Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses

Ocean microbes drive global-scale biogeochemical cycling, but do so under constraints imposed by viruses on host community composition, metabolism, and evolutionary trajectories. Due to sampling and cultivation challenges, genome-level viral diversity remains poorly described and grossly understudied in nature such that <1% of observed surface ocean viruses, even those that are abundant and ubiquitous, are ′known′. Here we analyze a global map of abundant, double stranded DNA (dsDNA) viruses and viral-encoded auxiliary metabolic genes (AMGs) with genomic and ecological contexts through the Global Ocean Viromes (GOV) dataset, which includes complete genomes and large genomic fragments from both surface and deep ocean viruses sampled during the Tara Oceans and Malaspina research expeditions. A total of 15,222 epi- and mesopelagic viral populations were identified that comprised 867 viral clusters (VCs, approximately genus-level groups). This roughly triples known ocean viral populations, doubles known candidate bacterial and archaeal virus genera, and near-completely samples epipelagic communities at both the population and VC level. Thirty-eight of the 867 VCs were identified as the most impactful dsDNA viral groups in the oceans, as these were locally or globally abundant and accounted together for nearly half of the viral populations in any GOV sample. Most of these were predicted in silico to infect dominant, ecologically relevant microbes, while two thirds of them represent newly described viruses that lacked any cultivated representative. Beyond these taxon-specific ecological observations, we identified 243 viral-encoded AMGs in GOV, only 95 of which were known. Deeper analyses of 4 of these AMGs revealed that abundant viruses directly manipulate sulfur and nitrogen cycling, and do so throughout the epipelagic ocean. Together these data provide a critically-needed organismal catalog and functional context to begin meaningfully integrating viruses into ecosystem models as key players in nutrient cycling and trophic networks

L-infinity algebra connections and applications to String- and Chern-Simons n-transport

We give a generalization of the notion of a Cartan-Ehresmann connection from Lie algebras to L-infinity algebras and use it to study the obstruction theory of lifts through higher String-like extensions of Lie algebras. We find (generalized) Chern-Simons and BF-theory functionals this way and describe aspects of their parallel transport and quantization. It is known that over a D-brane the Kalb-Ramond background field of the string restricts to a 2-bundle with connection (a gerbe) which can be seen as the obstruction to lifting the PU(H)-bundle on the D-brane to a U(H)-bundle. We discuss how this phenomenon generalizes from the ordinary central extension U(1) -> U(H) -> PU(H) to higher categorical central extensions, like the String-extension BU(1) -> String(G) -> G. Here the obstruction to the lift is a 3-bundle with connection (a 2-gerbe): the Chern-Simons 3-bundle classified by the first Pontrjagin class. For G = Spin(n) this obstructs the existence of a String-structure. We discuss how to describe this obstruction problem in terms of Lie n-algebras and their corresponding categorified Cartan-Ehresmann connections. Generalizations even beyond String-extensions are then straightforward. For G = Spin(n) the next step is "Fivebrane structures" whose existence is obstructed by certain generalized Chern-Simons 7-bundles classified by the second Pontrjagin class.Comment: 100 pages, references and clarifications added; correction to section 5.1 and further example to 9.3.1 adde

Expansions of algebras and superalgebras and some applications

After reviewing the three well-known methods to obtain Lie algebras and superalgebras from given ones, namely, contractions, deformations and extensions, we describe a fourth method recently introduced, the expansion of Lie (super)algebras. Expanded (super)algebras have, in general, larger dimensions than the original algebra, but also include the Inonu-Wigner and generalized IW contractions as a particular case. As an example of a physical application of expansions, we discuss the relation between the possible underlying gauge symmetry of eleven-dimensional supergravity and the superalgebra osp(1|32).Comment: Invited lecture delivered at the 'Deformations and Contractions in Mathematics and Physics Workshop', 15-21 January 2006, Mathematisches Forschungsinstitut Oberwolfach, German

The chemical enrichment of the ICM from hydrodynamical simulations

The study of the metal enrichment of the intra-cluster and inter-galactic media (ICM and IGM) represents a direct means to reconstruct the past history of star formation, the role of feedback processes and the gas-dynamical processes which determine the evolution of the cosmic baryons. In this paper we review the approaches that have been followed so far to model the enrichment of the ICM in a cosmological context. While our presentation will be focused on the role played by hydrodynamical simulations, we will also discuss other approaches based on semi-analytical models of galaxy formation, also critically discussing pros and cons of the different methods. We will first review the concept of the model of chemical evolution to be implemented in any chemo-dynamical description. We will emphasise how the predictions of this model critically depend on the choice of the stellar initial mass function, on the stellar life-times and on the stellar yields. We will then overview the comparisons presented so far between X-ray observations of the ICM enrichment and model predictions. We will show how the most recent chemo-dynamical models are able to capture the basic features of the observed metal content of the ICM and its evolution. We will conclude by highlighting the open questions in this study and the direction of improvements for cosmological chemo-dynamical models of the next generation.Comment: 25 pages, 11 figures, accepted for publication in Space Science Reviews, special issue "Clusters of galaxies: beyond the thermal view", Editor J.S. Kaastra, Chapter 18; work done by an international team at the International Space Science Institute (ISSI), Bern, organised by J.S. Kaastra, A.M. Bykov, S. Schindler & J.A.M. Bleeke

A search for periodic modulations of the solar neutrino flux in Super-Kamiokande-I

A search for periodic modulations of the solar neutrino flux was performed using the Super-Kamiokande-I data taken from May 31st, 1996 to July 15th, 2001. The detector's capability of measuring the exact time of events, combined with a relatively high yield of solar neutrino events, allows a search for short-time variations in the observed flux. We employed the Lomb test to look for periodic modulations of the observed solar neutrino flux. The obtained periodogram is consistent with statistical fluctuation and no significant periodicity was found

Search for Neutral Q-balls in Super-Kamiokande II

A search for Q-balls induced groups of successive contained events has been carried out in Super-Kamiokande II with 541.7 days of live time. Neutral Q-balls would emit pions when colliding with nuclei, generating a signal of successive contained pion events along a track. No candidate for successive contained event groups has been found in Super-Kamiokande II, so upper limits on the possible flux of such Q-balls have been obtained.Comment: 5 pages, 5 figures, Submitted to Phys. Lett.

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems

The Structure of Interpretations in Family Therapy: A Video-Enhanced Exploration *

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73991/1/j.1545-5300.2000.39204.x.pd

System Size and Energy Dependence of Jet-Induced Hadron Pair Correlation Shapes in Cu+Cu and Au+Au Collisions at sqrt(s_NN) = 200 and 62.4 GeV

We present azimuthal angle correlations of intermediate transverse momentum (1-4 GeV/c) hadrons from {dijets} in Cu+Cu and Au+Au collisions at sqrt(s_NN) = 62.4 and 200 GeV. The away-side dijet induced azimuthal correlation is broadened, non-Gaussian, and peaked away from \Delta\phi=\pi in central and semi-central collisions in all the systems. The broadening and peak location are found to depend upon the number of participants in the collision, but not on the collision energy or beam nuclei. These results are consistent with sound or shock wave models, but pose challenges to Cherenkov gluon radiation models.Comment: 464 authors from 60 institutions, 6 pages, 3 figures, 2 tables. Submitted to Physical Review Letters. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm