基于模型的景观格局与生态过程研究

景观格局与生态过程关系的研究是景观生态学的主要特色和理论核心之一。模型可以充分利用实验和观测数据并综合不同时间和空间尺度上的信息提炼规律或揭示内在机制,模拟景观格局与生态过程的动态与相互关系,成为景观生态学研究的有力工具。结合研究实例,总结了基于模型的景观格局研究、生态过程研究和格局-过程关系研究的发展现状和薄弱环节,同时探讨了通过构建耦合模型研究格局-过程相互关系的途径。总结了景观模型研究亟待发展的领域与发展趋势。     

Effects of kin-structured seed dispersal on the genetic structure of the clonal dioecious shrub ilex leucoclada

Nonrandom patterns of gene dispersal have been identified as possible causes of genetic structuring within populations. Attempts to model these patterns have generally focused solely on the effects of isolation by distance, but the processes involved are more complex than such modeling suggests. Here, we extend considerations of gene dispersal processes beyond simple isolation by distance effects by directly evaluating the effects of kin-structured gene dispersal mediated by the group dispersal of related seeds within fruits (i.e., kin-structured seed dispersal) by birds on genetic structure in Ilex leucoclada, a clonal dioecious shrub. To examine the genetic structure patterns, we established two 30x30 m plots (one with immature soils in old-growth forest and one in secondary forest, designated IM and SC, respectively) with different I. leucoclada stem densities. In these two plots 145 and 510 stems were found, representing 78 and 85 genets, respectively, identified by analyzing their genotypes at eight microsatellite loci. The clonal structure was stronger in the SC plot than in the IM plot. Correlograms of coancestry for genets in both plots exhibited significant, positive, high values in the shortest distance class, indicating the presence of strong genetic structure. However, Sp statistics revealed that the pattern of the genetic structure differed between the plots. In addition, to estimate the family structure within fruits, we sampled forty fruits, in total, from 15 randomly selected plants in the area around the IM and SC plots, and found that 80% of the fruits were multiseeded and 42-100% of the multiseeded fruits contained at least one pair of full sibs. Simulations based on these estimates demonstrated that the group dispersal of related seeds produced through correlated mating both within and across fruits, but not unstructured half-sib dispersal, could generate the observed magnitude and trends of genetic structure found in the IM plot. Furthermore, in addition to kin-structured seed dispersal, isolation by distance processes is also likely to promote genetic substructuring in the SC plot. After discussing possible ecological factors that may have contributed to the observed genetic structure, we contrast our results with those predicted by general isolation by distance models, and propose that kin-structured seed dispersal should promote some evolutionary phenomena, and thus should be incorporated, where appropriate, in models of gene dispersal in natural plant populations.     

Impact of periodic nutrient input rate on trophic chain properties

Marine ecosystems are characterized by a strong influence of hydrodynamics on biological processes. The associated models involve the coupling of physical to biological models and therefore require a large number of state variables. The consequent high complexity limits our capacity to perform a complete and detailed study and even prevents any complete mathematical study of these models. It is also difficult to disentangle among all the processes involved, which ones actually drive the system at any moment. Hydrodynamics, among other consequences, affect the way under which the nutrients are supplied to marine ecosystems. The variability of nutrient input rate in marine systems generally results from runs-off in coastal systems and from physical processes (wind forcing and hydrodynamics) in open ocean. This paper is devoted to the study of the effects of the nutrient input rate variability on the dynamics and the functioning of trophic chains. In this context, we aim to provide an understandable study, based on simplified system models. We consider a periodic nutrient input rate and analyze how this variability modifies some system properties: its dynamics, its functioning and its structure. The dynamics is obtained by numerical simulations and when possible, enlighten by already published mathematical results. The functioning is measured by the time averaged state variables during the simulation period, and their variability. The structure concerns the number of surviving populations, a proxy of specific biodiversity. We show how these properties can be affected and provide some conditions under which the modifications can occur. We also highlight that, even if the physical process is the main driving force in the global dynamics, the choice of the biological model is important to understand the biological response of the system to physical forcing.     

Combined LC/MS-platform for analysis of all major stratum corneum lipids,and the profiling of skin substitutes

Ceramides (CERs), cholesterol, and free fatty acids (FFAs) are the main lipid classes in human stratum corneum (SC, outermost skin layer), but no studies report on the detailed analysis of these classes in a single platform. The primary aims of this study were to 1) develop an LC/MS method for (semi-)quantitative analysis of all main lipid classes present in human SC; and 2) use this method to study in detail the lipid profiles of human skin substitutes and compare them to human SC lipids. By applying two injections of 10 μl, the developed method detects all major SC lipids using RPLC and negative ion mode APCI-MS for detection of FFAs, and NPLC using positive ion mode APCI-MS to analyze CERs and cholesterol. Validation showed this lipid platform to be robust, reproducible, sensitive, and fast. The method was successfully applied on ex vivo human SC, human SC obtained from tape strips and human skin substitutes (porcine SC and human skin equivalents). In conjunction with FFA profiles, clear differences in CER profiles were observed between these different SC sources. Human skin equivalents more closely mimic the lipid composition of human stratum corneum than porcine skin does, although noticeable differences are still present. These differences gave biologically relevant information on some of the enzymes that are probably involved in SC lipid processing. For future research, this provides an excellent method for (semi-)quantitative, ‘high-throughput’ profiling of SC lipids and can be used to advance the understanding of skin lipids and the biological processes involved.     

Responses to innocuous, but not noxious, somatosensory stimulation by neurons in the ferret superior colliculus

The intermediate and deep layers of the superior colliculus (SC) are known for their role in initiating orienting behaviors. To direct these orienting functions, the SC of some animals (e.g., primates, carnivores) is dominated by inputs from the distance senses (vision, audition). In contrast, the rodent SC relies more heavily on non-visual inputs, such as touch and nociception, possibly as an adaptive response to the proximity of dangers encountered during their somatosensory-dominant search behaviors. The ferret (a carnivore) seems to employ strategies of both groups: above ground they use visual/auditory cues, but during subterranean hunting ferrets must rely on non-visual signals to direct orienting. Therefore, the present experiments sought to determine whether the sensory inputs to the ferret SC reveal adaptations common to functioning in both environments. The results showed that the ferret SC is dominated (63%; 181/286) by visual/auditory inputs (like the cat), rather than by somatosensory inputs (as found in rodents). Furthermore, tactile responses were driven primarily from hair-receptors (like cats), not from the vibrissae (as in rodents). Additionally, while a majority of collicular neurons in rodents respond to brief noxious stimulation, no such neurons were encountered in the ferret SC. A small proportion (4%; 13/286) of the ferret SC neurons were responsive to long-duration (>5 s) noxious stimulation, but further tests could not establish these responses as nociceptive. Collectively, these data indicate that the ferret SC is best adapted for the animal's visuallacoustically guided activities and most closely resembles the SC of its phylogenetic relative, the cat.     

Environmental control of lineage plasticity and stem cell memory

Tissue-resident stem cells (SCs) are critical players in the maintenance of tissue homeostasis. SCs reside in complex and uniquely anatomically organized microenvironments (SC niches), that carefully control SC lineage outputs depending on localized tissue needs. Upon environmental perturbations and tissue stressors, SCs respond and restore the tissue to homeostasis, as well as protect it from secondary assaults. Critical to this function are two key processes, SC lineage plasticity and SC memory. In this review, we delineate the multifactorial determinants and key principles underlining these two remarkable SC behaviors. Understanding lineage plasticity and SC memory will be critical not only to design new regenerative therapies but also to determine how these processes are altered in a multitude of pathologies such as cancer and chronic tissue damage.     

Responses to innocuous,but not noxious,somatosensory stimulation by neurons in the ferret superior colliculus

The intermediate and deep layers of the superior colliculus (SC) are known for their role in initiating orienting behaviors. To direct these orienting functions, the SC of some animals (e.g., primates, carnivores) is dominated by inputs from the distance senses (vision, audition). In contrast, the rodent SC relies more heavily on non-visual inputs, such as touch and nociception, possibly as an adaptive response to the proximity of dangers encountered during their somatosensory-dominant search behaviors. The ferret (a carnivore) seems to employ strategies of both groups: above ground they use visual/auditory cues, but during subterranean hunting ferrets must rely on non-visual signals to direct orienting. Therefore, the present experiments sought to determine whether the sensory inputs to the ferret SC reveal adaptations common to functioning in both environments. The results showed that the ferret SC is dominated (63%; 181/286) by visual/auditory inputs (like the cat), rather than by somatosensory inputs (as found in rodents). Furthermore, tactile responses were driven primarily from hair-receptors (like cats), not from the vibrissae (as in rodents). Additionally, while a majority of collicular neurons in rodents respond to brief noxious stimulation, no such neurons were encountered in the ferret SC. A small proportion (4%; 13/286) of the ferret SC neurons were responsive to long-duration (> 5s) noxious stimulation, but further tests could not establish these responses as nociceptive. Collectively, these data indicate that the ferret SC is best adapted for the animal's visual/acoustically guided activities and most closely resembles the SC of its phylogenetic relative, the cat.     

Interdigitating reticulum cells in lymph nodes of Sézary syndrome. Freeze-fracture and ultrathin-section morphology

Lymph nodes with extensive leukemic infiltration from three patients with the Sézary syndrome were examined in ultrathin sections and in freeze-fracture replicas. Sézary cells (SC) and interdigitating reticulum cells (IDC) were the predominant cell types in the lymph nodes. Both were closely connected with each other by apparently interdigitating cytoplasmic processes. The projections between these cells were, in the main, processes from the IDC. In freeze-fracture replicas these cellular processes did not appear as interdigitations but were more bubble-like, and for this reason these cells are imprecisely described by the term "interdigitating." The SC were seen to possess only short cytoplasmic processes. The frequent polar grouping of cell organelles in SC in the region of the contact zone with IDC and the high organelle content of IDC ('activated IDC') could be the morphologic expression of intense interaction between IDC and SC. IDC displayed three features in freeze-fracture which are not specific to the Sézary syndrome, but should be applicable to IDC in general: (1) they exhibited an approximately equal density of intramembrane particles in both the E-face and the P-face, (2) some of the intramembrane particles in the P-face were assembled in clusters and (3) the surface showed bubble-like formations of the cytoplasmic processes. On the basis of these properties it was possible to distinguish IDC from macrophages and lymphocytes in freeze-fracture replicas.     

Investigating the eco-evolutionary response of microbiomes to environmental change

Microorganisms are the primary engines of biogeochemical processes and foundational to the provisioning of ecosystem services to human society. Free-living microbial communities (microbiomes) and their functioning are now known to be highly sensitive to environmental change. Given microorganisms' capacity for rapid evolution, evolutionary processes could play a role in this response. Currently, however, few models of biogeochemical processes explicitly consider how microbial evolution will affect biogeochemical responses to environmental change. Here, we propose a conceptual framework for explicitly integrating evolution into microbiome–functioning relationships. We consider how microbiomes respond simultaneously to environmental change via four interrelated processes that affect overall microbiome functioning (physiological acclimation, demography, dispersal and evolution). Recent evidence in both the laboratory and the field suggests that ecological and evolutionary dynamics occur simultaneously within microbiomes; however, the implications for biogeochemistry under environmental change will depend on the timescales over which these processes contribute to a microbiome's response. Over the long term, evolution may play an increasingly important role for microbially driven biogeochemical responses to environmental change, particularly to conditions without recent historical precedent.     

An introduction to the European Terrestrial Ecosystem Modelling Activity

The objective of the European Terrestrial Ecosystem Modelling Activity (ETEMA) was to address some of the major challenges in developing generalized models to examine responses of natural and seminatural ecosystems to environmental change at the regional to European scale. The approach described herein was to break down the totality of ecosystem functioning into its key components, each with its characteristic spatial and temporal scales. A conceptual framework was developed describing the configuration of these components as modules within a generalized simulation model. The framework describes the key inputs, outputs and state variables, their spatial and temporal contexts, and information flows between modules. The ‘backbone’ of the model is a system of nested timing loops corresponding to the disparate time scales at which different ecosystem processes occur. The framework is a theoretical construct into which ecosystem models at levels of complexity ranging from the very general to the highly detailed can be mapped, and thus provides a guide for development of models for novel, particularly regional‐scale, applications. A number of subsystem studies of the major components of ecosystem functioning, i.e. modules of the conceptual framework, are briefly introduced herein. The general aim of the subsystem studies was to identify the key alternative formulations (as opposed to minor variants) and test these against observational data. The various subsystem studies concern planetary boundary layer–ecosystem interactions, ecosystem CO₂ and H₂O fluxes, vegetation physiology and phenology, biogeography and vegetation dynamics, detritus and SOM dynamics, soil moisture and human and natural disturbances and, as individual papers, they complete this special ETEMA issue.     

Applications of metabolic modeling to drive bioprocess development for the production of value-added chemicals

Increasing numbers of value added chemicals are being produced using microbial fermentation strategies. Computational modeling and simulation of microbial metabolism is rapidly becoming an enabling technology that is driving a new paradigm to accelerate the bioprocess development cycle. In particular, constraint-based modeling and the development of genome-scale models of industrial microbes are finding increasing utility across many phases of the bioprocess development workflow. Herein, we review and discuss the requirements and trends in the industrial application of this technology as we build toward integrated computational/experimental platforms for bioprocess engineering. Specifically we cover the following topics: (1) genome-scale models as genetically and biochemically consistent representations of metabolic networks; (2) the ability of these models to predict, assess, and interpret metabolic physiology and flux states of metabolism; (3) the model-guided integrative analysis of high throughput ‘omics’ data; (4) the reconciliation and analysis of on- and off-line fermentation data as well as flux tracing data; (5) model-aided strain design strategies and the integration of calculated biotransformation routes; and (6) control and optimization of the fermentation processes. Collectively, constraint-based modeling strategies are impacting the iterative characterization of metabolic flux states throughout the bioprocess development cycle, while also driving metabolic engineering strategies and fermentation optimization.     

The SC15 protein of Schizophyllum commune mediates formation of aerial hyphae and attachment in the absence of the SC3 hydrophobin

Disruption of the SC3 gene in the basidiomycete Schizophyllum commune affected not only formation of aerial hyphae but also attachment to hydrophobic surfaces. However, these processes were not completely abolished, indicating involvement of other molecules. We here show that the SC15 protein mediates formation of aerial hyphae and attachment in the absence of SC3. SC15 is a secreted protein of 191 aa with a hydrophilic N-terminal half and a highly hydrophobic C-terminal half. It is not a hydrophobin as it lacks the eight conserved cysteine residues found in these proteins. Besides being secreted into the medium, SC15 was localized in the cell wall and the mucilage that binds aerial hyphae together. In a strain in which the SC15 gene was deleted (DeltaSC15) formation of aerial hyphae and attachment were not affected. However, these processes were almost completely abolished when the SC15 gene was deleted in the DeltaSC3 background. The absence of aerial hyphae in the DeltaSC3DeltaSC15 strain can be explained by the inability of the strain to lower the water surface tension and to make aerial hyphae hydrophobic.     

Are there links between responses of soil microbes and ecosystem functioning to elevated CO2, N deposition and warming? A global perspective

In recent years, there has been an increase in research to understand how global changes’ impacts on soil biota translate into altered ecosystem functioning. However, results vary between global change effects, soil taxa, and ecosystem processes studied, and a synthesis of relationships is lacking. Therefore, here we initiate such a synthesis to assess whether the effect size of global change drivers (elevated CO₂, N deposition, and warming) on soil microbial abundance is related with the effect size of these drivers on ecosystem functioning (plant biomass, soil C cycle, and soil N cycle) using meta‐analysis and structural equation modeling. For N deposition and warming, the global change effect size on soil microbes was positively associated with the global change effect size on ecosystem functioning, and these relationships were consistent across taxa and ecosystem processes. However, for elevated CO₂, such links were more taxon and ecosystem process specific. For example, fungal abundance responses to elevated CO₂ were positively correlated with those of plant biomass but negatively with those of the N cycle. Our results go beyond previous assessments of the sensitivity of soil microbes and ecosystem processes to global change, and demonstrate the existence of general links between the responses of soil microbial abundance and ecosystem functioning. Further we identify critical areas for future research, specifically altered precipitation, soil fauna, soil community composition, and litter decomposition, that are need to better quantify the ecosystem consequences of global change impacts on soil biodiversity.     

Cholesterol sulfate fluidizes the sterol fraction of the stratum corneum lipid phase and increases its permeability

Desulfation of cholesterol sulfate (CholS) to cholesterol (Chol) is an important event in epidermal homeostasis and necessary for stratum corneum (SC) barrier function. The CholS/Chol ratio decreases during SC maturation but remains high in pathological conditions, such as X-linked ichthyosis, characterized by dry and scaly skin. The aim of this study was to characterize the influence of the CholS/Chol molar ratio on the structure, dynamics, and permeability of SC lipid model mixtures. We synthesized deuterated CholS and investigated lipid models with specifically deuterated components using ²H solid-state NMR spectroscopy at temperatures from 25°C to 80°C. Although the rigid acyl chains in ceramides and fatty acids remained essentially rigid upon variation of the CholS/Chol ratio, both sterols were increasingly fluidized in lipid models containing higher CholS concentrations. We also show the X-ray repeat distance of the lipid lamellar phase (105 Å) and the orthorhombic chain packing of the ceramide’s acyl chains and long free fatty acids did not change upon the variation of the CholS content. However, the Chol phase separation visible in models with high Chol concentration disappeared at the 50:50 CholS/Chol ratio. This increased fluidity resulted in higher permeabilities to model markers of these SC models. These results reveal that a high CholS/Chol ratio fluidizes the sterol fraction and increases the permeability of the SC lipid phase while maintaining the lamellar lipid arrangement with an asymmetric sterol distribution.     

Modeling of Actual Eukaryotic Control Gene Subnetworks Based on the Method of Generalized Threshold Models

Mathematical and computational means are developed that take into consideration the specifics of control processes at the molecular level and allow one to obtain both qualitative and quantitative patterns of gene network dynamics. Using the method of generalized threshold models, models are constructed for the Arabidopsis thalianaflower morphogenesis control subsystem and gene subnetwork controlling the Drosophila melanogasterearly ontogeny. The dynamics of these systems are investigated: kinetic curves are computed for molecular components (RNA, proteins), possible modes of functioning and steady states of the nets are revealed and biologically interpreted. The models are shown to be adequate to the real processes. The effectiveness of the generalized threshold model method is evaluated in the analysis of the actual eukaryotic gene networks.     

Stochastic effects on endemic infection levels of disseminating versus local contacts

The effects of two levels of mixing on endemic infection levels are shown to differ for identically conformed deterministic compartmental (DC) and stochastic compartmental (SC) models. Both DC and SC models give similar endemic levels when populations are large, immunity is short lived, and mixing is universal. But local transmissions and/or transient immunity decrease overall population infection levels in SC but not in DC models. DC models also fail to detect the greater effects of eliminating disseminating transmissions in comparison to eliminating local transmissions shown by SC models. These differences in model behavior arise because localities that encounter few infections from distant sites and that have stochastically low infection levels have decreased infection rates while localities with stochastically high levels of infection do not decrease the rate at which they lose infection. At the extreme this generates local stochastic die out with subsequent build up of susceptibility in SC but not DC models. This phenomenon should act upon all endemic infections that have changing geographic or social foci of infection. Neither standard epidemiological investigations nor sufficient-component cause models can capture these effects because they occur in the absence of differences between individuals.     

Research Needs for Understanding and Predicting the Behavior of Managed Ecosystems: Lessons from the Study of Agroecosystems

Managed ecosystems are complex, dynamic systems with spatially varying inputs and outputs that are the result of interrelated physical, biological, and human decision-making processes. To gain an adequate understanding of these systems and predict their behavior, we believe that it is necessary to move beyond stylized theoretical models and loosely coupled disciplinary simulation models to what we describe as “fully integrated models.” Herein we present a conceptual framework for a more integrated approach to the study of managed ecosystems using the example of agricultural ecosystems. We then propose the implementation of a research agenda that fosters coordinated disciplinary research aimed at a better understanding and quantification of linkages across disciplinary models. Key research issues include the effects of spatial scale, the assessment of uncertainty in coupled models, and methods for collecting and analyzing spatially referenced data. Received 6 October 2000; accepted 10 April 2001.