Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163T and comparative genomic insights into plant pathogenicity

Smits THM, Jaenicke S, Rezzonico F, et al. Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163(T) and comparative genomic insights into plant pathogenicity. BMC Genomics. 2010;11(1): 2.Background: Erwinia pyrifoliae is a newly described necrotrophic pathogen, which causes fire blight on Asian (Nashi) pear and is geographically restricted to Eastern Asia. Relatively little is known about its genetics compared to the closely related main fire blight pathogen E. amylovora. Results: The genome of the type strain of E. pyrifoliae strain DSM 12163(T), was sequenced using both 454 and Solexa pyrosequencing and annotated. The genome contains a circular chromosome of 4.026 Mb and four small plasmids. Based on their respective role in virulence in E. amylovora or related organisms, we identified several putative virulence factors, including type III and type VI secretion systems and their effectors, flagellar genes, sorbitol metabolism, iron uptake determinants, and quorum-sensing components. A deletion in the rpoS gene covering the most conserved region of the protein was identified which may contribute to the difference in virulence/host-range compared to E. amylovora. Comparative genomics with the pome fruit epiphyte Erwinia tasmaniensis Et1/99 showed that both species are overall highly similar, although specific differences were identified, for example the presence of some phage gene-containing regions and a high number of putative genomic islands containing transposases in the E. pyrifoliae DSM 12163T genome. Conclusions: The E. pyrifoliae genome is an important addition to the published genome of E. tasmaniensis and the unfinished genome of E. amylovora providing a foundation for re-sequencing additional strains that may shed light on the evolution of the host-range and virulence/pathogenicity of this important group of plant-associated bacteria

Perceptions of, and reactions to, environmental heat: a brief note on issues of concern in relation to occupational health

Average temperatures around the world are already increasing, and climate change projections suggest that global mean temperatures will continue to rise. As the effects, and projected effects, of climate change are becoming clearer, it is more apparent that the health effects of heat exposure will need further investigation. The risks associated with heat exposure are especially relevant to understandings of occupational health for people involved in labouring or agricultural work in low-income countries. This review is a partial look at the ways in which issues surrounding heat exposure and occupational health have been treated in some of the available literature. This literature focuses on military-related medical understandings of heat exposure as well as heat exposure in working environments. The ways that these issues have been treated throughout the literature reflect the ways in which technologies of observation are intertwined with social attitudes. The effects of heat on the health of working people, as well as identification of risk groups, will require further research in order to promote prophylactic measures as well as to add to understandings of the actual and potential consequences of climatic change

Stochastic population growth in spatially heterogeneous environments

Classical ecological theory predicts that environmental stochasticity increases extinction risk by reducing the average per-capita growth rate of populations. To understand the interactive effects of environmental stochasticity, spatial heterogeneity, and dispersal on population growth, we study the following model for population abundances in $n$ patches: the conditional law of $X_{t+dt}$ given $X_t=x$ is such that when $dt$ is small the conditional mean of $X_{t+dt}^i-X_t^i$ is approximately $[x^i\mu_i+\sum_j(x^j D_{ji}-x^i D_{ij})]dt$, where $X_t^i$ and $\mu_i$ are the abundance and per capita growth rate in the $i$-th patch respectivly, and $D_{ij}$ is the dispersal rate from the $i$-th to the $j$-th patch, and the conditional covariance of $X_{t+dt}^i-X_t^i$ and $X_{t+dt}^j-X_t^j$ is approximately $x^i x^j \sigma_{ij}dt$. We show for such a spatially extended population that if $S_t=(X_t^1+...+X_t^n)$ is the total population abundance, then $Y_t=X_t/S_t$, the vector of patch proportions, converges in law to a random vector $Y_\infty$ as $t\to\infty$, and the stochastic growth rate $\lim_{t\to\infty}t^{-1}\log S_t$ equals the space-time average per-capita growth rate \sum_i\mu_i\E[Y_\infty^i] experienced by the population minus half of the space-time average temporal variation \E[\sum_{i,j}\sigma_{ij}Y_\infty^i Y_\infty^j] experienced by the population. We derive analytic results for the law of $Y_\infty$, find which choice of the dispersal mechanism $D$ produces an optimal stochastic growth rate for a freely dispersing population, and investigate the effect on the stochastic growth rate of constraints on dispersal rates. Our results provide fundamental insights into "ideal free" movement in the face of uncertainty, the persistence of coupled sink populations, the evolution of dispersal rates, and the single large or several small (SLOSS) debate in conservation biology.Comment: 47 pages, 4 figure

Multiple magnon modes and consequences for the Bose-Einstein condensed phase in BaCuSi2O6

The compound BaCuSi2O6 is a quantum magnet with antiferromagnetic dimers of S=1/2 moments on a quasi-2D square lattice. We have investigated its spin dynamics by inelastic neutron scattering experiments on single crystals with an energy resolution considerably higher than in an earlier study. We observe multiple magnon modes, indicating clearly the presence of magnetically inequivalent dimer sites. The more complex spin Hamiltonian revealed in our study leads to a distinct form of magnon Bose-Einstein condensate phase with a spatially modulated condensate amplitude

The prevalence, characteristics and effectiveness of Aichi Target 11 ' s "other effective area-based conservation measures" (OECMs) in Key Biodiversity Areas

Aichi Target 11 of the CBD Strategic Plan for Biodiversity commits countries to the effective conservation of areas of importance for biodiversity, through protected areas and “other effective area-based conservation measures” (OECMs). However, the prevalence and characteristics of OECMs are poorly known, particularly in sites of importance for biodiversity. We assess the prevalence of potential OECMs in 740 terrestrial Key Biodiversity Areas (KBAs) outside known or mapped protected areas across ten countries. A majority of unprotected KBAs (76.5%) were at least partly covered by one or more potential OECMs. The conservation of ecosystem services or biodiversity was a stated management aim in 73% of these OECMs. Local or central government bodies managed the highest number of potential OECMs, followed by local and indigenous communities and private landowners. There was no difference between unprotected KBAs with or without OECMs in forest loss or in a number of state-pressure-response metrics.The project was funded by the CCI Collaborative Fun

Computing and visually analyzing mutual information in molecular co-evolution

<p>Abstract</p> <p>Background</p> <p>Selective pressure in molecular evolution leads to uneven distributions of amino acids and nucleotides. In fact one observes correlations among such constituents due to a large number of biophysical mechanisms (folding properties, electrostatics, ...). To quantify these correlations the mutual information -after proper normalization - has proven most effective. The challenge is to navigate the large amount of data, which in a study for a typical protein cannot simply be plotted.</p> <p>Results</p> <p>To visually analyze mutual information we developed a matrix visualization tool that allows different views on the mutual information matrix: filtering, sorting, and weighting are among them. The user can interactively navigate a huge matrix in real-time and search e.g., for patterns and unusual high or low values. A computation of the mutual information matrix for a sequence alignment in FASTA-format is possible. The respective stand-alone program computes in addition proper normalizations for a null model of neutral evolution and maps the mutual information to <it>Z</it>-scores with respect to the null model.</p> <p>Conclusions</p> <p>The new tool allows to compute and visually analyze sequence data for possible co-evolutionary signals. The tool has already been successfully employed in evolutionary studies on HIV1 protease and acetylcholinesterase. The functionality of the tool was defined by users using the tool in real-world research. The software can also be used for visual analysis of other matrix-like data, such as information obtained by DNA microarray experiments. The package is platform-independently implemented in <monospace>Java</monospace> and free for academic use under a GPL license.</p

On the interpretation of a possible ∼ 750 GeV particle decaying into γγ

We consider interpretations of the recent ∼ 3σ reports by the CMS and ATLAS collaborations of a possible X (∼750 GeV) state decaying into γγ final states. We focus on the possibilities that this is a scalar or pseudoscalar electroweak isoscalar state produced by gluon-gluon fusion mediated by loops of heavy fermions. We consider several models for these fermions, including a single vector-like charge 2/3 T quark, a doublet of vector-like quarks (T, B), and a vector-like generation of quarks, with or without leptons that also contribute to the X → γγ decay amplitude. We also consider the possibility that X (750) is a dark matter mediator, with a neutral vector-like dark matter particle. These scenarios are compatible with the present and prospective direct limits on vector-like fermions from LHC Runs 1 and 2, as well as indirect constraints from electroweak precision measurements, and we show that the required Yukawa-like couplings between the X particle and the heavy vector-like fermions are small enough to be perturbative so long as the X particle has dominant decay modes into gg and γγ. The decays X → ZZ, Zγ and W+W− are interesting prospective signatures that may help distinguish between different vector-like fermion scenarios

SAMPI: Protein Identification with Mass Spectra Alignments

BACKGROUND: Mass spectrometry based peptide mass fingerprints (PMFs) offer a fast, efficient, and robust method for protein identification. A protein is digested (usually by trypsin) and its mass spectrum is compared to simulated spectra for protein sequences in a database. However, existing tools for analyzing PMFs often suffer from missing or heuristic analysis of the significance of search results and insufficient handling of missing and additional peaks. RESULTS: We present an unified framework for analyzing Peptide Mass Fingerprints that offers a number of advantages over existing methods: First, comparison of mass spectra is based on a scoring function that can be custom-designed for certain applications and explicitly takes missing and additional peaks into account. The method is able to simulate almost every additive scoring scheme. Second, we present an efficient deterministic method for assessing the significance of a protein hit, independent of the underlying scoring function and sequence database. We prove the applicability of our approach using biological mass spectrometry data and compare our results to the standard software Mascot. CONCLUSION: The proposed framework for analyzing Peptide Mass Fingerprints shows performance comparable to Mascot on small peak lists. Introducing more noise peaks, we are able to keep identification rates at a similar level by using the flexibility introduced by scoring schemes

Observation of one-way Einstein-Podolsky-Rosen steering

The distinctive non-classical features of quantum physics were first discussed in the seminal paper by A. Einstein, B. Podolsky and N. Rosen (EPR) in 1935. In his immediate response E. Schr\"odinger introduced the notion of entanglement, now seen as the essential resource in quantum information as well as in quantum metrology. Furthermore he showed that at the core of the EPR argument is a phenomenon which he called steering. In contrast to entanglement and violations of Bell's inequalities, steering implies a direction between the parties involved. Recent theoretical works have precisely defined this property. Here we present an experimental realization of two entangled Gaussian modes of light by which in fact one party can steer the other but not conversely. The generated one-way steering gives a new insight into quantum physics and may open a new field of applications in quantum information.Comment: 4 pages, 4 figure

Morphology and photoluminescence study of titania nanoparticles

Titania nanoparticles are prepared by sol–gel chemistry with a poly(ethylene oxide) methyl ether methacrylate-block-poly(dimethylsiloxane)-block-poly(ethylene oxide) methyl ether methacrylate triblock copolymer acting as the templating agent. The sol–gel components—hydrochloric acid, titanium tetraisopropoxide, and triblock copolymer—are varied to investigate their effect on the resulting titania morphology. An increased titania precursor or polymer content yields smaller primary titania structures. Microbeam grazing incidence small-angle X-ray scattering measurements, which are analyzed with a unified fit model, reveal information about the titania structure sizes. These small structures could not be observed via the used microscopy techniques. The interplay among the sol–gel components via our triblock copolymer results in different sized titania nanoparticles with higher packing densities. Smaller sized titania particles, (∼13–20 nm in diameter) in the range of exciton diffusion length, are formed by 2% by weight polymer and show good crystallinity with less surface defects and high oxygen vacancies