Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs

An important question of biological relevance is the polymorphism of the double-helical DNA structure in its free form, and the changes that it undergoes upon protein-binding. We have analysed a database of free DNA crystal structures to assess the inherent variability of the free DNA structure and have compared it with a database of protein-bound DNA crystal structures to ascertain the protein-induced variations.

The top 100 questions of importance to the future of global agriculture

Despite a significant growth in food production over the past half-century, one of the most important challenges facing society today is how to feed an expected population of some nine billion by the middle of the 20th century. To meet the expected demand for food without significant increases in prices, it has been estimated that we need to produce 70-100 per cent more food, in light of the growing impacts of climate change, concerns over energy security, regional dietary shifts and the Millennium Development target of halving world poverty and hunger by 2015. The goal for the agricultural sector is no longer simply to maximize productivity, but to optimize across a far more complex landscape of production, rural development, environmental, social justice and food consumption outcomes. However, there remain significant challenges to developing national and international policies that support the wide emergence of more sustainable forms of land use and efficient agricultural production. The lack of information flow between scientists, practitioners and policy makers is known to exacerbate the difficulties, despite increased emphasis upon evidence-based policy. In this paper, we seek to improve dialogue and understanding between agricultural research and policy by identifying the 100 most important questions for global agriculture. These have been compiled using a horizon-scanning approach with leading experts and representatives of major agricultural organizations worldwide. The aim is to use sound scientific evidence to inform decision making and guide policy makers in the future direction of agricultural research priorities and policy support. If addressed, we anticipate that these questions will have a significant impact on global agricultural practices worldwide, while improving the synergy between agricultural policy, practice and research. This research forms part of the UK Government's Foresight Global Food and Farming Futures project.

An estimate of equilibrium sensitivity of global terrestrial carbon cycle using NCAR CCSM4

Increasing concentrations of atmospheric CO2 influence climate, terrestrial biosphere productivity and ecosystem carbon storage through its radiative, physiological and fertilization effects. In this paper, we quantify these effects for a doubling of CO2 using a low resolution configuration of the coupled model NCAR CCSM4. In contrast to previous coupled climate-carbon modeling studies, we focus on the near-equilibrium response of the terrestrial carbon cycle. For a doubling of CO2, the radiative effect on the physical climate system causes global mean surface air temperature to increase by 2.14 K, whereas the physiological and fertilization on the land biosphere effects cause a warming of 0.22 K, suggesting that these later effects increase global warming by about 10 % as found in many recent studies. The CO2-fertilization leads to total ecosystem carbon gain of 371 Gt-C (28 %) while the radiative effect causes a loss of 131 Gt-C (10 %) indicating that climate warming damps the fertilization-induced carbon uptake over land. Our model-based estimate for the maximum potential terrestrial carbon uptake resulting from a doubling of atmospheric CO2 concentration (285-570 ppm) is only 242 Gt-C. This highlights the limited storage capacity of the terrestrial carbon reservoir. We also find that the terrestrial carbon storage sensitivity to changes in CO2 and temperature have been estimated to be lower in previous transient simulations because of lags in the climate-carbon system. Our model simulations indicate that the time scale of terrestrial carbon cycle response is greater than 500 years for CO2-fertilization and about 200 years for temperature perturbations. We also find that dynamic changes in vegetation amplify the terrestrial carbon storage sensitivity relative to a static vegetation case: because of changes in tree cover, changes in total ecosystem carbon for CO2-direct and climate effects are amplified by 88 and 72 %, respectively, in simulations with dynamic vegetation when compared to static vegetation simulations.

Wet and dry spell characteristics of global tropical rainfall

In this study, we analyze satellite-based daily rainfall observations to compare and contrast the wet and dry spell characteristics of tropical rainfall. Defining a wet (dry) spell as the number of consecutive rainy (nonrainy) days, we find that the distributions of wet spells appear to exhibit universality in the following sense. While both ocean and land regions with high seasonal rainfall accumulation (humid regions; e. g., India, Amazon, Pacific Ocean) show a predominance of 2-4 day wet spells, those regions with low seasonal rainfall accumulation (arid regions; e. g., South Atlantic, South Australia) exhibit a wet spell duration distribution that is essentially exponential in nature, with a peak at 1 day. The behavior that we observed for wet spells is reversed for the dry spell characteristics. In other words, the main contribution to the dry part of the season, in terms of the number of nonrainy days, appears to come from 3-4 day dry spells in the arid regions, as opposed to 1 day dry spells in the humid regions. The total rainfall accumulated in each wet spell has also been analyzed, and we find that the major contribution to seasonal rainfall for arid regions comes from 1-5 day wet spells; however, for humid regions, this contribution comes from wet spells of duration as long as 30 days. We also explore the role of chance as well as the influence of organized convection in determining some of the observed features.

Ontology analysis of global gene expression differences of human bone marrow stromal cells cultured on 3D scaffolds or 2D films

Differences in gene expression of human bone marrow stromal cells (hBMSCs) during culture in three-dimensional (3D) nanofiber scaffolds or on two-dimensional (2D) films were investigated via pathway analysis of microarray mRNA expression profiles. Previous work has shown that hBMSC culture in nanofiber scaffolds can induce osteogenic differentiation in the absence of osteogenic supplements (OS). Analysis using ontology databases revealed that nanofibers and OS regulated similar pathways and that both were enriched for TGF-beta and cell-adhesion/ECM-receptor pathways. The most notable difference between the two was that nanofibers had stronger enrichment for cell-adhesion/ECM-receptor pathways. Comparison of nanofibers scaffolds with flat films yielded stronger differences in gene expression than comparison of nanofibers made from different polymers, suggesting that substrate structure had stronger effects on cell function than substrate polymer composition. These results demonstrate that physical (nanofibers) and biochemical (OS) signals regulate similar ontological pathways, suggesting that these cues use similar molecular mechanisms to control hBMSC differentiation. Published by Elsevier Ltd.

Ranking of global climate models for India using multicriterion analysis

Eleven GCMs (BCCR-BCCM2.0, INGV-ECHAM4, GFDL2.0, GFDL2.1, GISS, IPSL-CM4, MIROC3, MRI-CGCM2, NCAR-PCMI, UKMO-HADCM3 and UKMO-HADGEM1) were evaluated for India (covering 73 grid points of 2.5 degrees x 2.5 degrees) for the climate variable `precipitation rate' using 5 performance indicators. Performance indicators used were the correlation coefficient, normalised root mean square error, absolute normalised mean bias error, average absolute relative error and skill score. We used a nested bias correction methodology to remove the systematic biases in GCM simulations. The Entropy method was employed to obtain weights of these 5 indicators. Ranks of the 11 GCMs were obtained through a multicriterion decision-making outranking method, PROMETHEE-2 (Preference Ranking Organisation Method of Enrichment Evaluation). An equal weight scenario (assigning 0.2 weight for each indicator) was also used to rank the GCMs. An effort was also made to rank GCMs for 4 river basins (Godavari, Krishna, Mahanadi and Cauvery) in peninsular India. The upper Malaprabha catchment in Karnataka, India, was chosen to demonstrate the Entropy and PROMETHEE-2 methods. The Spearman rank correlation coefficient was employed to assess the association between the ranking patterns. Our results suggest that the ensemble of GFDL2.0, MIROC3, BCCR-BCCM2.0, UKMO-HADCM3, MPIECHAM4 and UKMO-HADGEM1 is suitable for India. The methodology proposed can be extended to rank GCMs for any selected region.

CTFS-ForestGEO: a worldwide network monitoring forests in an era of global change

Global change is impacting forests worldwide, threatening biodiversity and ecosystem services including climate regulation. Understanding how forests respond is critical to forest conservation and climate protection. This review describes an international network of 59 long-term forest dynamics research sites (CTFS-ForestGEO) useful for characterizing forest responses to global change. Within very large plots (median size 25ha), all stems 1cm diameter are identified to species, mapped, and regularly recensused according to standardized protocols. CTFS-ForestGEO spans 25 degrees S-61 degrees N latitude, is generally representative of the range of bioclimatic, edaphic, and topographic conditions experienced by forests worldwide, and is the only forest monitoring network that applies a standardized protocol to each of the world's major forest biomes. Supplementary standardized measurements at subsets of the sites provide additional information on plants, animals, and ecosystem and environmental variables. CTFS-ForestGEO sites are experiencing multifaceted anthropogenic global change pressures including warming (average 0.61 degrees C), changes in precipitation (up to +/- 30% change), atmospheric deposition of nitrogen and sulfur compounds (up to 3.8g Nm(-2)yr(-1) and 3.1g Sm(-2)yr(-1)), and forest fragmentation in the surrounding landscape (up to 88% reduced tree cover within 5km). The broad suite of measurements made at CTFS-ForestGEO sites makes it possible to investigate the complex ways in which global change is impacting forest dynamics. Ongoing research across the CTFS-ForestGEO network is yielding insights into how and why the forests are changing, and continued monitoring will provide vital contributions to understanding worldwide forest diversity and dynamics in an era of global change.