Coevolutionary diversification creates nested-modular structure in phage-bacteria interaction networks

This is a post-print of an article published in Interface Focus. Please cite the published article.Phage and their bacterial hosts are the most diverse and abundant biological entities in the oceans, where their interactions have a major impact on marine ecology and ecosystem function. The structure of interaction networks for natural phage-bacteria communities offers insight into their coevolutionary origin. At small phylogenetic scales, observed communities typically show a nested structure, in which both hosts and phage can be ranked by their range of resistance and infectivity respectively. A qualitatively different multiscale structure is seen at larger phylogenetic scales; a natural assemblage sampled from the Atlantic Ocean displays large-scale modularity and local nestedness within each module. Here we show that such “nested-modular” interaction networks can be produced by a simple model of host-phage coevolution in which infection depends on genetic matching. Negative frequency-dependent selection causes diversification of hosts (to escape phage) and phage (to track their evolving hosts). This creates a diverse community of bacteria and phage, maintained by kill-the-winner ecological dynamics. When the resulting communities are visualised as bipartite networks of who-infects-whom, they show the nested-modular structure characteristic of the Atlantic sample. The statistical significance and strength of this observation varies depending on whether the interaction networks take into account the density of the interacting strains, with implications for interpretation of interaction networks constructed by different methods. Our results suggest that the apparently complex community structures associated with marine bacteria and phage may arise from relatively simple coevolutionary origins.University of Exete

Career toolbox - the decision paper: A tool to facilitate decision-making

Guidelines for writing a decision paper are presented. The purpose of the decision paper is to present complex issues in an organized format; it is especially helpful when timeliness is important. The writing style and format of the decision paper are described. The format for a decision paper includes the issue or problem statement, relevant background material, options or alternatives, discussion, recommendation, coordination/endorsement, and record of decision

Network analysis reveals open forums and echo chambers in social media discussions of climate change

Open Access articleAction to tackle the complex and divisive issue of climate change will be strongly influenced by public perception. Online social media and associated social networks are an increasingly important forum for public debate and are known to influence individual attitudes and behaviours yet online discussions and social networks related to climate change are not well understood. Here we construct several forms of social network for users communicating about climate change on the popular microblogging platform Twitter. We classify user attitudes to climate change based on message content and nd that social networks are characterised by strong attitude-based homophily and segregation into polarised "sceptic" and "activist" groups. Most users interact only with like-minded others, in communities dominated by a single view. However, we also nd mixed-attitude communities in which sceptics and activists frequently interact. Messages between like-minded users typically carry positive sentiment, while messages between sceptics and activists carry negative sentiment. We identify a number of general patterns in user behaviours relating to engagement with alternative views. Users who express negative sentiment are themselves the target of negativity. Users in mixed- attitude communities are less likely to hold a strongly polarised view, but more likely to express negative sentiment towards other users with di ering views. Overall, social media discussions of climate change often occur within polarising "echo chambers", but also within "open forums", mixed-attitude communities that reduce polarisation and stimulate debate. Our results have implications for public engagement with this important global challenge.Engineering and Physical Sciences Research Council (EPSRC) - Bridging the Gaps initiativ

A systematic review and meta-regression analysis of prophylactic gabapentin for postoperative pain

We searched MEDLINE, Embase, CINAHL, AMED and CENTRAL databases until December 2014 and included 133 randomised controlled trials of peri-operative gabapentin vs placebo. Gabapentin reduced mean (95% CI) 24-h morphine-equivalent consumption by 8.44 (7.26–9.62) mg, p < 0.001, whereas more specific reductions in morphine equivalents were predicted (R2 = 90%, p < 0.001) by the meta-regression equation: 3.73 + (−0.378 × control morphine consumption (mg)) + (−0.0023 × gabapentin dose (mg)) + (−1.917 × anaesthetic type), where ‘anaesthetic type’ is ‘1’ for general anaesthesia and ‘0’ for spinal anaesthesia. The type of surgery was not independently associated with gabapentin effect. Gabapentin reduced postoperative pain scores on a 10-point scale at 1 h, 2 h, 6 h, 12 h and 24 h by a mean (95% CI) of: 1.68 (1.35–2.01); 1.21 (0.88–1.55); 1.28 (0.98–1.57); 1.12 (0.91–1.33); and 0.71 (0.56–0.87), respectively, p < 0.001 for all. The risk ratios (95% CI) for postoperative nausea, vomiting, pruritus and sedation with gabapentin were: 0.78 (0.69–0.87), 0.67 (0.59–0.76), 0.64 (0.51–0.80) and 1.18 (1.09–1.28), respectively, p < 0.001 for all. Gabapentin reduced pre-operative anxiety and increased patient satisfaction on a 10-point scale by a mean (95% CI) of 1.52 (0.78–2.26) points and 0.89 (0.22–1.57) points, p < 0.001 and p = 0.01, respectively. All the effects of gabapentin may have been overestimated by statistically significant small study effects

Impact of vertical mixing on sea surface pCO2 in temperate seasonally stratified shelf seas

A key parameter in determining the exchange of CO2 across the ocean-atmosphere interface is the sea surface partial pressure of carbon dioxide (pCO2). Temperate seasonally stratified shelf seas represent a significant sink for atmospheric CO2. Here an analytical model is used to quantify the impact of vertical mixing across the seasonal thermocline on pCO2. The model includes the impacts of the resultant dissolved inorganic carbon, heat, salt, and alkalinity fluxes on the solubility of CO2 and the effect of the inorganic carbon sink created by the primary production fuelled by the flux of limiting nutrient. The results indicate that diapycnal mixing drives a modest but continuous change in pCO2 of order 1–10 µatm d−1. In quantifying the individual impacts of the fluxes of the different parameters, we find that the impact of the fluxes of DIC and nitrate fluxes dominate. In consequence, both the direction and magnitude of the change in pCO2 are strongly dependent on the C:N uptake ratio in primary production. While the smaller impacts of the heat and salt fluxes tend to compensate for each other at midshelf locations, the heat flux dominates close to the shelf break. The analysis highlights the importance of the accurate parameterization of the C:N uptake ratio, the surface-mixed layer depth, and the TKE dissipation rate within the seasonal thermocline in models to be used to predict the air-sea exchange of carbon dioxide in these regimes. The results implicate storms as key periods of pCO2 perturbation

Raman Scattering versus Infrared Conductivity: Evidence for one-dimensional Conduction in La_{2-x}Sr_{x}CuO_{4}

Raman and Infrared (IR) spectra of an underdoped La_{1.90}Sr_{0.10}CuO_{4} single crystal have been measured as a function of temperature. Both techniques provide unconventional low-energy spectra. The IR conductivity exhibits features peaked at finite frequencies which do not have a counterpart in the Raman response. Below approximately 100 K a transfer of both Raman and IR spectral weight towards lower energies is found and a new component in the Raman response builds up being characterized by a very long lifetime of electrons propagating along the Cu-O bonds.Comment: 4 pages, 3 eps figure

Ultrafast Spectroscopic Signatures of Coherent Electron-Transfer Mechanisms in a Transition Metal Complex

The prevalence of ultrafast electron-transfer processes in light-harvesting materials has motivated a deeper understanding of coherent reaction mechanisms. Kinetic models based on the traditional (equilibrium) form of Fermi's Golden Rule are commonly employed to understand photoinduced electron-transfer dynamics. These models fail in two ways when the electron-transfer process is fast compared to solvation dynamics and vibrational dephasing. First, electron-transfer dynamics may be accelerated if the photoexcited wavepacket traverses the point of degeneracy between donor and acceptor states in the solvent coordinate. Second, traditional kinetic models fail to describe electron-transfer transitions that yield products which undergo coherent nuclear motions. We address the second point in this work. Transient absorption spectroscopy and a numerical model are used to investigate coherent back-electron-transfer mechanisms in a transition metal complex composed of titanium and catechol, [Ti(cat)3]2-. The transient absorption experiments reveal coherent wavepacket motions initiated by the back-electron-transfer process. Model calculations suggest that the vibrationally coherent product states may originate in either vibrational populations or coherences of the reactant. That is, vibrational coherence may be produced even if the reactant does not undergo coherent nuclear motions. The analysis raises a question of broader significance: can a vibrational population-to-coherence transition (i.e., a nonsecular transition) accelerate electron-transfer reactions even when the rate is slower than vibrational dephasing

Communication: Uncovering correlated vibrational cooling and electron transfer dynamics with multidimensional spectroscopy

Analogues of 2D photon echo methods in which two population times are sampled have recently been used to expose heterogeneity in chemical kinetics. In this work, the two population times sampled for a transition metal complex are transformed into a 2D rate spectrum using the maximum entropy method. The 2D rate spectrum suggests heterogeneity in the vibrational cooling (VC) rate within the ensemble. In addition, a cross peak associated with VC and back electron transfer (BET) dynamics reveals correlation between the two processes. We hypothesize that an increase in the strength of solute-solvent interactions, which accelerates VC, drives the system toward the activationless regime of BET

Nonlinear dynamics for vortex lattice formation in a rotating Bose-Einstein condensate

We study the response of a trapped Bose-Einstein condensate to a sudden turn-on of a rotating drive by solving the two-dimensional Gross-Pitaevskii equation. A weakly anisotropic rotating potential excites a quadrupole shape oscillation and its time evolution is analyzed by the quasiparticle projection method. A simple recurrence oscillation of surface mode populations is broken in the quadrupole resonance region that depends on the trap anisotropy, causing stochastization of the dynamics. In the presence of the phenomenological dissipation, an initially irrotational condensate is found to undergo damped elliptic deformation followed by unstable surface ripple excitations, some of which develop into quantized vortices that eventually form a lattice. Recent experimental results on the vortex nucleation should be explained not only by the dynamical instability but also by the Landau instability; the latter is necessary for the vortices to penetrate into the condensate.Comment: RevTex4, This preprint includes no figures. You can download the complete article and figures at http://matter.sci.osaka-cu.ac.jp/bsr/cond-mat.htm

Vector meson production and nucleon resonance analysis in a coupled-channel approach for energies m_N < sqrt(s) < 2 GeV I: pion-induced results and hadronic parameters

We present a nucleon resonance analysis by simultaneously considering all pion- and photon-induced experimental data on the final states gamma N, pi N, 2 pi N, eta N, K Lambda, K Sigma, and omega N for energies from the nucleon mass up to sqrt(s) = 2 GeV. In this analysis we find strong evidence for the resonances P_{31}(1750), P_{13}(1900), P_{33}(1920), and D_{13}(1950). The omega N production mechanism is dominated by large P_{11}(1710) and P_{13}(1900) contributions. In this first part, we present the results of the pion-induced reactions and the extracted resonance and background properties with emphasis on the difference between global and purely hadronic fits.Comment: 54 pages, 26 figures, discussion extended, typos corrected, references updated, to appear in Phys. Rev.