Experiments on waves trapped over the continental slope and shelf in a continuously stratified rotating ocean, and their incidence on a canyon

Continental margins form a waveguide for topographic Rossby waves, which can be trapped to the bottom by continuous stratification and concentrated over the continental slope while propagating along the coast. We present results of laboratory wave simulations designed to keep as many dimensionless numbers (Rossby, Burger, normalized frequency, wave steepness, geometrical, Ekman, and Reynolds) as possible similar to those of coastal-trapped waves, such as are observed in coastal regions around the world. The 13-m diameter rotating tank is salt-stratified and a continental slope joins a shallow shelf region along the outer tank circumference to a deep central region. The velocity field is measured using a correlation-based digital particle image velocimetry technique at several depths. Current ellipses downstream from subinertial forcing indicate along-isobath propagation with energy concentrated at depth and three-dimensional structure in agreement with a numerical wave solution calculated using the experimental geometry, rotation rate, and buoyancy frequency. Contrasting the inviscid wave solution, experimental flow shows an asymmetry with positive time-mean uv correlations (u across isobaths toward deep water, v along isobaths with shallow water to the left), and phase variations perpendicular to isobaths with flow near the shelf break leading that farther inshore and offshore. Both of these attributes have been seen previously in ocean observations and are interpreted as the signature of frictional influences based on stratified slope-Kelvin wave behavior. When incident on a canyon that indents the slope and shelf, a wave propagates in to and out of it along isobaths while remaining concentrated over the sloping topography with only weakly modified amplitude and phase structure. Based on the limited range of parameter space studied, the implication is that alongshore wave propagation will remain largely unmodified by natural corrugations in the slope and shelf and loss of energy by scattering will be weak

Structure of the receptor-binding carboxy-terminal domain of the bacteriophage T5 L-shaped tail fibre with and without its intra-molecular chaperone

Bacteriophage T5, a Siphovirus belonging to the order Caudovirales, has a flexible, three-fold symmetric tail, to which three L-shaped fibres are attached. These fibres recognize oligo-mannose units on the bacterial cell surface prior to infection and are composed of homotrimers of the pb1 protein. Pb1 has 1396 amino acids, of which the carboxy-terminal 133 residues form a trimeric intra-molecular chaperone that is auto-proteolyzed after correct folding. The structure of a trimer of residues 970–1263 was determined by single anomalous dispersion phasing using incorporated selenomethionine residues and refined at 2.3 Å resolution using crystals grown from native, methionine-containing, protein. The protein inhibits phage infection by competition. The phage-distal receptor-binding domain resembles a bullet, with the walls formed by partially intertwined beta-sheets, conferring stability to the structure. The fold of the domain is novel and the topology unique to the pb1 structure. A site-directed mutant (Ser1264 to Ala), in which auto-proteolysis is impeded, was also produced, crystallized and its 2.5 Å structure solved by molecular replacement. The additional chaperone domain (residues 1263–1396) consists of a central trimeric alpha-helical coiled-coil flanked by a mixed alpha-beta domain. Three long beta-hairpin tentacles, one from each chaperone monomer, extend into long curved grooves of the bullet-shaped domain. The chaperone-containing mutant did not inhibit infection by competition.This research was sponsored by grants BFU2011-24843, BIO2011-14756-E, BFU2014-53425P (Mark J. van Raaij), and BFU2014-55475R (José R. Castón) and the BioFiViNet network (FIS2011-16090-E) from the Spanish Ministry of Economy and Competitiveness, grant S2013/MIT-2807 (José R. Castón) from the Comunidad Autónoma de Madrid and a joint networking grant from CSIC (2011FR0016; Mark J. van Raaij) and CNRS (2011EDC25326; Pascale Boulanger). Carmela Garcia-Doval was the recipient of a pre-doctoral FPU fellowship from the Spanish Ministry of Education, Culture and Sports and José M. Otero of a post-doctoral Plan I2C fellowship from the Xunta de Galicia. The research leading to these results has also received funding from the European Community’s Seventh Framework Programme (FP7/2007–2013) under BioStruct-X (grant agreement number 283570). We acknowledge support by the CSIC Open Access Publication Initiative through its Unit of Information Resources for Research (URICI).Peer Reviewe

Investigation of Linum flavum (L.) Hairy Root Cultures for the Production of Anticancer Aryltetralin Lignans.

Collaboration with: Université d’Orléans, 28000 Chartres, France, Université de Picardie Jules Verne, F-80037 Amiens, France De Montfort University Open access articleLinum flavum hairy root lines were established from hypocotyl pieces using Agrobacterium rhizogenes strains LBA 9402 and ATCC 15834. Both strains were effective for transformation but induction of hairy root phenotype was more stable with strain ATCC 15834. Whereas similar accumulation patterns were observed in podophyllotoxin-related compounds (6-methoxy-podophyllotoxin, podophyllotoxin and deoxypodophyllotoxin), significant quantitative variations were noted between root lines. The influence of culture medium and various treatments (hormone, elicitation and precursor feeding) were evaluated. The highest accumulation was obtained in Gamborg B5 medium. Treatment with methyl jasmonate, and feeding using ferulic acid increased the accumulation of aryltetralin lignans. These results point to the use of hairy root culture lines of Linum flavum as potential sources for these valuable metabolites as an alternative, or as a complement to Podophyllum collected from wild stands

ART: A machine learning Automated Recommendation Tool for synthetic biology

Biology has changed radically in the last two decades, transitioning from a descriptive science into a design science. Synthetic biology allows us to bioengineer cells to synthesize novel valuable molecules such as renewable biofuels or anticancer drugs. However, traditional synthetic biology approaches involve ad-hoc engineering practices, which lead to long development times. Here, we present the Automated Recommendation Tool (ART), a tool that leverages machine learning and probabilistic modeling techniques to guide synthetic biology in a systematic fashion, without the need for a full mechanistic understanding of the biological system. Using sampling-based optimization, ART provides a set of recommended strains to be built in the next engineering cycle, alongside probabilistic predictions of their production levels. We demonstrate the capabilities of ART on simulated data sets, as well as experimental data from real metabolic engineering projects producing renewable biofuels, hoppy flavored beer without hops, and fatty acids. Finally, we discuss the limitations of this approach, and the practical consequences of the underlying assumptions failing

Justice and Corporate Governance: New Insights from Rawlsian Social Contract and Sen’s Capabilities Approach

By considering what we identify as a problem inherent in the ‘nature of the firm’—the risk of abuse of authority—we propound the conception of a social contract theory of the firm which is truly Rawlsian in its inspiration. Hence, we link the social contract theory of the firm (justice at firm’s level) with the general theory of justice (justice at society’s level). Through this path, we enter the debate about whether firms can be part of Rawlsian theory of justice showing that corporate governance principles enter the “basic structure.” Finally, we concur with Sen’s aim to broaden the realm of social justice beyond what he calls the ‘transcendental institutional perfectionism’ of Rawls’ theory. We maintain the contractarian approach to justice but introduce Sen’s capability concept as an element of the constitutional and post-constitutional contract model of institutions with special reference to corporate governance. Accordingly, rights over primary goods and capabilities are (constitutionally) granted by the basic institutions of society, but many capabilities have to be turned into the functionings of many stakeholders through the operation of firms understood as post-constitutional institutional domains. The constitutional contract on the distribution of primary goods and capabilities should then shape the principles of corporate governance so that at post-constitutional level anyone may achieve her/his functionings in the corporate domain by exercising such capabilities. In the absence of such a condition, post-constitutional contracts would distort the process that descends from constitutional rights and capabilities toward social outcomes