Statistical characterization of the GxxxG glycine repeats in the flagellar biosynthesis protein FliH and its Type III secretion homologue YscL

<p>Abstract</p> <p>Background</p> <p>FliH is a protein involved in the export of components of the bacterial flagellum and we herein describe the presence of glycine-rich repeats in FliH of the form AxxxG(xxxG)_<it>m</it>xxxA, where the value of <it>m </it>varies considerably in FliH proteins from different bacteria. While GxxxG and AxxxA patterns have previously been described, the long glycine repeat segments in FliH proteins have yet to be characterized. The Type III secretion system homologue to FliH (YscL, AscL, PscL, etc.) also contains a similar GxxxG repeat, and hence the presence of the repeat is evolutionarily conserved in these proteins, suggesting an important structural role or biological function.</p> <p>Results</p> <p>A set of FliH and YscL protein sequences was downloaded from GenBank, and then filtered to reduce redundancy, to ensure the soundness of the sequences, and to eliminate, as much as possible, confounding phylogenetic signal between individual sequences by implementing a pairwise 25% sequence identity cut-off. The general features of the glycine-rich repeats in these proteins were examined, and it was found that the length of these repeat segments varied substantially among FliH proteins but was fairly consistent for the Type III (YscL) homologue sequences, with values of <it>m </it>ranging from 0 to 12 for FliH and 0 to 2 for YscL. The amino acid sequence distribution of each of the three positions in the GxxxG repeats was found to differ significantly from the overall amino acid composition of the FliH/YscL proteins. The high frequency of Glu, Gln, Lys and Ala residues in the repeat positions, which is not likely indicative of any contaminating phylogenetic signal, suggests an α-helical structure for this motif. In addition, we sought to determine whether certain pairs of amino acids, in certain pairs of positions, were found together significantly more often than would be predicted by chance. Several statistically significant correlations were uncovered, which may be important for maintaining helical stability or for forming helix-helix interactions. These correlations are likely not of a phylogenetic origin as the originating sequences for the pair correlations are derived from a low similarity set and the individual incidences of the pair correlations do not cluster in any obvious phylogenetic sense, nor is there much evidence of strict sequence conservation outside the positions of the glycine residues. Finally, the α-helices from a non-redundant set of proteins from the Protein Data Bank were searched for GxxxG repeats similar in length to those found in FliH, however there were no helices containing more than three contiguous glycine repeat segments; thus, long glycine repeats similar to those found in FliH are presumably quite rare in nature.</p> <p>Conclusion</p> <p>The glycine repeats in YscL and particularly FliH represent an intriguing amino acid sequence motif that is very rare in nature. Although we do not attempt to offer a mechanism whereby these repeats may have evolved, we do place the existence of the motif and some residue pairings within a rational structural context. While crystal structures of these proteins are necessary to fully elucidate the structural and functional significance of these repeats, the characterization reported here represents a first step in understanding this unique sequence feature.</p

X-33 Metallic TPS Tests in NASA-LaRC High Temperature Tunnel

Conclusions The first series of metallic TPS tests in the NASA-LaRC Mach 7 High Temperature Tunnel has been completed. Additional testing is 'in progress and shall provide data for off-design configurations for the metallic TPS. The available data are being analyzed and being used to correlate analytical models to be used for X-33 flight design analysis. The final paper shan present additional data from these tests and comparisons between the data and analytical predictions

Phase transition in a 2-dimensional Heisenberg model

We investigate the two-dimensional classical Heisenberg model with a nonlinear nearest-neighbor interaction V(s,s')=2K[(1+s.s')/2 ]^p. The analogous nonlinear interaction for the XY model was introduced by Domany, Schick, and Swendsen, who find that for large p the Kosterlitz-Thouless transition is preempted by a first-order transition. Here we show that, whereas the standard (p=1) Heisenberg model has no phase transition, for large enough p a first-order transition appears. Both phases have only short range order, but with a correlation length that jumps at the transition.Comment: 6 pages, 5 encapsulated postscript figures; to appear in Physical Review Letter

The HP0256 gene product is involved in motility and cell envelope architecture of Helicobacter pylori

Background: Helicobacter pylori is the causative agent for gastritis, and peptic and duodenal ulcers. The bacterium displays 5-6 polar sheathed flagella that are essential for colonisation and persistence in the gastric mucosa. The biochemistry and genetics of flagellar biogenesis in H. pylori has not been fully elucidated. Bioinformatics analysis suggested that the gene HP0256, annotated as hypothetical, was a FliJ homologue. In Salmonella, FliJ is a chaperone escort protein for FlgN and FliT, two proteins that themselves display chaperone activity for components of the hook, the rod and the filament. Results: Ablation of the HP0256 gene in H. pylori significantly reduced motility. However, flagellin and hook protein synthesis was not affected in the HP0256 mutant. Transmission electron transmission microscopy revealed that the HP0256 mutant cells displayed a normal flagellum configuration, suggesting that HP0256 was not essential for assembly and polar localisation of the flagella in the cell. Interestingly, whole genome microarrays of an HP0256 mutant revealed transcriptional changes in a number of genes associated with the flagellar regulon and the cell envelope, such as outer membrane proteins and adhesins. Consistent with the array data, lack of the HP0256 gene significantly reduced adhesion and the inflammatory response in host cells. Conclusions: We conclude that HP0256 is not a functional counterpart of FliJ in H. pylori. However, it is required for full motility and it is involved, possibly indirectly, in expression of outer membrane proteins and adhesins involved in pathogenesis and adhesion

The fading of Cassiopeia A, and improved models for the absolute spectrum of primary radio calibration sources

Based on five years of observations with the 40-foot telescope at Green Bank Observatory (GBO), Reichart & Stephens (2000) found that the radio source Cassiopeia A had either faded more slowly between the mid-1970s and late 1990s than Baars et al. (1977) had found it to be fading between the late 1940s and mid-1970s, or that it had rebrightened and then resumed fading sometime between the mid-1970s and mid-1990s, in L band (1.4 GHz). Here, we present 15 additional years of observations of Cas A and Cyg A with the 40-foot in L band, and three and a half additional years of observations of Cas A, Cyg A, Tau A, and Vir A with GBO's recently refurbished 20-meter telescope in L and X (9 GHz) bands. We also present a more sophisticated analysis of the 40-foot data, and a reanalysis of the Baars et al. (1977) data, which reveals small, but non-negligible differences. We find that overall, between the late 1950s and late 2010s, Cas A faded at an average rate of $0.670 \pm 0.019$ %/yr in L band, consistent with Reichart & Stephens (2000). However, we also find, at the 6.3$\sigma$ credible level, that it did not fade at a constant rate. Rather, Cas A faded at a faster rate through at least the late 1960s, rebrightened (or at least faded at a much slower rate), and then resumed fading at a similarly fast rate by, at most, the late 1990s. Given these differences from the original Baars et al. (1977) analysis, and given the importance of their fitted spectral and temporal models for flux-density calibration in radio astronomy, we update and improve on these models for all four of these radio sources. In doing so, we additionally find that Tau A is fading at a rate of $0.102^{+0.042}_{-0.043}$ %/yr in L band.Comment: 17 pages, 12 figures, accepted to MNRA

Counting Exceptional Instantons

We show how to obtain the instanton partition function of N=2 SYM with exceptional gauge group EFG using blow-up recursion relations derived by Nakajima and Yoshioka. We compute the two instanton contribution and match it with the recent proposal for the superconformal index of rank 2 SCFTs with E6, E7 global symmetry.Comment: 16 pages, references adde

Transcriptome analysis of pigeon milk production - role of cornification and triglyceride synthesis genes

BACKGROUND : The pigeon crop is specially adapted to produce milk that is fed to newly hatched young. The process of pigeon milk production begins when the germinal cell layer of the crop rapidly proliferates in response to prolactin, which results in a mass of epithelial cells that are sloughed from the crop and regurgitated to the young. We proposed that the evolution of pigeon milk built upon the ability of avian keratinocytes to accumulate intracellular neutral lipids during the cornification of the epidermis. However, this cornification process in the pigeon crop has not been characterised. RESULTS: We identified the epidermal differentiation complex in the draft pigeon genome scaffold and found that, like the chicken, it contained beta-keratin genes. These beta-keratin genes can be classified, based on sequence similarity, into several clusters including feather, scale and claw keratins. The cornified cells of the pigeon crop express several cornification-associated genes including cornulin, S100-A9 and A16-like, transglutaminase 6-like and the pigeon \u27lactating\u27 crop-specific annexin cp35. Beta-keratins play an important role in \u27lactating\u27 crop, with several claw and scale keratins up-regulated. Additionally, transglutaminase 5 and differential splice variants of transglutaminase 4 are up-regulated along with S100-A10. CONCLUSIONS: This study of global gene expression in the crop has expanded our knowledge of pigeon milk production, in particular, the mechanism of cornification and lipid production. It is a highly specialised process that utilises the normal keratinocyte cellular processes to produce a targeted nutrient solution for the young at a very high turnover

Dynamics of Wind Setdown at Suez and the Eastern Nile Delta

BACKGROUND: Wind setdown is the drop in water level caused by wind stress acting on the surface of a body of water for an extended period of time. As the wind blows, water recedes from the upwind shore and exposes terrain that was formerly underwater. Previous researchers have suggested wind setdown as a possible hydrodynamic explanation for Moses crossing the Red Sea, as described in Exodus 14. METHODOLOGY/PRINCIPAL FINDINGS: This study analyzes the hydrodynamic mechanism proposed by earlier studies, focusing on the time needed to reach a steady-state solution. In addition, the authors investigate a site in the eastern Nile delta, where the ancient Pelusiac branch of the Nile once flowed into a coastal lagoon then known as the Lake of Tanis. We conduct a satellite and modeling survey to analyze this location, using geological evidence of the ancient bathymetry and a historical description of a strong wind event in 1882. A suite of model experiments are performed to demonstrate a new hydrodynamic mechanism that can cause an angular body of water to divide under wind stress, and to test the behavior of our study location and reconstructed topography. CONCLUSIONS/SIGNIFICANCE: Under a uniform 28 m/s easterly wind forcing in the reconstructed model basin, the ocean model produces an area of exposed mud flats where the river mouth opens into the lake. This land bridge is 3-4 km long and 5 km wide, and it remains open for 4 hours. Model results indicate that navigation in shallow-water harbors can be significantly curtailed by wind setdown when strong winds blow offshore

Renormalized couplings and scaling correction amplitudes in the N-vector spin models on the sc and the bcc lattices

For the classical N-vector model, with arbitrary N, we have computed through order \beta^{17} the high temperature expansions of the second field derivative of the susceptibility \chi_4(N,\beta) on the simple cubic and on the body centered cubic lattices. (The N-vector model is also known as the O(N) symmetric classical spin Heisenberg model or, in quantum field theory, as the lattice O(N) nonlinear sigma model.) By analyzing the expansion of \chi_4(N,\beta) on the two lattices, and by carefully allowing for the corrections to scaling, we obtain updated estimates of the critical parameters and more accurate tests of the hyperscaling relation d\nu(N) +\gamma(N) -2\Delta_4(N)=0 for a range of values of the spin dimensionality N, including N=0 [the self-avoiding walk model], N=1 [the Ising spin 1/2 model], N=2 [the XY model], N=3 [the classical Heisenberg model]. Using the recently extended series for the susceptibility and for the second correlation moment, we also compute the dimensionless renormalized four point coupling constants and some universal ratios of scaling correction amplitudes in fair agreement with recent renormalization group estimates.Comment: 23 pages, latex, no figure