Metallicity dependence of the Hercules stream in Gaia/RAVE data -- explanation by non-closed orbits

The origin of the Hercules stream, the most prominent velocity substructure in the Solar neighbour disc stars, is still under debate. Recent accurate measurements of position, velocity, and metallicity provided by Tycho Gaia Astrometric Solution (TGAS) and RAdial Velocity Experiments (RAVE) have revealed that the Hercules stream is most clearly seen in the metal-rich region ([Fe/H] > 0), while it is not clearly seen in lower metallicity region ([Fe/H] < -0.25). By using a large number of chemo-dynamical 2D test-particle simulations with a rotating bar and/or spiral arms, we find that the observed [Fe/H] dependence of the Hercules stream is a natural consequence of the inside-out formation of the stellar disc and the existence of highly non-closed orbits in the rotating frame of the bar or spiral arms. Our successful models that reproduce the observed properties of the Hercules stream include not only fast-bar-only and fast-bar+spiral models, but also slow-bar+spiral models. This indicates that it is very difficult to estimate the pattern speed of the bar or spiral arms based only on the observations of the Hercules stream in the Solar neighbourhood. As a by-product of our simulations, we make some predictions about the locations across the Galactic plane where we can observe velocity bimodality that is not associated with the Hercules stream. These predictions can be tested by the forthcoming Gaia data, and such a test will improve our understanding of the evolution of the Milky Way stellar disc

Metallicity dependence of the Hercules stream in Gaia/RAVE data -- explanation by non-closed orbits

The origin of the Hercules stream, the most prominent velocity substructure in the Solar neighbour disc stars, is still under debate. Recent accurate measurements of position, velocity, and metallicity provided by Tycho Gaia Astrometric Solution (TGAS) and RAdial Velocity Experiments (RAVE) have revealed that the Hercules stream is most clearly seen in the metal-rich region ([Fe/H] > 0), while it is not clearly seen in lower metallicity region ([Fe/H] < -0.25). By using a large number of chemo-dynamical 2D test-particle simulations with a rotating bar and/or spiral arms, we find that the observed [Fe/H] dependence of the Hercules stream is a natural consequence of the inside-out formation of the stellar disc and the existence of highly non-closed orbits in the rotating frame of the bar or spiral arms. Our successful models that reproduce the observed properties of the Hercules stream include not only fast-bar-only and fast-bar+spiral models, but also slow-bar+spiral models. This indicates that it is very difficult to estimate the pattern speed of the bar or spiral arms based only on the observations of the Hercules stream in the Solar neighbourhood. As a by-product of our simulations, we make some predictions about the locations across the Galactic plane where we can observe velocity bimodality that is not associated with the Hercules stream. These predictions can be tested by the forthcoming Gaia data, and such a test will improve our understanding of the evolution of the Milky Way stellar disc

Identification of amino acids in antigen-binding site of class II HLA proteins independently associated with hepatitis B vaccine response

Background & aimsGenetic factors in class II human leukocyte antigen (HLA) have been reported to be associated with inter-individual variation in hepatitis B virus (HBV) vaccine response. However, the mechanism underlying the associations remains elusive. In particular, the broad linkage disequilibrium in HLA region complicates the localization of the independent effects of genetic variants. Thus, the present study aimed to identify the most probable causal variations in class II HLA loci involved in the immune response to HBV vaccine.MethodsWe performed a case-control study to assess whether HLA-DRB1, -DQB1, and -DPB1 4-digit alleles were associated with the response to primary HBV vaccination in 574 healthy Japanese students. To identify causative variants, we next assessed independently associated amino acid variants in these loci using conditional logistic regression analysis. Furthermore, to clarify the functional effects of these variants on HLA proteins, we performed computational structural studies.ResultsHLA-DRB1∗01:01, HLA-DRB1∗08:03, HLA-DQB1∗05:01, and HLA-DPB1∗04:02 were significantly associated with sufficient response, whereas HLA-DPB1∗05:01 was associated with poor response. We then identified amino acids independently associated with sufficient response, namely, leucine at position 26 of HLA-DRβ1 and glycine-glycine-proline-methionine at positions 84–87 of HLA-DPβ1. These amino acids were located in antigen-binding pocket 4 of HLA-DR and pocket 1 of HLA-DP, respectively, which are important structures for selective binding of antigenic peptides. In addition, the detected variations in HLA-DP protein were responsible for the differences in the electrostatic potentials of the pocket, which can explain in part the sufficient/poor vaccine responses.ConclusionHLA-DRβ1 position 26 and HLA-DPβ1 positions 84–87 are independently associated with anti-HBs production against HBV vaccine. Our results suggest that HBsAg presentation through these HLA pocket structures plays an important role in the inter-individual variability of HBV vaccination

Soliton excitations in halogen-bridged mixed-valence binuclear metal complexes

Motivated by recent stimulative observations in halogen (X)-bridged binuclear transition-metal (M) complexes, which are referred to as MMX chains, we study solitons in a one-dimensional three-quarter-filled charge-density-wave system with both intrasite and intersite electron-lattice couplings. Two distinct ground states of MMX chains are reproduced and the soliton excitations on them are compared. In the weak-coupling region, all the solitons are degenerate to each other and are uniquely scaled by the band gap, whereas in the strong-coupling region, they behave differently deviating from the scenario in the continuum limit. The soliton masses are calculated and compared with those for conventional mononuclear MX chains.Comment: 9 pages, 10 figures embedded, to be published in J. Phys. Soc. Jpn. 71, No. 1 (2002

Pathogenicity of highly pathogenic avian H5N1 influenza A viruses isolated from humans between 2003 and 2008 in northern Vietnam

Vietnam is one of the countries most affected by highly pathogenic H5N1 influenza A viruses. To evaluate the potential pathogenicity in mammals of H5N1 viruses isolated from humans in Vietnam, we determined the sequences of all eight genes of 22 human isolates collected between 2003 and 2008 and compared their virulence in mice. The isolates were classified into clade 1 and clade 2.3.4 and differed in pathogenicity for mice. Whilst lysine at position 627 of PB2 (PB2-627K) is a critical virulence determinant for clade 2.3.4 viruses, asparagine at position 701 of PB2 and other unknown virulence determinants appear to be involved in the high pathogenicity of clade 1 viruses, warranting further studies to determine the factors responsible for the high virulence of H5N1 viruses in mammals

Differences among epitopes recognized by neutralizing antibodies induced by SARS-CoV-2 infection or COVID-19 vaccination

SARS-CoV-2 has gradually acquired amino acid substitutions in its S protein that reduce the potency of neutralizing antibodies, leading to decreased vaccine efficacy. Here, we attempted to obtain mutant viruses by passaging SARS-CoV-2 in the presence of plasma samples from convalescent patients or vaccinees to determine which amino acid substitutions affect the antigenicity of SARS-CoV-2. Several amino acid substitutions in the S2 region, as well as the N-terminal domain (NTD) and receptor-binding domain (RBD), affected the neutralization potency of plasma samples collected from vaccinees, indicating that amino acid substitutions in the S2 region as well as those in the NTD and RBD affect neutralization by vaccine-induced antibodies. Furthermore, the neutralizing potency of vaccinee plasma samples against mutant viruses we obtained or circulating viruses differed among individuals. These findings suggest that genetic backgrounds of vaccinees influence the recognition of neutralizing epitopes

Mutation Analysis of 2009 Pandemic Influenza A(H1N1) Viruses Collected in Japan during the Peak Phase of the Pandemic

BACKGROUND: Pandemic influenza A(H1N1) virus infection quickly circulated worldwide in 2009. In Japan, the first case was reported in May 2009, one month after its outbreak in Mexico. Thereafter, A(H1N1) infection spread widely throughout the country. It is of great importance to profile and understand the situation regarding viral mutations and their circulation in Japan to accumulate a knowledge base and to prepare clinical response platforms before a second pandemic (pdm) wave emerges. METHODOLOGY: A total of 253 swab samples were collected from patients with influenza-like illness in the Osaka, Tokyo, and Chiba areas both in May 2009 and between October 2009 and January 2010. We analyzed partial sequences of the hemagglutinin (HA) and neuraminidase (NA) genes of the 2009 pdm influenza virus in the collected clinical samples. By phylogenetic analysis, we identified major variants of the 2009 pdm influenza virus and critical mutations associated with severe cases, including drug-resistance mutations. RESULTS AND CONCLUSIONS: Our sequence analysis has revealed that both HA-S220T and NA-N248D are major non-synonymous mutations that clearly discriminate the 2009 pdm influenza viruses identified in the very early phase (May 2009) from those found in the peak phase (October 2009 to January 2010) in Japan. By phylogenetic analysis, we found 14 micro-clades within the viruses collected during the peak phase. Among them, 12 were new micro-clades, while two were previously reported. Oseltamivir resistance-related mutations, i.e., NA-H275Y and NA-N295S, were also detected in sporadic cases in Osaka and Tokyo

Biological and Structural Characterization of a Host-Adapting Amino Acid in Influenza Virus

Two amino acids (lysine at position 627 or asparagine at position 701) in the polymerase subunit PB2 protein are considered critical for the adaptation of avian influenza A viruses to mammals. However, the recently emerged pandemic H1N1 viruses lack these amino acids. Here, we report that a basic amino acid at position 591 of PB2 can compensate for the lack of lysine at position 627 and confers efficient viral replication to pandemic H1N1 viruses in mammals. Moreover, a basic amino acid at position 591 of PB2 substantially increased the lethality of an avian H5N1 virus in mice. We also present the X-ray crystallographic structure of the C-terminus of a pandemic H1N1 virus PB2 protein. Arginine at position 591 fills the cleft found in H5N1 PB2 proteins in this area, resulting in differences in surface shape and charge for H1N1 PB2 proteins. These differences may affect the protein's interaction with viral and/or cellular factors, and hence its ability to support virus replication in mammals