Similar Microbial Communities Found on Two Distant Seafloor Basalts.

The oceanic crust forms two thirds of the Earth's surface and hosts a large phylogenetic and functional diversity of microorganisms. While advances have been made in the sedimentary realm, our understanding of the igneous rock portion as a microbial habitat has remained limited. We present the first comparative metagenomic microbial community analysis from ocean floor basalt environments at the Lō'ihi Seamount, Hawai'i, and the East Pacific Rise (EPR; 9°N). Phylogenetic analysis indicates the presence of a total of 43 bacterial and archaeal mono-phyletic groups, dominated by Alpha- and Gammaproteobacteria, as well as Thaumarchaeota. Functional gene analysis suggests that these Thaumarchaeota play an important role in ammonium oxidation on seafloor basalts. In addition to ammonium oxidation, the seafloor basalt habitat reveals a wide spectrum of other metabolic potentials, including CO2 fixation, denitrification, dissimilatory sulfate reduction, and sulfur oxidation. Basalt communities from Lō'ihi and the EPR show considerable metabolic and phylogenetic overlap down to the genus level despite geographic distance and slightly different seafloor basalt mineralogy

QCD on the Light-Front -- A Systematic Approach to Hadron Physics

Light-Front Hamiltonian theory provides a rigorous frame-independent framework for solving nonperturbative QCD. The valence Fock-state wavefunctions of the light-front QCD Hamiltonian satisfy a single-variable relativistic equation of motion, analogous to the nonrelativistic radial Schr\"odinger equation, with an effective confining potential U which systematically incorporates the effects of higher quark and gluon Fock states. Remarkably, the potential U has a unique form of a harmonic oscillator potential if one requires that the chiral QCD action remains conformally invariant. A mass gap arises when one extends the formalism of de Alfaro, Fubini and Furlan to light-front Hamiltonian theory. The valence LF meson wavefunctions for zero quark mass satisfy a single-variable relativistic equation of motion in the invariant variable $\zeta^2=b^2_\perp x(1-x)$, which is conjugate to the invariant mass squared. The result is a nonperturbative relativistic light-front quantum mechanical wave equation which incorporates color confinement and other essential spectroscopic and dynamical features of hadron physics, including a massless pion for zero quark mass and linear Regge trajectories with the same slope in the radial quantum number n and orbital angular momentum L. The corresponding light-front Dirac equation provides a model of nucleons. The same light-front equations arise from the holographic mapping of the soft-wall model modification of AdS_5 space with a unique dilaton profile to QCD (3+1) at fixed light-front time. Light-front holography thus provides a precise relation between amplitudes in the fifth dimension of AdS space and light-front wavefunctions. We also discuss the implications of the underlying conformal template of QCD for renormalization scale-setting, and the implications of light-front quantization for the value of the cosmological constant.Comment: Invited talk, presented by SJB at LightCone 2013+, May 20- May 24, 2013, Skiathos, Greece. arXiv admin note: text overlap with arXiv:1309.4856, arXiv:1308.5251, arXiv:1302.539

Light-Front Holographic QCD and the Confinement Potential

Light-Front Hamiltonian theory, derived from the quantization of the QCD Lagrangian at fixed light-front time \tau = t+z/c, provides a rigorous frame-independent framework for solving nonperturbative QCD. The eigenvalues of the light-front QCD Hamiltonian predict the hadronic mass spectrum, and the eigensolutions provide the light-front wavefunctions describing hadron structure. The valence Fock-state wavefunctions of the light-front QCD Hamiltonian satisfy a single-variable relativistic equation of motion, analogous to the nonrelativistic radial Schrodinger equation, with an effective confining potential U which systematically incorporates the effects of higher quark and gluon Fock states. The potential U has a unique form if one requires that the action for zero quark mass remains conformally invariant. The holographic mapping of gravity in AdS space to QCD with a specific soft-wall dilaton yields the same light-front Schrodinger equation. It also gives a precise relation between the bound-state amplitudes in the fifth dimension z of AdS space and the boost-invariant light-front wavefunctions describing the internal structure of hadrons in physical space-time. The elastic and transition form factors of the pion and the nucleons are found to be well described in this framework. The predictions include a zero-mass pion in the chiral limit, and linear Regge trajectories with the same slope in the radial quantum number n and orbital angular momentum L. The light-front AdS/QCD holographic approach thus gives a frame-independent representation of color-confining dynamics and the excitation spectra of light-quark hadrons in terms of a single mass parameter. We also discuss the implications of the underlying conformal template of QCD for renormalization scale-setting and the implications of light-front quantization for the value of the cosmological constant.Comment: Presented by SJB at Light-Cone 2012: Relativistic Hadronic and Particle Physics, 10 to 15 December, 2012 at the University of Delhi, New Delhi, Indi

Conformal Symmetry, Confinement, and Light-Front Holographic QCD

We show that (a) the conformal properties of Anti-de Sitter (AdS) space, (b) the properties of a field theory in one dimension under the full conformal group found by de Alfaro, Fubini and Furlan, and (c) the frame-independent single-variable light-front Schr\"odinger equation for bound states all lead to the same result: a relativistic nonperturbative model which successfully incorporates salient features of hadronic physics, including confinement, linear Regge trajectories, and results which are conventionally attributed to spontaneous chiral symmetry breaking.Comment: Presented by SJB at the Third Workshop on the QCD Structure of the Nucleon (QCD-N'12), Bilbao, Spain, October 22-26, 2012. This work was supported by the Department of Energy contract DE--AC02--76SF0051

Prospects for the Study of Evolution in the Deep Biosphere

Since the days of Darwin, scientists have used the framework of the theory of evolution to explore the interconnectedness of life on Earth and adaptation of organisms to the ever-changing environment. The advent of molecular biology has advanced and accelerated the study of evolution by allowing direct examination of the genetic material that ultimately determines the phenotypes upon which selection acts. The study of evolution has been furthered through examination of microbial evolution, with large population numbers, short generation times, and easily extractable DNA. Such work has spawned the study of microbial biogeography, with the realization that concepts developed in population genetics may be applicable to microbial genomes (Martiny et al., 2006; Manhes and Velicer, 2011). Microbial biogeography and adaptation has been examined in many different environments. Here we argue that the deep biosphere is a unique environment for the study of evolution and list specific factors that can be considered and where the studies may be performed. This publication is the result of the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) theme team on Evolution (www.darkenergybiosphere.org)

Meeting report : Ocean ‘omics science, technology and cyberinfrastructure : current challenges and future requirements (August 20-23, 2013)

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Standards in Genomic Sciences 9 (2014): 1251-1258, doi:10.4056/sigs.5749944.The National Science Foundation’s EarthCube End User Workshop was held at USC’s Wrigley Marine Science Center on Catalina Island, California in August 2013. The workshop was designed to explore and characterise the needs and tools available to the community focusing on microbial and physical oceanography research with a particular focus on ‘omic research. The assembled researchers outlined the existing concerns regarding the vast data resources that are being generated, and how we will deal with these resources as their volume and diversity increases. Particular attention was focused on the tools for handling and analysing the existing data, and on the need for the construction and curation of diverse federated databases, as well as development of shared interoperable, “big-data capable” analytical tools. The key outputs from this workshop include (i) critical scientific challenges and cyberinfrastructure constraints, (ii) the current and future ocean ‘omics science grand challenges and questions, and (iii) data management, analytical and associated and cyber-infrastructure capabilities required to meet critical current and future scientific challenges. The main thrust of the meeting and the outcome of this report is a definition of the ‘omics tools, technologies and infrastructures that facilitate continued advance in ocean science biology, marine biogeochemistry, and biological oceanography.We gratefully acknowledge support for the Ocean ‘Omics EarthCube end-user workshop by the Geo-sciences Division of the U.S. National Science Foundation

De Novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a aariable genomic landscape

Hypersaline systems near salt saturation levels represent an extreme environment, in which organisms grow and survive near the limits of life. One of the abundant members of the microbial communities in hypersaline systems is the square archaeon, Haloquadratum walsbyi. Utilizing a short-read metagenome from Lake Tyrrell, a hypersaline ecosystem in Victoria, Australia, we performed a comparative genomic analysis of H. walsbyi to better understand the extent of variation between strains/subspecies. Results revealed that previously isolated strains/subspecies do not fully describe the complete repertoire of the genomic landscape present in H. walsbyi. Rearrangements, insertions, and deletions were observed for the Lake Tyrrell derived Haloquadratum genomes and were supported by environmental de novo sequences, including shifts in the dominant genomic landscape of the two most abundant strains. Analysis pertaining to halomucins indicated that homologs for this large protein are not a feature common for all species of Haloquadratum. Further, we analyzed ATP-binding cassette transporters (ABC-type transporters) for evidence of niche partitioning between different strains/subspecies. We were able to identify unique and variable transporter subunits from all five genomes analyzed and the de novo environmental sequences, suggesting that differences in nutrient and carbon source acquisition may play a role in maintaining distinct strains/subspecies.Funding for this was provided by the National Science Foundation (NSF) MCB Award no. 0626526 to J. Banfield, E. Allen, and K. Heidelberg

The capabilities approach and critical social policy: lessons from the majority world?

The capabilities approach (CA) most closely associated with the thinner and thicker versions of Sen and Nussbaum has the potential to provide a paradigm shift for critical social policy, encompassing but also transcending some of the limitations associated with the Marshallian social citizenship approach. The article argues, however, that it cannot simply be imported from the majority world, rather there is a need to bear in mind the critical literature that developed around it. This is generally discussed and then critically applied to case studies of CA in the developed capitalist world, particularly the Equalities Review conducted for the Equality and Human Rights Commission

Neutrinoless Double Beta Decay in Gauge Theories

Neutrinoless double beta decay is a very important process both from the particle and nuclear physics point of view. Its observation will severely constrain the existing models and signal that the neutrinos are massive Majorana particles. From the elementary particle point of view it pops up in almost every model. In addition to the traditional mechanisms, like the neutrino mass, the admixture of right handed currents etc, it may occur due to the R-parity violating supersymmetric (SUSY) interactions. From the nuclear physics point of view it is challenging, because: 1) The relevant nuclei have complicated nuclear structure. 2) The energetically allowed transitions are exhaust a small part of all the strength. 3) One must cope with the short distance behavior of the transition operators, especially when the intermediate particles are heavy (eg in SUSY models). Thus novel effects, like the double beta decay of pions in flight between nucleons, have to be considered. 4) The intermediate momenta involved are about 100 MeV. Thus one has to take into account possible momentum dependent terms in the nucleon current. We find that, for the mass mechanism, such modifications of the nucleon current for light neutrinos reduce the nuclear matrix elements by about 25 per cent, almost regardless of the nuclear model. In the case of heavy neutrinos the effect is much larger and model dependent. Taking the above effects into account, the available nuclear matrix elements for the experimentally interesting nuclei A = 76, 82, 96, 100, 116, 128, 130, 136 and 150 and the experimental limits on the life times we have extracted new stringent limits on the average neutrino mass and on the R-parity violating coupling for various SUSY models.Comment: Latex, 24 pages, 1 postscript figure, uses iopconf.st