New understandings of thermostable and peizostable enzymes

Recent large-scale studies illustrate the importance of electrostatic interactions near the surface of proteins as a major factor in enhancing thermal stability. Mutagenesis studies have also demonstrated the importance of optimized charge interactions on the surface of the protein, which can significantly augment enzyme thermal stability. Directed evolution studies show that increased stability may be obtained by different routes, which may not mimic those used by nature. Despite observations that some of the most thermotolerant organisms grow under conditions of high pressure, little effort has been made to understand the correlation between pressure and temperature stability. One recent study demonstrates that the active-site volume may be important in increasing pressure stability.     

Organisms as Functional Machines: A Connectivity Explanation

Living organisms exist as a complex set of levels of organizationarranged in a pattern of strong ordering with none of theselevels being more important than others for a full understandingof life. Central to biological strong ordering is the organismallevel. Individual organisms are of special interest to biologistsbecause they are relevant to all biological processes regardlessof the operational level of the process. This is especiallytrue for investigations of the morphological-physiological propertiesof organisms. For such studies, living organisms must be consideredas complex machines with all of the sophisticated integrationand multifarious interactions of component parts typical ofcomplex systems. Understanding of the properties of any individualfeature in an organism depends as much, or possibly even more,on an appreciation of its connections and interactions withother features of that organism than on an understanding ofits intrinsic attributes. Learning the connectivity skills,including the modes of thinking, needed to comprehend the integrationof diverse components of any complex system requires a differenttraining than that needed to determine the detailed attributesof individual parts; both are necessary, however, to achieveproper advances in biological knowledge. Case studies of severalvertebrate features will be used to illustrate types of interactionswhich exist between structural/functional attributes, and howtheir recognition can lead to new and interesting questions.This "feeling for the organism" may be the major factor separatingthose biologists who are able to make important discoveriesfrom those who will only provide the subsequent, less excitingdetails of normal science.     

Molecular mechanisms of epistasis within and between genes

'Disease-causing' mutations do not cause disease in all individuals. One possible important reason for this is that the outcome of a mutation can depend upon other genetic variants in a genome. These epistatic interactions between mutations occur both within and between molecules, and studies in model organisms show that they are extremely prevalent. However, epistatic interactions are still poorly understood at the molecular level, and consequently difficult to predict de novo. Here I provide an overview of our current understanding of the molecular mechanisms that can cause epistasis, and areas where more research is needed. A more complete understanding of epistasis will be vital for making accurate predictions about the phenotypes of individuals.     

Plant metabolomics for plant chemical responses to belowground community change by climate change

General circulation models on global climate change predict increase in surface air temperature and changes in precipitation. Increases in air temperature (thus soil temperature) and altered precipitation are known to affect the species composition and function of soil microbial communities. Plant roots interact with diverse soil organisms such as bacteria, protozoa, fungi, nematodes, annelids and insects. Soil organisms show diverse interactions with plants (eg. competition, mutualism and parasitism) that may alter plant metabolism. Besides plant roots, various soil microbes such as bacteria and fungi can produce volatile organic compounds (VOCs), which can serve as infochemicals among soil organisms and plant roots. While the effects of climate change are likely to alter both soil communities and plant metabolism, it is equally probable that these changes will have cascading consequnces for grazers and subsequent food web components aboveground. Advances in plant metabolomics have made it possibile to track changes in plant metabolomes as they respond to biotic and abiotic environmental changes. Recent developments in analytical instrumentation and bioinformatics software have established metabolomics as an important research tool for studying ecological interactions between plants and other organisms. In this review, we will first summarize recent progress in plant metabolomics methodology and subsequently review recent studies of interactions between plants and soil organisms in relation to climate change issues.     

Resource selection by tropical frugivorous birds: integrating multiple interactions

Summary Resource selection is a function of interactions of organisms (competition, predation) as well as characteristics of the resource and organisms. I provide a quantitative model that integrates these factors. I use the model to predict profitability of fruits to tropical birds, but the model and its predictions are applicable to a wider array of systems and organisms. Profitability of a fruit is determined by rewards provided by the pericarp (mass and caloric yields) relative to costs (metabolic requirements, handling time, search time, behavioral interference, predator avoidance) associated with finding and eating that fruit (Fig. 1). Fruits increase in profitability with increases in fruit size until increases in handling time offset increases in pericarp mass. The fruit size at which increases in handling time offset increases in pericarp mass varies among bird species due to differences in bill and body size. Decreases in feeding rate due to decreasing numbers of fruits and increasing search time causes reduced profitability and this effect becomes more severe with decreasing fruit size and/or increasing frugivore size. Consequently, as fruit size decreases relative to frugivore size, fruit abundance becomes increasingly important to fruit selection by frugivores. However, while profitability of resources is a function of characteristics of the resources and the organisms, biological interactions can change profitability rankings; resources that may be more profitable in the absence of behavioral interference, exploitation competition, or predation risk can become less profitable in the face of these interactions. The proposed model integrates these interactions to provide predictions of resource selection and these predictions are supported by published studies.     

Environmental metabolomics: a critical review and future perspectives

Environmental metabolomics is the application of metabolomics to characterise the interactions of organisms with their environment. This approach has many advantages for studying organism–environment interactions and for assessing organism function and health at the molecular level. As such, metabolomics is finding an increasing number of applications in the environmental sciences, ranging from understanding organismal responses to abiotic pressures, to investigating the responses of organisms to other biota. These interactions can be studied from individuals to populations, which can be related to the traditional fields of ecophysiology and ecology, and from instantaneous effects to those over evolutionary time scales, the latter enabling studies of genetic adaptation. This review provides a comprehensive and current overview of environmental metabolomics research. We begin with an overview of metabolomic studies into the effects of abiotic pressures on organisms. In the field of ecophysiology, studies on the metabolic responses to temperature, water, food availability, light and circadian rhythms, atmospheric gases and season are reviewed. A section on ecotoxicogenomics discusses research in aquatic and terrestrial ecotoxicology, assessing organismal responses to anthropogenic pollutants in both the laboratory and field. We then discuss environmental metabolomic studies of diseases and biotic–biotic interactions, in particular herbivory. Finally, we critically evaluate the contribution that metabolomics has made to the environmental sciences, and highlight and discuss recommendations to advance our understanding of the environment, ecology and evolution using a metabolomics approach.     

Principles from community and metapopulation ecology: application to fungal entomopathogens

Fungal entomopathogens are often studied within the context of their use for biological control, yet these natural enemies are also excellent subjects for studies of ecological interactions. Here, we present selected principles from community ecology and discuss these in relation to fungal entomopathogens. We discuss the relevance of apparent competition, food web construction, intraguild predation and density-mediated and trait-mediated indirect effects. Although current knowledge of community interactions involving fungal entomopathogens are limited, fungal entomopathogens can be important, interactive members of communities and the activities of fungal entomopathogens should be evaluated in the context of ecological principles. We also discuss aspects of metapopulation ecology and the application of these principles to fungal entomopathogens. Knowledge of ecological interactions is crucial if we are to understand and predict the effects of fungal entomopathogens on host populations and understand the interactions among fungal entomopathogens and other organisms in the communities in which they occur.     

Chlamydia persistence -- a tool to dissect chlamydia--host interactions

Under stress, chlamydiae can enter a non-infectious but viable state termed persistence. In the absence of a tractable genetic system, persistence induction provides an important experimental tool with which to study these fascinating organisms. This review will discuss examples of: i) persistence studies that have illuminated critical chlamydiae/host interactions; and ii) novel persistence models that will do so in the future.     

How do belowground organisms influence plant-pollinator interactions?

Aims The majority of angiosperms are pollinated by animals, and this interaction is of enormous importance in both agricultural and natural systems. Pollinator behavior is influenced by plants' floral traits, and these traits may be modified by interactions with other community members. In recent years, knowledge of ecological linkages between above- and belowground organisms has grown tremendously. Soil communities are extremely diverse, and when their interactions with plants influence floral characteristics, they have the potential to alter pollinator attraction and visitation, but plant–pollinator interactions have been neglected in studies of the direct and indirect effects of soil organism–root interactions. Here, we review these belowground interactions, focusing on the effects of nitrogen-fixing bacteria, arbuscular mycorrhizal fungi and root-feeding herbivores, and their effects on floral traits and pollinators. Further, we identify gaps in our knowledge of these indirect effects and recommend promising directions and topics that should be addressed by future research.Important findings Belowground organisms can influence a wide variety of floral traits that are important mediators of pollinator attraction, including the number and size of flowers and nectar and pollen production. Other traits that are known to influence pollinators in some plant species, such as floral volatiles, color and nectar composition, have rarely or never been examined in the context of belowground plant interactions. Despite clear effects on flowers, relatively few studies have measured pollinator responses to belowground interactions. When these indirect effects have been studied, both arbuscular mycorrhizal fungi and root herbivores were found to shift pollinator visitation patterns. Depending on the interaction, these changes may either increase or decrease pollinator attraction. Finally, we discuss future directions for ecological studies that will more fully integrate belowground ecology with pollination biology. We advocate a multilevel approach to these questions to not only document indirect effect pathways between soil interactions and pollination but also identify the mechanisms driving changes in pollinator impacts and the resultant effects on plant fitness. A more thorough understanding of these indirect interactions will advance ecological theory and may inform management strategies in agriculture and conservation biology.     

Predator shadows: complex life histories as generators of spatially patterned indirect interactions across ecosystems

Ecological coupling by material exchanges or dispersal between spatially distinct communities has important impacts on ecological processes, such as diversity–stability relationships, ecosystem function, and food web dynamics. One important mode of coupling between ecosystems occurs via organisms with complex life histories, which often switch between distinct ecosystems during their life cycle, and so can be channels of material exchanges between these ecosystems. Some organisms with complex life histories (e.g. frogs, dragonflies) can be abundant and effective predators during one or more life stages, and so provide conduits for strong direct and indirect interactions across ecosystem boundaries, linking the dynamics of discrete and often quite dissimilar community types. We present simple models and a case study (tailored to pond ecosystems), to explore how interactions within larval habitats can indirectly impact ecological interactions in adult habitats. Using our case study as a springboard, we propose that cohorts of predators emerging from natal habitats (e.g. ponds) cast 'predation shadows' on the surrounding adult (e.g. terrestrial) landscape. Trophic interactions within ponds, and the distribution of ponds on the landscape, can thus affect the spatial pattern in the strength of these predation shadows, creating strong spatial patterning in terrestrial trophic cascades. Our findings emphasize the importance of organisms with complex life histories as generators of strong links across ecosystem boundaries, and as potential sources of spatial variation in the strength and indirect impacts of interspecific interactions.     

To charge or not to charge?

The ability to engineer proteins with increased thermostability will profoundly broaden their practical applications. Recent experimental results show that optimization of charge-charge interactions on the surface of proteins can be a useful strategy in the design of thermostable enzymes. Results also indicate a possibility that such optimized interactions provide structural determinants for enhanced stability of proteins from thermophilic organisms. In this article, the general strategy for design of thermostable proteins and perspectives for future studies are discussed.     

Interactions between mycorrhizal fungi and other soil organisms

Mycorrhizal fungi interact with a wide range of other soil organisms, in the root, in the rhizosphere and in the bulk soil. These interactions may be inhibitory or stimulatory; some are clearly competitive, others may be mutualistic. Effects can be seen at all stages of the mycorrhizal fungal life-cycle, from spore population dynamics (predation, dispersal and germination) through root colonization to external hyphal growth. Two areas that seem likely to be of particular importance to the functioning of the symbiosis are the role of bacteria in promoting mycorrhiza formation and of soil animals in grazing the external mycelium. Mycorrhizal fungi also modify the interactions of plants with other soil organisms, both pathogens, such as root-inhabiting nematodes and fungi, and mutualists, notably nitrogen-fixing bacteria. These interactions are probably important both in natural ecosystems, where pathogens are increasingly recognized as playing controlling roles, and in agricultural systems, where mycorrhizas may be valuable in designing integrated systems of pest control and growth stimulation.     

Complex interactions among a nematode parasite (Daubaylia potomaca), a commensalistic annelid (Chaetogaster limnaei limnaei), and trematode parasites in a snail host (Helisoma anceps)

Many biotic interactions can affect the prevalence and intensity of parasite infections in aquatic snails. Historically, these studies have centered on interactions between trematode parasites or between trematodes and other organisms. The present investigation focuses on the nematode parasite Daubaylia potomaca and its interactions with a commensal, Chaetogaster limnaei limnaei , and a variety of trematode species. It was found that the presence of C. l. limnaei indirectly increased the mean intensity of D. potomaca infections, apparently by acting as a restraint for various trematode parasites, particularly the rediae of Echinostoma sp. In turn, Echinostoma sp. rediae adversely affected the mean intensity of D. potomaca by their consumption of both juvenile and adult nematodes present in tissues of the snail. These organisms not only belong to 3 different phyla but occupy distinct trophic levels as well. The complex interactions among these 3 organisms in the snail host provide an excellent example of biotic interactions influencing the infection dynamics of parasites in aquatic snails.     

Characterizing Cell–Cell Interactions Induced Spatial Organization of Cell Phenotypes: Application to Density-Dependent Protein Nucleocytoplasmic Distribution

Cell–cell interactions play an important role in spatial organization (pattern formation) during the development of multicellular organisms. An understanding of these biological roles requires identifying cell phenotypes that are regulated by cell–cell interactions and characterizing the spatial organizations of the phenotypes. However, conventional methods for assaying cell–cell interactions are mainly applicable at a cell population level. These measures are incapable of elucidating the spatial organizations of the phenotypes, resulting in an incomplete view of cell–cell interactions. To overcome this issue, we developed an automated image-based method to investigate cell–cell interactions based on spatial localizations of cells. We demonstrated this method in cultured cells using cell density-dependent nucleocytoplasmic distribution of β-catenin and aryl hydrocarbon receptor as the phenotype. This novel method was validated by comparing with a conventional population-based method, and proved to be more sensitive and reliable. The application of the method characterized how the phenotypes were spatially organized in a population of cultured cells. We further showed that the spatial organization was governed by cell density and was protein-specific. This automated method is very simple, and will be applicable to study cell–cell interactions in different systems from prokaryotic colonies to multicellular organisms. We envision that the ability to extract and interpret how cell–cell interactions determine the spatial organization of a cell phenotype will provide new insights into biology that may be missed by traditional population-averaged studies.     

Protein-protein interaction networks: from interactions to networks

The goal of interaction proteomics that studies the protein-protein interactions of all expressed proteins is to understand biological processes that are strictly regulated by these interactions. The availability of entire genome sequences of many organisms and high-throughput analysis tools has led scientists to study the entire proteome (Pandey and Mann, 2000). There are various high-throughput methods for detecting protein interactions such as yeast two-hybrid approach and mass spectrometry to produce vast amounts of data that can be utilized to decipher protein functions in complicated biological networks. In this review, we discuss recent developments in analytical methods for large-scale protein interactions and the future direction of interaction proteomics.     

Integrating theory into disturbance interaction experiments to better inform ecosystem management

Managing multiple, interacting disturbances is a key challenge to biodiversity conservation, and one that will only increase as global change drivers continue to alter disturbance regimes. Theoretical studies have highlighted the importance of a mechanistic understanding of stressor interactions for improving the prediction and management of interactive effects. However, many conservation studies are not designed or interpreted in the context of theory and instead focus on case‐specific management questions. This is a problem as it means that few studies test the relationships highlighted in theoretical models as being important for ecological management. We explore the extent of this problem among studies of interacting disturbances by reviewing recent experimental studies of the interaction between fire and grazing in terrestrial ecosystems. Interactions between fire and grazing can occur via a number of pathways; one disturbance can modify the other's likelihood, intensity or spatial distribution, or one disturbance can alter the other's impacts on individual organisms. The strength of such interactions will vary depending on disturbance attributes (e.g. size or intensity), and this variation is likely to be nonlinear. We show that few experiments testing fire–grazing interactions are able to identify the mechanistic pathway driving an observed interaction, and most are unable to detect nonlinear effects. We demonstrate how these limitations compromise the ability of experimental studies to effectively inform ecological management. We propose a series of adjustments to the design of disturbance interaction experiments that would enable tests of key theoretical pathways and provide the deeper ecological understanding necessary for effective management. Such considerations are relevant to studies of a broad range of ecological interactions and are critical to informing the management of disturbance regimes in the context of accelerating global change.     

Uncovering the holes and cracks: from anecdote to testable hypotheses in predation studies

Biological interactions between organisms have long been believed to be very important in structuring communities and, when scaled up over geological time, in the evolution of organisms. Investigations of palaeontological evidence for predator–prey interactions have been popular pursuits, and a number of attractive hypotheses have been proposed which link increased predation pressure with a wide range of morphological and ecological changes which are apparent over the course of the Phanerozoic. In particular studies of fossil drill holes and repair scars in shelly prey have been common targets for research. However, the nature of some of our data has been rather anecdotal and restricted in range. Perhaps we should be more concerned that we are not picking up the true range of natural variability. This paper aims to highlight the sources of variability in our data and, going forward, to urge the collection of quantitative data from many more samples and (palaeo)environmental settings in order that we might properly be able to separate the intrinsic natural variability in our data from robust temporal or spatial trends.     

The importance of fungi in shaping the paleoecosystem

Although fungi have a long geologic history, many aspects regarding their origins and subsequent evolution remain impossible to document from the fossil record. As heterotrophs, fungi must interact with other organisms, and it is here that the fossil record can provide an important source of biological and paleoecological information about fungal interactions. Saprophytic, parasitic and biotrophic interactions among fungi and other organisms are ancient; examples of these interrelationships are discussed as they relate to the establishment and evolution of the biological and physical paleoecosystem.     

Wasp predation drives the assembly of fungal and fly communities on frog egg masses

Community ecology aims to understand how species interactions shape species diversity and abundance. Although less studied than predatory or competitive interactions, facilitative interactions can be important in communities associated with ephemeral microhabitats. Successful recruitment from these habitats requires species to rapidly colonize, develop, and disperse during brief periods of habitat suitability. Interactions between organisms, including processing chain interactions whereby initial consumers alter resources in ways that improve their quality for subsequent consumers, could aid these processes. The terrestrial egg masses of red-eyed treefrogs (Agalychnis callidryas) are a resource for predatory wasps (Agelaia spp., Polybia rejecta) and a microhabitat and resource for saprovoric and pathogenic fungi and saprovoric flies (Megaselia spp., Psychoda savaiiensis). We investigate how interactions with wasps might facilitate fly and fungal colonization of and survival on frog egg masses. Our results indicate that wasps facilitate fungal colonization, whereas flies appear not to, and that both wasps and fungi generate frog egg carrion that attracts saprovoric flies to oviposit and increases the survival of fly larvae. While studies of colonization order often focus on inhibition by early colonizers of subsequent arrivals, this study demonstrates how early colonizers can facilitate the establishment of later ones, by modifying resources in ways that promote the location of and survival in habitat patches. This research draws attention to the diversity of interactions that can occur within ephemeral communities and emphasizes the role that positive interactions may play. Processing chain interactions may be a generally important mechanism increasing the diversity of local communities, including very ephemeral ones.