Characterization of bacteriophage communities and CRISPR profiles from dental plaque.

BackgroundDental plaque is home to a diverse and complex community of bacteria, but has generally been believed to be inhabited by relatively few viruses. We sampled the saliva and dental plaque from 4 healthy human subjects to determine whether plaque was populated by viral communities, and whether there were differences in viral communities specific to subject or sample type.ResultsWe found that the plaque was inhabited by a community of bacteriophage whose membership was mostly subject-specific. There was a significant proportion of viral homologues shared between plaque and salivary viromes within each subject, suggesting that some oral viruses were present in both sites. We also characterized Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in oral streptococci, as their profiles provide clues to the viruses that oral bacteria may be able to counteract. While there were some CRISPR spacers specific to each sample type, many more were shared across sites and were highly subject specific. Many CRISPR spacers matched viruses present in plaque, suggesting that the evolution of CRISPR loci may have been specific to plaque-derived viruses.ConclusionsOur findings of subject specificity to both plaque-derived viruses and CRISPR profiles suggest that human viral ecology may be highly personalized

Engaging without over-powering: A case study of a FLOSS project

This is the post-print version of the published chapter. The original publication is available at the link below. Copyright @ 2010 IFIP International Federation for Information Processing.The role of Open Source Software (OSS) in the e-learning business has become more and more fundamental in the last 10 years, as long as corporate and government organizations have developed their educational and training programs based on OSS out-of-the-box tools. This paper qualitatively documents the decision of the largest UK e-learning provider, the Open University, to adopt the Moodle e-learning system, and how it has been successfully deployed in its site after a multi-million investment. A further quantitative study also provides evidence of how a commercial stakeholder has been engaged with, and produced outputs for, the Moodle community. Lessons learned from this experience by the stakeholders include the crucial factors of contributing to the OSS community, and adapting to an evolving technology. It also becomes evident how commercial partners helped this OSS system to achieve the transition from an “average” OSS system to a successful multi-site, collaborative and community-based OSS project

Reducing the fine-tuning of gauge-mediated SUSY breaking

Despite their appealing features, models with gauge-mediated supersymmetry breaking (GMSB) typically present a high degree of fine-tuning, due to the initial absence of the top trilinear scalar couplings, At = 0. In this paper, we carefully evaluate such a tuning, showing that is worse than per mil in the minimal model. Then, we examine some existing proposals to generate At ≠ 0 term in this context. We find that, although the stops can be made lighter, usually the tuning does not improve (it may be even worse), with some exceptions, which involve the generation of At at one loop or tree level. We examine both possibilities and propose a conceptually simplified version of the latter; which is arguably the optimum GMSB setup (with minimal matter content), concerning the fine-tuning issue. The resulting fine-tuning is better than one per mil, still severe but similar to other minimal supersymmetric standard model constructions. We also explore the so-called “little A2t /m2 problem”, i.e. the fact that a large At -term is normally accompanied by a similar or larger sfermion mass, which typically implies an increase in the fine-tuning. Finally, we find the version of GMSB for which this ratio is optimized, which, nevertheless, does not minimize the fine-tuningThis work has been partially supported by the MICINN, Spain, under contract FPA2013-44773-P, Consolider-Ingenio CPAN CSD2007-00042, as well as MULTIDARK CSD2009-00064. We also thank the Spanish MINECO Centro de excelencia Severo Ochoa Program under Grant SEV-2012-0249. S.R. is supported by the Campus of Excellence UAM+CSIC and K.R. by the Spanish Research Council (CSIC) within the JAE-Doc progra

Spin configuration in a frustrated ferromagnetic/antiferromagnetic thin film system

We have studied the magnetic configuration in ultrathin antiferromagnetic Mn films grown around monoatomic steps on an Fe(001) surface by spin-polarized scanning tunneling microscopy/spectroscopy and ab-initio-parametrized self-consistent real-space tight binding calculations in which the spin quantization axis is independent for each site thus allowing noncollinear magnetism. Mn grown on Fe(001) presents a layered antiferromagnetic structure. In the regions where the Mn films overgrows Fe steps the magnetization of the surface layer is reversed across the steps. Around these defects a frustration of the antiferromagnetic order occurs. Due to the weakened magnetic coupling at the central Mn layers, the amount of frustration is smaller than in Cr and the width of the wall induced by the step does not change with the thickness, at least for coverages up to seven monolayers.Comment: 10 pages, 5 figure

Sustainable Sorbent Materials Obtained from Orange Peel as an Alternative for Water Treatment

The presence of pollutants in water promotes negative impacts on aquatic organisms. Among the methods of wastewater treatment, the use of sorbent materials is one of the most outstanding due to its efficiencies and easy implementation. Orange peels had become value-added products for these purposes. Activated carbon as a sorbent material was prepared using orange peel as a precursor. The resulting material was physicochemically characterized by scanning electron microscope (SEM) and Fourier transform infrared radiation (FTIR); structural changes were identified and related to sorption capacity using a model pollutant. Results of sorption indicated natural dried orange peel which presented a sorption capacity of 149.26 mg/g, while sorbent-activated carbon presented a sorption capacity of 2342.91 mg/g. The recovery of orange peel to obtain potential interest materials provided benefits for wastewater treatment

The failure of stellar feedback, magnetic fields, conduction, and morphological quenching in maintaining red galaxies

The quenching "maintenance'" and related "cooling flow" problems are important in galaxies from Milky Way mass through clusters. We investigate this in halos with masses $\sim 10^{12}-10^{14}\,{\rm M}_{\odot}$, using non-cosmological high-resolution hydrodynamic simulations with the FIRE-2 (Feedback In Realistic Environments) stellar feedback model. We specifically focus on physics present without AGN, and show that various proposed "non-AGN" solution mechanisms in the literature, including Type Ia supernovae, shocked AGB winds, other forms of stellar feedback (e.g. cosmic rays), magnetic fields, Spitzer-Braginskii conduction, or "morphological quenching" do not halt or substantially reduce cooling flows nor maintain "quenched" galaxies in this mass range. We show that stellar feedback (including cosmic rays from SNe) alters the balance of cold/warm gas and the rate at which the cooled gas within the galaxy turns into stars, but not the net baryonic inflow. If anything, outflowing metals and dense gas promote additional cooling. Conduction is important only in the most massive halos, as expected, but even at $\sim 10^{14}\,{\rm M}_{\odot}$ reduces inflow only by a factor $\sim 2$ (owing to saturation effects and anisotropic suppression). Changing the morphology of the galaxies only slightly alters their Toomre-$Q$ parameter, and has no effect on cooling (as expected), so has essentially no effect on cooling flows or maintaining quenching. This all supports the idea that additional physics, e.g., AGN feedback, must be important in massive galaxies.Comment: 16 pages, 12 figure

Focusing on optic tectum circuitry through the lens of genetics

The visual pathway is tasked with processing incoming signals from the retina and converting this information into adaptive behavior. Recent studies of the larval zebrafish tectum have begun to clarify how the 'micro-circuitry' of this highly organized midbrain structure filters visual input, which arrives in the superficial layers and directs motor output through efferent projections from its deep layers. The new emphasis has been on the specific function of neuronal cell types, which can now be reproducibly labeled, imaged and manipulated using genetic and optical techniques. Here, we discuss recent advances and emerging experimental approaches for studying tectal circuits as models for visual processing and sensorimotor transformation by the vertebrate brain