Multiple domestications and their taxonomic consequences: the example of Phaseolus vulgaris

The evolutionary history of P. vulgaris is important to those working on its genetic resources, but is not reflected in its infraspecific taxonomy. Genetic isolation of wild populations between and also within Middle and South America has resulted in morphological and molecular differentiation. Populations from northern and southern ends of the range are assigned to different gene pools, though intermediates occur in intervening areas. Chloroplast haplotypes suggest three distinct lineages of wild beans and several intercontinental dispersals. The species was domesticated independently in both Middle and South America, probably several times in Middle America. This, together with further differentiation under human selection, has produced distinct races among domesticated beans. The informal categories of wild versus domesticated, gene pool, and race convey the evolutionary picture more clearly than the formal categories provided by the Codes of Nomenclature for wild or cultivated plants.

Fatty acids and immune function: new insights into mechanisms

Fatty acids are known to play diverse roles in immune cells. They are important as a source of energy, as structural components of cell membranes, as signaling molecules and as precursors for the synthesis of eicosanoids and similar mediators. Recent research has suggested that the localization and organisation of fatty acids into distinct cellular pools has a direct influence on the behaviour of a number of proteins involved in immune cell activation, including those associated with T cell responses, antigen presentation and fatty acid-derived inflammatory mediator production. This article reviews these studies and places them in the context of existing literature in the field. These studies indicate the existence of several novel mechanisms by which altered fatty acid availability can modulate immune responses and impact upon clinical outcomes

Fatty acids as gatekeepers of immune cell regulation

Fatty acids have diverse roles in all cells. They are important as a source of energy, as structural components of cell membranes, as signalling molecules and as precursors for the synthesis of eicosanoids. Recent research has suggested that the organization of fatty acids into distinct cellular pools has a particularly important role in cells of the immune system and that forms of lipid trafficking exist, which are as yet poorly understood. This Review examines the nature and regulation of cellular lipid pools in the immune system, their delivery of fatty acids or fatty acid derivatives to specific locations and their potential role in health and disease.

Understanding omega-3 polyunsaturated fatty acids

Current intakes of very long-chain omega-3 fatty acids, eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), are low in most individuals living in Western countries. A good natural source of these fatty acids is seafood, especially oily fish. Fish oil capsules contain these fatty acids also. Very long-chain omega-3 fatty acids are readily incorporated from capsules into transport (blood lipids), functional (cell and tissue), and storage (adipose) pools. This incorporation is dose-dependent and follows a kinetic pattern that is characteristic for each pool. At sufficient levels of incorporation, EPA and DHA influence the physical nature of cell membranes and membrane protein-mediated responses, lipid-mediator generation, cell signaling, and gene expression in many different cell types. Through these mechanisms, EPA and DHA influence cell and tissue physiology and the way cells and tissues respond to external signals. In most cases the effects seen are compatible with improvements in disease biomarker profiles or health-related outcomes. As a result, very long-chain omega-3 fatty acids play a role in achieving optimal health and in protection against disease. Long-chain omega-3 fatty acids not only protect against cardiovascular morbidity but also against mortality. In some conditions, for example rheumatoid arthritis, they may be beneficial as therapeutic agents. On the basis of the recognized health improvements brought about by long-chain omega-3 fatty acids, recommendations have been made to increase their intake. The plant omega-3 fatty acid, alpha-linolenic acid (ALA), can be converted to EPA, but conversion to DHA appears to be poor in humans. Effects of ALA on human health-related outcomes appear to be due to conversion to EPA, and since this is limited, moderately increased consumption of ALA may be of little benefit in improving health outcomes compared with increased intake of preformed EPA + DHA.

Omega-3 polyunsaturated fatty acids and human health outcomes

Current intakes of very long chain omega-3 fatty acids, eicosapentaenoic acid (EPA), and docosahexaenoic acid (DNA) are low in most individuals living in Western countries. A good natural source of these fatty acids is seafood, especially oily fish. Fish oil capsules contain these fatty acids too. Very long chain w-3 fatty acids are readily incorporated from capsules into transport, functional, and storage pools. This incorporation is dose-dependent and follows a kinetic pattern that is characteristic for each pool. At sufficient levels of incorporation, EPA and DHA influence the physical nature of cell membranes and membrane protein-mediated responses, eicosanoid generation, cell signaling and gene expression in many different cell types. Through these mechanisms, EPA and DHA influence cell and tissue physiology, and the way cells and tissues respond to external signals. In most cases, the effects seen are compatible with improvements in disease biomarker profiles or in health-related outcomes. As a result, very long chain omega-3 fatty acids play a role in achieving optimal health and in protection against disease. Long chain omega-3 fatty acids protect against cardiovascular morbidity and mortality, and might be beneficial in rheumatoid arthritis, inflammatory bowel diseases, childhood learning, and behavior, and adult psychiatric and neurodegenerative illnesses. DHA has an important structural role in the eye and brain, and its supply early in life is known to be of vital importance. On the basis of the recognized health improvements brought about by long chain omega-3 fatty acids, recommendations have been made to increase their intake. (C) 2009 International Union of Biochemistry and Molecular Biology, Inc. Volume 35, Number 3, May/June 2009, Pages 266-272. E-mail: pcc@soton.ac.uk

Collaborative grid infrastructure for molecular simulations: The eMinerals minigrid as a prototype integrated computer and data grid

This paper describes a prototype grid infrastructure, called the eMinerals minigrid, for molecular simulation scientists. which is based on an integration of shared compute and data resources. We describe the key components, namely the use of Condor pools, Linux/Unix clusters with PBS and IBM's LoadLeveller job handling tools, the use of Globus for security handling, the use of Condor-G tools for wrapping globus job submit commands, Condor's DAGman tool for handling workflow, the Storage Resource Broker for handling data, and the CCLRC dataportal and associated tools for both archiving data with metadata and making data available to other workers.

Chemical and aerosol characterisation of the troposphere over West Africa during the monsoon period as part of AMMA

During June, July and August 2006 five aircraft took part in a campaign over West Africa to observe the aerosol content and chemical composition of the troposphere and lower stratosphere as part of the African Monsoon Multidisciplinary Analysis (AMMA) project. These are the first such measurements in this region during the monsoon period. In addition to providing an overview of the tropospheric composition, this paper provides a description of the measurement strategy (flights performed, instrumental payloads, wing-tip to wing-tip comparisons) and points to some of the important findings discussed in more detail in other papers in this special issue. The ozone data exhibits an "S" shaped vertical profile which appears to result from significant losses in the lower troposphere due to rapid deposition to forested areas and photochemical destruction in the moist monsoon air, and convective uplift of ozone-poor air to the upper troposphere. This profile is disturbed, particularly in the south of the region, by the intrusions in the lower and middle troposphere of air from the southern hemisphere impacted by biomass burning. Comparisons with longer term data sets suggest the impact of these intrusions on West Africa in 2006 was greater than in other recent wet seasons. There is evidence for net photochemical production of ozone in these biomass burning plumes as well as in urban plumes, in particular that from Lagos, convective outflow in the upper troposphere and in boundary layer air affected by nitrogen oxide emissions from recently wetted soils. This latter effect, along with enhanced deposition to the forested areas, contributes to a latitudinal gradient of ozone in the lower troposphere. Biogenic volatile organic compounds are also important in defining the composition both for the boundary layer and upper tropospheric convective outflow. Mineral dust was found to be the most abundant and ubiquitous aerosol type in the atmosphere over Western Africa. Data collected within AMMA indicate that injection of dust to altitudes favourable for long-range transport (i.e. in the upper Sahelian planetary boundary layer) can occur behind the leading edge of mesoscale convective system (MCS) cold-pools. Research within AMMA also provides the first estimates of secondary organic aerosols across the West African Sahel and have shown that organic mass loadings vary between 0 and 2 μg m−3 with a median concentration of 1.07 μg m−3. The vertical distribution of nucleation mode particle concentrations reveals that significant and fairly strong particle formation events did occur for a considerable fraction of measurement time above 8 km (and only there). Very low concentrations were observed in general in the fresh outflow of active MCSs, likely as the result of efficient wet removal of aerosol particles due to heavy precipitation inside the convective cells of the MCSs. This wet removal initially affects all particle size ranges as clearly shown by all measurements in the vicinity of MCSs.

Model inter-comparison between statistical and dynamic model assessments of the long-term stability of blanket peat in Great Britain (1940-2099)

We compared output from 3 dynamic process-based models (DMs: ECOSSE, MILLENNIA and the Durham Carbon Model) and 9 bioclimatic envelope models (BCEMs; including BBOG ensemble and PEATSTASH) ranging from simple threshold to semi-process-based models. Model simulations were run at 4 British peatland sites using historical climate data and climate projections under a medium (A1B) emissions scenario from the 11-RCM (regional climate model) ensemble underpinning UKCP09. The models showed that blanket peatlands are vulnerable to projected climate change; however, predictions varied between models as well as between sites. All BCEMs predicted a shift from presence to absence of a climate associated with blanket peat, where the sites with the lowest total annual precipitation were closest to the presence/absence threshold. DMs showed a more variable response. ECOSSE predicted a decline in net C sink and shift to net C source by the end of this century. The Durham Carbon Model predicted a smaller decline in the net C sink strength, but no shift to net C source. MILLENNIA predicted a slight overall increase in the net C sink. In contrast to the BCEM projections, the DMs predicted that the sites with coolest temperatures and greatest total annual precipitation showed the largest change in carbon sinks. In this model inter-comparison, the greatest variation in model output in response to climate change projections was not between the BCEMs and DMs but between the DMs themselves, because of different approaches to modelling soil organic matter pools and decomposition amongst other processes. The difference in the sign of the response has major implications for future climate feedbacks, climate policy and peatland management. Enhanced data collection, in particular monitoring peatland response to current change, would significantly improve model development and projections of future change.

Biotic carbon feedbacks in a materially-closed soil-vegetation-atmosphere system

The magnitude and direction of the coupled feedbacks between the biotic and abiotic components of the terrestrial carbon cycle is a major source of uncertainty in coupled climate–carbon-cycle models1, 2, 3. Materially closed, energetically open biological systems continuously and simultaneously allow the two-way feedback loop between the biotic and abiotic components to take place4, 5, 6, 7, but so far have not been used to their full potential in ecological research, owing to the challenge of achieving sustainable model systems6, 7. We show that using materially closed soil–vegetation–atmosphere systems with pro rata carbon amounts for the main terrestrial carbon pools enables the establishment of conditions that balance plant carbon assimilation, and autotrophic and heterotrophic respiration fluxes over periods suitable to investigate short-term biotic carbon feedbacks. Using this approach, we tested an alternative way of assessing the impact of increased CO2 and temperature on biotic carbon feedbacks. The results show that without nutrient and water limitations, the short-term biotic responses could potentially buffer a temperature increase of 2.3 °C without significant positive feedbacks to atmospheric CO2. We argue that such closed-system research represents an important test-bed platform for model validation and parameterization of plant and soil biotic responses to environmental changes.

Elevated atmospheric CO2 changes phosphorus fractions in soils under a short rotation poplar plantation (EuroFACE)

Future high levels of atmospheric carbon dioxide (CO2) may increase biomass production of terrestrial plants and hence plant requirements for soil mineral nutrients to sustain a greater biomass production. Phosphorus (P), an element essential for plant growth, is found in soils both in inorganic and in organic forms. In this work, three genotypes of Populus were grown under ambient and elevated atmospheric CO2 concentrations (FACE) for 5 years. An N fertilisation treatment was added in years 4 and 5 after planting. Using a fractionation scheme, total P was sequentially extracted using H2O, NaOH, HCl and HNO3, and P determined as both molybdate (Mo) reactive and total P. Molybdate-reactive P is defined as mainly inorganic but also some labile organic P which is determined by Vanado-molybdophosphoric acid colorimetric methods. Organic P was also measured to assess all plant available and weatherable P pools. We tested the hypotheses that higher P demand due to increased growth is met by a depletion of easily weatherable soil P pools, and that increased biomass inputs increases the amount of organic P in the soil. The concentration of organic P increased under FACE, but was associated with a decrease in total soil organic matter. The greatest increase in the soil P due to elevated CO2 was found in the HCl-extractable P fraction in the non-fertilised treatment. In the NaOH-extractable fraction the Mo-reactive P increased under FACE, but total P did not differ between ambient and FACE. The increase in both the NaOH- and HCl-extractable fractions was smaller after N addition. The results showed that elevated atmospheric CO2 has a positive effect on soil P availability rather than leading to depletion.We suggest that the increase in the NaOH- and HCl-extractable fractions is biologically driven by organic matter mineralization, weathering and mycorrhizal hyphal turnover.

Forest soil carbon cycle under elevated CO2 – a case of increased throughput?

Forest soils account for a large part of the stable carbon pool held in terrestrial ecosystems. Future levels of atmospheric CO2 are likely to increase C input into the soils through increased above- and below-ground production of forests. This increased input will result in greater sequestration of C only if the additional C enters stable pools. In this review, we compare current observations from four large-scale Free Air FACE Enrichment (FACE) experiments on forest ecosystems (EuroFACE, Aspen-FACE, Duke FACE and ORNL-FACE) and consider their predictive power for long-term C sequestration. At all sites, FACE increased fine root biomass, and in most cases higher fine root turnover resulted in higher C input into soil via root necromass. However, at all sites, soil CO2 efflux also increased in excess of the increased root necromass inputs. A mass balance calculation suggests that a large part of the stimulation of soil CO2 efflux may be due to increased root respiration. Given the duration of these experiments compared with the life cycle of a forest and the complexity of processes involved, it is not yet possible to predict whether elevated CO2 will result in increased C storage in forest soil.

Modelling of the natural chlorine cycling in a coniferous stand: implications for chlorine-36 behaviour in a contaminated forest environment

Considered as one of the most available radionuclide in soileplant system, 36Cl is of potential concern for long-term management of radioactive wastes, due to its high mobility and its long half-life. To evaluate the risk of dispersion and accumulation of 36Cl in the biosphere as a consequence of a potential contamination, there is a need for an appropriate understanding of the chlorine cycling dynamics in the ecosystems. To date, a small number of studies have investigated the chlorine transfer in the ecosystem including the transformation of chloride to organic chlorine but, to our knowledge, none have modelled this cycle. In this study, a model involving inorganic as well as organic pools in soils has been developed and parameterised to describe the biogeochemical fate of chlorine in a pine forest. The model has been evaluated for stable chlorine by performing a range of sensitivity analyses and by comparing the simulated to the observed values. Finally a range of contamination scenarios, which differ in terms of external supply, exposure time and source, has been simulated to estimate the possible accumulation of 36Cl within the different compartments of the coniferous stand. The sensitivity study supports the relevancy of the model and its compartments, and has highlighted the chlorine transfers affecting the most the residence time of chlorine in the stand. Compared to observations, the model simulates realistic values for the chlorine content within the different forest compartments. For both atmospheric and underground contamination scenarios most of the chlorine can be found in its organic form in the soil. However, in case of an underground source, about two times less chlorine accumulates in the system and proportionally more chlorine leaves the system through drainage than through volatilisation.

The REFLEX project: Comparing different algorithms and implementations for the inversion of a terrestrial ecosystem model against eddy covariance data

We describe a model-data fusion (MDF) inter-comparison project (REFLEX), which compared various algorithms for estimating carbon (C) model parameters consistent with both measured carbon fluxes and states and a simple C model. Participants were provided with the model and with both synthetic net ecosystem exchange (NEE) of CO2 and leaf area index (LAI) data, generated from the model with added noise, and observed NEE and LAI data from two eddy covariance sites. Participants endeavoured to estimate model parameters and states consistent with the model for all cases over the two years for which data were provided, and generate predictions for one additional year without observations. Nine participants contributed results using Metropolis algorithms, Kalman filters and a genetic algorithm. For the synthetic data case, parameter estimates compared well with the true values. The results of the analyses indicated that parameters linked directly to gross primary production (GPP) and ecosystem respiration, such as those related to foliage allocation and turnover, or temperature sensitivity of heterotrophic respiration, were best constrained and characterised. Poorly estimated parameters were those related to the allocation to and turnover of fine root/wood pools. Estimates of confidence intervals varied among algorithms, but several algorithms successfully located the true values of annual fluxes from synthetic experiments within relatively narrow 90% confidence intervals, achieving >80% success rate and mean NEE confidence intervals <110 gC m−2 year−1 for the synthetic case. Annual C flux estimates generated by participants generally agreed with gap-filling approaches using half-hourly data. The estimation of ecosystem respiration and GPP through MDF agreed well with outputs from partitioning studies using half-hourly data. Confidence limits on annual NEE increased by an average of 88% in the prediction year compared to the previous year, when data were available. Confidence intervals on annual NEE increased by 30% when observed data were used instead of synthetic data, reflecting and quantifying the addition of model error. Finally, our analyses indicated that incorporating additional constraints, using data on C pools (wood, soil and fine roots) would help to reduce uncertainties for model parameters poorly served by eddy covariance data.