Constraint line methods and the applications in ecology北大核心CSCD

With increasing data availability in the big data era, many traditional statistical analyses based on the mean or median are insufficient or inappropriate to elucidate the complex patterns of variation. This is particularly the case when multiple factors are involved and the bivariate scatter occurs as scatter clouds. In such circumstances, constraint line (or envelope) method could be an alternative and effective tool to extract the data boundaries, thus improves our understanding of the complex relationships between limiting factor and response factor. Here, we synthesize the major findings and achievements in the field of applying the constraint line method in ecology. Specifically, we first describe the history and development of the constraint line method. We then discuss the techniques to establish the constraint lines with examples, and discuss the applications and implications of the constraint lines in species distribution, population performance, and optimization problem. We suggest simultaneously application of both constraint lines and regression techniques to the same datasets to achieve a comprehensive understanding of ecological process and underlying mechanisms. Such combined methods should be used with special attention to the role of spatial heterogeneity and scale dependency. We also discuss in detail the potential applicability of the constraint line method in studying the linkages between ecosystem services, and land system design.     

约束线方法在生态学研究中的应用

生态系统格局和过程往往受到多个因子的共同影响, 故此反映两个生态学变量相互关系的散点图常常会表现为有边界的散点云。基于数据均值或中值分析的传统统计方法不适用于散点云数据的分析。散点云所表征的不是两变量之间的相关关系, 而是限制作用关系。约束线(包络)方法为提取散点云边界、理解限制变量对响应变量的作用, 以及预测响应变量的潜在最大值提供了有效手段。该文对应用约束线方法研究生态学问题所取得的成果进行总结与归纳, 介绍了约束线概念的发展历程、提取方法, 从物种分布、种群行为及作物产量优化三个方面总结了约束线方法的优点及适用性, 概述了当前约束线方法应用研究面临的问题与挑战, 指出约束线方法应结合其他统计方法, 实现对生态过程的准确理解, 此外, 还应重视约束线方法的尺度依赖性。最后, 该文展望了约束线方法在研究生态系统服务关系和土地系统优化等方面的应用前景。     

植物边缘种群遗传多样性研究进展

边缘种群指地理分布边缘可检测到的一定数量的同种个体集合, 准确评价其遗传多样性对于理解第四纪冰期后气候变化对物种边缘扩展或收缩、遗传资源保护与利用以及物种形成等有重要意义。该文探讨了维持植物边缘种群遗传多样性的进化机制, 分析交配系统对物种边缘及其遗传多样性的影响, 比较了边缘与中心种群遗传多样性的差异及其形成的生态与进化过程, 并探讨了边缘种群遗传多样性与其所在的群落物种多样性的关系及理论基础。该文提出今后研究的重点是应用全基因组序列或转录组基因序列研究前缘-后缘种群之间或边缘-中心种群之间的适应性差异, 边缘种群与所在群落其他物种之间相互作用的分子机制, 深入解析边缘种群对环境的适应及边缘种群遗传多样性与群落物种多样性关系的生态与进化过程。     

Ecological thresholds: Concept,Methods and research outlooks

The concept of ecological thresholds was raised in the 1970s. However, it was subsequently given different definitions and interpretations depending on research fields or disciplines. For most scientists, ecological thresholds refer to the points or zones that link abrupt changes between alternative stable states of an ecosystem. The measurement and quantification of ecological thresholds have great theoretical and practical significance in ecological research for clarifying the structure and function of ecosystems, for planning sustainable development modes, and for delimiting ecological red lines in managing the ecosystems of a region. By reviewing the existing concepts and classifications of ecological thresholds, we propose a new concept and definition at two different levels: the ecological threshold points, i.e. the turning points of quantitative changes to qualitative changes, which can be considered as ecological red lines; the ecological threshold zones, i.e. the regime shifts of the quantitative changes among different stable states, which can be considered as the yellow and/or orange warning boundaries of the gradual ecological changes. The yellow thresholds mean that an ecosystem can return to a stable state by its self-adjustment, the orange thresholds indicate that the ecosystem will stay in the equilibrium state after interference factors being removed, whereas the red thresholds, as the critical threshold points, indicate that the ecosystem will undergo irreversible degradation or even collapse beyond those points. We also summarizes two types of popular Methods in determining ecological thresholds: statistical analysis and modeling based on data of field observations. The applications of ecological thresholds in ecosystem service, biodiversity conservation and ecosystem management research are also reviewed. Future research on ecological thresholds should focus on the following aspects: (1) methodological development for measurement and quantification of ecological thresholds; (2) emphasizing the scaling effect of ecological thresholds and establishment of national-scale observation system and network; and (3) implementation of ecological thresholds as early warning tools in ecosystem management and delimiting ecological red lines.     

Calibration of multivariate scatter plots for exploratory analysis of relations within and between sets of variables in genomic research

The scatter plot is a well known and easily applicable graphical tool to explore relationships between two quantitative variables. For the exploration of relations between multiple variables, generalisations of the scatter plot are useful. We present an overview of multivariate scatter plots focussing on the following situations. Firstly, we look at a scatter plot for portraying relations between quantitative variables within one data matrix. Secondly, we discuss a similar plot for the case of qualitative variables. Thirdly, we describe scatter plots for the relationships between two sets of variables where we focus on correlations. Finally, we treat plots of the relationships between multiple response and predictor variables, focussing on the matrix of regression coefficients. We will present both known and new results, where an important original contribution concerns a procedure for the inclusion of scales for the variables in multivariate scatter plots. We provide software for drawing such scales. We illustrate the construction and interpretation of the plots by means of examples on data collected in a genomic research program on taste in tomato.     

The mode of action of heparan and dermatan sulfates in the regulation of hepatocyte growth factor/scatter factor.

Hepatocyte growth factor/scatter factor, in addition to binding to its specific signal-transducing receptor, Met, also interacts with both heparan and dermatan sulfates with high affinity. We have investigated the comparative role of these two glycosaminoglycans in the activation of Met by hepatocyte growth factor/scatter factor. Using glycosaminoglycan-deficient CHO pgsA-745 cells we have shown that growth factor activity is critically dependent upon glycosaminoglycans, and that heparan sulfate and dermatan sulfate are equally potent as co-receptors. Cross-linked 1:1 conjugates of growth factor and either heparan or dermatan sulfate do not dimerize under physiological conditions and are biologically active. This implies that a ternary signaling complex with Met forms in vivo. Native Met isolated from CHO pgsA-745 cells shows only very weak intrinsic affinity for heparin in vitro. Also, a heparin-derived hexasaccharide, which is the minimal size for high affinity binding to the growth factor alone, is sufficient to induce biological activity. Together these observations imply that the role of these glycosaminoglycan may be primarily to effect a conformational change in hepatocyte growth factor/scatter factor, rather than to induce a necessary growth factor dimerization, or to stabilize a ternary complex by additionally interacting with Met.     

Reinforcing the LINC complex connection to actin filaments: the role of FHOD1 in TAN line formation and nuclear movement

Positioning the nucleus is critical for many cellular processes including cell division, migration and differentiation. The linker of nucleoskeleton and cytoskeleton (LINC) complex spans the inner and outer nuclear membranes and has emerged as a major factor in connecting the nucleus to the cytoskeleton for movement and positioning. Recently, we discovered that the diaphanous formin family member FHOD1 interacts with the LINC complex component nesprin-2 giant (nesprin-2G) and that this interaction plays essential roles in the formation of transmembrane actin-dependent nuclear (TAN) lines and nuclear movement during cell polarization in fibroblasts. We found that FHOD1 strengthens the connection between nesprin-2G and rearward moving dorsal actin cables by providing a second site of interaction between nesprin-2G and the actin cable. These results indicate that the LINC complex connection to the actin cytoskeleton can be enhanced by cytoplasmic factors and suggest a new model for TAN line formation. We discuss how the nesprin-2G-FHOD1 interaction may be regulated and its possible functional significance for development and disease.     

Effects of drought stress on photosynthesis,growth and root structure of transgenic PtPIP2;8 poplar 84K (Populus alba × P. glandulosa)

为研究水通道蛋白PtPIP2;8基因功能, 了解其不同表达水平的转基因84K杨(Populus alba × P. glandulossa)应对干旱胁迫的响应, 该文以转PtPIP2;8 84K杨抑制表达株系(抑制表达)、野生型(WT)和转PtPIP2;8 84K杨超表达株系(超表达)为试验材料, 测定PtPIP2;8表达水平、根系导度、光响应曲线、气体交换参数、生长及根系形态指标。结果显示: (1) WT植株PtPIP2;8仅在根系表达; 超表达植株PtPIP2;8除在根部显著表达外, 在茎和叶片中也显著表达; 抑制表达植株PtPIP2;8仅在根部有微量表达, 表达量分别是WT和超表达植株的1/20和1/80。(2)根系结构分析发现, 超表达植株总根长、总根表面积、总根体积、总根尖数显著低于WT和抑制表达植株, 根系导水率显著高于WT和抑制表达植株, 表明PtPIP2;8参与了植物根系水分运输, 提高了水分运输效率。(3)正常水分条件下, 抑制表达植株苗高、叶面积显著低于WT和超表达植株, 根冠比显著高于WT和超表达植株。干旱胁迫后, 抑制表达植株净光合速率(P_n)、气孔导度(G_s)下降幅度小, 仍能维持较高的P_n。气体交换参数显示抑制表达植株P_n、G_s日变化为“单峰”型, 属气孔因素引起的净光合速率下降;WT和超表达植株P_n、G_s日变化为“双峰”型, 干旱胁迫后, 抑制表达植株P_n略微下降, WT和超表达植株P_n均下降, 尤其是13:00、15:00下降显著, 表明WT和超表达植株对干旱胁迫更加敏感, 干旱对其影响更大。(4)干旱胁迫后, 抑制表达植株相对生长速率、总生物量降低的最少, 根冠比最高; 总根表面积、总根体积、总根尖数显著高于WT植株。表明PtPIP2;8直接参与水分运输并提高水分运输效率, 其转化影响了植株根系发育和生长。超表达植株根系发育的下降和叶面积的增大减弱了它的抗旱性, 而抑制表达植株矮小, 降低的叶面积, 增加的根系生长和根冠比提高了它的抗旱能力。从研究结果来看, 水通道蛋白提高了水分跨膜运输效率, 而非水通道蛋白导水机制对干旱有较强的耐受性。     

Automated quantitative analysis of epithelial cell scatter

Epithelial cell scatter is a well-known in vitro model for the study of epithelial-mesenchymal transition (EMT). Scatter recapitulates many of the events that occur during EMT, including the dissociation of multicellular structures and increased cell motility. Because it has been implicated in tumor invasion and metastasis, much effort has been made to identify the molecular signals that regulate EMT. To better understand the quantitative contributions of these signals, we have developed metrics that quantitatively describe multiple aspects of cell scatter. One metric (cluster size) quantifies the disruption of intercellular adhesions while a second metric (nearest-neighbor distance) quantifies cell dispersion. We demonstrate that these metrics delineate the effects of individual cues and detect synergies between them. Specifically, we find epidermal growth factor (EGF), cholera toxin (CT) and insulin to synergistically reduce cluster sizes and increase nearest-neighbor distances. To facilitate the rapid measurement of our metrics from live-cell images, we have also developed automated techniques to identify cell nuclei and cell clusters in fluorescence images. Taken together, these studies provide broadly applicable quantitative image analysis techniques and insight into the control of epithelial cell scatter, both of which will contribute to the understanding of EMT and metastasis.Key words: cell scatter, EMT, automated image analysis     

Progress in the studies of vivipary in mangrove plants

Vivipary in plants refers to a phenomenon that sexually reproduced offsprings germinate while still attached to the maternal bodies. This is mostly manifested in mangrove plants, which occur in tropical and subtropical intertidal zones and encounter harsh environmental conditions such as high salinity, high temperatures, waterlogging, hypoxia and tidal waves. Vivipary has long been recognized as one of the most important adaptive features under such a complex environment. Here we discuss four aspects of vivipary: morphological anatomy, physiology and biochemistry, molecular biology and ecological adaptation. We also discuss shortcomings in current studies and prospect of future directions. Differing from regular seed development, viviparous seeds in mangroves are evolved with many special structures, indicating a genetically based process. Hormones play an important role in regulating the process, whilst the dynamics of salt ion concentration during embryo and propagule development seems to be an adaptive feature. The ecological significance of vivipary is fully exhibited in the propagules that can effectively establish themselves on muddy tidal zones. Such a success heavily relies on sound functional features developed on the mother plants. However, the molecular mechanism and the regulation of viviparous seed development in mangroves remain elusive. Systematic studies of vivipary in mangroves not only help to understand the nature and evolutionary process of this distinct adaptive phenomenon, but also provide the foundation for mangrove forest restoration and protection in many parts of the world.     

An evaluation of four threshold selection methods in species occurrence modelling with random forest: Case studies with Davidia involucrata and Cunninghamia lanceolata

Aims Predictive species distribution models (SDMs) are increasingly applied in resource assessment, environmental conservation and biodiversity management. However, most SDM models often yield a predicted probability (suitability) surface map. In conservation and environmental management practices, the information presented as species presence/absence (binary) may be more practical than presented as probability or suitability. Therefore, a threshold is needed to transform the probability or suitability data to presence/absence data. However, little is known about the effects of different threshold-selection methods on model performance and species range changes induced by future climate. Of the numerous SDM models, random forest (RF) can produce probabilistic and binary species distribution maps based on its regression and classification algorisms, respectively. Studies dealing with the comparative test of the performances of RF regression and classification algorisms have not been reported.
Methods Here, the RF was used to simulate the current and project the future potential distributions of Davidia involucrata and Cunninghamia lanceolata. Then, four threshold-setting methods (Default 0.5, MaxKappa, MaxTSS and MaxACC) were selected and used to transform modelled probabilities of occurrence into binary predictions of species presence and absence. Lastly, we investigated the difference in model performance among the threshold selection methods by using five model accuracy measures (Kappa, TSS, Overall accuracy, Sensitivity and Specificity). We also used the map similarity measure, Kappa, for a cell-by-cell comparison of similarities and differences of distribution map under current and future climates.
Important findings We found that the choice of threshold method altered estimates of model performance, species habitat suitable area and species range shifts under future climate. The difference in selected threshold cut-offs among the four threshold methods was significant for D. involucrata, but was not significant for C. lanceolata. Species’ geographic ranges changed (area change and shifting distance) in response to climate change, but the projections of the four threshold methods did not differ significantly with respect to how much or in which direction, but they did differ against RF classification predictions. The pairwise similarity analysis of binary maps indicated that spatial correspondence among prediction maps was the highest between the MaxKappa and the MaxTSS, and lowest between RF classification algorism and the four threshold-setting methods. We argue that the MaxTSS and the MaxKappa are promising methods for threshold selection when RF regression algorism is used for the distribution modeling of species. This study also provides promising insights to our understanding of the uncertainty of threshold selection in species distribution modeling.     

New perspectives on forest soil carbon and nitrogen cycling processes: Roles of arbuscular mycorrhizal versus ectomycorrhizal tree species

Nearly all tree species develop symbiotic relationships with either arbuscular mycorrhizal (AM) or ectomycorrhizal (EM) fungi to acquire nutrients from soils, and hence influence soil carbon (C) and nitrogen (N) cycles in terrestrial ecosystems. It is crucial to understand the differences in soil C and N cycles between AM and EM forests and the underlying mechanisms. In this review, we first compared the differences in the soil C and N cycles between AM and EM forests, and synthesized the underlying mechanisms from perspectives of the inputs, stabilization, and outputs of soil C and N in forest ecosystems. We also compared the responses of soil C and N cycles between AM and EM forests to global changes. In this field, one major research priority is comparing the structure and function (including the soil C and N cycles) between AM and EM forest ecosystems to provide theoretical basis and solid data for improving forest productivity and ecosystem services. The second research focus is deepening the understanding of the effects of interactions between aboveground litter and belowground mycorrhiza and free-living microbes on soil C and N cycles to reveal the potential underlying mechanisms in forests with different mycorrhizal symbioses. Third, the research methodology and new techniques need refining and applying to explicitly focus on scaling up the fine-scale measurements to better expound and predict the C and N cycles in forest ecosystems. Finally, more studies on the stability of soil organic matter among different mycorrhizal forests are needed to precisely assess responses of the structure and function of forest ecosystems to global changes.     

Single molecule techniques in DNA repair: A primer

A powerful new approach has become much more widespread and offers insights into aspects of DNA repair unattainable with billions of molecules. Single molecule techniques can be used to image, manipulate or characterize the action of a single repair protein on a single strand of DNA. This allows search mechanisms to be probed, and the effects of force to be understood. These physical aspects can dominate a biochemical reaction, where at the ensemble level their nuances are obscured. In this paper we discuss some of the many technical advances that permit study at the single molecule level. We focus on DNA repair to which these techniques are actively being applied. DNA repair is also a process that encompasses so much of what single molecule studies benefit – searching for targets, complex formation, sequential biochemical reactions and substrate hand-off to name just a few. We discuss how single molecule biophysics is poised to transform our understanding of biological systems, in particular DNA repair.     

Data mining tools for biological sequences

We describe a methodology, as well as some related data mining tools, for analyzing sequence data. The methodology comprises three steps: (a) generating candidate features from the sequences, (b) selecting relevant features from the candidates, and (c) integrating the selected features to build a system to recognize specific properties in sequence data. We also give relevant techniques for each of these three steps. For generating candidate features, we present various types of features based on the idea of k-grams. For selecting relevant features, we discuss signal-to-noise, t-statistics, and entropy measures, as well as a correlation-based feature selection method. For integrating selected features, we use machine learning methods, including C4.5, SVM, and Naive Bayes. We illustrate this methodology on the problem of recognizing translation initiation sites. We discuss how to generate and select features that are useful for understanding the distinction between ATG sites that are translation initiation sites and those that are not. We also discuss how to use such features to build reliable systems for recognizing translation initiation sites in DNA sequences.     

Lab and field experiments: Are they the same animal?

To advance our understanding of biological processes we often plan our experiments based on published data. This can be confusing though, as data from experiments performed in a laboratory environment are sometimes different from, or completely opposite to, findings from similar experiments performed in the “real world”. In this mini-review, we discuss instances where results from laboratory experiments differ as a result of laboratory housing conditions, and where they differ from results gathered in the field environment. Experiments involving endocrinology and behavior appear to be particularly susceptible to influence from the environment in which they are performed.As such, we have attempted to promote discussion of the influence of housing environment on the reproductive axis, circadian biology and behavior, immune function, stress biology, neuroplasticity and photoperiodism. For example, why should a rodent species be diurnal in one housing environment yet nocturnal in another? Are data that are gathered from experiments in the laboratory applicable to the field environment, and vice-versa? We hope not only to highlight the need for experiments in both lab and field when looking at complex biological systems, but also to promote frank discussion of discordant data. Perhaps, just as study of individual variation has been gaining momentum in recent years, data from variation between experimental arenas can provide us with novel lines of research.     

Marine Ecosystems as Complex Adaptive Systems: Emergent Patterns,Critical Transitions,and Public Goods

Complex adaptive systems provide a unified framework for explaining ecosystem phenomena. In the past 20 years, complex adaptive systems have been sharpened from an abstract concept into a series of tools that can be used to solve concrete problems. These advances have been led by the development of new techniques for coupling ecological and evolutionary dynamics, for integrating dynamics across multiple scales of organization, and for using data to infer the complex interactions among different components of ecological systems. Focusing on the development and usage of these new methods, we discuss how they have led to an improved understanding of three universal features of complex adaptive systems, emergent patterns; tipping points and critical phenomena; and cooperative behavior. We restrict our attention primarily to marine ecosystems, which provide numerous successful examples of the application of complex adaptive systems. Many of these are currently undergoing dramatic changes due to anthropogenic perturbations, and we take the opportunity to discuss how complex adaptive systems can be used to improve the management of public goods and to better preserve critical ecosystem services.     

Order Release and Product Mix Coordination in a Complex PCB Manufacturing Line with Batch Processors

In this paper, we study the role of order releases and product mix coordination in a complex manufacturing line with batch processors. We develop a planning methodology for synchronizing production in such manufacturing lines and discuss the decision-making process in the context of a PCB production environment at Northern Telecom's Fiberworld Division. The planning methodology includes developing mathematical programming models for determining a configuration of batch processors, order releases to the shop floor, and daily loading decisions at the batch processors. The optimization models are linked to a simulation model of the shop, which provides key statistics like lead time, work in process, and utilization rates. The objective is to reduce lead time for manufacturing different products in this environment while meeting the demand. We analyze the performance of such a line, study the efficacy of various types of shop floor synchronization policies, and establish the role of batch processors in managing such complex lines effectively. We exhibit how batch processors (which are bottleneck operations) could be scheduled effectively to incorporate the logical constraints that govern their operations and react to variabilities in the manufacturing line.     

亚热带常绿阔叶林89种木本植物一级根直径的变异

细根直径变异是根系形态变化的常见形式, 对细根变异研究具有重要意义。为了揭示亚热带天然常绿阔叶林一级根直径变异特征, 该研究选取福建省建瓯市万木林自然保护区天然常绿阔叶林的89种木本植物进行研究。每个树种选取胸径或地径相近的3株, 用完整土块法进行根系取样, 用根序法对根系进行分级。采用单因素方差分析分别检验叶片习性(常绿、落叶树种)、生长型(乔木、小乔木或灌木、灌木)和主要科之间一级根直径的差异; 通过计算Blomberg’s K值以检验系统发育信号; 利用线性回归方法, 分析科水平的分化时间与一级根直径的相关性。结果显示: 1)亚热带常绿阔叶林一级根直径变异系数为23%; 2)常绿树种与落叶树种一级根直径没有显著差异, 但灌木一级根直径显著小于小乔木或灌木、乔木; 3)一级根直径系统发育信号不显著, 科水平分化时间与一级根直径呈正相关关系。研究结果表明, 亚热带天然常绿阔叶林木本植物一级根直径变异受系统发育影响较小, 但受生长型影响, 表现为一定的趋同适应。     

Scatter factor: molecular characteristics and effect on the invasiveness of epithelial cells

The generation of invasiveness in transformed cells represents an essential step of tumor progression. We have previously shown that MDCK epithelial cells, which are deprived of intracellular adhesion by the addition of anti-Arc-1/uvomorulin antibodies, become invasive for collagen gels and embryonal heart tissue (Behrens, J., M. M. Mareel, F. M. Van Roy, and W. Birchmeier. 1989. J. Cell Biol. 108: 2435-2447.). Here we examined whether invasiveness is also induced by scatter factor, which is known to dissociate epithelial cells (Stoker, M., E. Gherardi, M. Perryman, and J. Gray. 1987. Nature (Lond.). 327:239- 242.). Scatter factor was purified to homogeneity from conditioned medium of human fibroblasts by heparin-Sepharose chromatography, followed by cation exchange chromatography, gel filtration, or preparative SDS gel electrophoresis. We found that scatter factor represents a 92,000 mol wt glycoprotein which, apparently, is converted by limited proteolysis into disulfide-linked 62,000 and 34/32,000 mol wt subunits. Reversed phase HPLC and sequence analysis of tryptic peptides confirmed the suggested molecular structure, and revealed further that scatter factor exhibits sequence similarities to hepatocyte growth factor and to plasminogen. Purified scatter factor in fact induces the invasiveness into collagen matrices of MDCK epithelial cells, and induces or promotes the invasiveness of a number of human carcinoma cell lines. Apparently, the effect on the human cells depends on their respective degree of differentiation, i.e., cell lines with a less pronounced epithelial phenotype were more susceptible to the factor. Scatter factor does not seem to influence synthesis, steady- state level, and phosphorylation of the cell adhesion molecule Arc- 1/uvomorulin. Thus, scatter factor represents a clearly defined molecular species which induces, in vitro, the progression of epithelial cells to a more motile, i.e., invasive phenotype.