Cross–Scale Interactions and Changing Pattern–Process Relationships: Consequences for System Dynamics

Cross–scale interactions refer to processes at one spatial or temporal scale interacting with processes at another scale to result in nonlinear dynamics with thresholds. These interactions change the pattern–process relationships across scales such that fine-scale processes can influence a broad spatial extent or a long time period, or broad-scale drivers can interact with fine-scale processes to determine system dynamics. Cross–scale interactions are increasing recognized as having important influences on ecosystem processes, yet they pose formidable challenges for understanding and forecasting ecosystem dynamics. In this introduction to the special feature, “Cross–scale interactions and pattern–process relationships”, we provide a synthetic framework for understanding the causes and consequences of cross–scale interactions. Our framework focuses on the importance of transfer processes and spatial heterogeneity at intermediate scales in linking fine- and broad-scale patterns and processes. Transfer processes and spatial heterogeneity can either amplify or attenuate system response to broad-scale drivers. Providing a framework to explain cross–scale interactions is an important step in improving our understanding and ability to predict the impacts of propagating events and to ameliorate these impacts through proactive measures.     

Ecosystem dynamics based on plankton functional types for global ocean biogeochemistry models

Ecosystem processes are important determinants of the biogeochemistry of the ocean, and they can be profoundly affected by changes in climate. Ocean models currently express ecosystem processes through empirically derived parameterizations that tightly link key geochemical tracers to ocean physics. The explicit inclusion of ecosystem processes in models will permit ecological changes to be taken into account, and will allow us to address several important questions, including the causes of observed glacial–interglacial changes in atmospheric trace gases and aerosols, and how the oceanic uptake of CO₂ is likely to change in the future. There is an urgent need to assess our mechanistic understanding of the environmental factors that exert control over marine ecosystems, and to represent their natural complexity based on theoretical understanding. We present a prototype design for a Dynamic Green Ocean Model (DGOM) based on the identification of (a) key plankton functional types that need to be simulated explicitly to capture important biogeochemical processes in the ocean; (b) key processes controlling the growth and mortality of these functional types and hence their interactions; and (c) sources of information necessary to parameterize each of these processes within a modeling framework. We also develop a strategy for model evaluation, based on simulation of both past and present mean state and variability, and identify potential sources of validation data for each. Finally, we present a DGOM-based strategy for addressing key questions in ocean biogeochemistry. This paper thus presents ongoing work in ocean biogeochemical modeling, which, it is hoped will motivate international collaborations to improve our understanding of the role of the ocean in the climate system.     

Integrin and Growth Factor Receptor Alliance in Angiogenesis

A sequence of events in vascular and stromal cells maintained in a highly coordinated manner regulates angiogenesis and tissue remodeling. These processes are mediated by the ability of cells to respond to environmental cues and activate surface integrins. Physiological and pathological processes in vascular biology are dependent on the specificity of important signaling mechanisms that are activated through the association between growth factors, their receptors, integrins, and their specific extracellular matrix ligands. A large body of evidence from in vitro and in vivo models demonstrates the importance of coordination of signals from the extracellular environment that activates specific tyrosine kinase receptors and integrins in order to regulate angiogenic processes in vivo. In addition to complex formation between growth factor receptors and integrins, growth factors and cytokines also directly interact with integrins, depending upon their concentration levels in the environment, and differentially regulate integrin-related processes. Recent studies from a number of laboratories including ours have provided important novel insights into the involvement of many signaling events that improve our existing knowledge on the cross-talk between growth factor receptors and integrins in the regulation of angiogenesis. In this review, our focus will be on updating the recent developments in the field of integrin-growth factor receptor associations and their implications in the vascular processes.     

Historical foundations and future directions in macrosystems ecology

Macrosystems ecology is an effort to understand ecological processes and interactions at the broadest spatial scales and has potential to help solve globally important social and ecological challenges. It is important to understand the intellectual legacies underpinning macrosystems ecology: How the subdiscipline fits within, builds upon, differs from and extends previous theories. We trace the rise of macrosystems ecology with respect to preceding theories and present a new hypothesis that integrates the multiple components of macrosystems theory. The spatio‐temporal anthropogenic rescaling (STAR) hypothesis suggests that human activities are altering the scales of ecological processes, resulting in interactions at novel space–time scale combinations that are diverse and predictable. We articulate four predictions about how human actions are “expanding”, “shrinking”, “speeding up” and “slowing down” ecological processes and interactions, and thereby generating new scaling relationships for ecological patterns and processes. We provide examples of these rescaling processes and describe ecological consequences across terrestrial, freshwater and marine ecosystems. Rescaling depends in part on characteristics including connectivity, stability and heterogeneity. Our STAR hypothesis challenges traditional assumptions about how the spatial and temporal scales of processes and interactions operate in different types of ecosystems and provides a lens through which to understand macrosystem‐scale environmental change.     

Emergent and effective properties in ecology and evolution

Emergent properties are often discussed in arguments concerning relationships among different levels. However, the different definitions of emergent properties sometimes confuse the arguments about macro-level phenomena, since some authors regard emergent properties not only as observable global patterns but as properties that affect and cause change in ecological and evolutionary processes. Thus it is important to distinguish higher-level or larger-scale properties that can influence particular ecological and evolutionary processes from those that cannot. I call the former properties effective properties. I gave examples that show why the distinctions between effective and non-effective properties are important.

     

湿地氮素传输过程研究进展

综述了湿地氮素传输过程的研究进展。湿地氮素传输过程包括物理过程、化学过程和生物过程 ,与土壤、植物的发生、发育紧密联系在一起 ,并形成了空气 -水 -土 -生命系统中物质循环和能量流动的复杂网络。湿地硝态氮的淋失直接威胁着湿地地下水水质安全 ,N2 O源汇转变受土壤和水体等环境因子的制约 ,氨挥发则与水体 p H值密切相关排放。湿地氮素的化学转化过程是矿质养分供给和 N2 O产生的主要机制 ,受环境因子和人类活动干扰的影响 ;动力学模型可用于描述氮素的化学转化过程。湿地植物的吸收和累积以及微生物的分解过程是湿地氮素循环的重要环节。最后分析了当前国内外研究中存在的不足 ,并对未来研究的重点领域进行了展望     

Patterns and Processes of Microbial Community Assembly

SUMMARY

Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and often confusing terminology as well as unnecessarily polarizing debates. Thus, we review recent literature on microbial community assembly, using the framework of Vellend (Q. Rev. Biol. 85:183–206, 2010) in an effort to synthesize and unify these contributions. We begin by discussing patterns in microbial biogeography and then describe four basic processes (diversification, dispersal, selection, and drift) that contribute to community assembly. We also discuss different combinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generate hypotheses describing how these differences may be important for community assembly. We end by discussing the implications of microbial assembly processes for ecosystem function and biodiversity.     

“Third‐wave” cognitive and behavioral therapies and the emergence of a process‐based approach to intervention in psychiatry

For decades, cognitive and behavioral therapies (CBTs) have been tested in randomized controlled trials for specific psychiatric syndromes that were assumed to represent expressions of latent diseases. Although these protocols were more effective as compared to psychological control conditions, placebo treatments, and even active pharmacotherapies, further advancement in efficacy and dissemination has been inhibited by a failure to focus on processes of change. This picture appears now to be evolving, due both to a collapse of the idea that mental disorders can be classified into distinct, discrete categories, and to the more central attention given to processes of change in newer, so‐called “third‐wave” CBTs. Here we review the context for this historic progress and evaluate the impact of these newer methods and models, not as protocols for treating syndromes, but as ways of targeting an expanded range of processes of change. Five key features of “third‐wave” therapies are underlined: a focus on context and function; the view that new models and methods should build on other strands of CBT; a focus on broad and flexible repertoires vs. an approach to signs and symptoms; applying processes to the clinician, not just the client; and expanding into more complex issues historically more characteristic of humanistic, existential, analytic, or system‐oriented approaches. We argue that these newer methods can be considered in the context of an idiographic approach to process‐based functional analysis. Psychological processes of change can be organized into six dimensions: cognition, affect, attention, self, motivation and overt behavior. Several important processes of change combine two or more of these dimensions. Tailoring intervention strategies to target the appropriate processes in a given individual would be a major advance in psychiatry and an important step toward precision mental health care.     

Immunolocalisation of P2Y receptors in the rat eye

Nucleotides present an important role in ocular physiology which has been demonstrated by recent works that indicate their involvement in many ocular processes. P2Y are important among P2 receptors since they can control tear production, corneal wound healing, aqueous humour dynamics and retinal physiology. Commercial antibodies have allowed us to investigate the distribution of P2Y receptors in the cornea, anterior and posterior chamber of the eye and retina. The P2Y₁ receptor was present mainly in cornea, ciliary processes, and trabecular meshwork. The P2Y₂ receptors were present in cornea, ciliary processes and retinal pigmented epithelium. P2Y₄ was present in cornea, ciliary processes, photoreceptors, outer plexiform layer and ganglion cell layer. The P2Y₆ presented almost an identical distribution as the P2Y₄ receptor. The P2Y₁₁ was also detectable in the retinal pigmented epithelium. The detailed distribution of the receptors clearly supports the recent findings indicating the relevant role of nucleotides in the ocular function.     

Proteome characterization of Paracoccidioides lutzii conidia by using nanoUPLC-MSE

Fungi of the genus Paracoccidioides are the etiological agents of Paracoccidioidomycosis (PCM), the most prevalent mycosis in Latin America. Paracoccidioidomycosis infection is acquired by inhalation of Paracoccidioides conidia, which have first contact with the lungs and can subsequently spread to other organs/tissues. Until now, there have been no proteomic studies focusing on this infectious particle of Paracoccidioides. In order to identify the Paracoccidioides lutzii conidia proteome, conidia were produced and purified. Proteins were characterized by use of the nanoUPLC-MS^E approach. The strategy allowed us to identify a total of 242 proteins in P. lutzii conidia. In the conidia proteome, proteins were classified in functional categories such as protein synthesis, energy production, metabolism, cellular defense/virulence processes, as well as other processes that can be important for conidia survival. Through this analysis, a pool of ribosomal proteins was identified, which may be important for the initial processes of dimorphic transition. In addition, molecules related to energetic and metabolic processes were identified, suggesting a possible basal metabolism during this form of resistance of the fungus. In addition, adhesins and virulence factors were identified in the P. lutzii conidia proteome. Our results demonstrate the potential role that these molecules can play during early cell–host interaction processes, as well as the way in which these molecules are involved in environmental survival during this form of propagation.     

Soil Methane Sink Capacity Response to a Long-Term Wildfire Chronosequence in Northern Sweden

Boreal forests occupy nearly one fifth of the terrestrial land surface and are recognised as globally important regulators of carbon (C) cycling and greenhouse gas emissions. Carbon sequestration processes in these forests include assimilation of CO₂ into biomass and subsequently into soil organic matter, and soil microbial oxidation of methane (CH₄). In this study we explored how ecosystem retrogression, which drives vegetation change, regulates the important process of soil CH₄ oxidation in boreal forests. We measured soil CH₄ oxidation processes on a group of 30 forested islands in northern Sweden differing greatly in fire history, and collectively representing a retrogressive chronosequence, spanning 5000 years. Across these islands the build-up of soil organic matter was observed to increase with time since fire disturbance, with a significant correlation between greater humus depth and increased net soil CH₄ oxidation rates. We suggest that this increase in net CH₄ oxidation rates, in the absence of disturbance, results as deeper humus stores accumulate and provide niches for methanotrophs to thrive. By using this gradient we have discovered important regulatory controls on the stability of soil CH₄ oxidation processes that could not have not been explored through shorter-term experiments. Our findings indicate that in the absence of human interventions such as fire suppression, and with increased wildfire frequency, the globally important boreal CH₄ sink could be diminished.     

Spatial ecology of the steephead parrotfish (Chlorurus microrhinos): an evaluation using acoustic telemetry

Herbivory and other ecosystem processes are widely accepted as important factors in maintaining coral reef resilience. While the spatial scales over which these processes occur have been evaluated, the spatial ecology of individual taxa responsible for shaping these processes is almost entirely unknown. This study combined acoustic telemetry and ecological assessments to evaluate the movement patterns and feeding range of a functionally important coral reef fish, Chlorurus microrhinos (f. Labridae). The diurnal home range and feeding areas of C. microrhinos, on Orpheus Island, Great Barrier Reef, were quantified using active acoustic telemetry. The average diurnal home range of C. microrhinos was 7,830 m² ± 940 (SE). Core areas of activity (50% kernel utilization distributions) were relatively small, encompassing approximately 22% of an individual’s home range (1,690 m² ± 220). Core areas exhibited greater topographic complexity. C. microrhinos may select these areas because of decreased predation risk. Feeding intensities were not homogenous throughout the home range. Core areas were found to have a greater number of feeding scars and are thus exposed to increased bioerosion and algal removal by C. microrhinos. While important in shaping key ecosystem processes, the ecosystem impact of individual C. microrhinos in Pioneer Bay appears to be restricted to small areas within a narrow band along the reef crest.     

A genetic map of Xenopus tropicalis

Posttranslational modifications constitute a major field of emerging biological significance as mounting evidence demonstrates their key role in multiple physiological processes. Following in the footsteps of protein phosphorylation studies, new modifications are being shown to regulate protein properties and functions in vivo. Among such modifications, an important role belongs to protein arginylation — posttranslational tRNA-mediated addition of arginine, to proteins by arginyltransferase, ATE1. Recent studies show that arginylation is essential for embryogenesis in many organisms and that it regulates such important processes as heart development, angiogenesis, and tissue morphogenesis in mammals. This review summarizes the key data in the protein arginylation field since its original discovery to date.     

细菌中钙信号的作用

摘要：越来越多的实验证明二价钙离子（Ca2+）在细菌中有重要调控作用。本文从Ca2+ 信号对细菌生理的影响、细胞内Ca2+ 浓度及测定方法、细菌中Ca2+ 的运输和Ca2+ 结合蛋白四个方面综述了目前细菌中钙信号的研究进展。     

Top-down and bottom-up community regulation in marine rocky intertidal habitats

Strong top-down control by consumers has been demonstrated in rocky intertidal communities around the world. In contrast, the role of bottom-up effects (nutrients and productivity), known to have important influences in terrestrial and particularly freshwater ecosystems, is poorly known in marine hard-bottom communities. Recent studies in South Africa, New England, Oregon and New Zealand suggest that bottom-up processes can have important effects on rocky intertidal community structure. A significant aspect of all of these studies was the incorporation of processes varying on larger spatial scales than previously considered (10’s to 1000’s of km). In all four regions, variation in oceanographic factors (currents, upwelling, nutrients, rates of particle flux) was associated with different magnitudes of algal and/or phytoplankton abundance, availability of particulate food, and rates of recruitment. These processes led to differences in prey abundance and growth, secondary production, consumer growth, and consumer impact on prey resources. Oceanographic conditions therefore may vary on scales that generate ecologically significant variability in populations at the bottom of the food chain, and through upward-flowing food chain effects, lead to variation in top-down trophic effects. I conclude that top-down and bottom-up processes can be important joint determinants of community structure in rocky intertidal habitats, and predict that such effects will occur generally wherever oceanographic ‘discontinuities’ lie adjacent to rocky coastlines. I further argue that increased attention by researchers and of funding agencies to such benthic–pelagic coupling would dramatically enhance our understanding of the dynamics of marine ecosystems.     

Analysis of Thisbe and Pyramus functional domains reveals evidence for cleavage of <Emphasis Type="Italic">Drosophila</Emphasis> FGFs

Background  

As important regulators of developmental and adult processes in metazoans, Fibroblast Growth Factor (FGF) proteins are potent signaling molecules whose activities must be tightly regulated. FGFs are known to play diverse roles in many processes, including mesoderm induction, branching morphogenesis, organ formation, wound healing and malignant transformation; yet much more remains to be learned about the mechanisms of regulation used to control FGF activity.     

Comparison of estimation capabilities of response surface methodology (RSM) with artificial neural network (ANN) in lipase-catalyzed synthesis of palm-based wax ester

Background  

Wax esters are important ingredients in cosmetics, pharmaceuticals, lubricants and other chemical industries due to their excellent wetting property. Since the naturally occurring wax esters are expensive and scarce, these esters can be produced by enzymatic alcoholysis of vegetable oils. In an enzymatic reaction, study on modeling and optimization of the reaction system to increase the efficiency of the process is very important. The classical method of optimization involves varying one parameter at a time that ignores the combined interactions between physicochemical parameters. RSM is one of the most popular techniques used for optimization of chemical and biochemical processes and ANNs are powerful and flexible tools that are well suited to modeling biochemical processes.     

GeneMesh: a web-based microarray analysis tool for relating differentially expressed genes to MeSH terms

Background  

An important objective of DNA microarray-based gene expression experimentation is determining inter-relationships that exist between differentially expressed genes and biological processes, molecular functions, cellular components, signaling pathways, physiologic processes and diseases.     

Genome-Wide Screening of Aluminum Tolerance in <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis>

Genome-wide screening has identified 37 Al-tolerance genes in Saccharomyces cerevisiae. These genes can be roughly categorised into three groups on the basis of function, i.e., genes related to vesicle transport processes, signal transduction pathways, and protein mannosylation. The largest group is composed of genes related to vesicle transport processes; severe Al sensitivity was found in yeast strains lacking these genes. The retrograde transport of endosome-derived vesicles back to the Golgi apparatus is an important factor in determining the Al tolerance of the vesicle transport system. The PKC1-MAPK cascade signalling pathway is important in the Al tolerance of signal transduction. The lack of the gene implicated in this process leads to weakened cell wall architecture, rendering the yeast Al-sensitive. Alternatively, Al might attack the cell wall and/or plasma membrane, and, as signalling is prevented in cells devoid of the genes related to signalling processes, the cells may be unable to alleviate the damage. The genes for protein mannosylation are also associated with Al tolerance, demonstrating the importance of cell wall architecture. These genes are involved in cell integrity processes. An erratum to this article is available at .