Conformational analysis of nucleic acids revisited: Curves+

We describe Curves+, a new nucleic acid conformational analysis program which is applicable to a wide range of nucleic acid structures, including those with up to four strands and with either canonical or modified bases and backbones. The program is algorithmically simpler and computationally much faster than the earlier Curves approach, although it still provides both helical and backbone parameters, including a curvilinear axis and parameters relating the position of the bases to this axis. It additionally provides a full analysis of groove widths and depths. Curves+ can also be used to analyse molecular dynamics trajectories. With the help of the accompanying program Canal, it is possible to produce a variety of graphical output including parameter variations along a given structure and time series or histograms of parameter variations during dynamic

Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

We use cryo-electron microscopy (cryo-EM) to study the 3D shapes of 94-bp-long DNA minicircles and address the question of whether cyclization of such short DNA molecules necessitates the formation of sharp, localized kinks in DNA or whether the necessary bending can be redistributed and accomplished within the limits of the elastic, standard model of DNA flexibility. By comparing the shapes of covalently closed, nicked and gapped DNA minicircles, we conclude that 94-bp-long covalently closed and nicked DNA minicircles do not show sharp kinks while gapped DNA molecules, containing very flexible single-stranded regions, do show sharp kinks. We corroborate the results of cryo-EM studies by using Bal31 nuclease to probe for the existence of kinks in 94-bp-long minicircle

Structural motifs of biomolecules

Biomolecular structures are assemblies of emergent anisotropic building modules such as uniaxial helices or biaxial strands. We provide an approach to understanding a marginally compact phase of matter that is occupied by proteins and DNA. This phase, which is in some respects analogous to the liquid crystal phase for chain molecules, stabilizes a range of shapes that can be obtained by sequence-independent interactions occurring intra- and intermolecularly between polymeric molecules. We present a singularityfree self-interaction for a tube in the continuum limit and show that this results in the tube being positioned in the marginally compact phase. Our work provides a unified framework for understanding the building blocks of biomolecules.Comment: 13 pages, 5 figure

Plasmon Lifetime in K: A Case Study of Correlated Electrons in Solids Amenable to Ab Initio Theory

On the basis of a new ab initio, all-electron response scheme, formulated within time-dependent density-functional theory, we solve the puzzle posed by the anomalous dispersion of the plasmon linewidth in K. The key damping mechanism is shown to be decay into particle-hole pairs involving empty states of d-symmetry. While the effect of many-particle correlations is small, the correlations built into the "final-state" -d-bands play an important, and novel, role ---which is related to the phase-space complexity associated with these flat bands. Our case study of plasmon lifetime in K illustrates the importance of ab initio paradigms for the study of excitations in correlated-electron systems.Comment: 12 pages, 4 figures, for html browsing see http://web.utk.edu/~weik

Minimal versus specialist equipment for the delivery of pulmonary rehabilitation in COPD

Background: Evidence for pulmonary rehabilitation(PR)largely comes from trials where the intervention used specialist aerobic and/or resistance equipment.Limited data exist to demonstrate the efficacy of PR in community settings with minimal equipment. Aims: To compare completion rates and outcomes in COPD patients undergoing PR in a community setting with minimal equipment(PR-min)with a matched sample undergoing PR in a gym setting with specialist aerobic and resistance equipment(PR-gym). Methods: Using propensity score matching,318 patients with COPD referred for 8 weeks of PR-min were matched 1:1 with a control group of 318 patients who undertook 8 weeks of PR-gym. Completion rate(attendance≥8 supervised sessions)and changes in incremental shuttle walk(ISW),Chronic Respiratory Disease Questionnaire(CRQ)and quadriceps maximal voluntary contraction(QMVC)were compared. Results: Groups were matched for age(70.8v70.7years),FEV1%predicted(46.8v45.8),ISW(192v195m),%current smoking status(19v20)and depression scores(6.5v6.6).No between group differences were seen in ISW,CRQ or QMVC change. Completion rates were better in the PR-gym(73%)as opposed to the PR-min(64%);p=0.01. Conclusion: This case-control study shows that PR-min had similar benefits to PR-gym.A randomised non-inferiority trial is needed to confirm the findings of this study

On the nonlinear stability of mKdV breathers

A mathematical proof for the stability of mKdV breathers is announced. This proof involves the existence of a nonlinear equation satisfied by all breather profiles, and a new Lyapunov functional which controls the dynamics of small perturbations and instability modes. In order to construct such a functional, we work in a subspace of the energy one. However, our proof introduces new ideas in order to attack the corresponding stability problem in the energy space. Some remarks about the sine-Gordon case are also considered.Comment: 7 p

Conformational analysis of nucleic acids revisited: Curves

We describe Curves+, a new nucleic acid conformational analysis program which is applicable to a wide range of nucleic acid structures, including those with up to four strands and with either canonical or modified bases and backbones. The program is algorithmically simpler and computationally much faster than the earlier Curves approach, although it still provides both helical and backbone parameters, including a curvilinear axis and parameters relating the position of the bases to this axis. It additionally provides a full analysis of groove widths and depths. Curves+ can also be used to analyse molecular dynamics trajectories. With the help of the accompanying program Canal, it is possible to produce a variety of graphical output including parameter variations along a given structure and time series or histograms of parameter variations during dynamics

An assessment of the strength of knots and splices used as eye terminations in a sailing environment

Research into knots, splices and other methods of forming an eye termination has been limited, despite the fact that they are essential and strongly affect the performance of a rope. The aim of this study was to carry out a comprehensive initial assessment of the breaking strength of eye terminations commonly used in a sailing environment, thereby providing direction for further work in the field. Supports for use in a regular tensile testing machine were specially developed to allow individual testing of each sample and a realistic spread of statistical data to be obtained. Over 180 break tests were carried out on four knots (the bowline, double bowline, figure-of-eight loop and perfection loop) and two splices (three-strand eye splice and braid-on-braid splice). The factors affecting their strength were investigated. A statistical approach to the analysis of the results was adopted. The type of knot was found to have a significant effect on the strength. This same effect was seen in both types of rope construction (three-strand and braid-on-braid). Conclusions were also drawn as to the effect of splice length, eye size, manufacturer and rope diameter on the breaking strength of splices. Areas of development and further investigation were identified

Plasmonic excitations in noble metals: The case of Ag

The delicate interplay between plasmonic excitations and interband transitions in noble metals is described by means of {\it ab initio} calculations and a simple model in which the conduction electron plasmon is coupled to the continuum of electron-hole pairs. Band structure effects, specially the energy at which the excitation of the $d$-like bands takes place, determine the existence of a subthreshold plasmonic mode, which manifests itself in Ag as a sharp resonance at 3.8 eV. However, such a resonance is not observed in the other noble metals. Here, this different behavior is also analyzed and an explanation is provided.Comment: 9 pages, 8 figure

Novel cyclic di-GMP effectors of the YajQ protein family control bacterial virulence

Bis-(3 ',5 ') cyclic di-guanylate (cyclic di-GMP) is a key bacterial second messenger that is implicated in the regulation of many critical processes that include motility, biofilm formation and virulence. Cyclic di-GMP influences diverse functions through interaction with a range of effectors. Our knowledge of these effectors and their different regulatory actions is far from complete, however. Here we have used an affinity pull-down assay using cyclic di-GMP-coupled magnetic beads to identify cyclic di-GMP binding proteins in the plant pathogen Xanthomonas campestris pv. campestris (Xcc). This analysis identified XC_3703, a protein of the YajQ family, as a potential cyclic di-GMP receptor. Isothermal titration calorimetry showed that the purified XC_3703 protein bound cyclic di-GMP with a high affinity (K-d similar to 2 mu M). Mutation of XC_3703 led to reduced virulence of Xcc to plants and alteration in biofilm formation. Yeast two-hybrid and far-western analyses showed that XC_3703 was able to interact with XC_2801, a transcription factor of the LysR family. Mutation of XC_2801 and XC_3703 had partially overlapping effects on the transcriptome of Xcc, and both affected virulence. Electromobility shift assays showed that XC_3703 positively affected the binding of XC_2801 to the promoters of target virulence genes, an effect that was reversed by cyclic di-GMP. Genetic and functional analysis of YajQ family members from the human pathogens Pseudomonas aeruginosa and Stenotrophomonas maltophilia showed that they also specifically bound cyclic di-GMP and contributed to virulence in model systems. The findings thus identify a new class of cyclic di-GMP effector that regulates bacterial virulence