Evolution of the Kdo2-lipid A biosynthesis in bacteria

<p>Abstract</p> <p>Background</p> <p>Lipid A is the highly immunoreactive endotoxic center of lipopolysaccharide (LPS). It anchors the LPS into the outer membrane of most Gram-negative bacteria. Lipid A can be recognized by animal cells, triggers defense-related responses, and causes Gram-negative sepsis. The biosynthesis of Kdo₂-lipid A, the LPS substructure, involves with nine enzymatic steps.</p> <p>Results</p> <p>In order to elucidate the evolutionary pathway of Kdo₂-lipid A biosynthesis, we examined the distribution of genes encoding the nine enzymes across bacteria. We found that not all Gram-negative bacteria have all nine enzymes. Some Gram-negative bacteria have no genes encoding these enzymes and others have genes only for the first four enzymes (LpxA, LpxC, LpxD, and LpxB). Among the nine enzymes, five appeared to have arisen from three independent gene duplication events. Two of such events happened within the Proteobacteria lineage, followed by functional specialization of the duplicated genes and pathway optimization in these bacteria.</p> <p>Conclusions</p> <p>The nine-enzyme pathway, which was established based on the studies mainly in <it>Escherichia coli </it>K12, appears to be the most derived and optimized form. It is found only in <it>E. coli </it>and related Proteobacteria. Simpler and probably less efficient pathways are found in other bacterial groups, with Kdo₂-lipid A variants as the likely end products. The Kdo₂-lipid A biosynthetic pathway exemplifies extremely plastic evolution of bacterial genomes, especially those of Proteobacteria, and how these mainly pathogenic bacteria have adapted to their environment.</p

Theory of ω−4/3\omega^{-4/3} law of the power spectrum in dissipative flows

It is demonstrated that $\omega^{-4/3}$ law of the power spectrum with the angular frequency $\omega$ in dissipative flows is produced by the emission of dispersive waves from the antikink of an congested domain. The analytic theory predicts the spectrum is proportional to $\omega^{-2}$ for relatively low frequency and $\omega^{-4/3}$ for high frequency.Comment: 11 pages, 2 figure

Stability Analysis of Optimal Velocity Model for Traffic and Granular Flow under Open Boundary Condition

We analyzed the stability of the uniform flow solution in the optimal velocity model for traffic and granular flow under the open boundary condition. It was demonstrated that, even within the linearly unstable region, there is a parameter region where the uniform solution is stable against a localized perturbation. We also found an oscillatory solution in the linearly unstable region and its period is not commensurate with the periodicity of the car index space. The oscillatory solution has some features in common with the synchronized flow observed in real traffic.Comment: 4 pages, 6 figures. Typos removed. To appear in J. Phys. Soc. Jp

Fluctuation of the Top Location and Avalanches in the Formation Process of a Sandpile

We investigate the formation processes of a sandpile using numerical simulation. We find a new relation between the fluctuation of the motion of the top and the surface state of a sandpile. The top moves frequently as particles are fed one by one every time interval T. The time series of the top location has the power spectrum which obeys a power law, S(f)~f^{\alpha}, and its exponent \alpha depends on T and the system size w. The surface state is characterized by two time scales; the lifetime of an avalanche, T_{a}, and the time required to cause an avalanche, T_{s}. The surface state is fluid-like when T_{a}~T_{s}, and it is solid-like when T_{a}<<T_{s}. Our numerical results show that \alpha is a function of T_{s}/T_{a}.Comment: 15 pages, 13 figure

Mining the Arabidopsis thaliana genome for highly-divergent seven transmembrane receptors

To identify divergent seven-transmembrane receptor (7TMR) candidates from the Arabidopsis thaliana genome, multiple protein classification methods were combined, including both alignment-based and alignment-free classifiers. This resolved problems in optimally training individual classifiers using limited and divergent samples, and increased stringency for candidate proteins. We identified 394 proteins as 7TMR candidates and highlighted 54 with corresponding expression patterns for further investigation

Power-law behavior in the power spectrum induced by Brownian motion of a domain wall

We show that Brownian motion of a one-dimensional domain wall in a large but finite system yields a $\omega^{-3/2}$ power spectrum. This is successfully applied to the totally asymmetric simple exclusion process (TASEP) with open boundaries. An excellent agreement between our theory and numerical results is obtained in a frequency range where the domain wall motion dominates and discreteness of the system is not effective.Comment: 4 pages, 4 figure

Summing Up All Genus Free Energy of ABJM Matrix Model

The localization technique allows us to compute the free energy of the U(N)_k x U(N)_{-k} Chern-Simons-matter theory dual to type IIA strings on AdS_4 x CP^3 from weak to strong 't Hooft coupling \lambda = N / k at finite N, as demonstrated by Drukker, Marino, and Putrov. In this note we study further the free energy at large 't Hooft coupling with the aim of testing AdS/CFT at the quantum gravity level and, in particular, sum up all the 1/N corrections, apart from the worldsheet instanton contributions. The all genus partition function takes a remarkably simple form -- the Airy function, Ai (k^{4/3} \lambda_r), with the renormalized 't Hooft coupling \lambda_r.Comment: 18 pages, no figures, v2: typos corrected and references adde