insight for metabolomics and the future of isotopic tracers in metabolic research where the underlying physiology is complex or unknown.We acknowledge the support of NIH Grant DK58533 and the DuPont-MIT Alliance.     

FEMALE AND MALE GENETIC EFFECTS ON OFFSPRING PATERNITY: ADDITIVE GENETIC (CO)VARIANCES IN FEMALE EXTRA‐PAIR REPRODUCTION AND MALE PATERNITY SUCCESS IN SONG SPARROWS (MELOSPIZA MELODIA)

Ongoing evolution of polyandry, and consequent extra‐pair reproduction in socially monogamous systems, is hypothesized to be facilitated by indirect selection stemming from cross‐sex genetic covariances with components of male fitness. Specifically, polyandry is hypothesized to create positive genetic covariance with male paternity success due to inevitable assortative reproduction, driving ongoing coevolution. However, it remains unclear whether such covariances could or do emerge within complex polyandrous systems. First, we illustrate that genetic covariances between female extra‐pair reproduction and male within‐pair paternity success might be constrained in socially monogamous systems where female and male additive genetic effects can have opposing impacts on the paternity of jointly reared offspring. Second, we demonstrate nonzero additive genetic variance in female liability for extra‐pair reproduction and male liability for within‐pair paternity success, modeled as direct and associative genetic effects on offspring paternity, respectively, in free‐living song sparrows (Melospiza melodia). The posterior mean additive genetic covariance between these liabilities was slightly positive, but the credible interval was wide and overlapped zero. Therefore, although substantial total additive genetic variance exists, the hypothesis that ongoing evolution of female extra‐pair reproduction is facilitated by genetic covariance with male within‐pair paternity success cannot yet be definitively supported or rejected either conceptually or empirically.     

Comprehensive evaluation of multiple cropping systems on upland red soil

According to the principles and methods of ecology and system engineering, we set up an evaluation indicator system for multi-component and multiple cropping systems, evaluated the comprehensive benefits of multi-component and multiple cropping systems using grey relation clustering analysis and screened out the optimized model based on research done in the upland red soil in Jiangxi Agricultural University from 1984 to 2004. The results show that the grey relation degree of “cabbage/potato/maize — sesame” was the highest among 23 multi-component and multiple cropping systems and was clustered into the optimized system. This indicates that “cabbage/potato/maize — sesame” can bring the best social, economic and ecological benefits, increase product yield and farmers’ income and promote sustainable development of agricultural production. Therefore, it is suitable for promotion on upland red soil. The grey relation degree of “canola/Chinese milk vetch/maize/mung bean/maize” was second, which is suitable for implementation at the city outskirts. In conclusion, these two planting patterns are expected to play important roles in the reconstruction of the planting structure and optimization of the planting patterns on upland red soil. __________ Translated from Acta Ecologica Sinica, 2006, 26(8): 2532–2539 [译自: 生态学报]     

大豆对斜纹夜蛾幼虫抗性遗传的发展表达过程

采用植物数量性状遗传体系分离分析方法,通过4个感抗杂交组合研究了在网室人工接入斜纹夜蛾幼虫的条件下大豆抗斜纹夜蛾植株反应发育过程的遗传。不论P1、P2、F1、F2、F2：3多世代联合分析或单个分离世代分析,结果均表明大豆对斜纹夜蛾幼虫的抗性为两对主基因 多基因遗传模式。但在大豆生长发育的不同时期,随害虫数量的变化,其抗虫性遗传呈动态变化过程。在两对主基因充分表达日期,主基因的遗传率较高,达70.40%-99.21%,环境影响较小;多基因遗遗传率较低,为0.00%-22.29%。     

Alignments grow, secondary structure prediction improves.

Using information from sequence alignments significantly improves protein secondary structure prediction. Typically, more divergent profiles yield better predictions. Recently, various groups have shown that accuracy can be improved significantly by using PSI-BLAST profiles to develop new prediction methods. Here, we focused on the influences of various alignment strategies on two 8-year-old PHD methods. The following results stood out. (i) PHD using pairwise alignments predicts about 72% of all residues correctly in one of the three states: helix, strand, and other. Using larger databases and PSI-BLAST raised accuracy to 75%. (ii) More than 60% of the improvement originated from the growth of current sequence databases; about 20% resulted from detailed changes in the alignment procedure (substitution matrix, thresholds, and gap penalties). Another 20% of the improvement resulted from carefully using iterated PSI-BLAST searches. (iii) It is of interest that we failed to improve prediction accuracy further when attempting to refine the alignment by dynamic programming (MaxHom and ClustalW). (iv) Improvement through family growth appears to saturate at some point. However, most families have not reached this saturation. Hence, we anticipate that prediction accuracy will continue to rise with database growth.     

城市公园绿地可达性分析——以沈阳市铁西区为例

公园绿地作为城市重要的自然景观元素,其可达性是体现公园绿地所提供的自然服务能否被市民便捷、公平享用的一个重要指标.对可达性理论进行深入研究,从而更加准确、真实地对公园绿地可达性进行评价是目前亟需解决的问题.本文基于QuickBird卫星影像和GIS平台,以沈阳市铁西区为例,选取步行、非机动车、机动车和公共交通4种方式来定量评价公园绿地的可达性,并对4种交通方式下公园绿地可达区的空间分布、可达面积及可达人口的数量差异进行对比分析.结果表明： 沈阳市铁西区公园绿地数量较少且分布不均衡,表现为西南部及中心区域公园绿地的可达性较好,边缘区域可达性较差,东部和北部边缘可达性最差;各交通方式下公园绿地的可达性存在较大差异,机动车可达性最好,其次为非机动车和公共交通,步行可达性最差：近九成的居民可以采用步行30 min、非机动车和公共交通15 min、机动车10 min的方式到达最近的公园绿地.该研究对城市公园绿地可达性理论的深入、系统研究提供了一种新思路,对基于可达性的绿地空间布局优化具有重要的现实意义.     

酚酸类物质的抑草效应分析

运用正交旋转回归试验设计分析5种常见的化感物质替代物水饧酸、对羟基苯甲酸、肉桂酸、香草酸和阿魏酸对田间伴生杂草稗草的抑制效应．结果表明,肉桂酸对稗草根长抑制率的影响最显著。其关系函数的二次项系数为-6．18,达极显著水平,水杨酸、对羟基苯甲酸和阿魏酸对稗草根长的抑制效应趋势与肉桂酸相同,效应曲线均为“n”形抛物线;而香草酸的效应曲线则为“U”形抛物线．当水饧酸、对羟基苯甲酸、肉桂酸、香草酸和阿魏酸浓度水平分别为0．06、0．60、0．24、0．02和0．02mmol·L^-1时,混合物对稗草根长的抑制率最大,达到78．65％。     

基于多目标灰色局势决策的三峡库区防护林类型空间优化配置

基于2007年Landsat TM遥感影像和影响防护林的主导环境因子,对三峡库区的森林立地进行分类,并通过选取水源涵养量、生物量和林分生产力3个指标,利用多目标灰色局势决策模型对库区现有的针叶林、阔叶林、针阔混交林和灌木林4种防护林类型进行空间优化配置.结果表明： 2007年,三峡库区森林立地可划分为40种类型;空间配置优化后,研究区针叶林、阔叶林、针阔混交林和灌木林的面积比例分别为32.55%、29.43%、34.95%和3.07%.与优化前相比,优化后针叶林和灌木林的面积比例分别减少了8.79%和28.55%,阔叶林和针阔混交林分别增加了10.23%和27.11%.通过防护林类型的空间优化,三峡库区整体的水源涵养能力、生物量和林分生产力分别增加14.09×10⁸ m³、0.35×10⁸ t和1.08×10⁶ t.     

Subharmonics increase the auditory impact of female koala rejection calls

Although non‐linear phenomena are common in human and non‐human animal vocalisations, their functional relevance remains poorly understood. One theory posits that non‐linear phenomena generate unpredictability in vocalisations, which increases the auditory impact of vocal signals, and makes animals less likely to habituate to call repetition. Female koalas (Phascolarctos cinereus) produce vocal signals when they reject male copulation attempts that contain relatively high levels of non‐linear phenomena, and thus may function as attention grabbing vocal signals during the breeding season. To test this hypothesis, we used playback experiments: firstly, to determine whether female rejection calls induce heightened behavioural responses in free‐ranging male koalas during the breeding season, and secondly, to examine how the relative amount of non‐linear phenomena in rejection calls influences male behavioural response. The results show that male koalas look for longer towards speakers broadcasting playback sequences of male bellows followed by a series of female rejection calls than those broadcasting only male bellows. In addition, female rejection call sequences with more subharmonics, higher harmonics‐to‐noise ratios, and less biphonation produced the greatest male looking responses. Our findings support the hypothesis that female koala rejection calls function to grab male attention during the breeding season, and indicate that subharmonics are the main acoustic feature that increases the auditory impact of these vocal signals.