Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion

Conjugation of DNA through a type IV secretion system (T4SS) drives horizontal gene transfer. Yet little is known on the diversity of these nanomachines. We previously found that T4SS can be divided in eight classes based on the phylogeny of the only ubiquitous protein of T4SS (VirB4). Here, we use an ab initio approach to identify protein families systematically and specifically associated with VirB4 in each class. We built profiles for these proteins and used them to scan 2262 genomes for the presence of T4SS. Our analysis led to the identification of thousands of occurrences of 116 protein families for a total of 1623 T4SS. Importantly, we could identify almost always in our profiles the essential genes of well-studied T4SS. This allowed us to build a database with the largest number of T4SS described to date. Using profile-profile alignments, we reveal many new cases of homology between components of distant classes of T4SS. We mapped these similarities on the T4SS phylogenetic tree and thus obtained the patterns of acquisition and loss of these protein families in the history of T4SS. The identification of the key VirB4-associated proteins paves the way toward experimental analysis of poorly characterized T4SS classes.Funding. Spanish Ministry of Economy [BFU2011-26608]; European Seventh Framework Program [282004/FP7-HEALTH.2011, 612146/FP7-ICT-2013]; European Research Council Grant [EVOMOBILOME no. 281605]. Source of open access funding: European Research Council grant to the PI

Constraining Ceres' interior from its Rotational Motion

Context. Ceres is the most massive body of the asteroid belt and contains about 25 wt.% (weight percent) of water. Understanding its thermal evolution and assessing its current state are major goals of the Dawn Mission. Constraints on internal structure can be inferred from various observations. Especially, detailed knowledge of the rotational motion can help constrain the mass distribution inside the body, which in turn can lead to information on its geophysical history. Aims. We investigate the signature of the interior on the rotational motion of Ceres and discuss possible future measurements performed by the spacecraft Dawn that will help to constrain Ceres' internal structure. Methods. We compute the polar motion, precession-nutation, and length-of-day variations. We estimate the amplitudes of the rigid and non-rigid response for these various motions for models of Ceres interior constrained by recent shape data and surface properties. Results. As a general result, the amplitudes of oscillations in the rotation appear to be small, and their determination from spaceborne techniques will be challenging. For example, the amplitudes of the semi-annual and annual nutations are around ~364 and ~140 milli-arcseconds, and they show little variation within the parametric space of interior models envisioned for Ceres. This, combined with the very long-period of the precession motion, requires very precise measurements. We also estimate the timescale for Ceres' orientation to relax to a generalized Cassini State, and we find that the tidal dissipation within that object was probably too small to drive any significant damping of its obliquity since formation. However, combining the shape and gravity observations by Dawn offers the prospect to identify departures of non-hydrostaticity at the global and regional scale, which will be instrumental in constraining Ceres' past and current thermal state. We also discuss the existence of a possible Chandler mode in the rotational motion of Ceres, whose potential excitation by endogenic and/or exogenic processes may help detect the presence of liquid reservoirs within the asteroid.Comment: submitted to Astronomy and Astrophysic

Wave Number of Maximal Growth in Viscous Magnetic Fluids of Arbitrary Depth

An analytical method within the frame of linear stability theory is presented for the normal field instability in magnetic fluids. It allows to calculate the maximal growth rate and the corresponding wave number for any combination of thickness and viscosity of the fluid. Applying this method to magnetic fluids of finite depth, these results are quantitatively compared to the wave number of the transient pattern observed experimentally after a jump--like increase of the field. The wave number grows linearly with increasing induction where the theoretical and the experimental data agree well. Thereby a long-standing controversy about the behaviour of the wave number above the critical magnetic field is tackled.Comment: 19 pages, 15 figures, RevTex; revised version with a new figure and references added. submitted to Phys Rev

Tate Form and Weak Coupling Limits in F-theory

We consider the weak coupling limit of F-theory in the presence of non-Abelian gauge groups implemented using the traditional ansatz coming from Tate's algorithm. We classify the types of singularities that could appear in the weak coupling limit and explain their resolution. In particular, the weak coupling limit of SU(n) gauge groups leads to an orientifold theory which suffers from conifold singulaties that do not admit a crepant resolution compatible with the orientifold involution. We present a simple resolution to this problem by introducing a new weak coupling regime that admits singularities compatible with both a crepant resolution and an orientifold symmetry. We also comment on possible applications of the new limit to model building. We finally discuss other unexpected phenomena as for example the existence of several non-equivalent directions to flow from strong to weak coupling leading to different gauge groups.Comment: 34 page

A Digital Repository and Execution Platform for Interactive Scholarly Publications in Neuroscience

The CARMEN Virtual Laboratory (VL) is a cloud-based platform which allows neuroscientists to store, share, develop, execute, reproduce and publicise their work. This paper describes new functionality in the CARMEN VL: an interactive publications repository. This new facility allows users to link data and software to publications. This enables other users to examine data and software associated with the publication and execute the associated software within the VL using the same data as the authors used in the publication. The cloud-based architecture and SaaS (Software as a Service) framework allows vast data sets to be uploaded and analysed using software services. Thus, this new interactive publications facility allows others to build on research results through reuse. This aligns with recent developments by funding agencies, institutions, and publishers with a move to open access research. Open access provides reproducibility and verification of research resources and results. Publications and their associated data and software will be assured of long-term preservation and curation in the repository. Further, analysing research data and the evaluations described in publications frequently requires a number of execution stages many of which are iterative. The VL provides a scientific workflow environment to combine software services into a processing tree. These workflows can also be associated with publications and executed by users. The VL also provides a secure environment where users can decide the access rights for each resource to ensure copyright and privacy restrictions are met

Politicising government engagement with corporate social responsibility: “CSR” as an empty signifier

Governments are widely viewed by academics and practitioners (and society more generally) as the key societal actors who are capable of compelling businesses to practice corporate social responsibility (CSR). Arguably, such government involvement could be seen as a technocratic device for encouraging ethical business behaviour. In this paper, we offer a more politicised interpretation of government engagement with CSR where “CSR” is not a desired form of business conduct but an element of discourse that governments can deploy in structuring their relationships with other social actors. We build our argument through a historical analysis of government CSR discourse in the Russian Federation. Laclau and Mouffe's (Hegemony and socialist strategy: Towards a radical democratic politics,Verso Books, London, 1985) social theory of hegemony underpins our research. We find that “CSR” in the Russian government’s discourse served to legitimise its power over large businesses. Using this case, we contribute to wider academic debates by providing fresh empirical evidence that allows the development of critical evaluation tools in relation to governments’ engagement with “CSR”. We find that governments are capable of hijacking CSR for their own self-interested gain. We close the paper by reflecting on the merit of exploring the case of the Russian Federation. As a “non-core”, non-western exemplar, it provides a useful “mirror” with which to reflect on the more widely used test-bed of Western industrial democracies when scrutinising CSR. Based on our findings, we invite other scholars to adopt a more critical, politicised stance when researching the role of governments in relation to CSR in other parts of the world