PDB-Explorer: a web-based interactive map of the protein data bank in shape space

Background The RCSB Protein Data Bank (PDB) provides public access to experimentally determined 3D-structures of biological macromolecules (proteins, peptides and nucleic acids). While various tools are available to explore the PDB, options to access the global structural diversity of the entire PDB and to perceive relationships between PDB structures remain very limited. Methods A 136-dimensional atom pair 3D-fingerprint for proteins (3DP) counting categorized atom pairs at increasing through-space distances was designed to represent the molecular shape of PDB-entries. Nearest neighbor searches examples were reported exemplifying the ability of 3DP-similarity to identify closely related biomolecules from small peptides to enzyme and large multiprotein complexes such as virus particles. The principle component analysis was used to obtain the visualization of PDB in 3DP-space. Results The 3DP property space groups proteins and protein assemblies according to their 3D-shape similarity, yet shows exquisite ability to distinguish between closely related structures. An interactive website called PDB-Explorer is presented featuring a color-coded interactive map of PDB in 3DP-space. Each pixel of the map contains one or more PDB-entries which are directly visualized as ribbon diagrams when the pixel is selected. The PDB-Explorer website allows performing 3DP-nearest neighbor searches of any PDB-entry or of any structure uploaded as protein-type PDB file. All functionalities on the website are implemented in JavaScript in a platform-independent manner and draw data from a server that is updated daily with the latest PDB additions, ensuring complete and up-to-date coverage. The essentially instantaneous 3DP-similarity search with the PDB-Explorer provides results comparable to those of much slower 3D-alignment algorithms, and automatically clusters proteins from the same superfamilies in tight groups. Conclusion A chemical space classification of PDB based on molecular shape was obtained using a new atom-pair 3D-fingerprint for proteins and implemented in a web-based database exploration tool comprising an interactive color-coded map of the PDB chemical space and a nearest neighbor search tool. The PDB-Explorer website is freely available at www.​cheminfo.​org/​pdbexplorer and represents an unprecedented opportunity to interactively visualize and explore the structural diversity of the PDB.

Ethical considerations for a global concept of sustainable land use

The paper gives an overview of current land husbandry problems in different agro-ecological zones of the world. It then lists four ethical principles, conceived at the global level, needed to achieve sustainable land use (SLU). Finally, it develops guidelines which can be used to facilitate a more effective implementation and realization of SLU. In the year of the UN Conference on Environment and Development (UNCED), such recommendations are important for improving the competence of political and economic decision-makers in taking action at national and international levels.

Carbon-Based Ocean Productivity and Phytoplankton Physiology from Space

Ocean biogeochemical and ecosystem processes are linked by net primary production (NPP) in the ocean's surface layer, where inorganic carbon is fixed by photosynthetic processes. Determinations of NPP are necessarily a function of phytoplankton biomass and its physiological status, but the estimation of these two terms from space has remained an elusive target. Here we present new satellite ocean color observations of phytoplankton carbon (C) and chlorophyll (Chl) biomass and show that derived Chl:C ratios closely follow anticipated physiological dependencies on light, nutrients, and temperature. With this new information, global estimates of phytoplankton growth rates (mu) and carbon-based NPP are made for the first time. Compared to an earlier chlorophyll-based approach, our carbon-based values are considerably higher in tropical oceans, show greater seasonality at middle and high latitudes, and illustrate important differences in the formation and demise of regional algal blooms. This fusion of emerging concepts from the phycological and remote sensing disciplines has the potential to fundamentally change how we model and observe carbon cycling in the global oceans.

Evaluating the U.S. Global Health Policy Initiative

In understanding that the efforts made in improving global health affects the health of U.S. citizens, a policy analysis of President Barak Obama's Global Health Initiative was conducted. Using materials gathered from experts in the field of health and their findings and recommendations, paired with the current policies of other G8 countries that pledged to support the efforts of improving global health, the analysis was conducted using four specifically defined criteria. The set criteria determine the appropriateness, responsiveness, effectiveness and equity of Obama's GHI in comparison to other G8 country health policies and overall global health priorities. G8 countries without a specific global health policy, or with a policy that was not in English were excluded from this study and Switzerland, headquarters of the World Health Organization, was added due to its membership in the OECD, and the fact that it has a specific foreign health policy. In evaluating the U.S. Global Health Initiative it is clear that in terms of implementing foreign policy specific to health, the United States is on the forefront alongside the United Kingdom and Switzerland. Other G8 Countries have pledged monies and in order to Millennium Development Health Goals by 2015. The U.S. Global Health Policy does not address issues necessary to meet Millennium Development Goals in Health. Instead the Global Health Initiative is focused narrowly on Fighting and rolling back the HIV/Aids Epidemic based on President Bush's PEPFAR policy. Policy recommendations for a more effective and efficient Global Health Initiative include building upon the PEPFAR policy foundation in order to strengthen health systems worldwide, allowing individuals and communities to combat unnecessary death and disease through research, education, and other preventative methods.^

Global planktonic foraminifera seasonality

Shell fluxes of planktonic Foraminifera species vary intra-annually in a pattern that appears to follow the seasonal cycle. However, the variation in the timing and prominence of seasonal flux maxima in space and among species remains poorly constrained. Thus, although changing seasonality may result in a flux-weighted temperature offset of more than 5° C within a species, this effect is often ignored in the interpretation of Foraminifera-based paleoceanographic records. To address this issue we present an analysis of the intra-annual pattern of shell flux variability in 37 globally distributed time series. The existence of a seasonal component in flux variability was objectively characterised using periodic regression. This analysis yielded estimates of the number, timing and prominence of seasonal flux maxima. Over 80% of the flux series across all species showed a statistically significant periodic component, indicating that a considerable part of the intra-annual flux variability is predictable. Temperature appears to be a powerful predictor of flux seasonality, but its effect differs among species. Three different modes of seasonality are distinguishable. Tropical and subtropical species (Globigerinoides ruber (white and pink varieties), Neogloboquadrina dutertrei, Globigerinoides sacculifer, Orbulina universa, Globigerinella siphonifera, Pulleniatina obliquiloculata, Globorotalia menardii, Globoturborotalita rubescens, Globoturborotalita tenella and Globigerinoides conglobatus) appear to have a less predictable flux pattern, with random peak timing in warm waters. In colder waters, seasonality is more prevalent: peak fluxes occur shortly after summer temperature maxima and peak prominence increases. This tendency is stronger in species with a narrower temperature range, implying that warm-adapted species find it increasingly difficult to reproduce outside their optimum temperature range and that, with decreasing mean temperature, their flux is progressively more focussed in the warm season. The second group includes the temperate to cold-water species Globigerina bulloides, Globigerinita glutinata, Turborotalita quinqueloba, Neogloboquadrina incompta, Neogloboquadrina pachyderma, Globorotalia scitula, Globigerinella calida, Globigerina falconensis, Globorotalia theyeri and Globigerinita uvula. These species show a highly predictable seasonal pattern, with one to two peaks a year, which occur earlier in warmer waters. Peak prominence in this group is independent of temperature. The earlier-when-warmer pattern in this group is related to the timing of productivity maxima. Finally, the deep-dwelling Globorotalia truncatulinoides and Globorotalia inflata show a regular and pronounced peak in winter and spring. The remarkably low flux outside the main pulse may indicate a long reproductive cycle of these species. Overall, our analysis indicates that the seasonality of planktonic Foraminifera shell flux is predictable and reveals the existence of distinct modes of phenology among species. We evaluate the effect of changing seasonality on paleoceanographic reconstructions and find that, irrespective of the seasonality mode, the actual magnitude of environmental change will be underestimated. The observed constraints on flux seasonality can serve as the basis for predictive modelling of flux pattern. As long as the diversity of species seasonality is accounted for in such models, the results can be used to improve reconstructions of the magnitude of environmental change in paleoceanographic records.