Modeling metabolic adjustment in <Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis> upon treatment with isoniazid

Complex biological systems exhibit a property of robustness at all levels of organization. Through different mechanisms, the system tries to sustain stress such as due to starvation or drug exposure. To explore whether reconfiguration of the metabolic networks is used as a means to achieve robustness, we have studied possible metabolic adjustments in Mtb upon exposure to isoniazid (INH), a front-line clinical drug. The redundancy in the genome of M. tuberculosis (Mtb) makes it an attractive system to explore if alternate routes of metabolism exist in the bacterium. While the mechanism of action of INH is well studied, its effect on the overall metabolism is not well characterized. Using flux balance analysis, inhibiting the fluxes flowing through the reactions catalyzed by Rv1484, the target of INH, significantly changes the overall flux profiles. At the pathway level, activation or inactivation of certain pathways distant from the target pathway, are seen. Metabolites such as NADPH are shown to reduce drastically, while fatty acids tend to accumulate. The overall biomass also decreases with increasing inhibition levels. Inhibition studies, pathway level clustering and comparison of the flux profiles with the gene expression data indicate the activation of folate metabolism, ubiquinone metabolism, and metabolism of certain amino acids. This analysis provides insights useful for target identification and designing strategies for combination therapy. Insights gained about the role of individual components of a system and their interactions will also provide a basis for reconstruction of whole systems through synthetic biology approaches.     

小兴安岭7种典型林型林分生物量碳密度与固碳能力

森林生物碳储量作为森林生态系统碳库的重要组成部分, 在全球碳循环中发挥着重要作用。以小兴安岭7种典型林型为研究对象, 通过外业样地调查与室内实验分析相结合的方法, 从林分尺度对林分生物量与碳密度进行计量, 分析了林分生物碳储量的空间分配格局, 并对林分年固碳能力与碳汇潜力进行了探讨。结果表明: 小兴安岭不同林型从幼龄林到成熟林的乔木层碳密度增长速率为: 蒙古栎(Quercus mongolica)林>兴安落叶松(Larix gmelinii)林>云冷杉(Picea-Abies)林>樟子松(Pinus sylvestris var. mongolica)林>山杨(Populus davidiana)林>红松(Pinus koraiensis)林>白桦(Betula platyphylla)林。7种典型林型不同龄组(幼龄林、中龄林、近熟林和成熟林)林分生物量碳密度分别为: 红松林31.4、74.7、118.4和130.2 t·hm^-2; 兴安落叶松林28.9、44.3、74.2和113.3 t·hm^-2; 樟子松林22.8、52.0、71.1和92.6 t·hm^-2; 云冷杉林23.1、44.1、77.6和130.3 t·hm^-2; 白桦林18.8、35.3、66.6和88.5 t·hm^-2; 蒙古栎林25.0、20.0、47.5和68.9 t·hm^-2; 山杨林19.8、28.7、43.7和76.6 t·hm^-2。红松林、兴安落叶松林、樟子松林和蒙古栎林在幼龄林时林分年固碳量较高, 其他林型在成熟林时林分年固碳量较高。7种典型林型不同龄组的林分生物量碳密度均随林龄增长而增加, 但不同林型的碳汇功能存在差异, 同一林型不同林龄的生物量碳密度增幅差异也较大。林分年固碳量在0.4-2.8 t·hm^-2之间, 碳汇能力较强、碳汇潜力较大。尤其是小兴安岭目前林分质量较差, 幼龄林和中龄林所占的比重较大, 具有较大的碳汇潜力。研究结果可为森林经营管理及碳汇功能评价提供参考。     

集成高分辨率UAV影像与激光雷达点云的亚热带森林林分特征反演

该研究集成高分辨率无人机(UAV)影像和激光雷达(LiDAR)点云数据估算亚热带天然次生林林分基本特征变量。首先, 基于LiDAR点云和反距离加权插值法构建林下高精度数字高程模型(DEM); 然后利用UAV影像对序列构建植被冠层上层三维点云, 并借助DEM进行高度信息归一化, 提取高度和冠层点云密度相关的特征变量; 最后, 构建预测模型并估算Lorey’s高、林分密度、胸高断面积、蓄积量。结果表明: 联合提取的特征变量与Lorey’s高的敏感性最高, 蓄积量次之, 林分密度和胸高断面积最低; 利用UAV灵活快速的手段获取森林冠层信息, 辅以高精度LiDAR数据获取的地形信息, 两者互补实现一种可重复的快速、廉价和灵活的林分特征的反演方式。     

基于生物适应进化原理论证生物进化的动力

文章从现有主流生物进化理论存在的问题入手, 以生物适应进化原理为认识基础, 讨论生物进化的动力, 以求对生物进化机制有一个新的认识。在薛定谔“生命赖负熵生存”观点的指导下, 提出了“负熵流”包括能量流、物质流和信息流, 以及负熵流是生命生存和发育的动力的观点。作者在原有生物适应进化原理基础上, 修改完善并提出了“DNA、RNA和蛋白质在环境作用下的生物适应进化调控系统”理论, 并根据系统发育是个体发育的“积分”的观点, 推论得出生物与环境的负熵差引起的负熵流也是生命进化的动力, 对生物进化机制作出了新的理解。基于这样的生物进化机制的认识, 提出了“进化是一个子系统在其上一等级系统中, 将自身全部或部分信息遗传给下一代子系统, 并在其适应上一等级系统过程中, 产生一些新质, 终止一些旧质, 从而在其上一等级系统中得以延续的变化过程”的概念, 并探讨了一些与进化有关的其他争议问题。     

Dependence Calibration in Conditional Copulas: A Nonparametric Approach

Summary The study of dependence between random variables is a mainstay in statistics. In many cases, the strength of dependence between two or more random variables varies according to the values of a measured covariate. We propose inference for this type of variation using a conditional copula model where the copula function belongs to a parametric copula family and the copula parameter varies with the covariate. In order to estimate the functional relationship between the copula parameter and the covariate, we propose a nonparametric approach based on local likelihood. Of importance is also the choice of the copula family that best represents a given set of data. The proposed framework naturally leads to a novel copula selection method based on cross‐validated prediction errors. We derive the asymptotic bias and variance of the resulting local polynomial estimator, and outline how to construct pointwise confidence intervals. The finite‐sample performance of our method is investigated using simulation studies and is illustrated using a subset of the Matched Multiple Birth data.     

Assessing the effects of management on forest growth across France: insights from a new functional–structural model

Background and Aims

The structure of a forest stand, i.e. the distribution of tree size features, has strong effects on its functioning. The management of the structure is therefore an important tool in mitigating the impact of predicted changes in climate on forests, especially with respect to drought. Here, a new functional–structural model is presented and is used to assess the effects of management on forest functioning at a national scale.

Methods

The stand process-based model (PBM) Castanea was coupled to a stand structure module (SSM) based on empirical tree-to-tree competition rules. The calibration of the SSM was based on a thorough analysis of intersite and interannual variability of competition asymmetry. The coupled Castanea–SSM model was evaluated across France using forest inventory data, and used to compare the effect of contrasted silvicultural practices on simulated stand carbon fluxes and growth.

Key Results

The asymmetry of competition varied consistently with stand productivity at both spatial and temporal scales. The modelling of the competition rules enabled efficient prediction of changes in stand structure within the Castanea PBM. The coupled model predicted an increase in net primary productivity (NPP) with management intensity, resulting in higher growth. This positive effect of management was found to vary at a national scale across France: the highest increases in NPP were attained in forests facing moderate to high water stress; however, the absolute effect of management on simulated stand growth remained moderate to low because stand thinning involved changes in carbon allocation at the tree scale.

Conclusions

This modelling approach helps to identify the areas where management efforts should be concentrated in order to mitigate near-future drought impact on national forest productivity. Around a quarter of the French temperate oak and beech forests are currently in zones of high vulnerability, where management could thus mitigate the influence of climate change on forest yield     

The design and function of birds' nests

All birds construct nests in which to lay eggs and/or raise offspring. Traditionally, it was thought that natural selection and the requirement to minimize the risk of predation determined the design of completed nests. However, it is becoming increasingly apparent that sexual selection also influences nest design. This is an important development as while species such as bowerbirds build structures that are extended phenotypic signals whose sole purpose is to attract a mate, nests contain eggs and/or offspring, thereby suggesting a direct trade‐off between the conflicting requirements of natural and sexual selection. Nest design also varies adaptively in order to both minimize the detrimental effects of parasites and to create a suitable microclimate for parents and developing offspring in relation to predictable variation in environmental conditions. Our understanding of the design and function of birds' nests has increased considerably in recent years, and the evidence suggests that nests have four nonmutually exclusive functions. Consequently, we conclude that the design of birds' nests is far more sophisticated than previously realized and that nests are multifunctional structures that have important fitness consequences for the builder/s.     

庐山6种树木立地土壤溶液铝形态与溶解有机碳变化

于1999年夏季,采集了庐山植物园6种树木立地的不同层次土壤样品,提取土壤溶液,分析其溶液中的溶解铝和溶解有机碳。结果表明,尽管发育于同一发生性土类,不同立地下土壤溶液溶解铝含量有明显差异,而溶解性有机碳的差异相对较小,在6种树木立地中,香柏立地表层土壤溶解铝含量达4．95mg·kg^-1,为其它针叶林立地的2倍,是阔叶林立地的3倍。溶解铝积累与土壤酸化强度有密切关系,但溶解有机碳趋向于形成抑制毒性的单核铝,供试的不同立地土壤可以按溶液铝化学特点分为不同的生态化学类型。