A Polyhedral Approach to the Multi-Layer Crossing Minimization Problem

We study the multi-layer crossing minimization problem from a polyhedral point of view. After the introduction of an integer programming formulation of the multi-layer crossing minimization problem, we examine the 2-layer case and derive several classes of facets of the associated polytope. Preliminary computational results for 2- and 3-layer instances indicate, that the usage of the corresponding facet-defining inequalities in a branch-and-cut approach may only lead to a practically useful algorithm, if deeper polyhedral studies are conducted

The blackcap (Sylvia atricapilla) genome reveals a species-specific accumulation of LTR retrotransposons

Transposable elements are mobile genetic elements that have the ability to move around the genome, and as such can be a source of genome variability. Transposable elements (TEs) are ubiquitous and many are found within a wide variety of life. Based on their characteristics we can annotate TEs within the host genome and classify them into specific TE types and families. The increasing number of available high-quality genome references in recent years provides an excellent resource that will enhance the understanding of the role of recently active TEs on genetic variation and phenotypic evolution. Here we showcase this through a high-quality TE annotation of the Eurasian blackcap (Sylvia atricapilla), as our chromosome resolution reference genome allowed the reconstruction of difficult-to-assemble regions. We have the ability to distinguish species-specific and non-specific TEs. We investigate how these TE categories are distributed along the genome and evaluate their correlation with four genomic features: recombination rate, gene coverage, CpG island coverage and GC coverage. We found a marked difference between species-specific and non-specific TEs. While species-specific TEs were negatively correlated with both GC content and recombination rate, the correlation with recombination rate disappeared and turned positive for GC content when considering non-specific TEs

Extensive variation in the intelectin gene family in laboratory and wild mouse strains

Intelectins are a family of multimeric secreted proteins that bind microbe-specific glycans. Both genetic and functional studies have suggested that intelectins have an important role in innate immunity and are involved in the etiology of various human diseases, including inflammatory bowel disease. Experiments investigating the role of intelectins in human disease using mouse models are limited by the fact that there is not a clear one-to-one relationship between intelectin genes in humans and mice, and that the number of intelectin genes varies between different mouse strains. In this study we show by gene sequence and gene expression analysis that human intelectin-1 (ITLN1) has multiple orthologues in mice, including a functional homologue Itln1; however, human intelectin-2 has no such orthologue or homologue. We confirm that all sub-strains of the C57 mouse strain have a large deletion resulting in retention of only one intelectin gene, Itln1. The majority of laboratory strains have a full complement of six intelectin genes, except CAST, SPRET, SKIVE, MOLF and PANCEVO strains, which are derived from different mouse species/subspecies and encode different complements of intelectin genes. In wild mice, intelectin deletions are polymorphic in Mus musculus castaneus and Mus musculus domesticus. Further sequence analysis shows that Itln3 and Itln5 are polymorphic pseudogenes due to premature truncating mutations, and that mouse Itln1 has undergone recent adaptive evolution. Taken together, our study shows extensive diversity in intelectin genes in both laboratory and wild-mice, suggesting a pattern of birth-and-death evolution. In addition, our data provide a foundation for further experimental investigation of the role of intelectins in disease

Profilin-1 Is Expressed in Human Atherosclerotic Plaques and Induces Atherogenic Effects on Vascular Smooth Muscle Cells

.Here we monitored profilin-1 expression in human atherosclerotic plaques by immunofluorescent staining. The effects of recombinant profilin-1 on atherogenic signaling pathways and cellular responses such as DNA synthesis (BrdU-incorporation) and chemotaxis (modified Boyden-chamber) were evaluated in cultured rat aortic and human coronary vascular smooth muscle cells (VSMCs). Furthermore, the correlation between profilin-1 serum levels and the degree of atherosclerosis was assessed in humans.<0.001 vs. no atherosclerosis or control group).Profilin-1 expression is significantly enhanced in human atherosclerotic plaques compared to the normal vessel wall, and the serum levels of profilin-1 correlate with the degree of atherosclerosis in humans. The atherogenic effects exerted by profilin-1 on VSMCs suggest an auto-/paracrine role within the plaque. These data indicate that profilin-1 might critically contribute to atherogenesis and may represent a novel therapeutic target

Experimental constraints on the ω\omega-nucleus real potential

In a search for $\omega$ mesic states, the production of $\omega$-mesons in coincidence with forward going protons has been studied in photon induced reactions on $^{12}$C for incident photon energies of 1250 - 3100 MeV. The $\pi^0 \gamma$ pairs from decays of bound or quasi-free $\omega$-mesons have been measured with the CBELSA/TAPS detector system in coincidence with protons registered in the MiniTAPS forward array. Structures in the total energy distribution of the $\pi^0 \gamma$ pairs, which would indicate the population and decay of bound $\omega~^{11}$B states, are not observed. The $\pi^0 \gamma$ cross section of 0.3 nb/MeV/sr observed in the bound state energy regime between -100 and 0 MeV may be accounted for by yield leaking into the bound state regime because of the large in-medium width of the $\omega$-meson. A comparison of the measured total energy distribution with calculations suggests the real part $V_0$ of the $\omega~^{11}$B potential to be small and only weakly attractive with $V_0(\rho=\rho_0) = -15\pm$ 35(stat) $\pm$20(syst) MeV in contrast to some theoretical predictions of attractive potentials with a depth of 100 - 150 MeV.Comment: 13 pages, 8 figure