Towards data warehousing and mining of protein unfolding simulation data

OBJECTIVES: The prediction of protein structure and the precise understanding of protein folding and unfolding processes remains one of the greatest challenges in structural biology and bioinformatics. Computer simulations based on molecular dynamics (MD) are at the forefront of the effort to gain a deeper understanding of these complex processes. Currently, these MD simulations are usually on the order of tens of nanoseconds, generate a large amount of conformational data and are computationally expensive. More and more groups run such simulations and generate a myriad of data, which raises new challenges in managing and analyzing these data. Because the vast range of proteins researchers want to study and simulate, the computational effort needed to generate data, the large data volumes involved, and the different types of analyses scientists need to perform, it is desirable to provide a public repository allowing researchers to pool and share protein unfolding data. METHODS: To adequately organize, manage, and analyze the data generated by unfolding simulation studies, we designed a data warehouse system that is embedded in a grid environment to facilitate the seamless sharing of available computer resources and thus enable many groups to share complex molecular dynamics simulations on a more regular basis. RESULTS: To gain insight into the conformational fluctuations and stability of the monomeric forms of the amyloidogenic protein transthyretin (TTR), molecular dynamics unfolding simulations of the monomer of human TTR have been conducted. Trajectory data and meta-data of the wild-type (WT) protein and the highly amyloidogenic variant L55P-TTR represent the test case for the data warehouse. CONCLUSIONS: Web and grid services, especially pre-defined data mining services that can run on or 'near' the data repository of the data warehouse, are likely to play a pivotal role in the analysis of molecular dynamics unfolding data.

Adoption of green revolution services and poverty reduction in Ghana

In Sub-Saharan Africa (SSA) the technological advances of the Green Revolution (GR) have not been very successful. However, the efforts being made to re-introduce the revolution call for more socio-economic research into the adoption and the effects of the new technologies. The paper discusses an investigation on the effects of GR technology adoption on poverty among households in Ghana. Maximum likelihood estimation of a poverty model within the framework of Heckman's two stage method of correcting for sample selection was employed. Technology adoption was found to have positive effects in reducing poverty. Other factors that reduce poverty include education, credit, durable assets, living in the forest belt and in the south of the country. Technology adoption itself was also facilitated by education, credit, non-farm income and household labour supply as well as living in urban centres. Inarguably, technology adoption can be taken seriously by increasing the levels of complementary inputs such as credit, extension services and infrastructure. Above all, the fundamental problems of illiteracy, inequality and lack of effective markets must be addressed through increasing the levels of formal and non-formal education, equitable distribution of the 'national cake' and a more pragmatic management of the ongoing Structural Adjustment Programme.

The impact of NTFP sales on rural households’ cash income in India’s dry deciduous forest

In recent years, researchers and policy makers have recognized that nontimber forest products (NTFPs) extracted from forests by rural people can make a significant contribution to their well-being and to the local economy. This study presents and discusses data that describe the contribution of NTFPs to cash income in the dry deciduous forests of Orissa and Jharkhand, India. In its focus on cash income, this study sheds light on how the sale of NTFPs and products that use NTFPs as inputs contribute to the rural economy. From analysis of a unique data set that was collected over the course of a year, the study finds that the contribution of NTFPs to cash income varies across ecological settings, seasons, income level, and caste. Such variation should inform where and when to apply NTFP forest access and management policies.

Forest livelihoods: beekeeping as men's work in western Tanzania

This chapter takes the example of local African beekeeping to explore how the forest can act as an important locus for men's work in Western Tanzania. Here we scrutinise how beekeeping enables its practitioners to situate themselves in the forest locality and observe how the social relationships, interactions and everyday practices entailed in living and working together are a means through which beekeepers generate a sense of belonging and identity. As part and parcel of this process, men transmit their skills to a new generation, thus reproducing themselves and their social environment.

Pollen-based differentiation of Amazonian rainforest communities and implications for lowland palaeoecology in tropical South America

An ongoing controversy in Amazonian palaeoecology is the manner in which Amazonian rainforest communities have responded to environmental change over the last glacial–interglacial cycle. Much of this controversy results from an inability to identify the floristic heterogeneity exhibited by rainforest communities within fossil pollen records. We apply multivariate (Principal Components Analysis) and classification (Unweighted Pair Group with Arithmetic Mean Agglomerative Classification) techniques to floral-biometric, modern pollen trap and lake sediment pollen data situated within different rainforest communities in the tropical lowlands of Amazonian Bolivia. Modern pollen rain analyses from artificial pollen traps show that evergreen terra firme (well-drained), evergreen terra firme liana, evergreen seasonally inundated, and evergreen riparian rainforests may be readily differentiated, floristically and palynologically. Analogue matching techniques, based on Euclidean distance measures, are employed to compare these pollen signatures with surface sediment pollen assemblages from five lakes: Laguna Bella Vista, Laguna Chaplin, and Laguna Huachi situated within the Madeira-Tapajós moist forest ecoregion, and Laguna Isirere and Laguna Loma Suarez, which are situated within forest patches in the Beni savanna ecoregion. The same numerical techniques are used to compare rainforest pollen trap signatures with the fossil pollen record of Laguna Chaplin.

Global vegetation and terrestrial carbon cycle changes after the last ice age

•In current models, the ecophysiological effects of CO2 create both woody thickening and terrestrial carbon uptake, as observed now, and forest cover and terrestrial carbon storage increases that took place after the last glacial maximum (LGM). Here, we aimed to assess the realism of modelled vegetation and carbon storage changes between LGM and the pre-industrial Holocene (PIH). •We applied Land Processes and eXchanges (LPX), a dynamic global vegetation model (DGVM), with lowered CO2 and LGM climate anomalies from the Palaeoclimate Modelling Intercomparison Project (PMIP II), and compared the model results with palaeodata. •Modelled global gross primary production was reduced by 27–36% and carbon storage by 550–694 Pg C compared with PIH. Comparable reductions have been estimated from stable isotopes. The modelled areal reduction of forests is broadly consistent with pollen records. Despite reduced productivity and biomass, tropical forests accounted for a greater proportion of modelled land carbon storage at LGM (28–32%) than at PIH (25%). •The agreement between palaeodata and model results for LGM is consistent with the hypothesis that the ecophysiological effects of CO2 influence tree–grass competition and vegetation productivity, and suggests that these effects are also at work today.

Relationship between classroom authority and epistemological beliefs as espoused by primary school mathematics teachers from the very high and very low socio-economic regions in Thailand

This article presents findings of a larger single-country comparative study which set out to better understand primary school teachers’ mathematics education-related beliefs in Thailand. By combining the interview and observation data collected in the initial stage of this study with data gathered from the relevant literature, the 8-belief / 22-item ‘Thai Teachers’ Mathematics Education-related Beliefs’ (TTMEB) Scale was developed. The results of the Mann-Whitney U Test showed that Thai teachers in the two examined socio-economic regions espouse statistically different beliefs concerning the source and stability of mathematical knowledge, as well as classroom authority. Further, these three beliefs are found to be significantly and positively correlated.

The role of sky conditions on gross primary production in a mixed deciduous forest

The role of different sky conditions on diffuse PAR fraction (ϕ), air temperature (Ta), vapor pressure deficit (vpd) and GPP in a deciduous forest is investigated using eddy covariance observations of CO2 fluxes and radiometer and ceilometer observations of sky and PAR conditions on hourly and growing season timescales. Maximum GPP response occurred under moderate to high PAR and ϕ and low vpd. Light response models using a rectangular hyperbola showed a positive linear relation between ϕ and effective quantum efficiency (α = 0.023ϕ + 0.012, r2 = 0.994). Since PAR and ϕ are negatively correlated, there is a tradeoff between the greater use efficiency of diffuse light and lower vpd and the associated decrease in total PAR available for photosynthesis. To a lesser extent, light response was also modified by vpd and Ta. The net effect of these and their relation with sky conditions helped enhance light response under sky conditions that produced higher ϕ. Six sky conditions were classified from cloud frequency and ϕ data: optically thick clouds, optically thin clouds, mixed sky (partial clouds within hour), high, medium and low optical aerosol. The frequency and light responses of each sky condition for the growing season were used to predict the role of changing sky conditions on annual GPP. The net effect of increasing frequency of thick clouds is to decrease GPP, changing low aerosol conditions has negligible effect. Increases in the other sky conditions all lead to gains in GPP. Sky conditions that enhance intermediate levels of ϕ, such as thin or scattered clouds or higher aerosol concentrations from volcanic eruptions or anthropogenic emissions, will have a positive outcome on annual GPP, while an increase in cloud cover will have a negative impact. Due to the ϕ/PAR tradeoff and since GPP response to changes in individual sky conditions differ in sign and magnitude, the net response of ecosystem GPP to future sky conditions is non-linear and tends toward moderation of change.

Pollen-based reconstructions of biome distributions for Australia, Southeast Asia and the Pacific (SEAPAC region) at 0,6000 and 18,000 14C yr B.P.

Aim  This paper documents reconstructions of the vegetation patterns in Australia, Southeast Asia and the Pacific (SEAPAC region) in the mid-Holocene and at the last glacial maximum (LGM). Methods  Vegetation patterns were reconstructed from pollen data using an objective biomization scheme based on plant functional types. The biomization scheme was first tested using 535 modern pollen samples from 377 sites, and then applied unchanged to fossil pollen samples dating to 6000 ± 500 or 18,000 ± 1000 14C yr bp. Results  1. Tests using surface pollen sample sites showed that the biomization scheme is capable of reproducing the modern broad-scale patterns of vegetation distribution. The north–south gradient in temperature, reflected in transitions from cool evergreen needleleaf forest in the extreme south through temperate rain forest or wet sclerophyll forest (WSFW) and into tropical forests, is well reconstructed. The transitions from xerophytic through sclerophyll woodlands and open forests to closed-canopy forests, which reflect the gradient in plant available moisture from the continental interior towards the coast, are reconstructed with less geographical precision but nevertheless the broad-scale pattern emerges. 2. Differences between the modern and mid-Holocene vegetation patterns in mainland Australia are comparatively small and reflect changes in moisture availability rather than temperature. In south-eastern Australia some sites show a shift towards more moisture-stressed vegetation in the mid-Holocene with xerophytic woods/scrub and temperate sclerophyll woodland and shrubland at sites characterized today by WSFW or warm-temperate rain forest (WTRF). However, sites in the Snowy Mountains, on the Southern Tablelands and east of the Great Dividing Range have more moisture-demanding vegetation in the mid-Holocene than today. South-western Australia was slightly drier than today. The single site in north-western Australia also shows conditions drier than today in the mid-Holocene. Changes in the tropics are also comparatively small, but the presence of WTRF and tropical deciduous broadleaf forest and woodland in the mid-Holocene, in sites occupied today by cool-temperate rain forest, indicate warmer conditions. 3. Expansion of xerophytic vegetation in the south and tropical deciduous broadleaf forest and woodland in the north indicate drier conditions across mainland Australia at the LGM. None of these changes are informative about the degree of cooling. However the evidence from the tropics, showing lowering of the treeline and forest belts, indicates that conditions were between 1 and 9 °C (depending on elevation) colder. The encroachment of tropical deciduous broadleaf forest and woodland into lowland evergreen broadleaf forest implies greater aridity. Main conclusions  This study provides the first continental-scale reconstruction of mid-Holocene and LGM vegetation patterns from Australia, Southeast Asia and the Pacific (SEAPAC region) using an objective biomization scheme. These data will provide a benchmark for evaluation of palaeoclimate simulations within the framework of the Palaeoclimate Modelling Intercomparison Project.

Cation distribution and mixing thermodynamics in Fe/Ni thiospinels

The structural analogy between Ni-doped greigite minerals (Fe3S4) and the (Fe,Ni)S clusters present in biological enzymes has led to suggestions that these minerals could have acted as catalysts for the origin of life. However, little is known about the distribution and stability of Ni dopants in the greigite structure. We present here a theoretical investigation of mixed thiospinels (Fe1

What Tenants Want: UK occupiers’ requirements when renting commercial property and strategic implications for landlords

Businesses need property in order to generate turnover and profits. If real estate owners are to be able to provide properties and related services that are desirable, it is crucial that they understand tenants’ requirements and preferences. Changes in the way businesses operate might well lead to an overall reduction in space requirements in all sectors. Faced with reductions in demand, landlords will find themselves in an increasingly competitive marketplace for tenants. Of the array of strategies available to landlords, what strategies should they employ for maximum effect? This paper examines what United Kingdom tenants want from commercial property (retail, industrial and office). The first part provides an analysis of data from several hundred interviews with occupiers of commercial properties owned by some of the largest UK real estate investment companies. Results are presented for each of the asset classes separately. The second part compares the findings with previous research and discusses the strategic implications for landlords.

Forests of the tropical eastern Andean flank during the middle pleistocene

Inter-bedded volcanic and organic sediments from Erazo (Ecuador) indicate the presence of four different forest assemblages on the eastern Andean flank during the middle Pleistocene. Radiometric dates (40Ar–39Ar) obtained fromthe volcanic ash indicate that deposition occurred between 620,000 and 192,000 years ago. Examination of the organic sediment composition and the fossil pollen, wood and charcoal it contains provides insight into depositional environment, vegetation assemblage and fire history. The high organic content and abundance of macro fossils found throughout the sediment suggest that during the period of deposition the local environment was either a swamp or a shallow water body. The correlation of fire activity (peaks in charcoal abundance) with volcanic ash deposits through most of the record suggests that volcanoes were the main source of ignition. The low abundance of grass (typically b10%) throughout the sedimentary sequence along with the low abundance of other taxa indicative of open vegetation suggests the persistence of forest at Erazo. Four types of forest assemblage were identified (with the first taxa as the most dominant): i) Alnus-Arecaceae, ii) Miconia- Melastomataceae/Combretaceae-Moraceae/Urticaceae, iii) Arecaceae-Alnus, and iv) Podocarpus with Oreopanax sp. and Melastomataceae/Combretaceae. Changes in the forest floristic composition indicate high vegetation turnover and reassortment of taxa between upper and lower montane forests during the middle Pleistocene as well as the persistence of forest cover.

Locking-in carbon, locking-out livelihoods? ASM and REDD in Sub-Saharan Africa

This paper examines the potential mutual conflict between interventions aimed at formalising artisanal and small-scale mining (ASM) on the one hand, and policies implemented in response to the Reducing Emissions from Deforestation and Forest Degradation (REDD) initiative on the other. Deforestation caused by ASM undermines sound forest management, and potentially threatens the implementation of REDD. Conversely, the adoption of REDD could further marginalise and criminalise the ASM sector, reducing its contribution to poverty alleviation. Reviewing a series of commonalities between ASM and forest management highlights many difficulties facing policy-makers. Potentially, contradictory outcomes of evolving governance arrangements means novel cross-sectoral institutions will be required in order to realise the full potential of REDD and ASM to address poverty reduction in a complementary fashion. The analysis reiterates the centrality of livelihoods to REDD and the need for policies to take into account local contexts.

Simple measures of climate, soil properties and plant traits predict national scale grassland soil carbon stocks

1. Soil carbon (C) storage is a key ecosystem service. Soil C stocks play a vital role in soil fertility and climate regulation, but the factors that control these stocks at regional and national scales are unknown, particularly when their composition and stability are considered. As a result, their mapping relies on either unreliable proxy measures or laborious direct measurements. 2. Using data from an extensive national survey of English grasslands we show that surface soil (0-7cm) C stocks in size fractions of varying stability can be predicted at both regional and national scales from plant traits and simple measures of soil and climatic conditions. 3. Soil C stocks in the largest pool, of intermediate particle size (50-250 µm), were best explained by mean annual temperature (MAT), soil pH and soil moisture content. The second largest C pool, highly stable physically and biochemically protected particles (0.45-50 µm), was explained by soil pH and the community abundance weighted mean (CWM) leaf nitrogen (N) content, with the highest soil C stocks under N rich vegetation. The C stock in the small active fraction (250-4000 µm) was explained by a wide range of variables: MAT, mean annual precipitation, mean growing season length, soil pH and CWM specific leaf area; stocks were higher under vegetation with thick and/or dense leaves. 4. Testing the models describing these fractions against data from an independent English region indicated moderately strong correlation between predicted and actual values and no systematic bias, with the exception of the active fraction, for which predictions were inaccurate. 5. Synthesis and Applications: Validation indicates that readily available climate, soils and plant survey data can be effective in making local- to landscape-scale (1-100,000 km2) soil C stock predictions. Such predictions are a crucial component of effective management strategies to protect C stocks and enhance soil C sequestration.