Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis.

Mapping short reads against a reference genome is classically the first step of many next-generation sequencing data analyses, and it should be as accurate as possible. Because of the large number of reads to handle, numerous sophisticated algorithms have been developped in the last 3 years to tackle this problem. In this article, we first review the underlying algorithms used in most of the existing mapping tools, and then we compare the performance of nine of these tools on a well controled benchmark built for this purpose.

Interaction of measles virus (Hallé strain) with CD46: evidence that a common binding site on CD46 facilitates both CD46 downregulation and MV infection.

CD46 acts as a cellular receptor for vaccine strains of measles virus (MV). The MV/CD46 interaction-mediated by the MV attachment glycoprotein, the hemagglutinin (H)-not only facilitates infection but also induces CD46 downregulation. A conflict of opinion exists as to whether a single MVH binding site on CD46, or two separate sites, facilitates the two phenomena.

Characterization of a natural mutation in an antigenic site on the fusion protein of measles virus that is involved in neutralization.

Although measles virus is an antigenically monotypic virus, nucleotide sequence analysis of the hemagglutinin and nucleoprotein genes has permitted the differentiation of a number of genotypes. In contrast, the fusion (F) protein is highly conserved; only three amino acid changes have been reported over a 40-year period. We have isolated a measles virus strain which did not react with an anti-F monoclonal antibody (MAb) which we had previously shown to be directed against a dominant antigenic site.

Canine distemper virus DNA vaccination induces humoral and cellular immunity and protects against a lethal intracerebral challenge.

We have studied the immune responses to the two glycoproteins of the Morbillivirus canine distemper virus (CDV) after DNA vaccination of BALB/c mice. The plasmids coding for both CDV hemagglutinin (H) and fusion protein (F) induce high levels of antibodies which persist for more than 6 months. Intramuscular inoculation of the CDV DNA induces a predominantly immunoglobulin G2a (IgG2a) response (Th1 response), whereas gene gun immunization with CDV H evokes exclusively an IgG1 response (Th2 response).

Measles virus DNA vaccination: antibody isotype is determined by the method of immunization and by the nature of both the antigen and the coimmunized antigen.

Plasmids encoding the measles virus hemagglutinin (HA) and nucleoprotein (NP) proteins inoculated into the skin of BALB/c mice by the gene gun method induced both humoral and cytotoxic lymphocyte class I-restricted immune responses. Although intramuscular immunization induces the immunoglobulin G2a (IgG2a) antibody isotype for both antigens, with gene gun immunization, the NP still generated mainly IgG2a and the major isotype induced by the HA was IgG1. Interestingly, gene gun coimmunization of HA and NP plasmids resulted in a dominant IgG1 HA response and the switching of antibodies generated against the NP to the IgG1 isotype.

Immunization with plasmid DNA encoding for the measles virus hemagglutinin and nucleoprotein leads to humoral and cell-mediated immunity.

We have evaluated the DNA vaccination strategy for measles virus (MV) hemagglutinin (HA) and nucleoprotein (NP) genes. Plasmids encoding either the MV, HA, or NP proteins inoculated intramuscularly into Balb/c mice induced both humoral and CTL class I restricted responses. Antibody responses were not increased by multiple inoculations.

Identification of two amino acids in the hemagglutinin glycoprotein of measles virus (MV) that govern hemadsorption, HeLa cell fusion, and CD46 downregulation: phenotypic markers that differentiate vaccine and wild-type MV strains.

We have used site-directed mutagenesis of the hemagglutinin (H) glycoprotein of measles virus (MV) to investigate the molecular basis for the phenotypic differences observed between MV vaccine strains and recently isolated wild-type MV strains. The former downregulate CD46, the putative cellular receptor of MV, are positive for hemadsorption, and are fusogenic in HeLa cells, whereas the latter are negative for these phenotypic markers. CD46 downregulation in particular, could have profound consequences for the immunopathology of MV infection, as this molecule protects the cell from complement lysis.

Measles virus fusion: role of the cysteine-rich region of the fusion glycoprotein.

Measles virus (MV) fusion requires the participation of both the fusion (F) and hemagglutinin (H) glycoproteins. The canine distemper virus fusion protein (CDVF) cannot substitute for the measles virus fusion protein (MVF) in this process. Introduction of restriction enzyme sites into the cDNAs of CDVF and MVF by site-directed mutagenesis facilitated the production of chimeric F proteins which were tested for their capacity to give fusion when coexpressed with MVH.

Effects of atrial pacing on right ventricular contractility after coronary artery surgery.

Increasing heart rate enhances the strength of contraction of cardiac fibers. This has been demonstrated in vitro and recently for the left ventricle. To study this phenomenon on the right ventricle, the effects of increasing heart rate by atrial pacing on right ventricular (RV) contractility were observed after coronary artery surgery in 20 patients.