A review of the global ecology, genomics, and biogeography of the toxic cyanobacterium, Microcystis spp.

This review summarizes the present state of knowledge regarding the toxic, bloom-forming cyanobacterium, Microcystis, with a specific focus on its geographic distribution, toxins, genomics, phylogeny, and ecology. A global analysis found documentation suggesting geographic expansion of Microcystis, with recorded blooms in at least 108 countries, 79 of which have also reported the hepatatoxin microcystin. The production of microcystins (originally “Fast-Death Factor”) by Microcystis and factors that control synthesis of this toxin are reviewed, as well as the putative ecophysiological roles of this metabolite. Molecular biological analyses have provided significant insight into the ecology and physiology of Microcystis, as well as revealed the highly dynamic, and potentially unstable, nature of its genome. A genetic sequence analysis of 27 Microcystis species, including 15 complete/draft genomes are presented. Using the strictest biological definition of what constitutes a bacterial species, these analyses indicate that all Microcystis species warrant placement into the same species complex since the average nucleotide identity values were above 95%, 16S rRNA nucleotide identity scores exceeded 99%, and DNA–DNA hybridization was consistently greater than 70%. The review further provides evidence from around the globe for the key role that both nitrogen and phosphorus play in controlling Microcystis bloom dynamics, and the effect of elevated temperature on bloom intensification. Finally, highlighted is the ability of Microcystis assemblages to minimize their mortality losses by resisting grazing by zooplankton and bivalves, as well as viral lysis, and discuss factors facilitating assemblage resilience

Are direct photons a clean signal of a thermalized quark gluon plasma?

Direct photon production from a quark gluon plasma (QGP) in thermal equilibrium is studied directly in real time. In contrast to the usual S-matrix calculations, the real time approach is valid for a QGP that formed and reached LTE a short time after a collision and of finite lifetime ($\sim 10-20 \mathrm{fm}/c$ as expected at RHIC or LHC). We point out that during such finite QGP lifetime the spectrum of emitted photons carries information on the initial state. There is an inherent ambiguity in separating the virtual from the observable photons during the transient evolution of the QGP. We propose a real time formulation to extract the photon yield which includes the initial stage of formation of the QGP parametrized by an effective time scale of formation $\Gamma^{-1}$. This formulation coincides with the S-matrix approach in the infinite lifetime limit. It allows to separate the virtual cloud as well as the observable photons emitted during the pre- equilibrium stage from the yield during the QGP lifetime. We find that the lowest order contribution $\mathcal{O}(\alpha_{em})$ which does \emph{not} contribute to the S-matrix approach, is of the same order of or larger than the S-matrix contribution during the lifetime of the QGP for a typical formation time $\sim 1 \mathrm{fm}/c$. The yield for momenta $\gtrsim 3 \mathrm{Gev}/c$ features a power law fall-off $\sim T^3 \Gamma^2/k^{5}$ and is larger than that obtained with the S-matrix for momenta $\geq 4 \mathrm{Gev}/c$. We provide a comprehensive numerical comparison between the real time and S-matrix yields and study the dynamics of the build-up of the photon cloud and the different contributions to the radiative energy loss. The reliability of the current estimates on photon emission is discussed.Comment: 31 pages, 12 eps figures, version to appear in PR

Non-Markovian entanglement dynamics in coupled superconducting qubit systems

We theoretically analyze the entanglement generation and dynamics by coupled Josephson junction qubits. Considering a current-biased Josephson junction (CBJJ), we generate maximally entangled states. In particular, the entanglement dynamics is considered as a function of the decoherence parameters, such as the temperature, the ratio $r\equiv\omega_c/\omega_0$ between the reservoir cutoff frequency $\omega_c$ and the system oscillator frequency $\omega_0$, % between $\omega_0$ the characteristic frequency of the %quantum system of interest, and $\omega_c$ the cut-off frequency of %Ohmic reservoir and the energy levels split of the superconducting circuits in the non-Markovian master equation. We analyzed the entanglement sudden death (ESD) and entanglement sudden birth (ESB) by the non-Markovian master equation. Furthermore, we find that the larger the ratio $r$ and the thermal energy $k_BT$, the shorter the decoherence. In this superconducting qubit system we find that the entanglement can be controlled and the ESD time can be prolonged by adjusting the temperature and the superconducting phases $\Phi_k$ which split the energy levels.Comment: 13 pages, 3 figure

Presupernova Structure of Massive Stars

Issues concerning the structure and evolution of core collapse progenitor stars are discussed with an emphasis on interior evolution. We describe a program designed to investigate the transport and mixing processes associated with stellar turbulence, arguably the greatest source of uncertainty in progenitor structure, besides mass loss, at the time of core collapse. An effort to use precision observations of stellar parameters to constrain theoretical modeling is also described.Comment: Proceedings for invited talk at High Energy Density Laboratory Astrophysics conference, Caltech, March 2010. Special issue of Astrophysics and Space Science, submitted for peer review: 7 pages, 3 figure

The global Microcystis interactome

Bacteria play key roles in the function and diversity of aquatic systems, but aside from study of specific bloom systems, little is known about the diversity or biogeography of bacteria associated with harmful cyanobacterial blooms (cyanoHABs). CyanoHAB species are known to shape bacterial community composition and to rely on functions provided by the associated bacteria, leading to the hypothesized cyanoHAB interactome, a coevolved community of synergistic and interacting bacteria species, each necessary for the success of the others. Here, we surveyed the microbiome associated with Microcystis aeruginosa during blooms in 12 lakes spanning four continents as an initial test of the hypothesized Microcystis interactome. We predicted that microbiome composition and functional potential would be similar across blooms globally. Our results, as revealed by 16S rRNA sequence similarity, indicate that M. aeruginosa is cosmopolitan in lakes across a 280° longitudinal and 90° latitudinal gradient. The microbiome communities were represented by a wide range of operational taxonomic units and relative abundances. Highly abundant taxa were more related and shared across most sites and did not vary with geographic distance, thus, like Microcystis, revealing no evidence for dispersal limitation. High phylogenetic relatedness, both within and across lakes, indicates that microbiome bacteria with similar functional potential were associated with all blooms. While Microcystis and the microbiome bacteria shared many genes, whole-community metagenomic analysis revealed a suite of biochemical pathways that could be considered complementary. Our results demonstrate a high degree of similarity across global Microcystis blooms, thereby providing initial support for the hypothesized Microcystis interactome

Outstanding challenges in the transferability of ecological models

Predictive models are central to many scientific disciplines and vital for informing management in a rapidly changing world. However, limited understanding of the accuracy and precision of models transferred to novel conditions (their ‘transferability’) undermines confidence in their predictions. Here, 50 experts identified priority knowledge gaps which, if filled, will most improve model transfers. These are summarized into six technical and six fundamental challenges, which underlie the combined need to intensify research on the determinants of ecological predictability, including species traits and data quality, and develop best practices for transferring models. Of high importance is the identification of a widely applicable set of transferability metrics, with appropriate tools to quantify the sources and impacts of prediction uncertainty under novel conditions

Astronomical Distance Determination in the Space Age: Secondary Distance Indicators

The formal division of the distance indicators into primary and secondary leads to difficulties in description of methods which can actually be used in two ways: with, and without the support of the other methods for scaling. Thus instead of concentrating on the scaling requirement we concentrate on all methods of distance determination to extragalactic sources which are designated, at least formally, to use for individual sources. Among those, the Supernovae Ia is clearly the leader due to its enormous success in determination of the expansion rate of the Universe. However, new methods are rapidly developing, and there is also a progress in more traditional methods. We give a general overview of the methods but we mostly concentrate on the most recent developments in each field, and future expectations. © 2018, The Author(s)

Search for Supernova Neutrino-Bursts with the AMANDA Detector

The core collapse of a massive star in the Milky Way will produce a neutrino burst, intense enough to be detected by existing underground detectors. The AMANDA neutrino telescope located deep in the South Pole ice can detect MeV neutrinos by a collective rate increase in all photo-multipliers on top of dark noise. The main source of light comes from positrons produced in the CC-reaction of anti-electron neutrinos on free protons \antinue + p \to e^+ + n. This paper describes the first supernova search performed on the full sets of data taken during 1997 and 1998 (215 days of live time) with 302 of the detector's optical modules. No candidate events resulted from this search. The performance of the detector is calculated, yielding a 70% coverage of the Galaxy with one background fake per year with 90% efficiency for the detector configuration under study. An upper limit at the 90% c.l. on the rate of stellar collapses in the Milky Way is derived, yielding 4.3 events per year. A trigger algorithm is presented and its performance estimated. Possible improvements of the detector hardware are reviewed.Comment: 20 pages, 14 figures. Submitted to Astroparticle Physic

Large-Eddy Simulations of Magnetohydrodynamic Turbulence in Heliophysics and Astrophysics

We live in an age in which high-performance computing is transforming the way we do science. Previously intractable problems are now becoming accessible by means of increasingly realistic numerical simulations. One of the most enduring and most challenging of these problems is turbulence. Yet, despite these advances, the extreme parameter regimes encountered in space physics and astrophysics (as in atmospheric and oceanic physics) still preclude direct numerical simulation. Numerical models must take a Large Eddy Simulation (LES) approach, explicitly computing only a fraction of the active dynamical scales. The success of such an approach hinges on how well the model can represent the subgrid-scales (SGS) that are not explicitly resolved. In addition to the parameter regime, heliophysical and astrophysical applications must also face an equally daunting challenge: magnetism. The presence of magnetic fields in a turbulent, electrically conducting fluid flow can dramatically alter the coupling between large and small scales, with potentially profound implications for LES/SGS modeling. In this review article, we summarize the state of the art in LES modeling of turbulent magnetohydrodynamic (MHD) ows. After discussing the nature of MHD turbulence and the small-scale processes that give rise to energy dissipation, plasma heating, and magnetic reconnection, we consider how these processes may best be captured within an LES/SGS framework. We then consider several special applications in heliophysics and astrophysics, assessing triumphs, challenges,and future directions