Machine-learning based patient classification using Hepatitis B virus full-length genome quasispecies from Asian and European cohorts

Chronic infection with Hepatitis B virus (HBV) is a major risk factor for the development of advanced liver disease including fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). The relative contribution of virological factors to disease progression has not been fully defined and tools aiding the deconvolution of complex patient virus profiles is an unmet clinical need. Vari

Several Distinct Polycomb Complexes Regulate and Co-Localize on the INK4a Tumor Suppressor Locus

Misexpression of Polycomb repressive complex 1 (PRC1) components in human cells profoundly influences the onset of cellular senescence by modulating transcription of the INK4a tumor suppressor gene. Using tandem affinity purification, we find that CBX7 and CBX8, two Polycomb (Pc) homologs that repress INK4a, both participate in PRC1-like complexes with at least two Posterior sex combs (Psc) proteins, MEL18 and BMI1. Each complex contains a single representative of the Pc and Psc families. In primary human fibroblasts, CBX7, CBX8, MEL18 and BMI1 are present at the INK4a locus and shRNA-mediated knockdown of any one of these components results in de-repression of INK4a and proliferative arrest. Sequential chromatin immunoprecipitation (ChIP) reveals that CBX7 and CBX8 bind simultaneously to the same region of chromatin and knockdown of one of the Pc or Psc proteins results in release of the other, suggesting that the binding of PRC1 complexes is interdependent. Our findings provide the first evidence that a single gene can be regulated by several distinct PRC1 complexes and raise important questions about their configuration and relative functions

Novel spontaneous deletion of artemis exons 10 and 11 in mice leads to T- and B-cell deficiency.

Here we describe a novel, spontaneous, 4035 basepairs long deletion in the DNA cross-link repair 1C (Dclre1c)-locus in C57BL/6-mice, which leads to loss of exons 10 and 11 of the gene encoding for Artemis, a protein involved into V(D) J-recombination of antigen receptors of T and B cells. While several spontaneous mutations of Artemis have been described to cause SCID in humans, in mice, only targeted deletions by knockout technology are known to cause the same phenotype so far. The deletion we observed causes a loss of Artemis function in the C57BL/6 strain and, consequently, the absence of T and B cells, in presence of normal numbers of NK cells and cells of the myeloid lineage. Thus, for the first time we present T(-)B(-)NK(+) severe combined immunodeficiency (SCID) phenotype after spontaneously occurring modification of Artemis gene in mice. Our mouse model may serve as a valuable tool to study mechanisms as well as potential therapies of SCID in humans

Sequencing of <i>Dclre1c-</i>gene.

<p>(A) Two heterogeneous and four homogeneous mutant mice were analyzed using next-generation-sequencing techniques. Displayed is the coverage of the bases in exons 9 to 12. (B) Graphical representation of the genomic organization of <i>Dclr1c</i> between exons 9 and 12. Exons are indicated by black boxes, while arrows indicate primer binding-sites. The upper row represents the organization in the wild-type genome while the lower row represents the gene in the mutant. (C) Results of PCR reactions with the indicated primer sets. DNA was visualized on ethidium bromide agarose gels. (D) Primer p3f and p8r were used to amplify DNA from mutant animals and the purified PCR products were used for Sanger DNA-sequencing. The resulting sequences were aligned to the <i>Dclre1c</i>-sequence according to the “Gene” database of NCBI. (*) indicates matching bases, (-) indicates gaps in the alignment. Shown is the 5´ beginning of the deletion (before //) as well as the 3´ end of the deletion (after //).</p

Phage-mediated Dispersal of Biofilm and Distribution of Bacterial Virulence Genes Is Induced by Quorum Sensing

The microbiome and the phage meta-genome within the human gut are influenced by antibiotic treatments. Identifying a novel mechanism, here we demonstrate that bacteria use the universal communication molecule AI-2 to induce virulence genes and transfer them via phage release. High concentrations (i.e. 100 mu M) of AI-2 promote dispersal of bacteria from already established biofilms, and is associated with release of phages capable of infecting other bacteria. Enterococcus faecalis V583 Delta ABC harbours 7 prophages in its genome, and a mutant deficient in one of these prophages (i.e. prophage 5) showed a greatly reduced dispersal of biofilm. Infection of a probiotic E. faecalis strain without lytic prophages with prophage 5 resulted in increased biofilm formation and also in biofilm dispersal upon induction with AI-2. Infection of the probiotic E. faecalis strain with phage-containing supernatants released through AI-2 from E. faecalis V583 Delta ABC resulted in a strong increase in pathogenicity of this strain. The polylysogenic probiotic strain was also more virulent in a mouse sepsis model and a rat endocarditis model. Both AI-2 and ciprofloxacin lead to phage release, indicating that conditions in the gastrointestinal tract of hospitalized patients treated with antibiotics might lead to distribution of virulence genes to apathogenic enterococci and possibly also to other commensals or even to beneficial probiotic strains

Initial characterization of cell subsets in the spleens of mutant mice.

<p>(A) Single cell suspensions of spleens were stained for B cells (CD19⁺B220⁺) or T cells (CD4⁺ or CD8⁺), which were further analyzed for expression of CD3 (lower panel). Cells were gated on live lymphocytes. (B) Single cell suspensions of spleens were stained with the indicated antibodies to identify DC (CD11c⁺MHCII⁺), NK cells (NK1.1 ⁺ CD3^-), granulocytes (Gr1 ⁺ CD3^-) and CD11b⁺ monocytes. FACS-plots and statistics are representative results from one out of six experiments with similar outcome (n=3 mice per group). Bar graphs represent mean number of live cells ± SD in the respective gate.</p