From Multiple Voices to a Common Language: Ecosystem Approaches to Human Health as an Emerging Paradigm

The International Forum on Ecosystem Approaches to Human Health, held in Montreal, May 18–23, 2003, was one product of a new paradigm or framework linking health, ecosystems, and sustainable development that emerged in recent decades. This profile aims to provide a backdrop for the contents of this supplementary issue by outlining some of the key principles of the Ecosystem Approaches to Human Health (Ecohealth) framework. It also discusses some of the activities supported by the Ecosystem Approaches to Human Health Program Initiative of the International Development Research Centre (IDRC) to build on the success of the Forum. In doing so, the intention is to frame the 2003 Forum as one in a series of opportunities to reflect and learn from precedents of research and practice from an ecohealth perspective and to foster the development of a community of practice on Ecohealth (COPEH). The profile not only places the contents of the supplement and the Forum within a larger context, but also provides an overview of other IDRC activities that are building capacity for future research and practice, and are strengthening the emerging COPEH.     

Guest Editors' Introduction to the Special Section: Computational Intelligence Approaches in Computational Biology and Bioinformatics

The ten papers in this special section focus on computational intelligence approaches on computational biology and bioinformatics.     

The Development of a Novel High Throughput Computational Tool for Studying Individual and Collective Cellular Migration

Understanding how cells migrate individually and collectively during development and cancer metastasis can be significantly aided by a computation tool to accurately measure not only cellular migration speed, but also migration direction and changes in migration direction in a temporal and spatial manner. We have developed such a tool for cell migration researchers, named Pathfinder, which is capable of simultaneously measuring the migration speed, migration direction, and changes in migration directions of thousands of cells both instantaneously and over long periods of time from fluorescence microscopy data. Additionally, we demonstrate how the Pathfinder software can be used to quantify collective cell migration. The novel capability of the Pathfinder software to measure the changes in migration direction of large populations of cells in a spatiotemporal manner will aid cellular migration research by providing a robust method for determining the mechanisms of cellular guidance during individual and collective cell migration.     

药物重定位的计算分析方法

全新结构药物的研发存在周期长、耗资大、风险高的问题.通过各种技术预测已有药物的新适应症,即药物重定位,可以缩短药物研发时间、降低研发成本和风险.由于疾病种类和已知药物的数量繁多,完全通过实验筛选已知药物的新用途仍然具有很高的成本.随着组学和药物信息学数据的积累,药物重定位进入到了理性设计和实验筛选相结合的阶段,药物重定位的计算预测已经成为计算生物学和系统生物学的重要研究方向.本文将目前药物重定位计算分析的策略归纳为药物-靶标关系分析、药物-药物关系分析和药物-疾病关系分析,对已报道的技术方法及其成功应用实例进行了综述.     

Application of TILLING and EcoTILLING as Reverse Genetic Approaches to Elucidate the Function of Genes in Plants and Animals

With the fairly recent advent of inexpensive, rapid sequencing technologies that continue to improve sequencing efficiency and accuracy, many species of animals, plants, and microbes have annotated genomic information publicly available. The focus on genomics has thus been shifting from the collection of whole sequenced genomes to the study of functional genomics. Reverse genetic approaches have been used for many years to advance from sequence data to the resulting phenotype in an effort to deduce the function of a gene in the species of interest. Many of the currently used approaches (RNAi, gene knockout, site-directed mutagenesis, transposon tagging) rely on the creation of transgenic material, the development of which is not always feasible for many plant or animal species. TILLING is a non-transgenic reverse genetics approach that is applicable to all animal and plant species which can be mutagenized, regardless of its mating / pollinating system, ploidy level, or genome size. This approach requires prior DNA sequence information and takes advantage of a mismatch endonuclease to locate and detect induced mutations. Ultimately, it can provide an allelic series of silent, missense, nonsense, and splice site mutations to examine the effect of various mutations in a gene. TILLING has proven to be a practical, efficient, and an effective approach for functional genomic studies in numerous plant and animal species. EcoTILLING, which is a variant of TILLING, examines natural genetic variation in populations and has been successfully utilized in animals and plants to discover SNPs including rare ones. In this review, TILLING and EcoTILLING techniques, beneficial applications and limitations from plant and animal studies are discussed.Key Words: Reverse genetics, functional genomics, TILLING (target induced local lesions in genomes), EcoTILLING (Ecotype TILLING), sequencing, SNP (single nucleotide polymorphism), genetic stocks.     

Effects of Individual and Group Characteristics on Feeding Behaviors in Wild Leontopithecus rosalia

Studies have linked variation in feeding and foraging success to variation in survival and reproductive success, which makes exploring influences on feeding invaluable. In the current study, we quantified energy contents of foods consumed by wild golden lion tamarins (Leontopithecus rosalia, GLT) and feeding behaviors of 34 GLT from March 1998 to March 1999. Our objective was to test predictions regarding effects of characteristics of the 1) individual, 2) group, 3) environment, and 4) other behaviors on 3 feeding behaviors: feeding on plant matter, searching for prey, and feeding on prey. We hypothesized that environmental characteristics, e.g., resource availability, in addition to group characteristics e.g., group size, would influence feeding on plant matter, because several individuals in a group often consume fruit in the same fruit tree. We hypothesized that environmental characteristics and individual characteristics, e.g., age, would influence searching for and consuming prey because the individual often searches for and consumes prey while it is alone at a substrate. We used SAS mixed models to determine the relative influence of these characteristics on the feeding behaviors. We found that group characteristics more significantly influenced feeding on plant matter, while individual characteristics more significantly influenced searching for prey. The results emphasize the distinctly different influences of individual and group characteristics on feeding. That influences other than competition may affect feeding on plant matter warrants further exploration.     

Individual and Collective Rationality in Pastoral Production: Evidence From Northern Kenya

This study explores the individual and collective rationality of livestock accumulation in pastoral production using data gathered in northern Kenya. Results suggest accumulating wealth in livestock even when facing the prospect of sudden dramatic loss makes sense at the household level, and that there is limited empirical support to the contention that herd accumulation at the household level imposes a cost on other households. I conclude by arguing the record of failure in pastoral development may be at least partially due to a faulty conceptual foundation, and suggest facilitating herd accumulation may offer more promise than discouraging it.     

3D Computational Mechanics Elucidate the Evolutionary Implications of Orbit Position and Size Diversity of Early Amphibians

For the first time in vertebrate palaeontology, the potential of joining Finite Element Analysis (FEA) and Parametrical Analysis (PA) is used to shed new light on two different cranial parameters from the orbits to evaluate their biomechanical role and evolutionary patterns. The early tetrapod group of Stereospondyls, one of the largest groups of Temnospondyls is used as a case study because its orbits position and size vary hugely within the members of this group. An adult skull of Edingerella madagascariensis was analysed using two different cases of boundary and loading conditions in order to quantify stress and deformation response under a bilateral bite and during skull raising. Firstly, the variation of the original geometry of its orbits was introduced in the models producing new FEA results, allowing the exploration of the ecomorphology, feeding strategy and evolutionary patterns of these top predators. Secondly, the quantitative results were analysed in order to check if the orbit size and position were correlated with different stress patterns. These results revealed that in most of the cases the stress distribution is not affected by changes in the size and position of the orbit. This finding supports the high mechanical plasticity of this group during the Triassic period. The absence of mechanical constraints regarding the orbit probably promoted the ecomorphological diversity acknowledged for this group, as well as its ecological niche differentiation in the terrestrial Triassic ecosystems in clades as lydekkerinids, trematosaurs, capitosaurs or metoposaurs.     

Collective Management of Water Resources in Coastal Bangladesh: Formal and Substantive Approaches

We examine the processes of collective management of water resources for agriculture within the wider context of environmental change in a coastal region of Bangladesh. We argue that while the formal propositions of rational-actor theories (such as the Institutional Analysis and Design Framework) help to identify the potential constraints to collective action (e.g., the free rider problem), these propositions need to be seen in the substantive social context of any given case. Findings show that the pattern of collective water management is crucially dependent on the individual economic incentives for participation as well as the social structures and norms that influence the behaviour of different classes of actor, including those with conflicting economic incentives. By examining the substantive processes of negotiation and decision-making around specific problems of water management, we are able to identify the contingent set of factors that shape the responses of different actors, enabling or constraining desirable collective outcomes.     

Approaches for Quantifying the Metabolism of Physical Economies: A Comparative Survey: Part II: Review of Individual Approaches

This article is the second of a two-part series that describes and compares the essential features of nine "physical economy" approaches for mapping and quantifying the material demands of the human economy upon the natural environ-ment. These approaches are critical tools in the design and implementation of industrial ecology strategies for greater eco-efficiency and reduced environmental impacts of human economic activity. Part I of the series provided an overview, meth-odological classification, and comparison of a selected set of major materials flow analysis (MFA) and related techniques. This sequel includes a convenient reference and overview of the major metabolism measurement approaches in the form of a more detailed summary of the key specific analytical and other features of the approaches introduced in part I. The surveyed physical economy related environmental analysis ap-proaches include total material requirement and output mod-els, bulk MFA (IFF (Department of Social Ecology, Institute for Interdiscplinary Studies of Austrian Universities) material flow balance model variant), physical input-output tables, substance flow analysis, ecological footprint analysis, environmental space, material intensity per unit service, life-cycle assessment (LCA), the sustainable process index, and company-level MFA.     

Towards Precision Medicine: Advances in Computational Approaches for the Analysis of Human Variants

Variations and similarities in our individual genomes are part of our history, our heritage, and our identity. Some human genomic variants are associated with common traits such as hair and eye color, while others are associated with susceptibility to disease or response to drug treatment. Identifying the human variations producing clinically relevant phenotypic changes is critical for providing accurate and personalized diagnosis, prognosis, and treatment for diseases. Furthermore, a better understanding of the molecular underpinning of disease can lead to development of new drug targets for precision medicine. Several resources have been designed for collecting and storing human genomic variations in highly structured, easily accessible databases. Unfortunately, a vast amount of information about these genetic variants and their functional and phenotypic associations is currently buried in the literature, only accessible by manual curation or sophisticated text text-mining technology to extract the relevant information. In addition, the low cost of sequencing technologies coupled with increasing computational power has enabled the development of numerous computational methodologies to predict the pathogenicity of human variants. This review provides a detailed comparison of current human variant resources, including HGMD, OMIM, ClinVar, and UniProt/Swiss-Prot, followed by an overview of the computational methods and techniques used to leverage the available data to predict novel deleterious variants. We expect these resources and tools to become the foundation for understanding the molecular details of genomic variants leading to disease, which in turn will enable the promise of precision medicine.     

Biomimetic Leukocyte Adhesion： A Review of Microfluidic and Computational Approaches and Applications

Leukocyte rolling and adhesion are complex physiological processes that have received a great deal of attention over the past decade. Significant increases in the knowledge base related to how leukocytes adhere in shear flows have occurred as a result of the development of novel experimental and computational techniques. Micro- and nano-fabrication techniques have enabled the development of novel flow devices for studying leukocyte adhesion in simple and complex geometries. Improvements in computer technology have enabled simulations of complex flow processes to be developed. As a result of these advances in knowledge related to leukocyte adhesion, numerous novel devices have been developed that mimic the leukocyte rolling and adhesion process. Examples of these devices include cell separation and enrichment devices and targeted ultrasound contrast agents. Future advances related to leukocyte rolling and adhesion processes hold great promise for advancing our knowledge of disease processes as well as development of novel therapeutic devices.     

Effect of Group Size on Individual and Collective Vigilance in Greater Rheas

We studied the effect of group size on the proportion of time that greater rheas, Rhea americana, allocated to vigilance and feeding during the non‐breeding season. We tested whether: (1) the proportion of time that one bird allocates to vigilance (individual vigilance) decreases with group size, and (2) the proportion of time that at least one bird of the group is vigilant (collective vigilance) increases with group size. We analyzed video‐recordings of birds that were foraging alone or in groups from two to 12 birds. The proportion of time allocated to individual vigilance decreased and the proportion of time spent feeding increased with group size. In both cases the main significant difference was between birds foraging alone and in groups. Collective vigilance did not vary with group size and it was lower than expected if vigilance bouts were random or sequential. Our results indicate that rheas foraging in large groups would not receive the benefit of an increase in collective vigilance, although they could still benefit from a reduction of predation risk by the dilution effect.