Chlamydomonas: Fast tracking from genomics

Elucidating biological processes has relied on the establishment of model organisms, many of which offer advantageous features such as rapid axenic growth, extensive knowledge of their physiological features and gene content, and the ease with which they can be genetically manipulated. The unicellular green alga Chlamydomonas reinhardtii has been an exemplary model that has enabled many scientific breakthroughs over the decades, especially in the fields of photosynthesis, cilia function and biogenesis, and the acclimation of photosynthetic organisms to their environment. Here, we discuss recent molecular/technological advances that have been applied to C. reinhardtii and how they have further fostered its development as a “flagship” algal system. We also explore the future promise of this alga in leveraging advances in the fields of genomics, proteomics, imaging, and synthetic biology for addressing critical future biological issues.     

Management of ectoparasites with biological control organisms

Biological control is not a new concept, but for many reasons it is gaining interest for control of livestock ectoparasites. These reasons will be discussed, both from a political view and from environmental and economic views. The US government has vowed to reduce pesticide use by the year 2000, but other forces may drive this change even faster. Pesticide costs are high, and efficacy against some pests is questionable. Also, many producers are concerned about the environment, and are anxious to do their part to reduce chemical pollution. Specialised training is required to reduce on-the-farm difficulties involved with the use of biological-control organisms. Otherwise, how do producers or veterinarians purchase and use biocontrol organisms, and how do they critique what has been purchased? Included is a short summary of the three most common ectoparasites of livestock, and the type of biological-control strategies being developed to combat them. Much of the classical work has been done on filth fly control, most likely because of the nuisance status of flies, and because of the availability of candidate beneficial organisms, particularly parasitic wasps. And finally, two fly-control success stories will be briefly described. Tremendous strides have been made in house-fly and stable-fly control with parasitic wasps on feedlots, but more work is needed to better understand the habits of immature fly populations. A predaceous fly is being tested for pest fly control in dairies. Larvae of this fly can kill 15-20 house-fly larvae daily, and the adults do not become pestiferous on farms or around homes. Biological control will be an important part of livestock pest control in the future, but its implementation will require a corps of educated producers who are confident that biological control can work for them.     

New technologies for 21st century plant science

Plants are one of the most fascinating and important groups of organisms living on Earth. They serve as the conduit of energy into the biosphere, provide food, and shape our environment. If we want to make headway in understanding how these essential organisms function and build the foundation for a more sustainable future, then we need to apply the most advanced technologies available to the study of plant life. In 2009, a committee of the National Academy highlighted the "understanding of plant growth" as one of the big challenges for society and part of a new era which they termed "new biology." The aim of this article is to identify how new technologies can and will transform plant science to address the challenges of new biology. We assess where we stand today regarding current technologies, with an emphasis on molecular and imaging technologies, and we try to address questions about where we may go in the future and whether we can get an idea of what is at and beyond the horizon.     

Evolutionary remnants as widely accessible evidence for evolution: the structure of the argument for application to evolution education

Evolution education, in both schools and informal education, often focuses on natural selection and the fit of organisms through natural selection to their environment and way of life. Examples of evidence that evolution has occurred are therefore often limited to a modest number of classic but exotic cases, with little attention to how one might apply principles to more familiar organisms. Many of these classic examples are examples of adaptation; adaptation to local environments is, however, an outcome that could in principle also be explained by supernatural creation or design. A frequent result is the perception among the public is that examples of evolution are rare, and that the existence of well-adapted organisms may just as easily be explained metaphysically. We argue that among categories of evidence of evolution accessible to non-specialists in any environment, the most compelling evidence of common ancestry consists of remnants of evolutionary history evident in homologous features, particularly when those homologies are related to lack of fit of organisms to their way of life (“vestiges”) or to better fit that involves complicated combinations of parts usually assigned other functions (“contrivances”). Darwin emphasized the critical nature of this argument from imperfections, and it has been part of traditional catalogs of “evidence for evolution” for more than a century. Yet while remnants of history are widely used as a category of evidence for evolution, their utility in education of comparative anatomy to document body parts passed on through descent is underemphasized in evolution education at all levels. We explore the use of evolutionary remnants to document common ancestry and evidence for evolution, for application to evolution education.     

How corals made rocks through the ages

Hard, or stony, corals make rocks that can, on geological time scales, lead to the formation of massive reefs in shallow tropical and subtropical seas. In both historical and contemporary oceans, reef‐building corals retain information about the marine environment in their skeletons, which is an organic–inorganic composite material. The elemental and isotopic composition of their skeletons is frequently used to reconstruct the environmental history of Earth's oceans over time, including temperature, pH, and salinity. Interpretation of this information requires knowledge of how the organisms formed their skeletons. The basic mechanism of formation of calcium carbonate skeleton in stony corals has been studied for decades. While some researchers consider coral skeletons as mainly passive recorders of ocean conditions, it has become increasingly clear that biological processes play key roles in the biomineralization mechanism. Understanding the role of the animal in living stony coral biomineralization and how it evolved has profound implications for interpreting environmental signatures in fossil corals to understand past ocean conditions. Here we review historical hypotheses and discuss the present understanding of how corals evolved and how their skeletons changed over geological time. We specifically explain how biological processes, particularly those occurring at the subcellular level, critically control the formation of calcium carbonate structures. We examine the different models that address the current debate including the tissue–skeleton interface, skeletal organic matrix, and biomineralization pathways. Finally, we consider how understanding the biological control of coral biomineralization is critical to informing future models of coral vulnerability to inevitable global change, particularly increasing ocean acidification.     

Genetically modified crops: success, safety assessment, and public concern

With the emergence of transgenic technologies, new ways to improve the agronomic performance of crops for food, feed, and processing applications have been devised. In addition, ability to express foreign genes using transgenic technologies has opened up options for producing large quantities of commercially important industrial or pharmaceutical products in plants. Despite this high adoption rate and future promises, there is a multitude of concerns about the impact of genetically modified (GM) crops on the environment. Potential contamination of the environment and food chains has prompted detailed consideration of how such crops and the molecules that they produce can be effectively isolated and contained. One of the reasonable steps after creating a transgenic plant is to evaluate its potential benefits and risks to the environment and these should be compared to those generated by traditional agricultural practices. The precautionary approach in risk management of GM plants may make it necessary to monitor significant wild and weed populations that might be affected by transgene escape. Effective risk assessment and monitoring mechanisms are the basic prerequisites of any legal framework to adequately address the risks and watch out for new risks. Several agencies in different countries monitor the release of GM organisms or frame guidelines for the appropriate application of recombinant organisms in agro-industries so as to assure the safe use of recombinant organisms and to achieve sound overall development. We feel that it is important to establish an internationally harmonized framework for the safe handling of recombinant DNA organisms within a few years.This is IMTECH Communication No. 038/2005.     

土壤中抗生素的环境风险及污染土壤的生物修复技术

抗生素的广泛使用导致其在环境中普遍存在,所引发的抗性基因问题已对全球公共卫生构成重大威胁。土壤是环境中抗生素的重要汇,抗生素暴露会对土壤生物带来危害,甚至会间接对人体健康造成潜在风险,因此需采取有效手段修复抗生素污染的土壤。文中综述了抗生素对土壤植物表型生长指标、土壤动物生理特征及群落分布、微生物群落组成与功能的影响,以及抗生素抗性基因在土壤生物间的传播风险等;总结了利用耐受土壤植物、动物、微生物以及其互作关系修复抗生素污染土壤的潜力与前景,指出了已有土壤中抗生素环境风险和生物修复研究中尚存在的问题,展望了未来的研究方向。     

Ant biodiversity and its relationship to ecosystem functioning: a review

Ants are important components of ecosystems not only because they constitute a great part of the animal biomass but also because they act as ecosystem engineers. Ant biodiversity is incredibly high and these organisms are highly responsive to human impact, which obviously reduces its richness. However, it is not clear how such disturbance damages the maintenance of ant services to the ecosystem. Ants are important in below ground processes through the alteration of the physical and chemical environment and through their effects on plants, microorganisms, and other soil organisms. This review summarizes the information available on ant biodiversity patterns, how it can be quantified, and how biodiversity is affected by human impacts such as land use change, pollution, invasions, and climate change. The role of ants in ecosystems is discussed, mainly from the perspective of the effects of ground-dwelling ants on soil processes and function, emphasizing their role as ecosystem engineers. Some lines of research are suggested after demonstrating the gaps in our current information on ant-soil interactions.     

Dissecting the Rhizosphere complexity: The truffle-ground study case

The word Rhizosphere describes the part of the soil which is immediately adjacent to and affected by plant roots. This is a very dynamic environment where plants, soil and microorganisms interact. The plant releases, in addition to biologically active substances, nutritive substances (exudates), which create a privileged habitat for many microbial populations. The same microbes that live in the rhizosphere may be useful for the plant. Interest in this fascinating environment has increased over the years. However, our knowledge of the biology and diversity of microbial populations in the rhizosphere is still limited, because it has always been linked to traditional culture-based techniques. These methods, which only allow the study of cultured microorganisms, do not allow the majority of the organisms existing in nature to be characterized. Over the last few years, this limitation has been overcome through the introduction of methodologies that are independent of culture techniques. This different approach, which has revolutionized scientific research, is known as metagenomics. In this review, the rhizosphere environment is considered with particular attention to the fungal and symbiotic organisms, which populate it. The new environmental genomic techniques and how these have been applied to the study of the various environments and the rhizosphere are described. Finally, a specific rhizosphere, a truffle-ground, is described as our study case.      

Lessons from the genomes of bifidobacteria

The gut microbiota is a complex ecosystem composed of hundreds of different bacterial species that altogether play an important role in the physiology of their host. In the past few years the complete genome sequence of a number of bacterial strains isolated from the human gastrointestinal tract has been established including that of Bifidobacterium longum NCC2705 isolated from the feces of a healthy infant. Bifidobacteria are among the first species to colonise the human gastrointestinal tract and as such are believed to play an important role in gut homeostasis and normal development. The genome sequence of NCC2705 has revealed a number of features that suggest how this bacterium has adapted to its environment and that could help understanding how it interacts with its host. Here, we review general features of bifidobacteria and illustrate how genome-based approaches can help us better understand the biology of these organisms.     

Physiological indicators of fitness in benthic invertebrates: a useful measure for ecological health assessment and experimental ecology

Physiological indicators of fitness present a measure of an organism’s response to a changing environment. An analysis of how these organisms allocate and store their energy resources provides an understanding of how they cope with such environmental changes. Each individual has to balance the investment necessary to acquire a certain resource with the energy gained by it. This trade-off can be monitored by measuring several physiological indicators of fitness such as energy storage components, metabolic state or RNA/DNA ratio. Because environmental adaptations and ecological strategies of survival are best examined within the natural environment, our research has to rely on the physiological indicators that are easily accessible in the field. The physiological indicators presented here are significant for an individual’s fitness and in turn lead to reliable values in field-collected samples. Based on our own expertise and on a literature survey, the physiological relevance of the presented indicators is explained. Furthermore, some consideration to the analytical methods used to obtain the physiological indicators is given, and possible errors introduced at the sampling site and during the laboratory procedures are discussed. This work demonstrates that the integration of ecological and physiological expertise facilitates the identification of future ecological problems much earlier than separate approaches of both disciplines alone.     

Recombinant entomopathogenic agents: a review of biotechnological approaches to pest insect control

Although the use of chemical pesticides has decreased in recent years, it is still a common method of pest control. However, chemical use leads to challenging problems. The harm caused by these chemicals and the length of time that they will remain in the environment is of great concern to the future and safety of humans. Therefore, developing new pest control agents that are safer and environmentally compatible, as well as assuring their widespread use is important. Entomopathogenic agents are microorganisms that play an important role in the biological control of pest insects and are eco-friendly alternatives to chemical control. They consist of viruses (non-cellular organisms), bacteria (prokaryotic organisms), fungi and protists (eukaryotic organisms), and nematodes (multicellular organisms). Genetic modification (recombinant technology) provides potential new methods for developing entomopathogens to manage pests. In this review, we focus on the important roles of recombinant entomopathogens in terms of pest insect control, placing them into perspective with other views to discuss, examine and evaluate the use of entomopathogenic agents in biological control.     

滩涂底栖动物有机污染生态学研究进展

底栖动物由于对有机污染物具有较强的吸收能力,再加上其移动能力较差、生活方式比较固定,而被广泛运用于滩涂有机污染的研究.目前这些研究主要集中在如下几个方面：（1）有机污染物在底栖动物体内的分布特征及在底栖食物链中的动力学研究;（2）底栖动物对有机污染物的生理响应研究;（3）污染物对底栖动物群落组成和结构影响研究;（4）底栖动物在滩涂有机污染检测中的应用研究.研究结果表明：滩涂底栖动物对有机污染物的累积具有选择性和季节波动性;有机污染物可以在底栖食物链中传递;底栖动物体内的有机污染物成分和含量可以有效地指示其生存环境的有机污染状况;底栖动物的混合功能氧化酶和抗氧化酶系统对体内有机污染物的累积产生积极的响应;有机污染物对底栖动物的免疫系统造成不利影响,并对遗传物质造成破坏;有机污染对底栖动物的群落组成和结构具有显著的影响.     

Introduction. Integration of ecology and endocrinology in avian reproduction: a new synthesis

Birds are some of the most familiar organisms of global ecosystems. Changes in the visibility and abundance of birds are therefore excellent indicators of population and physiological responses to habitat changes and are a major focus for public concern about detrimental environmental changes. In order to understand how birds respond to these challenges, it is essential to determine how the environment affects reproduction under natural conditions. The continuum from environmental variables (cues) to reproductive life-history traits depends upon a cascade of neural and physiological processes that determine the extent and rate at which birds will be able to adapt to changes in their environment. For a full understanding of this ability to adapt, ecologists and endocrinologists need to collaborate and build a common framework. The objective of this theme issue is to bring together a series of papers addressing how evolutionary ecologists and endocrinologists can collaborate directly using avian reproduction as a model system. First, we address the need to integrate ecology and endocrinology and what benefits to biological knowledge will be gained. The papers collected in this issue represent a new synthesis of ecology and endocrinology as discussed in three E-BIRD workshops. The three main foci are trade-offs and constraints, maternal effects and individual variation. Authors within each group present ecological and endocrinological aspects of their topics and many go on to outline testable hypotheses. Finally, we discuss where the major problems remain and how this issue points out where these need collaborative efforts of ecologists and endocrinologists. Specific challenges are raised to future researchers to break through intellectual barriers and explore new frontiers. This framework of topics will ultimately apply to all taxa because the principles involved are universal and hopefully will have direct application to programmes integrating organisms and genes throughout biological sciences.     

The evolutionary ecology of individual phenotypic plasticity in wild populations

The ability of individual organisms to alter morphological and life-history traits in response to the conditions they experience is an example of phenotypic plasticity which is fundamental to any population's ability to deal with short-term environmental change. We currently know little about the prevalence, and evolutionary and ecological causes and consequences of variation in life history plasticity in the wild. Here we outline an analytical framework, utilizing the reaction norm concept and random regression statistical models, to assess the between-individual variation in life history plasticity that may underlie population level responses to the environment at both phenotypic and genetic levels. We discuss applications of this framework to date in wild vertebrate populations, and illustrate how natural selection and ecological constraint may alter a population's response to the environment through their effects at the individual level. Finally, we present future directions and challenges for research into individual plasticity.     

Genomics of natural history collections for understanding evolution in the wild

A long‐standing question in biology is how organisms change through time and space in response to their environment. This knowledge is of particular relevance to predicting how organisms might respond to future environmental changes caused by human‐induced global change. Usually researchers make inferences about past events based on an understanding of current static genetic patterns, but these are limited in their capacity to inform on underlying past processes. Natural history collections (NHCs) represent a unique and critical source of information to provide temporally deep and spatially broad time‐series of samples. By using NHC samples, researchers can directly observe genetic changes over time and space and link those changes with specific ecological/evolutionary events. Until recently, such genetic studies were hindered by the intrinsic challenges of NHC samples (i.e. low yield of highly fragmented DNA). However, recent methodological and technological developments have revolutionized the possibilities in the novel field of NHC genomics. In this Special Feature, we compile a range of studies spanning from methodological aspects to particular case studies which demonstrate the enormous potential of NHC samples for accessing large genomic data sets from the past to advance our knowledge on how populations and species respond to global change at multiple spatial–temporal scales. We also highlight possible limitations, recommendations and a few opportunities for future researchers aiming to study NHC genomics.     

The impairment argument for the immorality of abortion revisited

Eric Vogelstein has defended Don Marquis' ‘future-like-ours' argument for the immorality of abortion against what is known as the Identity Objection, which contends that for a fetus to have a future like ours, it must be numerically identical to an entity like us that possesses valuable experiences some time in the future. On psychological accounts of personal identity, there is no identity relationship between the fetus and the entity with valuable experiences that it will become. Vogelstein maintains that a non-sentient fetus nonetheless has a future like ours because it is numerically identical with a future organism that has a mind that bears valuable experiences. Skott Brill, drawing on Jeff McMahan's embodied mind account, denies that human organisms directly have experiences, claiming that they only have experiences derivatively by virtue of their thinking part, and the loss of a future like ours is not transferred to the organism. I show that on McMahan's account, a strong case can be made for the organism having experiences directly, and the subject having these experiences derivatively. This negates Brill's reasoning, although it does imply that non-sentient fetuses do not have a future like ours in quite the same way as we do. I conclude that this is not problematic for Marquis' argument.     

The neuroecology of chemical defenses

Chemicals are a frequent means whereby organisms defend themselves against predators, competitors, parasites, microbes, and other potentially harmful organisms. Much progress has been made in understanding how a phylogenetic diversity of organisms living in a variety of environments uses chemical defenses. Chief among these advances is determining the molecular identity of defensive chemicals and the roles they play in shaping interactions between individuals. Some progress has been made in deciphering the molecular, cellular, and systems level mechanisms underlying these interactions, as well as how these interactions can lead to structuring of communities and even ecosystems. The neuroecological approach unifies practices and principles from these diverse disciplines and at all scales as it attempts to explain in a single conceptual framework the abundances of organisms and the distributions of species within natural habitats. This article explores the neuroecology of chemical defenses with a focus on aquatic organisms and environments. We review the concept of molecules of keystone significance, including examples of how saxitoxin and tetrodotoxin can shape the organization and dynamics of marine and riparian communities, respectively. We also describe the current status and future directions of a topic of interest to our research group-the use of ink by marine molluscs, especially sea hares, in their defense. We describe a diversity of molecules and mechanisms mediating the protective effects of sea hares' ink, including use as chemical defenses against predators and as alarm cues toward conspecifics, and postulate that some defensive molecules may function as molecules of keystone significance. Finally, we propose future directions for studying the neuroecology of the chemical defenses of sea hares and their molluscan relatives, the cephalopods.