Order of the phase transition in models of DNA thermal denaturation

We examine the behavior of a model which describes the melting of double-stranded DNA chains. The model, with displacement-dependent stiffness constants and a Morse on-site potential, is analyzed numerically; depending on the stiffness parameter, it is shown to have either (i) a second-order transition with "nu_perpendicular" = - beta = 1, "nu_parallel" = gamma/2 = 2 (characteristic of short range attractive part of the Morse potential) or (ii) a first-order transition with finite melting entropy, discontinuous fraction of bound pairs, divergent correlation lengths, and critical exponents "nu_perpendicular" = - beta = 1/2, "nu_parallel" = gamma/2 = 1.Comment: 4 pages of Latex, including 4 Postscript figures. To be published in Phys. Rev. Let

Past and Future Land Use Impacts of Canadian Oil Sands and Greenhouse Gas Emissions

The Canadian oil sands underlie 142,000 km2 of the boreal forest in northeastern Alberta. Oil sands production greenhouse gas (GHG) emissions increased from 15 million tonnes (Mt) to 55 Mt between 1990 and 2011. Their production represents the fastest-growing source of GHG emissions in Canada. A large body of studies show that oil sands industries have large environmental impacts, including effects on climate, land, water, and air quality but GHG emissions from oil sands land use disturbance and future land use impacts have yet to be examined in detail and the associated literature is scarce and incomplete. Our paper examines the historical and potential land use change and GHG emissions associated with oil sands development in Canada. Disturbance occurred between 1985 and 2009 from oil sands development were identified using remote sensing technique and mapped onto spatially explicit soil, biomass and peatlands carbon maps. We found that land use and GHG disturbance of oil sands production, especially in-situ technology that will be the dominant technology of choice for future oil sands development, are greater than previously reported. We estimate additional 500 km2 and 2,400 km2 of boreal forest including carbon-rich peatlands would be disturbed from surface mining and in-situ production, respectively, between 2012 and 2030; releasing additional 107–182 million tonnes of GHG from land use alone. Future efforts to monitor land use impacts of in-situ production are needed to reduce landscape impacts and associated GHG emissions. In addition, land reclamation after oil sands projects needs to be enforced for broad ecological benefits together with GHG benefits

Precautionary Regulation in Europe and the United States: A Quantitative Comparison

Much attention has been addressed to the question of whether Europe or the United States adopts a more precautionary stance to the regulation of potential environmental, health, and safety risks. Some commentators suggest that Europe is more risk-averse and precautionary, whereas the US is seen as more risk-taking and optimistic about the prospects for new technology. Others suggest that the US is more precautionary because its regulatory process is more legalistic and adversarial, while Europe is more lax and corporatist in its regulations. The flip-flop hypothesis claims that the US was more precautionary than Europe in the 1970s and early 1980s, and that Europe has become more precautionary since then. We examine the levels and trends in regulation of environmental, health, and safety risks since 1970. Unlike previous research, which has studied only a small set of prominent cases selected non-randomly, we develop a comprehensive list of almost 3,000 risks and code the relative stringency of regulation in Europe and the US for each of 100 risks randomly selected from that list for each year from 1970 through 2004. Our results suggest that: (a) averaging over risks, there is no significant difference in relative precaution over the period, (b) weakly consistent with the flip-flop hypothesis, there is some evidence of a modest shift toward greater relative precaution of European regulation since about 1990, although (c) there is a diversity of trends across risks, of which the most common is no change in relative precaution (including cases where Europe and the US are equally precautionary and where Europe or the US has been consistently more precautionary). The overall finding is of a mixed and diverse pattern of relative transatlantic precaution over the period

Breakthrough Capability for UVOIR Space Astronomy: Reaching the Darkest Sky

We describe how availability of new solar electric propulsion (SEP) technology can substantially increase the science capability of space astronomy missions working within the near-UV to far-infrared (UVOIR) spectrum by making dark sky orbits accessible for the first time. We present a proof of concept case study in which SEP is used to enable a 700 kg Explorer-class observatory payload to reach an orbit beyond where the zodiacal dust limits observatory sensitivity. The resulting scientific performance advantage relative to a Sun-Earth L2 point orbit is presented and discussed. We find that making SEP available to astrophysics Explorers can enable this small payload program to rival the science performance of much larger long development-time systems. We also present flight dynamics analysis which illustrates that this concept can be extended beyond Explorers to substantially improve the sensitivity performance of heavier (7000 kg) flagship-class astrophysics payloads such as the UVOIR successor to the James Webb Space Telescope by using high power SEP that is being developed for the Asteroid Redirect Robotics Mission

Fourier transform ion cyclotron resonance mass spectrometric detection of small Ca2+-induced conformational changes in the regulatory domain of human cardiac troponin C

AbstractTroponin C (TnC), a calcium-binding protein of the thin filament of muscle, plays a regulatory role in skeletal and cardiac muscle contraction. NMR reveals a small conformational change in the cardiac regulatory N-terminal domain of TnC (cNTnC) on binding of Ca2+ such that the total exposed hydrophobic surface area increases very slightly from 3090 ± 86 Å2 for apo-cNTnC to 3108 ± 71 Å2 for Ca2+-cNTnC. Here, we show that measurement of solvent accessibility for backbone amide protons by means of solution-phase hydrogen/deuterium (H/D) exchange followed by pepsin digestion, high-performance liquid chromatography, and electrospray ionization high-field (9.4 T) Fourier transform Ion cyclotron resonance mass spectrometry is sufficiently sensitive to detect such small ligand binding-induced conformational changes of that protein. The extent of deuterium incorporation increases significantly on binding of Ca2+ for each of four proteolytic segments derived from pepsin digestion of the apo- and Ca2+-saturated forms of cNTnC. The present results demonstrate that H/D exchange monitored by mass spectrometry can be sufficiently sensitive to detect and identify even very small conformational changes in proteins, and should therefore be especially informative for proteins too large (or too insoluble or otherwise intractable) for NMR analysis

Spatial and topological organization of DNA chains induced by gene co-localization

Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into discrete spatial foci called transcription factories. However, the mechanisms underlying the formation of these foci and the resulting topological order of the chromosome remain to be elucidated. Here we consider a thermodynamic framework based on a worm-like chain model of chromosomes where sparse designated sites along the DNA are able to interact whenever they are spatially close-by. This is motivated by recurrent evidence that there exists physical interactions between genes that operate together. Three important results come out of this simple framework. First, the resulting formation of transcription foci can be viewed as a micro-phase separation of the interacting sites from the rest of the DNA. In this respect, a thermodynamic analysis suggests transcription factors to be appropriate candidates for mediating the physical interactions between genes. Next, numerical simulations of the polymer reveal a rich variety of phases that are associated with different topological orderings, each providing a way to increase the local concentrations of the interacting sites. Finally, the numerical results show that both one-dimensional clustering and periodic location of the binding sites along the DNA, which have been observed in several organisms, make the spatial co-localization of multiple families of genes particularly efficient.Comment: Figures and Supplementary Material freely available on http://dx.doi.org/10.1371/journal.pcbi.100067

Structure calculation, refinement and validation using CcpNmr Analysis

CcpNmr Analysis provides a streamlined pipeline for both NMR chemical shift assignment and structure determination of biological macromolecules. In addition, it encompasses tools to analyse the many additional experiments that make NMR such a pivotal technique for research into complex biological questions. This report describes how CcpNmr Analysis can seamlessly link together all of the tasks in the NMR structure-determination process. It details each of the stages from generating NMR restraints [distance, dihedral,hydrogen bonds and residual dipolar couplings (RDCs)],exporting these to and subsequently re-importing them from structure-calculation software (such as the programs CYANA or ARIA) and analysing and validating the results obtained from the structure calculation to, ultimately, the streamlined deposition of the completed assignments and the refined ensemble of structures into the PDBe repository. Until recently, such solution-structure determination by NMR has been quite a laborious task, requiring multiple stages and programs. However, with the new enhancements to CcpNmr Analysis described here, this process is now much more intuitive and efficient and less error-prone

Breakthrough Capability for UVOIR Space Astronomy: Reaching the Darkest Sky

We describe how availability of new solar electric propulsion (SEP) technology can substantially increase the science capability of space astronomy missions working within the near-UV to far-infrared (UVOIR) spectrum by making dark sky orbits accessible for the first time. We present two case studies in which SEP is used to enable a 700 kg Explorer-class and 7000 kg flagship-class observatory payload to reach an orbit beyond where the zodiacal dust limits observatory sensitivity. The resulting scientific performance advantage relative to a Sun-Earth L2 point (SEL2) orbit is presented and discussed. We find that making SEP available to astrophysics Explorers can enable this small payload program to rival the science performance of much larger long development-time systems. Similarly, we find that astrophysics utilization of high power SEP being developed for the Asteroid Redirect Robotics Mission (ARRM) can have a substantial impact on the sensitivity performance of heavier flagship-class astrophysics payloads such as the UVOIR successor to the James Webb Space Telescope

Salerno's model of DNA reanalysed: could solitons have biological significance?

We investigate the sequence-dependent behaviour of localised excitations in a toy, nonlinear model of DNA base-pair opening originally proposed by Salerno. Specifically we ask whether ``breather'' solitons could play a role in the facilitated location of promoters by RNA polymerase. In an effective potential formalism, we find excellent correlation between potential minima and {\em Escherichia coli} promoter recognition sites in the T7 bacteriophage genome. Evidence for a similar relationship between phage promoters and downstream coding regions is found and alternative reasons for links between AT richness and transcriptionally-significant sites are discussed. Consideration of the soliton energy of translocation provides a novel dynamical picture of sliding: steep potential gradients correspond to deterministic motion, while ``flat'' regions, corresponding to homogeneous AT or GC content, are governed by random, thermal motion. Finally we demonstrate an interesting equivalence between planar, breather solitons and the helical motion of a sliding protein ``particle'' about a bent DNA axis.Comment: Latex file 20 pages, 5 figures. Manuscript of paper to appear in J. Biol. Phys., accepted 02/09/0

On the nonlinear dynamics of topological solitons in DNA

Dynamics of topological solitons describing open states in the DNA double helix are studied in the frameworks of the model which takes into account asymmetry of the helix. It is shown that three types of topological solitons can occur in the DNA double chain. Interaction between the solitons, their interactions with the chain inhomogeneities and stability of the solitons with respect to thermal oscillations are investigated.Comment: 16 pages, 16 figure