利用遥感技术实现作物模拟模型区域应用的研究进展

作物模拟模型从单点发展到区域应用时,模型中一些宏观资料的获取和参数的区域化方面出现困难,利用遥感技术将实现作物模拟模型的区域应用．文中综述了近年来遥感反演作物模型所需的地表生物物理参数的方法、利用遥感信息直接获取生物量的途径和遥感信息与作物模拟模型之间时空匹配问题等方面的研究概况,重点介绍了利用遥感技术实现作物模拟模型区域应用的3种解决方案(强迫型、调控型和验证型)及其研究进展,并讨论了目前存在的问题和今后研究的方向．     

城市街道空气污染物扩散模型综述

城市街道是城市居民的活动场所,其空气质量与居民健康密切相关.空气污染扩散模型是模拟和评估街道空气质量的重要方法,近年来广受关注,但模型应用存在问题,亟待解决.本文介绍了4种常用的空气污染物扩散模型:ENVI-met、FLUENT、MISKAM和OSPM.通过工作原理、运算流程、时空分辨率等的对比分析,明确了各模型的适用范围及其对街道峡谷内空气质量模拟能力的差异,阐述了各模型在时间尺度、物理建模、天气模拟、湍流模拟及光化学污染方面处理能力的局限性,提出了模型优化途径.通过综合分析4种模型的研究案例,总结了模型应用中存在的问题,提出未来研究可以通过激光雷达等新技术提高模型参数的获得精度,并强调综合模拟污染效应与热效应等对评估城市街道空气质量的重要性.     

用遥感和地理信息系统研究传染病时空分布

和其他物种迁移或生物入侵过程类似, 传染病的时空传播与流行伴随着人类活动的全球化而加剧. 以血吸虫病时空传播流行定量模拟为例, 提出一种对已知传染源→媒介→宿主传播关系前提下的疾病传播的时空动态概念模型. 用西昌郊区血吸虫病流行区为例, 证明这类概念模型的可行性. 展示了遥感和地理信息系统在这类模型中具体的应用方法. 利用建立的模型, 模拟给不同村居民服药所达到的不同效果, 证明这类模型在传染病防治和控制中可以起到空间决策支持的作用. 本文介绍的模拟方法对鼠疫、肾综合征出血热、莱姆病等传染病有直接借鉴意义; 遥感和地理信息系统方法对其他有关的传染病, 甚至生物入侵过程的研究有所帮助.     

FARSITE火行为模型的原理、结构及其应用

应用空间直观火行为模型模拟大的时空尺度上的林火蔓延过程成为林火管理、规划和科学分析的有效工具。FARSITE(Fire Area Simulator)是一个基于热物理、燃烧学和试验理论为一体的空间直观火行为模型,它集成了现有的地表火、树冠火、飞火和火加速等子模型。FARSITE能够利用GIS和RS提供的空间数据,模拟大时空尺度的林火蔓延,模拟结果能够以地图形式输出,反映林火行为的瞬时状态。本文介绍了FARSITE模型的基本原理、结构和运行机制,并将其应用到丰林自然保护区林火蔓延模拟,以期为国内林火管理和火行为模型的开发提供参考。     

植被对河道水流影响的研究进展

植被是自然河流的组成部分.明确植被与水流的相互影响,对于动植物栖息地的保护、水体富营养化的控制、河流和湖泊的生态修复,以及河道整治等方面均具有重要的科学和实践意义.本文回顾了国内外对河道植被与水流相互作用的研究状况,综述了植被对阻力系数、水流结构影响的研究,介绍了数值模拟在该领域的应用进展;基于文献资料,分析了河道断面形状、植株个体形态、植被分布格局等诸多因素对含植被水流流态的影响,阐述了在河流形态、时空尺度上植被变化、植被段内部水流分布、三维紊动模拟等方面深入研究河道植被水力学机制的重要性.     

作物模型区域应用两种参数校准方法的比较

区域模拟的目的是利用有限的空间数据模拟出产量等作物性状的时空变异规律.然而站点作物模型应用到区域范围时涉及到数据归一化、参数简化、模型的校准和验证等问题.利用CERES-Rice模型对作物模型在我国的区域应用进行了尝试并对部分参数进行了校准.首先利用田间观测数据在各实验点上对模型进行了详细的站点校准,以验证模型在我国的模拟能力;其次,以我国水稻种植区(精确到亚区)为单位,运用平均值和标准差(RMSE)两种方法进行了区域校准和验证,即找出能反映出品种空间差异的代表性品种参数集;然后分别运用两种方法的校准结果,模拟水稻产量和成熟期,并将模拟结果与实测值进行了比较.结果表明:区域校准能反映出水稻生育期和产量的时空变化规律,其中RMSE法较平均值法效果好.目前作物模型区域应用过程中还存在大量的误差来源,有待进一步研究.     

昆虫生态学试验设计中时空转换的技巧

时空转换最初是研究植物群落演替的方法,目前作为一种理论推断在社会科学、地理信息和地质分析等领域应用,在昆虫生态学中的应用很少,本文介绍了空间换取时间与时间换取空间两种方法,能够巧妙地缩短很多昆虫生态学的试验时间,或增加研究范围内的样本数,在大尺度景观研究昆虫迁移、预测预报、栖境恢复等方面具有重要意义。这种时空转换的技巧在昆虫生态学的研究的有广阔的应用前景。     

芦苇湿地多时空尺度蒸散模拟研究进展

湿地蒸散是湿地水分损失的主要途径,由于其对气候变化的高度敏感性和重要的反馈作用而倍受关注。湿地蒸散过程可以分为叶片、植株、冠层、景观至区域等多种尺度,如何实现不同时空尺度的过程和参数耦合成为湿地蒸散研究的重点和难点。本文回顾了湿地蒸散模拟研究的发展历程,着重总结了芦苇湿地蒸散监测及模拟方面的技术和方法,并从不同时间尺度(日、月、年)和不同空间尺度(叶片、植株、冠层、区域)以及实现不同时空尺度拓展的关键技术研究等方面进行归纳和总结,探讨了今后的研究重点。实现不同时空尺度的芦苇湿地蒸散过程的准确模拟,关键在于大气-植被-土壤界面的参数耦合,而目前针对不同尺度的芦苇湿地蒸散参数化研究很少,因此,有必要探讨适合芦苇湿地多尺度蒸散模拟及参数化方法,为芦苇湿地蒸散评估模型的选择提供理论支持。     

生态退耕与植被演替的时空格局

综述了多重尺度上生态退耕的时空格局及其对植被演替时空变异影响的研究进展,提出了生态退耕与植被演替的时空格局研究方向.在自然和人文等因子的驱动下,全球兴起了生态退耕的热潮,生态退耕类型正在由人工恢复为主向自然弃耕为主发展.尽管国内外很多学者开始关注不同尺度上生态退耕的时空格局及其影响因子,但是生态退耕的时空变异性研究仍然比较薄弱,尤其缺乏多重尺度上生态退耕时空格局及其驱动因子的综合研究,在很大程度上限制了研究结果外推.研究表明,受到多因子的综合影响,生态退耕后植被演替呈现出复杂多样的时空变化特征;退耕植被演替研究从植物群落结构特征分析为主向群落功能分析发展,从传统的演替过程规律分析转向退耕植被演替的时空变异性分析;相对来说,生态退耕后植被演替的时空分异、影响因子和机制方面的研究比较薄弱.加强多重尺度上生态退耕时空格局与植被演替时空变异的综合研究是将来的研究重点.     

森林生态系统与大气边界层相互作用的数值模拟

基于大气边界层和植被冠层微气象学基本原理,建立了一个森林生态系统与大气边界层相互作用的数值模式．应用该模式模拟了森林生态系统的热量平衡、植被温度、植被冠层内空气温度、地表温度日变化特征,及森林生态系统下垫面大气边界层风速、位温、比湿、湍流交换系数的时空分布和廓线的日变化特征．该模式还可应用于不同下垫面,模拟陆面物理过程与大气边界层相互作用机制及其区域气候效应的研究,这将为气候模式与生物圈的耦合研究奠定一个良好的基础．     

Fluid Dynamics of Heart Development

The morphology, muscle mechanics, fluid dynamics, conduction properties, and molecular biology of the developing embryonic heart have received much attention in recent years due to the importance of both fluid and elastic forces in shaping the heart as well as the striking relationship between the heart’s evolution and development. Although few studies have directly addressed the connection between fluid dynamics and heart development, a number of studies suggest that fluids may play a key role in morphogenic signaling. For example, fluid shear stress may trigger biochemical cascades within the endothelial cells of the developing heart that regulate chamber and valve morphogenesis. Myocardial activity generates forces on the intracardiac blood, creating pressure gradients across the cardiac wall. These pressures may also serve as epigenetic signals. In this article, the fluid dynamics of the early stages of heart development is reviewed. The relevant work in cardiac morphology, muscle mechanics, regulatory networks, and electrophysiology is also reviewed in the context of intracardial fluid dynamics.     

Theoretical studies of viral capsid proteins

Recent results in structural biology and increases in computer power have prompted initial theoretical studies on capsids of nonenveloped icosahedral viruses. The macromolecular assembly of 60 to 180 protein copies into a protein shell results in a structure of considerable size for molecular dynamics simulations. Nonetheless, progress has been made in examining these capsid assemblies from molecular dynamics calculations and kinetic models. The goals of these studies are to understand capsid function and structural properties, including quarternary structural stability, effects of antiviral compounds that bind the capsid and the self-assembly process. The insight that can be gained from the detailed information provided by simulations is demonstrated in studies of human rhinovirus; an entropic basis for the antiviral activity of hydrophobic compounds, predicted from calculated compressibility values, has been corroborated by experimental measurements on poliovirus.     

Boolean dynamics of biological networks with multiple coupled feedback loops

Boolean networks have been frequently used to study the dynamics of biological networks. In particular, there have been various studies showing that the network connectivity and the update rule of logical functions affect the dynamics of Boolean networks. There has been, however, relatively little attention paid to the dynamical role of a feedback loop, which is a circular chain of interactions between Boolean variables. We note that such feedback loops are ubiquitously found in various biological systems as multiple coupled structures and they are often the primary cause of complex dynamics. In this article, we investigate the relationship between the multiple coupled feedback loops and the dynamics of Boolean networks. We show that networks have a larger proportion of basins corresponding to fixed-point attractors as they have more coupled positive feedback loops, and a larger proportion of basins for limit-cycle attractors as they have more coupled negative feedback loops.     

The Dynamic keyhole-key model of coexistence to explain diversity of plants in limestone and other grasslands

Abstract. This paper is a tribute to A.S. Watt who published his ‘Pattern and process in the plant community’ almost 50 years ago. Watt's interpretation of the plant community “as a working mechanism, which maintains and regenerates itself” is still highly relevant, although the keywords have changed. ‘Process’ in Watt's view involves both upgrade and downgrade aspects, whereas ‘Pattern’ was not specified, neither quantified. Nowadays. process is mainly approached as ‘disturbance’, that is natural disturbance and ‘pattern’ as patch structure. Together they make up the ‘patch dynamics’ of the community. Some implications of patch dynamics for phytosociology are discussed. A ‘Wattian’ concept of the plant community combines the Gleasonian idea of individualistic behaviour of species with the Clementsian (or rather Braun-Blanquetian) notion of community dynamics. Later work by Harper (demography), Grubb (regeneration niche) and earlier work of Sernander (forest gap dynamics) is significant for the understanding of the patch-dynamic nature of the community. Recent interest in plant species mobility can easily be linked to the concept of patch dynamics. Examples of mobility in a limestone grassland are given and a system of mobility types is proposed. Some perspectives for the study of patch dynamics are mentioned. Numerical pattern analysis should have a more prominent place in this type of study; the significance of the study of small permanent plots in a stand is emphasized, and unprejudiced demographic studies, as well as experimental studies of small-scale species replacement are recommended.     

Local Synchronization of Resting-State Dynamics Encodes Gray’s Trait Anxiety

The Behavioral Inhibition System (BIS) as defined within the Reinforcement Sensitivity Theory (RST) modulates reactions to stimuli indicating aversive events. Gray’s trait Anxiety determines the extent to which stimuli activate the BIS. While studies have identified the amygdala-septo-hippocampal circuit as the key-neural substrate of this system in recent years and measures of resting-state dynamics such as randomness and local synchronization of spontaneous BOLD fluctuations have recently been linked to personality traits, the relation between resting-state dynamics and the BIS remains unexplored. In the present study, we thus examined the local synchronization of spontaneous fMRI BOLD fluctuations as measured by Regional Homogeneity (ReHo) in the hippocampus and the amygdala in twenty-seven healthy subjects. Correlation analyses showed that Gray’s trait Anxiety was significantly associated with mean ReHo in both the amygdala and the hippocampus. Specifically, Gray’s trait Anxiety explained 23% and 17% of resting-state ReHo variance in the left amygdala and the left hippocampus, respectively. In summary, we found individual differences in Gray’s trait Anxiety to be associated with ReHo in areas previously associated with BIS functioning. Specifically, higher ReHo in resting-state neural dynamics corresponded to lower sensitivity to punishment scores both in the amygdala and the hippocampus. These findings corroborate and extend recent findings relating resting-state dynamics and personality while providing first evidence linking properties of resting-state fluctuations to Gray’s BIS.     

AFM for analysis of structure and dynamics of DNA and protein-DNA complexes

This paper describes protocols for studies of structure and dynamics of DNA and protein-DNA complexes with atomic force microscopy (AFM) utilizing the surface chemistry approach. The necessary specifics for the preparation of functionalized surfaces and AFM probes with the use of silanes and silatranes, including the protocols for synthesis of silatranes are provided. The methodology of studies of local and global conformations DNA with the major focus on the time-lapse imaging of DNA in aqueous solutions is illustrated by the study of dynamics of Holliday junctions including branch migration. The analysis of nucleosome dynamics is selected as an example to illustrate the application of the time-lapse AFM to studies of dynamics of protein-DNA complexes. The force spectroscopy is the modality of AFM with a great importance to various fields of biomedical studies. The AFM force spectroscopy approach for studies of specific protein-DNA complexes is illustrated by the data on analysis of dynamics of synaptic SfiI-DNA complexes. When necessary, additional specifics are added to the corresponding example.     

Protein dynamics from NMR

This review surveys recent investigations of conformational fluctuations of proteins in solution using NMR techniques. Advances in experimental methods have provided more accurate means of characterizing fast and slow internal motions as well as overall diffusion. The information obtained from NMR dynamics experiments provides insights into specific structural changes or configurational energetics associated with function. A variety of applications illustrate that studies of protein dynamics provide insights into protein-protein interactions, target recognition, ligand binding, and enzyme function.     

Betaine enhances the cellular survival via mitochondrial fusion and fission factors,MFN2 and DRP1

Betaine is a key metabolite of the methionine cycle and known for attenuating alcoholic steatosis in the liver. Recent studies have focused on the protection effect of betaine in mitochondrial regulation through the enhanced oxidative phosphorylation system. However, the mechanisms of its beneficial effects have not been clearly identified yet. Mitochondrial dynamics is important for the maintenance of functional mitochondria and cell homeostasis. A defective mitochondrial dynamics and oxidative phosphorylation system have been closely linked to several pathologies, raising the possibility that novel drugs targeting mitochondrial dynamics may present a therapeutic potential to restore the cellular homeostasis. In this study, we investigated betaine’s effect on mitochondrial morphology and physiology and demonstrated that betaine enhances mitochondrial function by increasing mitochondrial fusion and improves cell survival. Furthermore, it rescued the unbalance of the mitochondrial dynamics from mitochondrial oxidative phosphorylation dysfunction induced by oligomycin and rotenone. The elongation properties by betaine were accompanied by lowering DRP1 and increasing MFN2 expression. These data suggest that betaine could play an important role in remodeling mitochondrial dynamics to enhance mitochondrial function and cell viability.     

Eco-evolutionary maintenance of diversity in fluctuating environments

Growing evidence suggests that temporally fluctuating environments are important in maintaining variation both within and between species. To date, however, studies of genetic variation within a population have been largely conducted by evolutionary biologists (particularly population geneticists), while population and community ecologists have concentrated more on diversity at the species level. Despite considerable conceptual overlap, the commonalities and differences of these two alternative paradigms have yet to come under close scrutiny. Here, we review theoretical and empirical studies in population genetics and community ecology focusing on the ‘temporal storage effect’ and synthesise theories of diversity maintenance across different levels of biological organisation. Drawing on Chesson's coexistence theory, we explain how temporally fluctuating environments promote the maintenance of genetic variation and species diversity. We propose a further synthesis of the two disciplines by comparing models employing traditional frequency-dependent dynamics and those adopting density-dependent dynamics. We then address how temporal fluctuations promote genetic and species diversity simultaneously via rapid evolution and eco-evolutionary dynamics. Comparing and synthesising ecological and evolutionary approaches will accelerate our understanding of diversity maintenance in nature.     

The role of epistatic gene interactions in the response to selection and the evolution of evolvability

It has been argued that the architecture of the genotype-phenotype map determines evolvability, but few studies have attempted to quantify these effects. In this article we use the multilinear epistatic model to study the effects of different forms of epistasis on the response to directional selection. We derive an analytical prediction for the change in the additive genetic variance, and use individual-based simulations to understand the dynamics of evolvability and the evolution of genetic architecture. This shows that the major determinant for the evolution of the additive variance, and thus the evolvability, is directional epistasis. Positive directional epistasis leads to an acceleration of evolvability, while negative directional epistasis leads to canalization. In contrast, pure non-directional epistasis has little effect on the response to selection. One consequence of this is that the classical epistatic variance components, which do not distinguish directional and non-directional effects, are useless as predictors of evolutionary dynamics. The build-up of linkage disequilibrium also has negligible effects. We argue that directional epistasis is likely to have major effects on evolutionary dynamics and should be the focus of empirical studies of epistasis.