InParanoid 6: eukaryotic ortholog clusters with inparalogs

The InParanoid eukaryotic ortholog database (http://InParanoid.sbc.su.se/) has been updated to version 6 and is now based on 35 species. We collected all available ‘complete’ eukaryotic proteomes and Escherichia coli, and calculated ortholog groups for all 595 species pairs using the InParanoid program. This resulted in 2 642 187 pairwise ortholog groups in total. The orthology-based species relations are presented in an orthophylogram. InParanoid clusters contain one or more orthologs from each of the two species. Multiple orthologs in the same species, i.e. inparalogs, result from gene duplications after the species divergence. A new InParanoid website has been developed which is optimized for speed both for users and for updating the system. The XML output format has been improved for efficient processing of the InParanoid ortholog clusters

Equine West Nile encephalitis, United States.

After the 1999 outbreak of West Nile (WN) encephalitis in New York horses, a case definition was developed that specified the clinical signs, coupled with laboratory test results, required to classify cases of WN encephalitis in equines as either probable or confirmed. In 2000, 60 horses from seven states met the criteria for a confirmed case. The cumulative experience from clinical observations and diagnostic testing during the 1999 and 2000 outbreaks of WN encephalitis in horses will contribute to further refinement of diagnostic criteria

Phonon Localization in One-Dimensional Quasiperiodic Chains

Quasiperiodic long range order is intermediate between spatial periodicity and disorder, and the excitations in 1D quasiperiodic systems are believed to be transitional between extended and localized. These ideas are tested with a numerical analysis of two incommensurate 1D elastic chains: Frenkel-Kontorova (FK) and Lennard-Jones (LJ). The ground state configurations and the eigenfrequencies and eigenfunctions for harmonic excitations are determined. Aubry's "transition by breaking the analyticity" is observed in the ground state of each model, but the behavior of the excitations is qualitatively different. Phonon localization is observed for some modes in the LJ chain on both sides of the transition. The localization phenomenon apparently is decoupled from the distribution of eigenfrequencies since the spectrum changes from continuous to Cantor-set-like when the interaction parameters are varied to cross the analyticity--breaking transition. The eigenfunctions of the FK chain satisfy the "quasi-Bloch" theorem below the transition, but not above it, while only a subset of the eigenfunctions of the LJ chain satisfy the theorem.Comment: This is a revised version to appear in Physical Review B; includes additional and necessary clarifications and comments. 7 pages; requires revtex.sty v3.0, epsf.sty; includes 6 EPS figures. Postscript version also available at http://lifshitz.physics.wisc.edu/www/koltenbah/koltenbah_homepage.htm

Deletion of Macrophage Vitamin D Receptor Promotes Insulin Resistance and Monocyte Cholesterol Transport to Accelerate Atherosclerosis in Mice

Intense effort has been devoted to understanding predisposition to chronic systemic inflammation because it contributes to cardiometabolic disease. We demonstrate that deletion of the macrophage vitamin D receptor (VDR) in mice (KODMAC) is sufficient to induce insulin resistance by promoting M2 macrophage accumulation in the liver as well as increasing cytokine secretion and hepatic glucose production. Moreover, VDR deletion increases atherosclerosis by enabling lipid-laden M2 monocytes to adhere, migrate, and carry cholesterol into the atherosclerotic plaque and by increasing macrophage cholesterol uptake and esterification. Increased foam cell formation results from lack of VDR-SERCA2b interaction, causing SERCA dysfunction, activation of ER stress-CaMKII-JNKp-PPARγ signaling, and induction of the scavenger receptors CD36 and SR-A1. Bone marrow transplant of VDR-expressing cells into KODMAC mice improved insulin sensitivity, suppressed atherosclerosis, and decreased foam cell formation. The immunomodulatory effects of vitamin D in macrophages are thus critical in diet-induced insulin resistance and atherosclerosis in mice

Whole genome sequencing and phylogenetic analysis of \u3ci\u3eBluetongue virus\u3c/i\u3e serotype 2 strains isolated in the Americas including a novel strain from the western United States

Bluetongue is a potentially fatal arboviral disease of domestic and wild ruminants that is characterized by widespread edema and tissue necrosis. Bluetongue virus (BTV) serotypes 10, 11, 13, and 17 occur throughout much of the United States, whereas serotype 2 (BTV-2) was previously only detected in the southeastern United States. Since 1998, 10 other BTV serotypes have also been isolated from ruminants in the southeastern United States. In 2010, BTV-2 was identified in California for the first time, and preliminary sequence analysis indicated that the virus isolate was closely related to BTV strains circulating in the southeastern United States. In the current study, the whole genome sequence of the California strain of BTV-2 was compared with those of other BTV-2 strains in the Americas. The results of the analysis suggest co-circulation of genetically distinct viruses in the southeastern United States, and further suggest that the 2010 western isolate is closely related to southeastern strains of BTV. Although it remains uncertain as to how this novel virus was translocated to California, the findings of the current study underscore the need for ongoing surveillance of this economically important livestock disease

Hidden dimers and the matrix maps: Fibonacci chains re-visited

The existence of cycles of the matrix maps in Fibonacci class of lattices is well established. We show that such cycles are intimately connected with the presence of interesting positional correlations among the constituent `atoms' in a one dimensional quasiperiodic lattice. We particularly address the transfer model of the classic golden mean Fibonacci chain where a six cycle of the full matrix map exists at the centre of the spectrum [Kohmoto et al, Phys. Rev. B 35, 1020 (1987)], and for which no simple physical picture has so far been provided, to the best of our knowledge. In addition, we show that our prescription leads to a determination of other energy values for a mixed model of the Fibonacci chain, for which the full matrix map may have similar cyclic behaviour. Apart from the standard transfer-model of a golden mean Fibonacci chain, we address a variant of it and the silver mean lattice, where the existence of four cycles of the matrix map is already known to exist. The underlying positional correlations for all such cases are discussed in details.Comment: 14 pages, 2 figures. Submitted to Physical Review