University of Auckland

A comparative risk assessment of burden of disease and injury attributable to 67 risk factors and risk factor clusters in 21 regions, 1990–2010: a systematic analysis for the Global Burden of Disease Study 2010

Disability-adjusted life years (DALYs) for 291 diseases and injuries in 21 regions, 1990–2010: a systematic analysis for the Global Burden of Disease Study 2010

Years lived with disability (YLDs) for 1160 sequelae of 289 diseases and injuries 1990–2010: a systematic analysis for the Global Burden of Disease Study 2010

Journal of Universal Computer Science

Almost all researchers in computer science have access to Internet by now: with some 2 million Internet nodes at the time of writing an estimated 30 million people can connect to Internet, many of them directly from their desk. Internet has become an increasingly powerful information, communication

The systems biology markup language (SBML): a medium forrepresentation and exchange of biochemical network models

MOTIVATION: Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively. RESULTS: We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others. AVAILABILITY: The specification of SBML Level 1 is freely available from http://www.sbml.org/

The Systems Biology Graphical Notation

Applying evolutionary biology to address global challenges

BACKGROUND Differences among species in their ability to adapt to environmental change threaten biodiversity, human health, food security, and natural resource availability. Pathogens, pests, and cancers often quickly evolve resistance to control measures, whereas crops, livestock, wild species, and human beings often do not adapt fast enough to cope with climate change, habitat loss, toxicants, and lifestyle change. To address these challenges, practices based on evolutionary biology can promote sustainable outcomes via strategic manipulation of genetic, developmental, and environmental factors. Successful strategies effectively slow unwanted evolution and reduce fitness in costly species or improve performance of valued organisms by reducing phenotype-environment mismatch or increasing group productivity. Tactics of applied evolutionary biology range broadly, from common policies that promote public health or preserve habitat for threatened species—but are easily overlooked as having an evolutionary rationale, to the engineering of new genomes. ADVANCES The scope and development of current tactics vary widely. In particular, genetic engineering attracts much attention (and controversy) but now is used mainly for traits under simple genetic control. Human gene therapy, which mainly involves more complex controls, has yet to be applied successfully at large scales. In contrast, other methods to alter complex traits are improving. These include artificial selection for drought- and flood-tolerant crops through bioinformatics and application of “life course” approaches in medicine to reduce human metabolic disorders. Successful control of unwanted evolution depends on governance initiatives that address challenges arising from both natural and social factors. Principal among these challenges are (i) global transfer of genes and selection agents; (ii) interlinked evolution across traditional sectors of society (environment, food, and health); and (iii) conflicts between individual and group incentives that threaten regulation of antibiotic use and crop refuges. Evolutionarily informed practices are a newer prospect in some fields and require more systematic research, as well as ethical consideration—for example, in attempts to protect wild species through assisted migration, in the choice of source populations for restoration, or in genetic engineering. OUTLOOK A more unified platform will better convey the value of evolutionary methods to the public, scientists, and decision-makers. For researchers and practitioners, applications may be expanded to other disciplines, such as in the transfer of refuge strategies that slow resistance evolution in agriculture to slow unwanted evolution elsewhere (for example, cancer resistance or harvest-induced evolution). For policy-makers, adoption of practices that minimize unwanted evolution and reduce phenotype-environment mismatch in valued species is likely essential to achieve the forthcoming Sustainable Development Goals and the 2020 Aichi Biodiversity Targets.

Biology and Ecology of the Globally Significant Kelp Ecklonia radiata

Ecklonia radiata is one of the most widespread kelps globally, dominating temperate reefs throughout much of Australasia and southeastern Africa. Throughout much of its range, it is the only laminarian kelp and hence plays a key role in facilitating biodiversity and driving food webs, and it underpins immense ecological and socioeconomic values. This review synthesises the growing literature on E. radiata from its phylogeny and distribution through to its biology, ecology and recent changes. 266 It provides an assessment of the state of knowledge and identifies gaps in our understanding of this important species. Despite being tolerant of a wide range of abiotic conditions, recent environmental change has caused direct and indirect loss of E. radiata forests, with extensive areas transitioning to turf and urchin barrens. Ongoing climate change may require application of multifaceted and novel strategies to increase its resistance and resilience to future conditions. By integrating variation across space, time and environmental change, this review provides a description of the current status and possible future trajectories of E. radiata forests.

Harmonizing semantic annotations for computational models in biology

Life science researchers use computational models to articulate and test hypotheses about the behavior of biological systems. Semantic annotation is a critical component for enhancing the interoperability and reusability of such models as well as for the integration of the data needed for model parameterization and validation. Encoded as machine-readable links to knowledge resource terms, semantic annotations describe the computational or biological meaning of what models and data represent. These annotations help researchers find and repurpose models, accelerate model composition and enable knowledge integration across model repositories and experimental data stores. However, realizing the potential benefits of semantic annotation requires the development of model annotation standards that adhere to a community-based annotation protocol. Without such standards, tool developers must account for a variety of annotation formats and approaches, a situation that can become prohibitively cumbersome and which can defeat the purpose of linking model elements to controlled knowledge resource terms. Currently, no consensus protocol for semantic annotation exists among the larger biological modeling community. Here, we report on the landscape of current annotation practices among the COmputational Modeling in BIology NEtwork community and provide a set of recommendations for building a consensus approach to semantic annotation.

Oceanography and Marine Biology

Coastal plankton show fluctuations in abundance and species composition. Resting stage (cyst) production is a common strategy adopted by hundreds of plankton species to ensure reproduction and to avoid adverse conditions. During the resting period, these species are normally absent from the water column, and cysts produced in the plankton accumulate in the sediment where they wait for the return of suitable conditions. A portion of the cyst bank does not hatch, instead undergoing a dormancy that may extend for decades. Confined coastal areas accumulate cysts in sediment due to one or more possibilities, including reduced water movement/hydrodynamics, high population density, abundance of cyst-producing species, and the absence or scarcity of possible cyst consumers in the benthos. The pelagic-benthic nexus, which affects both the sediment and the water column (and possibly sea ice) is still poorly understood. In fact, the presence of cysts in the life cycle of organisms is likely to have considerable consequences for the ecology of coastal plankton, as well as the evolution and biogeography of species. This review aims to depict the presence (and even abundance) of resting stages in marine environments and their impact on ecosystem functioning. The review starts with a description of encysted resting stages in all marine planktonic taxa, listing a total of 501 species with known cysts, and methods and tools for their collection and study. The physiology and timing of the rest period is then described for various taxa, followed by a discussion of the evolutionary implications of resting. The presence of encysted stages in different realms and phyla of plankton suggests an ancient origin and a successive diversification of morphologies that, today, roughly characterise each taxa. Ecological and biogeographical implications stem from this general framework and support the hypothesis of seasonal occurrences of planktonic life in ecosystems where productivity is suspended for a long time (e.g. in polar seas). The potential to suspend or resume life has implications for human activities, such as the risk of translocations through ship ballast water and contamination of water and seafood with toxins but also the benefit of cysts for the production of aquaculture feed. The review concludes with perspectives on present knowledge and outstanding questions to address in future studies.