Assessing antibiotic sorption in soil: a literature review and new case studies on sulfonamides and macrolides

The increased use of veterinary antibiotics in modern agriculture for therapeutic uses and growth promotion has raised concern regarding the environmental impacts of antibiotic residues in soil and water. The mobility and transport of antibiotics in the environment depends on their sorption behavior, which is typically predicted by extrapolating from an experimentally determined soil-water distribution coefficient (K(d)). Accurate determination of K(d) values is important in order to better predict the environmental fate of antibiotics. In this paper, we examine different analytical approaches in assessing K(d) of two major classes of veterinary antibiotics (sulfonamides and macrolides) and compare the existing literature data with experimental data obtained in our laboratory. While environmental parameters such as soil pH and organic matter content are the most significant factors that affect the sorption of antibiotics in soil, it is important to consider the concentrations used, the analytical method employed, and the transformations that can occur when determining K(d) values. Application of solid phase extraction and liquid chromatography/mass spectrometry can facilitate accurate determination of K(d) at environmentally relevant concentrations. Because the bioavailability of antibiotics in soil depends on their sorption behavior, it is important to examine current practices in assessing their mobility in soil

Binary and Millisecond Pulsars at the New Millennium

We review the properties and applications of binary and millisecond pulsars. Our knowledge of these exciting objects has greatly increased in recent years, mainly due to successful surveys which have brought the known pulsar population to over 1300. There are now 56 binary and millisecond pulsars in the Galactic disk and a further 47 in globular clusters. This review is concerned primarily with the results and spin-offs from these surveys which are of particular interest to the relativity community.Comment: 59 pages, 26 figures, 5 tables. Accepted for publication in Living Reviews in Relativity (http://www.livingreviews.org

Functional divergence in the role of N-linked glycosylation in smoothened signaling

The G protein-coupled receptor (GPCR) Smoothened (Smo) is the requisite signal transducer of the evolutionarily conserved Hedgehog (Hh) pathway. Although aspects of Smo signaling are conserved from Drosophila to vertebrates, significant differences have evolved. These include changes in its active sub-cellular localization, and the ability of vertebrate Smo to induce distinct G protein-dependent and independent signals in response to ligand. Whereas the canonical Smo signal to Gli transcriptional effectors occurs in a G protein-independent manner, its non-canonical signal employs Gαi. Whether vertebrate Smo can selectively bias its signal between these routes is not yet known. N-linked glycosylation is a post-translational modification that can influence GPCR trafficking, ligand responsiveness and signal output. Smo proteins in Drosophila and vertebrate systems harbor N-linked glycans, but their role in Smo signaling has not been established. Herein, we present a comprehensive analysis of Drosophila and murine Smo glycosylation that supports a functional divergence in the contribution of N-linked glycans to signaling. Of the seven predicted glycan acceptor sites in Drosophila Smo, one is essential. Loss of N-glycosylation at this site disrupted Smo trafficking and attenuated its signaling capability. In stark contrast, we found that all four predicted N-glycosylation sites on murine Smo were dispensable for proper trafficking, agonist binding and canonical signal induction. However, the under-glycosylated protein was compromised in its ability to induce a non-canonical signal through Gαi, providing for the first time evidence that Smo can bias its signal and that a post-translational modification can impact this process. As such, we postulate a profound shift in N-glycan function from affecting Smo ER exit in flies to influencing its signal output in mice

Nonlinear dynamics and chaos in an optomechanical beam

[EN] Optical nonlinearities, such as thermo-optic mechanisms and free-carrier dispersion, are often considered unwelcome effects in silicon-based resonators and, more specifically, optomechanical cavities, since they affect, for instance, the relative detuning between an optical resonance and the excitation laser. Here, we exploit these nonlinearities and their intercoupling with the mechanical degrees of freedom of a silicon optomechanical nanobeam to unveil a rich set of fundamentally different complex dynamics. By smoothly changing the parameters of the excitation laser we demonstrate accurate control to activate two-and four-dimensional limit cycles, a period-doubling route and a six-dimensional chaos. In addition, by scanning the laser parameters in opposite senses we demonstrate bistability and hysteresis between two-and four-dimensional limit cycles, between different coherent mechanical states and between four-dimensional limit cycles and chaos. Our findings open new routes towards exploiting silicon-based optomechanical photonic crystals as a versatile building block to be used in neurocomputational networks and for chaos-based applications.This work was supported by the European Comission project PHENOMEN (H2020-EU-713450), the Spanish Severo Ochoa Excellence program and the MINECO project PHENTOM (FIS2015-70862-P). DNU, PDG and MFC gratefully acknowledge the support of a Ramon y Cajal postdoctoral fellowship (RYC-2014-15392), a Beatriu de Pinos postdoctoral fellowship (BP-DGR 2015 (B) and a Severo Ochoa studentship, respectively. We would like to acknowledge Jose C. Sabina de Lis, J.M. Plata Suarez, A. Trifonova and C. Masoller for fruitful discussions.Navarro-Urrios, D.; Capuj, NE.; Colombano, MF.; García, PD.; Sledzinska, M.; Alzina, F.; Griol Barres, A.... (2017). Nonlinear dynamics and chaos in an optomechanical beam. Nature Communications. 8. https://doi.org/10.1038/ncomms14965S8Strogatz, S. H. Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering Westview Press (2014).Lorenz, E. N. Deterministic nonperiodic ow. J. Atmos. Sci. 20, 130–141 (1963).Sparrow, C. The Lorenz Attractor: Bifurcations, Chaos and Strange Attractors Springer (1982).Aspelmeyer, M., Kippenberg, T. & Marquardt, F. Cavity optomechanics. Rev. Mod. Phys. 86, 1391 (2014).Kippenberg, T., Rokhsari, H., Carmon, T., Scherer, A. & Vahala, K. Analysis of radiation-pressure induced mechanical oscillation of an optical microcavity. Phys. Rev. Lett. 95, 033901 (2005).Marquardt, F., Harris, J. G. E. & Girvin, S. M. Dynamical multistability induced by radiation pressure in high-finesse micromechanical optical cavities. Phys. Rev. Lett. 96, 103901 (2006).Krause, A. G. et al. Nonlinear radiation pressure dynamics in an optomechanical crystal. Phys. Rev. Lett. 115, 233601 (2015).Metzger, C. et al. Self-induced oscillations in an optomechanical system driven by bolometric backaction. Phys. Rev. Lett. 101, 133903 (2008).Bakemeier, L., Alvermann, A. & Fehske, H. Route to chaos in optomechanics. Phys. Rev. Lett. 114, 013601 (2015).Sciamanna, M. & Shore, K. A. Physics and applications of laser diode chaos. Nat. Photon. 9, 151–162 (2015).Williams, C. R. et al. Experimental observations of group synchrony in a system of chaotic optoelectronic oscillators. Phys. Rev. Lett. 110, 064104 (2013).Sciamanna, M. Optomechanics: vibrations copying optical chaos. Nat. Photon. 10, 366–368 (2016).Carmon, T., Cross, M. C. & Vahala, K. J. Chaotic quivering of micron-scaled on-chip resonators excited by centrifugal optical pressure. Phys. Rev. Lett. 98, 167203 (2007).Carmon, T., Rokhsari, H., Yang, L., Kippenberg, T. J. & Vahala, K. J. Temporal behavior of radiation-pressure-induced vibrations of an optical microcavity phonon mode. Phys. Rev. Lett. 94, 223902 (2005).Monifi, F. et al. Optomechanically induced stochastic resonance and chaos transfer between optical fields. Nat. Photon. 10, 399–405 (2016).Wu, J. et al. Dynamical chaos in chip-scale optomechanical oscillators. Preprint at https://arxiv.org/abs/1608.05071 (2016).Navarro-Urrios, D., Tredicucci, A. & Sotomayor-Torres, C. M. Coherent phonon generation in optomechanical crystals. SPIE Newsroom, doi:10.1117/2.1201507.006036 (2015).Navarro-Urrios, D. et al. A self-stabilized coherent phonon source driven by optical forces. Sci. Rep. 5, 15733 (2015).Johnson, T. J., Borselli, M. & Painter, O. Self-induced optical modulation of the transmission through a high-Q silicon microdisk resonator. Opt. Express 14, 817–831 (2006).Navarro-Urrios, D. et al. Self-sustained coherent phonon generation in optomechanical cavities. J. Opt. 18, 094006 (2016).Kemiktarak, U., Durand, M., Metcalfe, M. & Lawall, J. Mode competition and anomalous cooling in a multimode phonon laser. Phys. Rev. Lett. 113, 030802 (2014).Rosenstein, M. T., Collins, J. J. & De Luca, C. J. A practical method for calculating largest Lyapunov exponents from small data sets. Physica D 65, 117–134 (1993).Sprott, J. C. Chaos and Time-Series Analysis Vol. 69, Citeseer (2003).Grassberger, P. & Procaccia, I. Characterization of strange attractors. Phys. Rev. Lett. 50, 346–349 (1983).Hoppensteadt, F. C. & Izhikevich, E. M. Synchronization of MEMS resonators and mechanical neurocomputing. IEEE Trans. Circuits Syst. I, Reg. Papers 48, 133–138 (2001).Pennec, Y. et al. Band gaps and cavity modes in dual phononic and photonic strip waveguides. AIP Adv. 1, 041901 (2011).Gomis-Bresco, J. et al. A one-dimensional optomechanical crystal with a complete phononic band gap. Nat. Commun. 5, 4452 (2014).Johnson, S. G. et al. Perturbation theory for Maxwells equations with shifting material boundaries. Phys. Rev. E 65, 066611 (2002).Chan, J., Safavi-Naeini, A. H., Hill, J. T., Meenehan, S. & Painter, O. Optimized optomechanical crystal cavity with acoustic radiation shield. Appl. Phys. Lett. 101, 081115 (2012).Pennec, Y. et al. Modeling light-sound interaction in nanoscale cavities and waveguides. Nanophotonics 3, 413–440 (2014)

A direct physical interaction between Nanog and Sox2 regulates embryonic stem cell self-renewal

Embryonic stem (ES) cell self-renewal efficiency is determined by the Nanog protein level. However, the protein partners of Nanog that function to direct self-renewal are unclear. Here, we identify a Nanog interactome of over 130 proteins including transcription factors, chromatin modifying complexes, phosphorylation and ubiquitination enzymes, basal transcriptional machinery members, and RNA processing factors. Sox2 was identified as a robust interacting partner of Nanog. The purified Nanog–Sox2 complex identified a DNA recognition sequence present in multiple overlapping Nanog/Sox2 ChIP-Seq data sets. The Nanog tryptophan repeat region is necessary and sufficient for interaction with Sox2, with tryptophan residues required. In Sox2, tyrosine to alanine mutations within a triple-repeat motif (S X T/S Y) abrogates the Nanog–Sox2 interaction, alters expression of genes associated with the Nanog-Sox2 cognate sequence, and reduces the ability of Sox2 to rescue ES cell differentiation induced by endogenous Sox2 deletion. Substitution of the tyrosines with phenylalanine rescues both the Sox2–Nanog interaction and efficient self-renewal. These results suggest that aromatic stacking of Nanog tryptophans and Sox2 tyrosines mediates an interaction central to ES cell self-renewal

Contrasting changes in the abundance and diversity of North American bird assemblages from 1971 to 2010

This article is based upon work from COST Action ES1101 "Harmonising Global Biodiversity Modelling" (Harmbio), supported by COST (European Cooperation in Science and Technology).Although it is generally recognized that global biodiversity is declining, few studies have examined long-term changes in multiple biodiversity dimensions simultaneously. In this study we quantified and compared temporal changes in the abundance, taxonomic diversity, functional diversity and phylogenetic diversity of bird assemblages, using roadside monitoring data of the North American Breeding Bird Survey from 1971 to 2010. We calculated 12 abundance and diversity metrics based on five year average abundances of 519 species for each of 768 monitoring routes. We did this for all bird species together as well as for four sub-groups based on breeding habitat affinity (grassland, woodland, wetland and shrubland breeders). The majority of the biodiversity metrics increased or remained constant over the study period, whereas the overall abundance of birds showed a pronounced decrease, primarily driven by declines of the most abundant species. These results highlight how stable or even increasing metrics of taxonomic, functional or phylogenetic diversity may occur in parallel with substantial losses of individuals. We further found that patterns of change differed among the species sub-groups, with both abundance and diversity increasing for woodland birds and decreasing for grassland breeders. The contrasting changes between abundance and diversity and among the breeding habitat groups underscore the relevance of a multi-faceted approach to measuring biodiversity change. Our findings further stress the importance of monitoring the overall abundance of individuals in addition to metrics of taxonomic, functional or phylogenetic diversity, thus confirming the importance of population abundance as an essential biodiversity variable.Publisher PDFPeer reviewe

Biological strategy for the fabrication of highly ordered aragonite helices: The microstructure of the cavolinioidean gastropods

The Cavolinioidea are planktonic gastropods which construct their shells with the so-called aragonitic helical fibrous microstructure, consisting of a highly ordered arrangement of helically coiled interlocking continuous crystalline aragonite fibres. Our study reveals that, despite the high and continuous degree of interlocking between fibres, every fibre has a differentiated organic-rich thin external band, which is never invaded by neighbouring fibres. In this way, fibres avoid extinction. These intra-fibre organic-rich bands appear on the growth surface of the shell as minuscule elevations, which have to be secreted differentially by the outer mantle cells. We propose that, as the shell thickens during mineralization, fibre secretion proceeds by a mechanism of contact recognition and displacement of the tips along circular trajectories by the cells of the outer mantle surface. Given the sizes of the tips, this mechanism has to operate at the subcellular level. Accordingly, the fabrication of the helical microstructure is under strict biological control. This mechanism of fibre-by-fibre fabrication by the mantle cells is unlike that any other shell microstructure.Funding was provided by Research Projects CGL2013-48247-P of the Spanish Ministerio de Economía y Competitividad (MINECO) and Fondo Europeo de Desarrollo Regional (FEDER), and P10-RNM6433 of the Andalusian Consejería de Economía, Investigación, Ciencia y Empleo, of the Junta de Andalucía, and by the Research Group RNM363 (latter Institution)

Seeking legitimacy through CSR: Institutional Pressures and Corporate Responses of Multinationals in Sri Lanka

Arguably, the corporate social responsibility (CSR) practices of multinational enterprises (MNEs) are influenced by a wide range of both internal and external factors. Perhaps most critical among the exogenous forces operating on MNEs are those exerted by state and other key institutional actors in host countries. Crucially, academic research conducted to date offers little data about how MNEs use their CSR activities to strategically manage their relationship with those actors in order to gain legitimisation advantages in host countries. This paper addresses that gap by exploring interactions between external institutional pressures and firm-level CSR activities, which take the form of community initiatives, to examine how MNEs develop their legitimacy-seeking policies and practices. In focusing on a developing country, Sri Lanka, this paper provides valuable insights into how MNEs instrumentally utilise community initiatives in a country where relationship-building with governmental and other powerful non-governmental actors can be vitally important for the long-term viability of the business. Drawing on neo-institutional theory and CSR literature, this paper examines and contributes to the embryonic but emerging debate about the instrumental and political implications of CSR. The evidence presented and discussed here reveals the extent to which, and the reasons why, MNEs engage in complex legitimacy-seeking relationships with Sri Lankan institutions

Magnetic Coupling in the Quiet Solar Atmosphere

Three kinds of magnetic couplings in the quiet solar atmosphere are highlighted and discussed, all fundamentally connected to the Lorentz force. First the coupling of the convecting and overshooting fluid in the surface layers of the Sun with the magnetic field. Here, the plasma motion provides the dominant force, which shapes the magnetic field and drives the surface dynamo. Progress in the understanding of the horizontal magnetic field is summarized and discussed. Second, the coupling between acoustic waves and the magnetic field, in particular the phenomenon of wave conversion and wave refraction. It is described how measurements of wave travel times in the atmosphere can provide information about the topography of the wave conversion zone, i.e., the surface of equal Alfv\'en and sound speed. In quiet regions, this surface separates a highly dynamic magnetic field with fast moving magnetosonic waves and shocks around and above it from the more slowly evolving field of high-beta plasma below it. Third, the magnetic field also couples to the radiation field, which leads to radiative flux channeling and increased anisotropy in the radiation field. It is shown how faculae can be understood in terms of this effect. The article starts with an introduction to the magnetic field of the quiet Sun in the light of new results from the Hinode space observatory and with a brief survey of measurements of the turbulent magnetic field with the help of the Hanle effect.Comment: To appear in "Magnetic Coupling between the Interior and the Atmosphere of the Sun", eds. S.S. Hasan and R.J. Rutten, Astrophysics and Space Science Proceedings, Springer-Verlag, Heidelberg, Berlin, 200