Results from the Covered Catchment Experiment at Gårdsjön, Sweden, after ten years of clean precipitation treatment

The Covered Catchment Experiment at Gordsjon is a large scale forest ecosystem manipulation, where acid precipitation was intercepted by a 7000 m(2) plastic roof and replaced by 'clean precipitation' sprinkled below the roof for ten years between 1991 and 2001. The treatment resulted in a strong positive response of runoff quality. The runoff sulphate, inorganic aluminium and base cations decreased, while there was a strong increase in runoff ANC and a moderate increase in pH. The runoff continued to improve over the whole duration of the experiment. The achieved quality was, however, after ten years still considerably worse than estimated pre-industrial runoff at the site. Stable isotopes of sulphur were analysed to study the soil sulphur cycling. At the initial years of the experiment, the desorption of SO4 from the mineral soil appeared to control the runoff SO4 concentration. However, as the experiment proceeded, there was growing evidence that net mineralisation of soil organic sulphur in the humus layer was an additional source of SO4 in runoff. This might provide a challenge to current acidification models. The experiment convincingly demonstrated on a catchment scale, that reduction in acid deposition causes an immediate improvement of surface water quality even at heavily acidified sites. The improvement of the runoff appeared to be largely a result of cation exchange processes in the soil due to decreasing concentrations of the soil solution, while any potential change in soil base saturation seemed to be less important for the runoff chemistry over the short time period of one decade. These findings should be considered when interpreting and extrapolating regional trends in surface water chemistry to the terrestrial parts of ecosystems.

The ModFOLD server for the quality assessment of protein structural models

The reliable assessment of the quality of protein structural models is fundamental to the progress of structural bioinformatics. The ModFOLD server provides access to two accurate techniques for the global and local prediction of the quality of 3D models of proteins. Firstly ModFOLD, which is a fast Model Quality Assessment Program (MQAP) used for the global assessment of either single or multiple models. Secondly ModFOLDclust, which is a more intensive method that carries out clustering of multiple models and provides per-residue local quality assessment.

Benchmarking consensus model quality assessment for protein fold recognition

Background: Selecting the highest quality 3D model of a protein structure from a number of alternatives remains an important challenge in the field of structural bioinformatics. Many Model Quality Assessment Programs (MQAPs) have been developed which adopt various strategies in order to tackle this problem, ranging from the so called "true" MQAPs capable of producing a single energy score based on a single model, to methods which rely on structural comparisons of multiple models or additional information from meta-servers. However, it is clear that no current method can separate the highest accuracy models from the lowest consistently. In this paper, a number of the top performing MQAP methods are benchmarked in the context of the potential value that they add to protein fold recognition. Two novel methods are also described: ModSSEA, which based on the alignment of predicted secondary structure elements and ModFOLD which combines several true MQAP methods using an artificial neural network. Results: The ModSSEA method is found to be an effective model quality assessment program for ranking multiple models from many servers, however further accuracy can be gained by using the consensus approach of ModFOLD. The ModFOLD method is shown to significantly outperform the true MQAPs tested and is competitive with methods which make use of clustering or additional information from multiple servers. Several of the true MQAPs are also shown to add value to most individual fold recognition servers by improving model selection, when applied as a post filter in order to re-rank models. Conclusion: MQAPs should be benchmarked appropriately for the practical context in which they are intended to be used. Clustering based methods are the top performing MQAPs where many models are available from many servers; however, they often do not add value to individual fold recognition servers when limited models are available. Conversely, the true MQAP methods tested can often be used as effective post filters for re-ranking few models from individual fold recognition servers and further improvements can be achieved using a consensus of these methods.

Strained relations: a critical analysis of the mining conflict in Prestea, Ghana

This paper examines the dynamics of the ongoing conflict in Prestea, Ghana, where indigenous galamsey mining groups are operating illegally on a concession awarded to Bogoso Gold Limited (BGL), property of the Canadian-listed multinational Gold Star Resources. Despite being issued firm orders by the authorities to abandon their activities, galamsey leaders maintain that they are working areas of the concession that are of little interest to the company; they further counter that there are few alternative sources of local employment, which is why they are mining in the first place. Whilst the Ghanaian Government is in the process of setting aside plots to relocate illegal mining parties and is developing alternative livelihood projects, efforts are far from encouraging: in addition to a series of overlooked logistical problems, the areas earmarked for relocation have not yet been prospected to ascertain gold content, and the alternative income-earning activities identified are inappropriate. As has been the case throughout mineral-rich sub-Saharan Africa, the conflict in Prestea has come about largely because the national mining sector reform program, which prioritizes the expansion of predominantly foreign-controlled large-scale projects, has neglected the concerns of indigenous subsistence groups.

The budget and the WTO: driving forces behind the ‘Health Check’?

The chapter examines the evidence for budget concerns or external (WTO) pressures being the drivers for the 'Health Check' reform of the European Union's common agricultural policy.

The long-term safety and efficacy of bilateral transplantation of human fetal striatal tissue in patients with mild to moderate Huntington's disease.

Huntington's disease (HD) is a fatal autosomal dominant neurodegenerative disease involving progressive motor, cognitive and behavioural decline, leading to death approximately 20 years after motor onset. The disease is characterised pathologically by an early and progressive striatal neuronal cell loss and atrophy, which has provided the rationale for first clinical trials of neural repair using fetal striatal cell transplantation. Between 2000 and 2003, the 'NEST-UK' consortium carried out bilateral striatal transplants of human fetal striatal tissue in five HD patients. This paper describes the long-term follow up over a 3-10-year postoperative period of the patients, grafted and non-grafted, recruited to this cohort using the 'Core assessment program for intracerebral transplantations-HD' assessment protocol. No significant differences were found over time between the patients, grafted and non-grafted, on any subscore of the Unified Huntington's Disease Rating Scale, nor on the Mini Mental State Examination. There was a trend towards a slowing of progression on some timed motor tasks in four of the five patients with transplants, but overall, the trial showed no significant benefit of striatal allografts in comparison with a reference cohort of patients without grafts. Importantly, no significant adverse or placebo effects were seen. Notably, the raclopride positron emission tomography (PET) signal in individuals with transplants, indicated that there was no obvious surviving striatal graft tissue. This study concludes that fetal striatal allografting in HD is safe. While no sustained functional benefit was seen, we conclude that this may relate to the small amount of tissue that was grafted in this safety study compared with other reports of more successful transplants in patients with HD.

Are sulfurous soil amendments (S0, Fe(II)SO4, Fe(III)SO4) an effective tool in the restoration of heathland and acidic grassland after four decades of rock phosphate Fertilization?

This paper deals with the complex issue of reversing long-term improvements of fertility in soils derived from heathlands and acidic grasslands using sulfur-based amendments. The experiment was conducted on a former heathland and acid grassland in the U.K. that was heavily fertilized and limed with rock phosphate, chalk, and marl. The experimental work had three aims. First, to determine whether sulfurous soil amendments are able to lower pH to a level suitable for heathland and acidic grassland re-creation (approximately 3 pH units). Second, to determine what effect the soil amendments have on the available pool of some basic cations and some potentially toxic acidic cations that may affect the plant community. Third, to determine whether the addition of Fe to the soil system would sequester PO4− ions that might be liberated from rock phosphate by the experimental treatments. The application of S0 and Fe(II)SO4− to the soil was able to reduce pH. However, only the highest S0 treatment (2,000 kg/ha S) lowered pH sufficiently for heathland restoration purposes but effectively so. Where pH was lowered, basic cations were lost from the exchangeable pool and replaced by acidic cations. Where Fe was added to the soil, there was no evidence of PO4− sequestration from soil test data (Olsen P), but sequestration was apparent because of lower foliar P in the grass sward. The ability of the forb Rumex acetosella to apparently detoxify Al3+, prevalent in acidified soils, appeared to give it a competitive advantage over other less tolerant species. We would anticipate further changes in plant community structure through time, driven by Al3+ toxicity, leading to the competitive exclusion of less tolerant species. This, we suggest, is a key abiotic driver in the restoration of biotic (acidic plant) communities.