A decadal view of biodiversity informatics: challenges and priorities

Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. Great strides have been made in the past decade establishing a framework for sharing data, where taxonomy and systematics has been perceived as the most prominent discipline involved. To some extent this is inevitable, given the use of species names as the pivot around which information is organised. To address the urgent questions around conservation, land-use, environmental change, sustainability, food security and ecosystem services that are facing Governments worldwide, we need to understand how the ecosystem works. So, we need a systems approach to understanding biodiversity that moves significantly beyond taxonomy and species observations. Such an approach needs to look at the whole system to address species interactions, both with their environment and with other species.It is clear that some barriers to progress are sociological, basically persuading people to use the technological solutions that are already available. This is best addressed by developing more effective systems that deliver immediate benefit to the user, hiding the majority of the technology behind simple user interfaces. An infrastructure should be a space in which activities take place and, as such, should be effectively invisible.This community consultation paper positions the role of biodiversity informatics, for the next decade, presenting the actions needed to link the various biodiversity infrastructures invisibly and to facilitate understanding that can support both business and policy-makers. The community considers the goal in biodiversity informatics to be full integration of the biodiversity research community, including citizens' science, through a commonly-shared, sustainable e-infrastructure across all sub-disciplines that reliably serves science and society alike.

Oxygen-dependent hydroxylation by Factor Inhibiting HIF (FIH) regulates the TRPV3 ion channel

Factor Inhibiting HIF (FIH) is an oxygen-dependent asparaginyl hydroxylase that regulates the hypoxia-inducible factors (HIFs). Several proteins containing ankyrin repeat domains have been characterised as substrates of FIH, although there is little evidence for a functional consequence of hydroxylation on these substrates. This study demonstrates that the transient receptor potential vanilloid 3 (TRPV3) channel is hydroxylated by FIH on asparagine 242 within the cytoplasmic ankyrin repeat domain. Hypoxia, FIH inhibitors and mutation of asparagine 242 all potentiated TRPV3-mediated current, without altering TRPV3 protein levels, indicating that oxygen-dependent hydroxylation inhibits TRPV3 activity. This novel mechanism of channel regulation by oxygendependent asparaginyl hydroxylation is likely to extend to other ion channels.

Big Data and ecosystem research programmes

The size and complexity of data sets generated within ecosystem-level programmes merits their capture, curation, storage and analysis, synthesis and visualisation using Big Data approaches. This review looks at previous attempts to organise and analyse such data through the International Biological Programme and draws on the mistakes made and the lessons learned for effective Big Data approaches to current Research Councils United Kingdom (RCUK) ecosystem-level programmes, using Biodiversity and Ecosystem Service Sustainability (BESS) and Environmental Virtual Observatory Pilot (EVOp) as exemplars. The challenges raised by such data are identified, explored and suggestions are made for the two major issues of extending analyses across different spatio-temporal scales and for the effective integration of quantitative and qualitative data.

Measuring the economic value of pollination services: principles, evidence and knowledge gaps

An increasing degree of attention is being given to the ecosystem services which insect pollinators supply, and the economic value of these services. Recent research suggests that a range of factors are contributing to a global decline in pollination services, which are often used as a “headline” ecosystem service in terms of communicating the concept of ecosystem services, and how this ties peoples׳ well-being to the condition of ecosystems and the biodiversity found therein. Our paper offers a conceptual framework for measuring the economic value of changes in insect pollinator populations, and then reviews what evidence exists on the empirical magnitude of these values (both market and non-market). This allows us to highlight where the largest gaps in knowledge are, where the greatest conceptual and empirical challenges remain, and where research is most needed.

Mechanisms Associated with Large Daily Rainfall Events in Northeast Brazil

The mechanisms resulting in large daily rainfall events in Northeast Brazil are analyzed using data filtering to exclude periods longer than 30 days. Composites of circulation fields that include all independent events do not reveal any obvious forcing mechanisms as multiple patterns contribute to Northeast Brazil precipitation variability. To isolate coherent patterns, subsets of events are selected based on anomalies that precede the Northeast Brazil precipitation events at different locations. The results indicate that at 10 degrees S, 40 degrees W, the area of lowest annual rainfall in Brazil, precipitation occurs mainly in association with trailing midlatitude synoptic wave trains originating in either hemisphere. Closer to the equator at 5 degrees S, 37.5 degrees W, an additional convection precursor is found to the west, with a spatial structure consistent with that of a Kelvin wave. Although these two sites are located within only several hundred kilometers of each other and the midlatitude patterns that induce precipitation appear to be quite similar, the dates on which large precipitation anomalies occur at each location are almost entirely independent, pointing to separate forcing mechanisms.

Origin of Convectively Coupled Kelvin Waves over South America

Convectively coupled Kelvin waves over the South American continent are examined through the use of temporal and spatial filtering of reanalysis, satellite, and gridded rainfall data. They are most prominent from November to April, the season analyzed herein. The following two types of events are isolated: those that result from preexisting Kelvin waves over the eastern Pacific Ocean propagating into the continent, and those that apparently originate over Amazonia, forced by disturbances propagating equatorward from central and southern South America. The events with precursors in the Pacific are mainly upper-level disturbances, with almost no signal at the surface. Those events with precursors over South America, on the other hand, originate as upper-level synoptic wave trains that pass over the continent and resemble the ""cold surges`` documented by Garreaud and Wallace. As the wave train propagates over the Andes, it induces a southerly low-level wind that advects cold air to the north. Precipitation associated with a cold front reaches the equator a few days later and subsequently propagates eastward with the characteristics of a Kelvin wave. The structures of those waves originating over the Pacific are quite similar to those originating over South America as they propagate to eastern South America and into the Atlantic. South America Kelvin waves that originate over neither the Pacific nor the midlatitudes of South America can also be identified. In a composite sense, these form over the eastern slope of the Andes Mountains, close to the equator. There are also cases of cold surges that reach the equator yet do not form Kelvin waves. The interannual variability of the Pacific-originating events is related to sea surface temperatures in the central-eastern Pacific Ocean. When equatorial oceanic conditions are warm, there tends to be an increase in the number of disturbances that reach South America from the Pacific.

On the Use of Agents in a Bioinformatics Grid

MyGrid is an e-Science Grid project that aims to help biologists and bioinformaticians to perform workflow-based in silico experiments, and help them to automate the management of such workflows through personalisation, notification of change and publication of experiments. In this paper, we describe the architecture of myGrid and how it will be used by the scientist. We then show how myGrid can benefit from agents technologies. We have identified three key uses of agent technologies in myGrid: user agents, able to customize and personalise data, agent communication languages offering a generic and portable communication medium, and negotiation allowing multiple distributed entities to reach service level agreements.