Genetic diversity of Mycobacterium tuberculosis isolates from foreign-born and Japan-born residents in Tokyo

AbstractSequences of the full genomes of 259 clinical isolates of Mycobacterium tuberculosis, obtained from foreign-born and Japan-born patients in Tokyo, Japan, were determined, and a phylogenetic tree constructed by concatenated single-nucleotide polymorphism (SNP) sequences. The 259 isolates were clustered into four clades: Lineage 2 (East Asian or “Beijing” genotype; n = 182, 70.3%), Lineage 4 (Euro-American, n = 46, 17.8%), Lineage 1 (Indo-Oceanic, n = 23, 8.9%), and Lineage 3 (East African-Indian, n = 8, 3.1%). Of the 259, 36 (13.9%) were resistant to at least one drug. There was no multi-drug-resistant isolate. Drug resistance was greater for the strains in Lineage 2 than the non-Lineage 2. The proportion of Lineage 2 isolates was significantly smaller in foreign-born (n = 43/91, 47.3%) than in Japan-born (n = 139/168, 82.7%) patients, whereas the proportion of Lineage 1 isolates was significantly larger in foreign-born (n = 19/91, 20.9%) than in Japan-born (n = 4/168, 2.4%) patients. We also found eight SNPs specific to the typical Beijing sub-genotype in Lineage 2, including 4 non-synonymous SNPs. Of the 259 isolates, 244 had strain-specific SNP(s) and small (1–30-bp) insertions and deletions (indels). The numbers of strain-specific SNPs and indels per isolate were significantly larger from foreign-born (median 89, range 0–520) than from Japan-born (median 23, range 0–415) (p 3.66E-15) patients. These results suggested that M. tuberculosis isolates from foreign-born patients had more genetic diversity than those from Japan-born patients

Study of intrinsic spin and orbital Hall effects in Pt based on a (6s, 6p, 5d) tight-binding model

We study the origin of the intrinsic spin Hall conductivity (SHC) and the d-orbital Hall conductivity (OHC) in Pt based on a multiorbital tight-binding model with spin-orbit interaction. We find that the SHC reaches 1000 \hbar/e\Omega cm when the resistivity \rho is smaller than ~10 \mu\Omega cm, whereas it decreases to 300 \hbar/e\Omega cm when \rho ~ 100 \mu\Omega cm. In addition, the OHC is still larger than the SHC. The origin of huge SHE and OHE in Pt is the large ``effective magnetic flux'' that is induced by the interorbital transition between d_{xy}- and d_{x2-y2}-orbitals with the aid of the strong spin-orbit interaction.Comment: 5 page

Genomic view of the evolution of the complement system

The recent accumulation of genomic information of many representative animals has made it possible to trace the evolution of the complement system based on the presence or absence of each complement gene in the analyzed genomes. Genome information from a few mammals, chicken, clawed frog, a few bony fish, sea squirt, fruit fly, nematoda and sea anemone indicate that bony fish and higher vertebrates share practically the same set of complement genes. This suggests that most of the gene duplications that played an essential role in establishing the mammalian complement system had occurred by the time of the teleost/mammalian divergence around 500 million years ago (MYA). Members of most complement gene families are also present in ascidians, although they do not show a one-to-one correspondence to their counterparts in higher vertebrates, indicating that the gene duplications of each gene family occurred independently in vertebrates and ascidians. The C3 and factor B genes, but probably not the other complement genes, are present in the genome of the cnidaria and some protostomes, indicating that the origin of the central part of the complement system was established more than 1,000 MYA

Measurement of the Bottom-Strange Meson Mixing Phase in the Full CDF Data Set

We report a measurement of the bottom-strange meson mixing phase \beta_s using the time evolution of B0_s -> J/\psi (->\mu+\mu-) \phi (-> K+ K-) decays in which the quark-flavor content of the bottom-strange meson is identified at production. This measurement uses the full data set of proton-antiproton collisions at sqrt(s)= 1.96 TeV collected by the Collider Detector experiment at the Fermilab Tevatron, corresponding to 9.6 fb-1 of integrated luminosity. We report confidence regions in the two-dimensional space of \beta_s and the B0_s decay-width difference \Delta\Gamma_s, and measure \beta_s in [-\pi/2, -1.51] U [-0.06, 0.30] U [1.26, \pi/2] at the 68% confidence level, in agreement with the standard model expectation. Assuming the standard model value of \beta_s, we also determine \Delta\Gamma_s = 0.068 +- 0.026 (stat) +- 0.009 (syst) ps-1 and the mean B0_s lifetime, \tau_s = 1.528 +- 0.019 (stat) +- 0.009 (syst) ps, which are consistent and competitive with determinations by other experiments.Comment: 8 pages, 2 figures, Phys. Rev. Lett 109, 171802 (2012

Oxidative stress in hepatitis C infected end-stage renal disease subjects

BACKGROUND: Both uremia and hepatitis C infection is associated with increased oxidative stress. In the present study, we aimed to find out whether hepatitis C infection has any impact on oxidative stress in hemodialysis subjects. METHODS: Sixteen hepatitis C (+) hemodialysis subjects, 24 hepatitis C negative hemodialysis subjects and 24 healthy subjects were included. Total antioxidant capacity, total peroxide level and oxidative stress index were determined in all subjects. RESULTS: Total antioxidant capacity was significantly higher in controls than hemodialysis subjects with or without hepatitis C infection (all p < 0.05/3), while total peroxide level and oxidative stress index were significantly lower (all p < 0.05/3). Hepatitis C (-) hemodialysis subjects had higher total antioxidant capacity compared to hepatitis C (+) hemodialysis subjects (all p < 0.05/3). Total peroxide level and oxidative stress index was comparable between hemodialysis subjects with or without hepatitis C infection (p > 0.05/3). CONCLUSION: Oxidative stress is increased in both hepatitis C (+) and hepatitis C (-) hemodialysis subjects. However, hepatitis C infection seems to not cause any additional increase in oxidative stress in hemodialysis subjects and it may be partly due to protective effect of dialysis treatment on hepatitis C infection

Ion cyclotron range of frequency heating experiments on the large helical device and high energy ion behavior

Ion cyclotron range of frequency (ICRF) heating experiments on the Large Helical Device (LHD) [O. Motojima et al. Fus. Eng. Des. 20, 3 (1993)] achieved significant advances during the third experimental campaign carried out in 1999. They showed significant results in two heating modes; these are modes of the ICH-sustained plasma with large plasma stored energy and the neutral beam injection (NBI) plasma under additional heating. A long-pulse operation of more than 1 minute was achieved at a level of 1 MW. The characteristics of the ICRF heated plasma are the same as those of the NBI heated plasma. The energy confinement time is longer than that of International Stellarator Scaling 95. Three keys to successful ICRF heating are as follows: (1) an increase in the magnetic field strength, (2) the employment of an inward shift of the magnetic axis, (3) the installation of actively cooled graphite plates along the divertor legs. Highly energetic protons accelerated by the ICRF electric field were experimentally observed in the energy range from 30 to 250 keV and the tail temperature depended on the energy balance between the wave heating and the electron drag. The transfer efficiency from the high energy ions to the bulk plasma was deduced from the increase in the energy confinement time due to the high energy ions in the lower density discharge, which agrees fairly well with the result obtained by the Monte Carlo simulation. The transfer efficiency is expected to be 95% at an electron density of more than n_e=5.0×10^19 m^?3 even in the high power heating of 10 MW. The accumulation of impurities, e.g., FeXVI and OV was not observed in high rf power and long pulse operation. The well-defined divertor intrinsic to LHD is believed to be useful in reducing the impurity influx

A Novel PAN/Apple Domain-Containing Protein from Toxoplasma gondii: Characterization and Receptor Identification

Toxoplasma gondii is an intracellular parasite that invades nucleated cells, causing toxoplasmosis in humans and animals worldwide. The extremely wide range of hosts susceptible to T. gondii is thought to be the result of interactions between T. gondii ligands and receptors on its target cells. In this study, a host cell-binding protein from T. gondii was characterized, and one of its receptors was identified. P104 (GenBank Access. No. CAJ20677) is 991 amino acids in length, containing a putative 26 amino acid signal peptide and 10 PAN/apple domains, and shows low homology to other identified PAN/apple domain-containing molecules. A 104-kDa host cell-binding protein was detected in the T. gondii lysate. Immunofluorescence assays detected P104 at the apical end of extracellular T. gondii. An Fc-fusion protein of the P104 N-terminus, which contains two PAN/apple domains, showed strong affinity for the mammalian and insect cells evaluated. This binding was not related to protein-protein or protein-lipid interactions, but to a protein-glycosaminoglycan (GAG) interaction. Chondroitin sulfate (CS), a kind of GAG, was shown to be involved in adhesion of the Fc-P104 N-terminus fusion protein to host cells. These results suggest that P104, expressed at the apical end of the extracellular parasite, may function as a ligand in the attachment of T. gondii to CS or other receptors on the host cell, facilitating invasion by the parasite

ヨウリョクタイガタ フェレドキシン ノ コウゾウ カイセキ 2.8Å ブンカイノウ

Remarkable progress in the physical parameters of net-current free plasmas has been made in the Large Helical Device (LHD) since the last Fusion Energy Conference in Chengdu, 2006 (O.Motojima et al., Nucl. Fusion 47 (2007) S668). The beta value reached 5 % and a high beta state beyond 4.5% from the diamagnetic measurement has been maintained for longer than 100 times the energy confinement time. The density and temperature regimes also have been extended. The central density has exceeded 1.0 x 10^21 m^-3 due to the formation of an Internal Diffusion Barrier (IDB). The ion temperature has reached 6.8 keV at the density of 2 x 10^19m^-3, which is associated with the suppression of ion heat conduction loss. Although these parameters have been obtained in separated discharges, each fusion-reactor relevant parameter has elucidated the potential of net-current free heliotron plasmas. Diversified studies in recent LHD experiments are reviewed in this paper