Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics.

The genetic dissection of complex disease remains a significant challenge. Sample-tracking and the recording, processing and storage of high-throughput laboratory data with public domain data, require integration of databases, genome informatics and genetic analyses in an easily updated and scaleable format. To find genes involved in multifactorial diseases such as type 1 diabetes (T1D), chromosome regions are defined based on functional candidate gene content, linkage information from humans and animal model mapping information. For each region, genomic information is extracted from Ensembl, converted and loaded into ACeDB for manual gene annotation. Homology information is examined using ACeDB tools and the gene structure verified. Manually curated genes are extracted from ACeDB and read into the feature database, which holds relevant local genomic feature data and an audit trail of laboratory investigations. Public domain information, manually curated genes, polymorphisms, primers, linkage and association analyses, with links to our genotyping database, are shown in Gbrowse. This system scales to include genetic, statistical, quality control (QC) and biological data such as expression analyses of RNA or protein, all linked from a genomics integrative display. Our system is applicable to any genetic study of complex disease, of either large or small scale.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Bostonia: The Boston University Alumni Magazine. Volume 12

Founded in 1900, Bostonia magazine is Boston University’s main alumni publication

Does trapped O2 form in the bulk of LiNiO2 during charging?

LiNiO2 remains a critical archetypal material for high energy density Li-ion batteries, forming the basis of Ni-rich cathodes in use today. Nevertheless, there are still uncertainties surrounding the charging mechanism at high states of charge and the potential role of oxygen redox. We show that oxidation of O2− across the 4.2 V vs. Li+/Li plateau forms O2 trapped in the particles and is accompanied by the formation of 8% Ni vacancies on the transition metal sites of previously fully dense transition metal layers. Such Ni vacancy formation on charging activates O-redox by generating non-bonding O 2p orbitals and is necessary to form vacancy clusters to accommodate O2 in the particles. Ni accumulates at and near the surface of the particles on charging, forming a Ni-rich shell approximately 5 nm thick; enhanced by loss of O2 from the surface, the resulting shell composition is Ni2.3+1.75O2. The overall Ni oxidation state of the particles measured by XAS in fluorescence yield mode after charging across the plateau to 4.3 V vs. Li+/Li is approximately +3.8; however, taking account of the shell thickness and the shell Ni oxidation state of +2.3, this indicates a Ni oxidation state in the core closer to +4 for compositions beyond the plateau

Vaccine-mediated protection of pigs against infection with pandemic H1N1 2009 swine influenza A virus requires a close antigenic match between the vaccine antigen and challenge virus

Swineandnbsp;influenza A virusandnbsp;(SwIV) infection has considerable economic and animal welfare consequences and, because of the zoonotic potential, can also have public health implications. The 2009 pandemicandnbsp;H1N1andnbsp;andlsquo;swine-originandrsquo; infection is now endemic in both pigs and humans. In Europe, avian-like H1avN1, human-like H1huN2, human-like swineandnbsp;H3N2andnbsp;and, since 2009, pandemic H1N1 (pH1N1) lineage viruses andandnbsp;reassortants, constitute the dominant subtypes. In this study, we used a swine pH1N1 challenge virus to investigate the efficacy ofandnbsp;whole inactivated virus vaccinesandnbsp;homologous or heterologous to the challenge virus as well as a commercial vaccine. We found that vaccine-mediated protection was most effective when vaccine antigen and challenge virus were homologous and correlated with the specific production ofandnbsp;neutralising antibodiesandnbsp;and a cellular response to the challenge virus. We conclude that a conventional whole inactivated SwIV vaccine must be antigenically matched to the challenge strain to be an effective control measure.</p

Understanding the re-entrant phase transition in a non-magnetic scheelite

The stereochemical activity of lone pair electrons plays a central role in determining the structural and electronic properties of both chemically simple materials such as H2O, as well as more complex condensed phases such as photocatalysts or thermoelectrics. TlReO4 is a rare example of a non-magnetic material exhibiting a re-entrant phase transition and emphanitic behavior in the long-range structure. Here, we describe the role of the Tl+ 6s2 lone pair electrons in these unusual phase transitions and illustrate its tunability by chemical doping, which has broad implications for functional materials containing lone pair bearing cations. First-principles density functional calculations clearly show the contribution of the Tl+ 6s2 in the valence band region. Local structure analysis, via neutron total scattering, revealed that changes in the long-range structure of TlReO4 occur due to changes in the correlation length of the Tl+ lone pairs. This has a significant effect on the anion interactions, with long-range ordered lone pairs creating a more densely packed structure. This resulted in a trade-off between anionic repulsions and lone pair correlations that lead to symmetry lowering upon heating in the long-range structure, whereby lattice expansion was necessary for the Tl+ lone pairs to become highly correlated. Similarly, introducing lattice expansion through chemical pressure allowed long-range lone pair correlations to occur over a wider temperature range, demonstrating a method for tuning the energy landscape of lone pair containing functional materials

Challenge of Pigs with Classical Swine Fever Viruses after C-Strain Vaccination Reveals Remarkably Rapid Protection and Insights into Early Immunity

Pre-emptive culling is becoming increasingly questioned as a means of controlling animal diseases, including classical swine fever (CSF). This has prompted discussions on the use of emergency vaccination to control future CSF outbreaks in domestic pigs. Despite a long history of safe use in endemic areas, there is a paucity of data on aspects important to emergency strategies, such as how rapidly CSFV vaccines would protect against transmission, and if this protection is equivalent for all viral genotypes, including highly divergent genotype 3 strains. To evaluate these questions, pigs were vaccinated with the Riemser® C-strain vaccine at 1, 3 and 5 days prior to challenge with genotype 2.1 and 3.3 challenge strains. The vaccine provided equivalent protection against clinical disease caused by for the two challenge strains and, as expected, protection was complete at 5 days post-vaccination. Substantial protection was achieved after 3 days, which was sufficient to prevent transmission of the 3.3 strain to animals in direct contact. Even by one day post-vaccination approximately half the animals were partially protected, and were able to control the infection, indicating that a reduction of the infectious potential is achieved very rapidly after vaccination. There was a close temporal correlation between T cell IFN-γ responses and protection. Interestingly, compared to responses of animals challenged 5 days after vaccination, challenge of animals 3 or 1 days post-vaccination resulted in impaired vaccine-induced T cell responses. This, together with the failure to detect a T cell IFN-γ response in unprotected and unvaccinated animals, indicates that virulent CSFV can inhibit the potent antiviral host defences primed by C-strain in the early period post vaccination