Enabling comparative modeling of closely related genomes: Example genus Brucella

For many scientific applications, it is highly desirable to be able to compare metabolic models of closely related genomes. In this short report, we attempt to raise awareness to the fact that taking annotated genomes from public repositories and using them for metabolic model reconstructions is far from being trivial due to annotation inconsistencies. We are proposing a protocol for comparative analysis of metabolic models on closely related genomes, using fifteen strains of genus Brucella, which contains pathogens of both humans and livestock. This study lead to the identification and subsequent correction of inconsistent annotations in the SEED database, as well as the identification of 31 biochemical reactions that are common to Brucella, which are not originally identified by automated metabolic reconstructions. We are currently implementing this protocol for improving automated annotations within the SEED database and these improvements have been propagated into PATRIC, Model-SEED, KBase and RAST. This method is an enabling step for the future creation of consistent annotation systems and high-quality model reconstructions that will support in predicting accurate phenotypes such as pathogenicity, media requirements or type of respiration.We thank Jean Jacques Letesson, Maite Iriarte, Stephan Kohler and David O'Callaghan for their input on improving specific annotations. This project has been funded by the United States National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN272200900040C, awarded to BW Sobral, and from the United States National Science Foundation under Grant MCB-1153357, awarded to CS Henry. J.P.F. acknowledges funding from [FRH/BD/70824/2010] of the FCT (Portuguese Foundation for Science and Technology) Ph.D. scholarship

Electrophoretic Properties of Highly Charged Colloids: A Hybrid MD/LB Simulation Study

Using computer simulations, the electrophoretic motion of a positively charged colloid (macroion) in an electrolyte solution is studied in the framework of the primitive model. Hydrodynamic interactions are fully taken into account by applying a hybrid simulation scheme, where the charged ions (i.e. macroion and electrolyte), propagated via molecular dynamics (MD), are coupled to a Lattice Boltzmann (LB) fluid. In a recent experiment it was shown that, for multivalent salt ions, the mobility $\mu$ initially increases with charge density $\sigma$, reaches a maximum and then decreases with further increase of $\sigma$. The aim of the present work is to elucidate the behaviour of $\mu$ at high values of $\sigma$. Even for the case of monovalent microions, we find a decrease of $\mu$ with $\sigma$. A dynamic Stern layer is defined that includes all the counterions that move with the macroion while subject to an external electrical field. The number of counterions in the Stern layer, $q_0$, is a crucial parameter for the behavior of $\mu$ at high values of $\sigma$. In this case, the mobility $\mu$ depends primarily on the ratio $q_0/Q$ (with $Q$ the valency of the macroion). The previous contention that the increase in the distortion of the electric double layer (EDL) with increasing $\sigma$ leads to the lowering of $\mu$ does not hold for high $\sigma$. In fact, we show that the deformation of the EDL decreases with increase of $\sigma$. The role of hydrodynamic interactions is inferred from direct comparisons to Langevin simulations where the coupling to the LB fluid is switched off. Moreover, systems with divalent counterions are considered. In this case, at high values of $\sigma$ the phenomenon of charge inversion is found.Comment: accepted in J. Chem Phys., 10 pages, 9 figure

NGC 7789: An Open Cluster Case Study

We have obtained high-resolution spectra of 32 giants in the open cluster NGC 7789 using the Wisconsin-Indiana-Yale-NOAO Hydra spectrograph. We explore differences in atmospheric parameters and elemental abundances caused by the use of the linelist developed for the Gaia-ESO Survey (GES) compared to one based on Arcturus used in our previous work. [Fe/H] values decrease when using the GES linelist instead of the Arcturus-based linelist; these differences are probably driven by systematically lower (~ -0.1 dex) GES surface gravities. Using the GES linelist we determine abundances for 10 elements - Fe, Mg, Si, Ca, Ti, Na, Ni, Zr, Ba, and La. We find the cluster's average metallicity [Fe/H] = 0.03 +/- 0.07 dex, in good agreement with literature values, and a lower [Mg/Fe] abundance than has been reported before for this cluster (0.11 +/- 0.05 dex). We also find the neutron-capture element barium to be highly enhanced - [Ba/Fe] = +0.48 +/- 0.08 - and disparate from cluster measurements of neutron-capture elements La and Zr (-0.08 +/- 0.05 and 0.08 +/- 0.08, respectively). This is in accordance with recent discoveries of supersolar Ba enhancement in young clusters along with more modest enhancement of other neutron-capture elements formed in similar environments.Comment: 15 pages, 9 figures, Table 1 typo fixe

Many-body interactions and melting of colloidal crystals

We study the melting behavior of charged colloidal crystals, using a simulation technique that combines a continuous mean-field Poisson-Boltzmann description for the microscopic electrolyte ions with a Brownian-dynamics simulation for the mesoscopic colloids. This technique ensures that many-body interactions between the colloids are fully taken into account, and thus allows us to investigate how many-body interactions affect the solid-liquid phase behavior of charged colloids. Using the Lindemann criterion, we determine the melting line in a phase-diagram spanned by the colloidal charge and the salt concentration. We compare our results to predictions based on the established description of colloidal suspensions in terms of pairwise additive Yukawa potentials, and find good agreement at high-salt, but not at low-salt concentration. Analyzing the effective pair-interaction between two colloids in a crystalline environment, we demonstrate that the difference in the melting behavior observed at low salt is due to many-body interactions

Decreasing diagrams with two labels are complete for confluence of countable systems

Like termination, confluence is a central property of rewrite systems. Unlike for termination, however, there exists no known complexity hierarchy for confluence. In this paper we investigate whether the decreasing diagrams technique can be used to obtain such a hierarchy. The decreasing diagrams technique is one of the strongest and most versatile methods for proving confluence of abstract reduction systems, it is complete for countable systems, and it has many well-known confluence criteria as corollaries. So what makes decreasing diagrams so powerful? In contrast to other confluence techniques, decreasing diagrams employ a labelling of the steps ? with labels from a well-founded order in order to conclude confluence of the underlying unlabelled relation. Hence it is natural to ask how the size of the label set influences the strength of the technique. In particular, what class of abstract reduction systems can be proven confluent using decreasing diagrams restricted to 1 label, 2 labels, 3 labels, and so on? Surprisingly, we find that two labels su ce for proving confluence for every abstract rewrite system having the cofinality property, thus in particular for every confluent, countable system. We also show that this result stands in sharp contrast to the situation for commutation of rewrite relations, where the hierarchy does not collapse. Finally, as a background theme, we discuss the logical issue of first-order definability of the notion of confluence

Decreasing diagrams for confluence and commutation

Like termination, confluence is a central property of rewrite systems. Unlike for termination, however, there exists no known complexity hierarchy for confluence. In this paper we investigate whether the decreasing diagrams technique can be used to obtain such a hierarchy. The decreasing diagrams technique is one of the strongest and most versatile methods for proving confluence of abstract rewrite systems. It is complete for countable systems, and it has many well-known confluence criteria as corollaries. So what makes decreasing diagrams so powerful? In contrast to other confluence techniques, decreasing diagrams employ a labelling of the steps with labels from a wellfounded order in order to conclude confluence of the underlying unlabelled relation. Hence it is natural to ask how the size of the label set influences the strength of the technique. In particular, what class of abstract rewrite systems can be proven confluent using decreasing diagrams restricted to 1 label, 2 labels, 3 labels, and so on? Surprisingly, we find that two labels suffice for proving confluence for every abstract rewrite system having the cofinality property, thus in particular for every confluent, countable system. Secondly, we show that this result stands in sharp contrast to the situation for commutation of rewrite relations, where the hierarchy does not collapse. Thirdly, investigating the possibility of a confluence hierarchy, we determine the first-order (non-)definability of the notion of confluence and related properties, using techniques from finite model theory. We find that in particular Hanf ’s theorem is fruitful for elegant proofs of undefinability of properties of abstract rewrite systems

Properties of bacterial endophytes and their proposed role in plant growth

Bacterial endophytes live inside plants for at least part of their life cycle. Studies of the interaction of endophytes with their host plants and their function within their hosts are important to address the ecological relevance of endophytes. The modulation of ethylene levels in plants by bacterially produced 1-aminocyclopropane-1-carboxylate deaminase is a key trait that enables interference with the physiology of the host plant. Endophytes with this capacity might profit from association with the plant, because colonization is enhanced. In turn, host plants benefit by stress reduction and increased root growth. This mechanism leads to the concept of 'competent' endophytes, defined as endophytes that are equipped with genes important for maintenance of plant-endophyte associations. The ecological role of these endophytes and their relevance for plant growth are discussed here.</p

Self-similarity of complex networks

Complex networks have been studied extensively due to their relevance to many real systems as diverse as the World-Wide-Web (WWW), the Internet, energy landscapes, biological and social networks \cite{ab-review,mendes,vespignani,newman,amaral}. A large number of real networks are called ``scale-free'' because they show a power-law distribution of the number of links per node \cite{ab-review,barabasi1999,faloutsos}. However, it is widely believed that complex networks are not {\it length-scale} invariant or self-similar. This conclusion originates from the ``small-world'' property of these networks, which implies that the number of nodes increases exponentially with the ``diameter'' of the network \cite{erdos,bollobas,milgram,watts}, rather than the power-law relation expected for a self-similar structure. Nevertheless, here we present a novel approach to the analysis of such networks, revealing that their structure is indeed self-similar. This result is achieved by the application of a renormalization procedure which coarse-grains the system into boxes containing nodes within a given "size". Concurrently, we identify a power-law relation between the number of boxes needed to cover the network and the size of the box defining a finite self-similar exponent. These fundamental properties, which are shown for the WWW, social, cellular and protein-protein interaction networks, help to understand the emergence of the scale-free property in complex networks. They suggest a common self-organization dynamics of diverse networks at different scales into a critical state and in turn bring together previously unrelated fields: the statistical physics of complex networks with renormalization group, fractals and critical phenomena.Comment: 28 pages, 12 figures, more informations at http://www.jamlab.or