Darkness visible: reflections on underground ecology

1 Soil science and ecology have developed independently, making it difficult for ecologists to contribute to urgent current debates on the destruction of the global soil resource and its key role in the global carbon cycle. Soils are believed to be exceptionally biodiverse parts of ecosystems, a view confirmed by recent data from the UK Soil Biodiversity Programme at Sourhope, Scotland, where high diversity was a characteristic of small organisms, but not of larger ones. Explaining this difference requires knowledge that we currently lack about the basic biology and biogeography of micro-organisms. 2 It seems inherently plausible that the high levels of biological diversity in soil play some part in determining the ability of soils to undertake ecosystem-level processes, such as carbon and mineral cycling. However, we lack conceptual models to address this issue, and debate about the role of biodiversity in ecosystem processes has centred around the concept of functional redundancy, and has consequently been largely semantic. More precise construction of our experimental questions is needed to advance understanding. 3 These issues are well illustrated by the fungi that form arbuscular mycorrhizas, the Glomeromycota. This ancient symbiosis of plants and fungi is responsible for phosphate uptake in most land plants, and the phylum is generally held to be species-poor and non-specific, with most members readily colonizing any plant species. Molecular techniques have shown both those assumptions to be unsafe, raising questions about what factors have promoted diversification in these fungi. One source of this genetic diversity may be functional diversity. 4 Specificity of the mycorrhizal interaction between plants and fungi would have important ecosystem consequences. One example would be in the control of invasiveness in introduced plant species: surprisingly, naturalized plant species in Britain are disproportionately from mycorrhizal families, suggesting that these fungi may play a role in assisting invasion. 5 What emerges from an attempt to relate biodiversity and ecosystem processes in soil is our extraordinary ignorance about the organisms involved. There are fundamental questions that are now answerable with new techniques and sufficient will, such as how biodiverse are natural soils? Do microbes have biogeography? Are there rare or even endangered microbes

Molecular basis for bacterial peptidoglycan recognition by LysM domains.

Carbohydrate recognition is essential for growth, cell adhesion and signalling in all living organisms. A highly conserved carbohydrate binding module, LysM, is found in proteins from viruses, bacteria, fungi, plants and mammals. LysM modules recognize polysaccharides containing N-acetylglucosamine (GlcNAc) residues including peptidoglycan, an essential component of the bacterial cell wall. However, the molecular mechanism underpinning LysM-peptidoglycan interactions remains unclear. Here we describe the molecular basis for peptidoglycan recognition by a multimodular LysM domain from AtlA, an autolysin involved in cell division in the opportunistic bacterial pathogen Enterococcus faecalis. We explore the contribution of individual modules to the binding, identify the peptidoglycan motif recognized, determine the structures of free and bound modules and reveal the residues involved in binding. Our results suggest that peptide stems modulate LysM binding to peptidoglycan. Using these results, we reveal how the LysM module recognizes the GlcNAc-X-GlcNAc motif present in polysaccharides across kingdoms

Comparative study of density functional theories of the exchange-correlation hole and energy in silicon

We present a detailed study of the exchange-correlation hole and exchange-correlation energy per particle in the Si crystal as calculated by the Variational Monte Carlo method and predicted by various density functional models. Nonlocal density averaging methods prove to be successful in correcting severe errors in the local density approximation (LDA) at low densities where the density changes dramatically over the correlation length of the LDA hole, but fail to provide systematic improvements at higher densities where the effects of density inhomogeneity are more subtle. Exchange and correlation considered separately show a sensitivity to the nonlocal semiconductor crystal environment, particularly within the Si bond, which is not predicted by the nonlocal approaches based on density averaging. The exchange hole is well described by a bonding orbital picture, while the correlation hole has a significant component due to the polarization of the nearby bonds, which partially screens out the anisotropy in the exchange hole.Comment: 16 pages, 5 figures, RevTeX, added conten

A unified approach to energy conservation and potential vorticity dynamics for arbitrarily-structured C-grids

Copyright © 2010 Elsevier. NOTICE: this is the author’s version of a work that was accepted for publication in Journal of Computational Physics. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Journal of Computational Physics, Vol. 229, Issue 9 (2010), DOI: 10.1016/j.jcp.2009.12.007A numerical scheme applicable to arbitrarily-structured C-grids is presented for the nonlinear shallow-water equations. By discretizing the vector-invariant form of the momentum equation, the relationship between the nonlinear Coriolis force and the potential vorticity flux can be used to guarantee that mass, velocity and potential vorticity evolve in a consistent and compatible manner. Underpinning the consistency and compatibility of the discrete system is the construction of an auxiliary thickness equation that is staggered from the primary thickness equation and collocated with the vorticity field. The numerical scheme also exhibits conservation of total energy to within time-truncation error. Simulations of the standard shallow-water test cases confirm the analysis and show convergence rates between 1st1st- and 2nd2nd-order accuracy when discretizing the system with quasi-uniform spherical Voronoi diagrams. The numerical method is applicable to a wide class of meshes, including latitude–longitude grids, Voronoi diagrams, Delaunay triangulations and conformally-mapped cubed-sphere meshes

Functional diversity of chemokines and chemokine receptors in response to viral infection of the central nervous system.

Encounters with neurotropic viruses result in varied outcomes ranging from encephalitis, paralytic poliomyelitis or other serious consequences to relatively benign infection. One of the principal factors that control the outcome of infection is the localized tissue response and subsequent immune response directed against the invading toxic agent. It is the role of the immune system to contain and control the spread of virus infection in the central nervous system (CNS), and paradoxically, this response may also be pathologic. Chemokines are potent proinflammatory molecules whose expression within virally infected tissues is often associated with protection and/or pathology which correlates with migration and accumulation of immune cells. Indeed, studies with a neurotropic murine coronavirus, mouse hepatitis virus (MHV), have provided important insight into the functional roles of chemokines and chemokine receptors in participating in various aspects of host defense as well as disease development within the CNS. This chapter will highlight recent discoveries that have provided insight into the diverse biologic roles of chemokines and their receptors in coordinating immune responses following viral infection of the CNS

Tensor polarization in elastic electron-deuteron scattering in the momentum transfer range 3.8≤Q≤4.6 fm-1

The tensor polarization of the recoil deuteron in elastic electron-deuteron scattering has been measured at the Bates Linear Accelerator Center at three values of four-momentum transfer Q=3.78, 4.22, and 4.62 fm-1, corresponding to incident electron energies of 653, 755, and 853 MeV. The scattered electrons and the recoil deuterons were detected in coincidence. The recoil deuterons were transported to a liquid hydrogen target to undergo a second scattering. The angular distribution of the d→-p scattering was measured using a polarimeter. The polarimeter was calibrated in an auxiliary experiment using a polarized deuteron beam at the Laboratoire National Saturne. A Monte Carlo procedure was used to generate interpolated calibration data because the energy spread in the deuteron energies in the Bates experiment spanned the range of deuteron energies in the calibration experiment. The extracted values of t20 are compared to predictions of different theoretical models of the electromagnetic form factors of the deuteron: nonrelativistic and relativistic nucleon-meson dynamics, Skyrme model, quark models, and perturbative quantum chromodynamics. Along with the world data the structure functions A(Q) and B(Q) are used to separate the charge monopole and charge quadrupole form factors of the deuteron. A node in the charge monopole form factor is observed at Q=4.39±0.16 fm-1

Measurement of tensor polarization in elastic electron-deuteron scattering in the momentum-transfer range 3.8≤q≤4.6 fm-1

The tensor polarization t20 of the recoil deuteron in elastic e-d scattering has been measured for three values of four-momentum transfer, q=3.78, 4.22, and 4.62 fm-1. The data have been used to locate the first node in the charge monopole form factor of the deuteron at q=4.39±0.16 fm-1. The results for t20 are in reasonable agreement with expectations based on the nucleon-meson description of nuclear dynamic

The PHENIX Experiment at RHIC

The physics emphases of the PHENIX collaboration and the design and current status of the PHENIX detector are discussed. The plan of the collaboration for making the most effective use of the available luminosity in the first years of RHIC operation is also presented.Comment: 5 pages, 1 figure. Further details of the PHENIX physics program available at http://www.rhic.bnl.gov/phenix